Malak Tfaily

Interests

Research

Integration of multidisciplinary science to implement field- and laboratory-based investigations to advance understanding of how soil carbon responds to global change and the underlying microbial mechanisms and interactions that determine its response.Expertise: Analytical chemistry, Aquatic and terrestrial organic geochemist, peatland and permafrost biogeochemistry, multi-omics approaches, global change, mass spectrometry, gas fluxes and isotopes, plant-soil-microbiome interactions.

Teaching

Soil chemistry; Environmental Chemistry; Carbon cycling; Analytical Chemistry; Ecosystem science

Courses

Scholarly Contributions

Chapters

• Tfaily, M., & Wilson, R. (2019). Revisiting the Role of Bio- and Photodegradation on the Global Distribution and Degradation of Dissolved Organic Matter in Watersheds. In Open Watershed Science by Design: Leveraging Distributed Research Networks to Understand Watershed Systems.

Journals/Publications

• C, H., MM, L., Fudyma, J. D., Krongauz, A., Solonenko, N. E., Zayed, A. A., Andreopoulos, W. B., Olson, H. M., Kim, Y. M., Kyle, J. E., Del, G., Adkins, J. N., Tfaily, M. M., Paul, S., Sullivan, M. B., & Duhaime, M. B. (2025). Environment-specific virocell metabolic reprogramming. LID - 10.1093/ismejo/wrae055 [doi] LID - wrae055.
• Cory, A. B., Wilson, R. M., Holmes, M. E., Riley, W. J., Li, Y. F., Tfaily, M. M., Bagby, S. C., , I. F., , E. P., Crill, P. M., Ernakovich, J. G., Rich, V. I., & Chanton, J. P. (2025). A climatically significant abiotic mechanism driving carbon loss and nitrogen limitation in peat bogs. Scientific reports, 15(1), 2560.
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  Sphagnum-dominated bogs are climatically impactful systems that exhibit two puzzling characteristics: CO:CH ratios are greater than those predicted by electron balance models and C decomposition rates are enigmatically slow. We hypothesized that Maillard reactions partially explain both phenomena by increasing apparent CO production via eliminative decarboxylation and sequestering bioavailable nitrogen (N). We tested this hypothesis using incubations of sterilized Maillard reactants, and live and sterilized bog peat. Consistent with our hypotheses, CO production in the sterilized peat was equivalent to 8-13% of CO production in unsterilized peat, and the increased formation of aromatic N compounds decreased N-availability. Numerous sterility assessments rule out biological contamination or extracellular enzyme activity as significant sources of this CO. These findings suggest a need for a reevaluation of the fixed CO:CH production ratios commonly used in wetland biogeochemical models, which could be improved by incorporating abiotic sources of CO production and N sequestration.
• Anderson, C. G., Tfaily, M. M., Chu, R. K., Nikola, T., Fox, P. M., Nico, P. S., Fendorf, S., & Keiluweit, M. (2024). Seasonal Controls on Microbial Depolymerization and Oxidation of Organic Matter in Floodplain Soils. Environmental Science & Technology, 58(38), 16815-16823.
• Anderson, C. G., Tfaily, M. M., Chu, R. K., Tolić, N., Fox, P. M., Nico, P. S., Fendorf, S., & Keiluweit, M. (2024). Seasonal Controls on Microbial Depolymerization and Oxidation of Organic Matter in Floodplain Soils. Environmental science & technology.
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  Floodplain soils are vast reservoirs of organic carbon often attributed to anaerobic conditions that impose metabolic constraints on organic matter degradation. What remains elusive is how such metabolic constraints respond to dynamic flooding and drainage cycles characteristic of floodplain soils. Here we show that microbial depolymerization and respiration of organic compounds, two rate-limiting steps in decomposition, vary spatially and temporally with seasonal flooding of mountainous floodplain soils (Gothic, Colorado, USA). Combining metabolomics and -proteomics, we found a lower abundance of oxidative enzymes during flooding coincided with the accumulation of aromatic, high-molecular weight compounds, particularly in surface soils. In subsurface soils, we found that a lower oxidation state of carbon coincided with a greater abundance of chemically reduced, energetically less favorable low-molecular weight metabolites, irrespective of flooding condition. Our results suggest that seasonal flooding temporarily constrains oxidative depolymerization of larger, potentially plant-derived compounds in surface soils; in contrast, energetic constraints on microbial respiration persist in more reducing subsurface soils regardless of flooding. Our work underscores that the potential vulnerability of these distinct anaerobic carbon storage mechanisms to changing flooding dynamics should be considered, particularly as climate change shifts both the frequency and extent of flooding in floodplains globally.
• Bouranis, J. A., & Tfaily, M. M. (2024). Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism. Trends in microbiology, 32(12), 1170-1178.
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  Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.
• Coker, H. R., Lin, H. A., Shackelford, C. E., Tfaily, M. M., Smith, A. P., & Howe, J. A. (2024). Drought stimulates root exudation of organic nitrogen in cotton (). Frontiers in plant science, 15, 1431004.
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  Root exudation of N is a plant input to the soil environment and may be differentially regulated by the plant during drought. Organic N released by root systems has important implications in rhizosphere biogeochemical cycling considering the intimate coupling of C and N dynamics by microbial communities. Besides amino acids, diverse molecules exuded by root systems constitute a significant fraction of root exudate organic N but have yet to receive a metabolomic and quantitative investigation during drought. To observe root exudation of N during drought, mature cotton plants received progressive drought and recovery treatments in an aeroponic system throughout their reproductive stage and were compared to control plants receiving full irrigation. Root exudates were nondestructively sampled from the same plants at 9 timepoints over 18 days. Total organic C and N were quantified by combustion, inorganic N with spectrophotometric methods, free amino acids by high performance liquid chromatography (HPLC), and untargeted metabolomics by Fourier-transform ion cyclotron resonance-mass spectrometry (FT-ICR-MS). Results indicate that organic N molecules in root exudates were by far the greatest component of root exudate total N, which accounted for 20-30% of root exudate mass. Drought increased root exudation of organic N (62%), organic C (6%), and free amino acid-N (562%), yet free amino acids were
• Ellenbogen, J. B., Borton, M. A., McGivern, B. B., Cronin, D. R., Hoyt, D. W., Freire-Zapata, V., McCalley, C. K., Varner, R. K., Crill, P. M., Wehr, R. A., Chanton, J. P., Woodcroft, B. J., Tfaily, M. M., Tyson, G. W., Rich, V. I., & Wrighton, K. C. (2024). Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems, 9(1), e0069823.
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  While wetlands are major sources of biogenic methane (CH), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for and MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for , they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.
• Freire-Zapata, V., Holland-Moritz, H., Cronin, D. R., Aroney, S., Smith, D. A., Wilson, R. M., Ernakovich, J. G., Woodcroft, B. J., Bagby, S. C., , E. 2., , E. B., Rich, V. I., Sullivan, M. B., Stegen, J. C., & Tfaily, M. M. (2024). Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature microbiology, 9(11), 2892-2908.
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  Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO and CH porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.
• Howard-Varona, C., Lindback, M. M., Fudyma, J. D., Krongauz, A., Solonenko, N. E., Zayed, A. A., Andreopoulos, W. B., Olson, H. M., Kim, Y. M., Kyle, J. E., Glavina Del Rio, T., Adkins, J. N., Tfaily, M. M., Paul, S., Sullivan, M. B., & Duhaime, M. B. (2024). Environment-specific virocell metabolic reprogramming. The ISME journal, 18(1).
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  Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
• Kew, W., Myers-Pigg, A. .., Chang, C. H., Colby, S. M., Eder, J., Tfaily, M. M., Hawkes, J., Chu, R. K., & Stegen, J. C. (2024). Reviews and syntheses: Opportunities for robust use of peak intensities from high-resolution mass spectrometry in organic matter studies. Biogeosciences, 21(20), 4665-4679.
• Lin, H. A., Coker, H. R., Park, S., Finlayson, S. A., Tfaily, M. M., Nagy, E. M., Hague, S., Antony-Babu, S., Howe, J. A., & Smith, A. P. (2024). Aeroponic approach for nondestructive root exudate collection and simulation of variable water stress trialed on cotton (Gossypium hirsutum). Scientific reports, 14(1), 28615.
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  Analyzing root exudates during drought poses a serious challenge; sampling root exudates in soil is destructive to roots and leads to biased molecular analysis, along with microbial decomposition and exudate sorption to soil components. Hydroponic approaches are useful to overcome these problems but lack the utility to induce drought. Nondestructive sampling techniques are thus needed to analyze root exudates from the same plants over time in combination with highly controlled variable water/nutrient stress. The proposed aeroponic approach demonstrated that cotton could be grown to maturity in the aeroponic system, then a progressive drought treatment applied while simultaneously collecting root exudates from the same plants over time. Treatments of varying irrigation rates consisted of well-watered cotton (control) that was compared to cotton given progressive water stress (drought) and subsequent drought recovery for two weeks. Plants were entering flowering as drought treatment was applied. Nondestructive morphological measurements of plant productivity were made. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was employed to analyze the molecular profile of exudates, whereas gas chromatography-mass spectroscopy (GC-MS) was used to quantify abscisic acid (ABA). Plant development was highly responsive to reduced irrigation intervals with decreased canopy height, number of green leaves, biomass, and water content. As revealed by FT-ICR MS, the complexity and connectivity of unique biochemical transformation networks in response to drought was greatest at 9 days after treatment, where severe visual symptoms were observed. Overall, the aeroponic approach is a promising technology to simulate drought while sampling root exudates nondestructively, advancing root system research and plant-stress response mechanisms.
• McGivern, B. B., Cronin, D. R., Ellenbogen, J. B., Borton, M. A., Knutson, E. L., Freire-Zapata, V., Bouranis, J. A., Bernhardt, L., Hernandez, A. I., Flynn, R. M., Woyda, R., Cory, A. B., Wilson, R. M., Chanton, J. P., Woodcroft, B. J., Ernakovich, J. G., Tfaily, M. M., Sullivan, M. B., Tyson, G. W., , Rich, V. I., et al. (2024). Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature microbiology, 9(6), 1454-1466.
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  With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.
• McGivern, B. B., Ellenbogen, J. B., Hoyt, D. W., Bouranis, J. A., Stemple, B. P., Daly, R. A., Bosman, S. H., Sullivan, M. B., Hagerman, A. E., Chanton, J. P., Tfaily, M. M., & Wrighton, K. C. (2024). Polyphenol rewiring of the microbiome reduces methane emissions. bioRxiv : the preprint server for biology.
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  Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens, either through direct toxic effects or by diverting their substrates and energy, to gain traction. Problematically, current microbial methane mitigation knowledge derives from rumen studies and lacks detailed microbiome-centered insights, limiting translation across ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a novel catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes also co-expressed hydrogen-uptake genes, suggesting that hydrogenases may act as a hydrogen sink during catechin degradation, depriving methanogens of substrates. This was supported by decreased gene expression in hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. We also saw reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.
• Rajakaruna, S., Makke, G., Grachet, N. G., Ayala-Ortiz, C., Bouranis, J., Hoyt, D. W., Toyoda, J., Denis, E. H., Moran, J. J., Song, T., Sun, X., Eder, E. K., Wong, A. R., Chu, R., Heyman, H., Kolton, M., Chanton, J. P., Wilson, R. M., Kostka, J., & Tfaily, M. M. (2024). Adding labile carbon to peatland soils triggers deep carbon breakdown. Communications Earth & Environment, 5(1), 792.
• Smith, A. P., Rod, K. A., Campell, T., Patel, K. F., Dohnalkova, A., Tfaily, M., Renteria, L., Bailey, V. L., & Renslow, R. (2024). Moisture-mineral interactions drive bacterial and organic matter turnover in glacier-sourced riparian sediments undergoing pedogenesis. Soil Biology and Biochemistry, 199, 109617.
• VanZomeren, C. M., Bhomia, R. K., Tfaily, M. M., Inglett, K. S., Cooper, W. T., White, J. R., & Reddy, K. R. (2024). Influence of vegetation on soil organic nitrogen composition and mineralization in a subtropical wetland. Ecological Engineering, 200, 107186.
• Wyatt, M., Choudhury, A., Von Dohlen, G., Heileson, J. L., Forsse, J. S., Rajakaruna, S., Zec, M., Tfaily, M. M., & Greathouse, L. (2024). Randomized control trial of moderate dose vitamin D alters microbiota stability and metabolite networks in healthy adults. Microbiology spectrum, 12(10), e0008324.
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  Evidence indicates that both vitamin D and the gut microbiome are involved in the process of colon carcinogenesis. However, it is unclear what effects supplemental vitamin D has on the gut microbiome and its metabolites in healthy adults. We conducted a double-blind, randomized, placebo-controlled trial to identify the acute and long-term microbiota structural and metabolite changes that occur in response to a moderate dose (4,000 IU) of vitamin D for 12 weeks in healthy adults. Our results demonstrated a significant increase in serum 25-hydroxy-vitamin D (25(OH)D) in the treatment group compared to placebo ( < 0.0001). Vitamin D significantly increased compositional similarity ( < 0.0001) in the treatment group, and enriched members of the Bifidobacteriaceae family. We also identified a significant inverse relationship between the percent change in serum 25(OH)D and microbial stability in the treatment group ( = -0.52, < 0.019). Furthermore, vitamin D supplementation resulted in notable metabolic shifts, in addition to resulting in a drastic rewiring of key gut microbial-metabolic associations. In conclusion, we show that a moderate dose of vitamin D among healthy adults has unique acute and persistent effects on the fecal microbiota, and suggest novel mechanisms by which vitamin D may affect the host-microbiota relationship.
• AminiTabrizi, R., Graf-Grachet, N., Chu, R. K., Toyoda, J. G., Hoyt, D. W., Hamdan, R., Wilson, R. M., & Tfaily, M. M. (2023). Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils. Global change biology, 29(7), 1951-1970.
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  Peatlands are among the largest natural sources of atmospheric methane (CH ) worldwide. Microbial processes play a key role in regulating CH emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi-omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome-metabolome interactions; then explore the competition between methanogens and sulfate-reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO production with temperature. In contrast, the decrease in CH production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait-based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non-limiting sulfate concentrations at 21°C, thereby reducing CH emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low-molecular-weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.
• Ayala-Ortiz, C., Graf-Grachet, N., Freire-Zapata, V., Fudyma, J., Hildebrand, G., AminiTabrizi, R., Howard-Varona, C., Corilo, Y. E., Hess, N., Duhaime, M. B., Sullivan, M. B., & Tfaily, M. M. (2023). MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data. Microbiome, 11(1), 28.
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  Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.
• Furlong, M. A., Liu, T., Snider, J. M., Tfaily, M. M., Itson, C., Beitel, S., Parsawar, K., Keck, K., Galligan, J., Walker, D. I., Gulotta, J. J., & Burgess, J. L. (2023). Evaluating changes in firefighter urinary metabolomes after structural fires: an untargeted, high resolution approach. Scientific reports, 13(1), 20872.
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  Firefighters have elevated rates of urinary tract cancers and other adverse health outcomes, which may be attributable to environmental occupational exposures. Untargeted metabolomics was applied to characterize this suite of environmental exposures and biological changes in response to occupational firefighting. 200 urine samples from 100 firefighters collected at baseline and two to four hours post-fire were analyzed using untargeted liquid-chromatography and high-resolution mass spectrometry. Changes in metabolite abundance after a fire were estimated with fixed effects linear regression, with false discovery rate (FDR) adjustment. Partial least squares discriminant analysis (PLS-DA) was also used, and variable important projection (VIP) scores were extracted. Systemic changes were evaluated using pathway enrichment for highly discriminating metabolites. Metabolome-wide-association-study (MWAS) identified 268 metabolites associated with firefighting activity at FDR q 
• Hildebrand, G. A., Honeker, L. K., Freire-Zapata, V., Ayala-Ortiz, C., Rajakaruna, S., Fudyma, J., Daber, L. E., AminiTabrizi, R., Chu, R. L., Toyoda, J., Flowers, S. E., Hoyt, D. W., Hamdan, R., Gil-Loaiza, J., Shi, L., Dippold, M. A., Ladd, S. N., Werner, C., Meredith, L. K., & Tfaily, M. M. (2023). Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants. The Science of the total environment, 899, 165689.
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  Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.
• Honeker, L. K., Pugliese, G., Ingrisch, J., Fudyma, J., Gil-Loaiza, J., Carpenter, E., Singer, E., Hildebrand, G., Shi, L., Hoyt, D. W., Chu, R. K., Toyoda, J., Krechmer, J. E., Claflin, M. S., Ayala-Ortiz, C., Freire-Zapata, V., Pfannerstill, E. Y., Daber, L. E., Meeran, K., , Dippold, M. A., et al. (2023). Author Correction: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nature microbiology.
• Honeker, L. K., Pugliese, G., Ingrisch, J., Fudyma, J., Gil-Loaiza, J., Carpenter, E., Singer, E., Hildebrand, G., Shi, L., Hoyt, D. W., Chu, R. K., Toyoda, J., Krechmer, J. E., Claflin, M. S., Ayala-Ortiz, C., Freire-Zapata, V., Pfannerstill, E. Y., Daber, L. E., Meeran, K., , Dippold, M. A., et al. (2023). Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nature microbiology, 8(8), 1480-1494.
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  Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking C from position-specific C-pyruvate into CO and VOCs in parallel with multi-omics. During drought, efflux of C-enriched acetate, acetone and CHO (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,C-CO efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.
• Lin, H. A., Coker, H. R., Howe, J. A., Tfaily, M. M., Nagy, E. M., Antony-Babu, S., Hague, S., & Smith, A. P. (2023). Progressive drought alters the root exudate metabolome and differentially activates metabolic pathways in cotton (). Frontiers in plant science, 14, 1244591.
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  Root exudates comprise various primary and secondary metabolites that are responsive to plant stressors, including drought. As increasing drought episodes are predicted with climate change, identifying shifts in the metabolome profile of drought-induced root exudation is necessary to understand the molecular interactions that govern the relationships between plants, microbiomes, and the environment, which will ultimately aid in developing strategies for sustainable agriculture management. This study utilized an aeroponic system to simulate progressive drought and recovery while non-destructively collecting cotton () root exudates. The molecular composition of the collected root exudates was characterized by untargeted metabolomics using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) and mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Over 700 unique drought-induced metabolites were identified throughout the water-deficit phase. Potential KEGG pathways and KEGG modules associated with the biosynthesis of flavonoid compounds, plant hormones (abscisic acid and jasmonic acid), and other secondary metabolites were highly induced under severe drought, but not at the wilting point. Additionally, the associated precursors of these metabolites, such as amino acids (phenylalanine and tyrosine), phenylpropanoids, and carotenoids, were also mapped. The potential biochemical transformations were further calculated using the data generated by FT-ICR MS. Under severe drought stress, the highest number of potential biochemical transformations, including methylation, ethyl addition, and oxidation/hydroxylation, were identified, many of which are known reactions in some of the mapped pathways. With the application of FT-ICR MS, we revealed the dynamics of drought-induced secondary metabolites in root exudates in response to drought, providing valuable information for drought-tolerance strategies in cotton.
• Meredith, L. K., Ledford, S. M., Riemer, K., Geffre, P., Graves, K., Honeker, L. K., LeBauer, D., Tfaily, M. M., & Krechmer, J. (2023). Automating methods for estimating metabolite volatility. Frontiers in microbiology, 14, 1267234.
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  The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With , we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.
• Tfaily, M., S. R., J., R. P., Y., & D. H., M. (2023). Root exudates induced coupled carbon and phosphorus cycling in a soil with low phosphorus availability. Plant and Soil.
• AminiTabrizi, R., Dontsova, K., Graf Grachet, N., & Tfaily, M. M. (2022). Elevated temperatures drive abiotic and biotic degradation of organic matter in a peat bog under oxic conditions. The Science of the total environment, 804, 150045.
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  Understanding the effects of elevated temperatures on soil organic matter (SOM) decomposition pathways in northern peatlands is central to predicting their fate under future warming. Peatlands role as carbon (C) sink is dependent on both anoxic conditions and low temperatures that limit SOM decomposition. Previous studies have shown that elevated temperatures due to climate change can disrupt peatland's C balance by enhancing SOM decomposition and increasing CO emissions. However, little is known about how SOM decomposition pathways change at higher temperatures. Here, we used an integrated research approach to investigate the mechanisms behind enhanced CO emissions and SOM decomposition under elevated temperatures of surface peat soil collected from a raised and Sphagnum dominated mid-continental bog (S1 bog) peatland at the Marcel Experimental Forest in Minnesota, USA, incubated under oxic conditions at three different temperatures (4, 21, and 35 °C). Our results indicated that elevated temperatures could destabilize peatland's C pool via a combination of abiotic and biotic processes. In particular, temperature-driven changes in redox conditions can lead to abiotic destabilization of Fe-organic matter (phenol) complexes, previously an underestimated decomposition pathway in peatlands, leading to increased CO production and accumulation of polyphenol-like compounds that could further inhibit extracellular enzyme activities and/or fuel the microbial communities with labile compounds. Further, increased temperatures can alter strategies of microbial communities for nutrient acquisition via changes in the activities of extracellular enzymes by priming SOM decomposition, leading to enhanced CO emission from peatlands. Therefore, coupled biotic and abiotic processes need to be incorporated into process-based climate models to predict the fate of SOM under elevated temperatures and to project the likely impacts of environmental change on northern peatlands and CO emissions.
• Baalousha, M., Sikder, M., Poulin, B. A., Tfaily, M. M., & Hess, N. J. (2022). Natural organic matter composition and nanomaterial surface coating determine the nature of platinum nanomaterial-natural organic matter corona. The Science of the total environment, 806(Pt 1), 150477.
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  Natural organic matter corona (NOM corona) is an interfacial area between nanomaterials (NMs) and the surrounding environment, which gives rise to NMs' unique surface identity. While the importance of the formation of natural organic matter (NOM) corona on engineered nanomaterials (NMs) to NM behavior, fate, and toxicity has been well-established, the understanding of how NOM molecular properties affect NOM corona composition remains elusive due to the complexity and heterogeneity of NOM. This is further complicated by the variation of NOMs from different origins. Here we use eight NOM isolates of different molecular composition and ultrahigh resolution Fourier-transform ion cyclotron resonance-mass spectrometry (ESI-FT-ICR-MS) to determine the molecular composition of platinum NM-NOM corona as a function of NOM composition and NM surface coating. We observed that the composition of PtNM-NOM corona varied with the composition of the original NOM. The percentage of NOM formulas that formed PVP-PtNM-NOM corona was higher than those formed citrate-PtNM-NOM corona, due to increased sorption of NOM formulas, in particular condensed hydrocarbons, to the PVP coating. The relative abundance of heteroatom formulas (CHON, CHOS, and CHOP) was higher in the PVP-PtNM-NOM corona than in citrate-PtNM-corona which was in turn higher than those in the original NOM isolate, indicating preferential partitioning of heteroatom-rich molecules to NM surfaces. The relative abundance of CHO, CHON, CHOS, CHOP and condensed hydrocarbons in PtNM-NOM corona increased with their increase in NOM isolates. Furthermore, PtNM-NOM corona is rich with compounds with high molecular weight. This study demonstrates that the composition and properties of PtNM-NOM corona depend on NOM molecular properties and PtNM surface coating. The results here provide evidence of molecular interactions between NOM and NMs, which are critical to understanding NM colloidal properties (e.g., surface charge and stability), interaction forces (e.g., van der Waals and hydrophobic), environmental behaviors (e.g., aggregation, dissolution, sulfidation, etc.), and biological effects (e.g., uptake, bioaccumulation, and toxicity).
• Campbell, T. P., Ulrich, D., Toyoda, J., Thompson, J., Munsky, B., Albright, M., Bailey, V. L., Tfaily, M. M., & Dunbar, J. (2022). Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition. Frontiers in Microbiology, 12.
• Cates, A. M., Jilling, A., Tfaily, M. M., & Jackson, R. D. (2022). Temperature and moisture alter organic matter composition across soil fractions. Geoderma, 409, 115628.
• Colleary, C., O'Reilly, S., Dolocan, A., Toyoda, J. G., Chu, R. K., Tfaily, M. M., Hochella, M. F., & Nesbitt, S. J. (2022). Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments. Biology, 11(9).
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  Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.
• Dohnalkova, A. C., Tfaily, M. M., Chu, R. K., Smith, A. P., Brislawn, C. J., Varga, T., Crump, A. R., Kovarik, L., Thomashow, L. S., Harsh, J. B., Keller, C. K., & Balogh-Brunstad, Z. (2022). Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-Scale Approach. Frontiers in Earth Science, 10.
• Fofana, A., Anderson, D., McCalley, C. K., Hodgkins, S., Wilson, R. M., Cronin, D., Raab, N., Torabi, M., Varner, R. K., Crill, P., Saleska, S. R., Chanton, J. P., Tfaily, M. M., & Rich, V. I. (2022). Mapping substrate use across a permafrost thaw gradient. Soil Biology and Biochemistry, 175, 108809.
• Honeker, L. K., Hildebrand, G. A., Fudyma, J. D., Daber, L. E., Hoyt, D., Flowers, S. E., Gil-Loaiza, J., Kübert, A., Bamberger, I., Anderton, C. R., Cliff, J., Leichty, S., AminiTabrizi, R., Kreuzwieser, J., Shi, L., Bai, X., Velickovic, D., Dippold, M. A., Ladd, S. N., , Werner, C., et al. (2022). Elucidating Drought-Tolerance Mechanisms in Plant Roots through H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques. Environmental science & technology.
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  As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in sp. and roots, signifying different defense mechanisms; sp. enhanced root structural defense via recalcitrant compounds including lignin, while enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, , a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.
• Hough, M., McCabe, S., Vining, S. R., Pickering Pedersen, E., Wilson, R. M., Lawrence, R., Chang, K. Y., Bohrer, G., , I. C., Riley, W. J., Crill, P. M., Varner, R. K., Blazewicz, S. J., Dorrepaal, E., Tfaily, M. M., Saleska, S. R., & Rich, V. I. (2022). Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland. Global change biology, 28(3), 950-968.
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  Permafrost thaw is a major potential feedback source to climate change as it can drive the increased release of greenhouse gases carbon dioxide (CO ) and methane (CH ). This carbon release from the decomposition of thawing soil organic material can be mitigated by increased net primary productivity (NPP) caused by warming, increasing atmospheric CO , and plant community transition. However, the net effect on C storage also depends on how these plant community changes alter plant litter quantity, quality, and decomposition rates. Predicting decomposition rates based on litter quality remains challenging, but a promising new way forward is to incorporate measures of the energetic favorability to soil microbes of plant biomass decomposition. We asked how the variation in one such measure, the nominal oxidation state of carbon (NOSC), interacts with changing quantities of plant material inputs to influence the net C balance of a thawing permafrost peatland. We found: (1) Plant productivity (NPP) increased post-thaw, but instead of contributing to increased standing biomass, it increased plant biomass turnover via increased litter inputs to soil; (2) Plant litter thermodynamic favorability (NOSC) and decomposition rate both increased post-thaw, despite limited changes in bulk C:N ratios; (3) these increases caused the higher NPP to cycle more rapidly through both plants and soil, contributing to higher CO and CH  fluxes from decomposition. Thus, the increased C-storage expected from higher productivity was limited and the high global warming potential of CH contributed a net positive warming effect. Although post-thaw peatlands are currently C sinks due to high NPP offsetting high CO release, this status is very sensitive to the plant community's litter input rate and quality. Integration of novel bioavailability metrics based on litter chemistry, including NOSC, into studies of ecosystem dynamics, is needed to improve the understanding of controls on arctic C stocks under continued ecosystem transition.
• Leewis, M., Lawrence, C. R., Schulz, M. S., Tfaily, M. M., Ayala-Ortiz, C. O., Flores, G. E., Mackelprang, R., & McFarland, J. W. (2022). The influence of soil development on the depth distribution and structure of soil microbial communities. Soil Biology and Biochemistry, 174, 108808.
• Meredith, L. K., & Tfaily, M. M. (2022). Capturing the microbial volatilome: an oft overlooked 'ome'. Trends in microbiology.
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  Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. Advances in VOC detection now allow simultaneous observation of the numerous VOCs constituting the 'volatilome' of microbial systems. We present a roadmap for integrating and advancing VOC and other 'omics approaches and highlight the potential for realtime VOC measurements to help overcome limitations in discrete 'omics sampling. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.
• Stegen, J. C., Fansler, S. J., Tfaily, M. M., Garayburu-Caruso, V. A., Goldman, A. E., Danczak, R. E., Chu, R. K., Renteria, L., Tagestad, J., & Toyoda, J. (2022). Organic matter transformations are disconnected between surface water and the hyporheic zone. Biogeosciences, 19(12), 3099--3110.
• Tfaily, M., Graf Grachet, N., Dontsova, K. M., & Amini-Tabrizi, R. (2022). Elevated temperatures drive abiotic and biotic degradation of organic matter in a peat bog under oxic conditions. Science of The Total Environment, 804, 150045.
• Wilhelm, R. C., Lynch, L., Webster, T. M., Schweizer, S., Inagaki, T. M., Tfaily, M. M., Kukkadapu, R., Hoeschen, C., Buckley, D. H., & Lehmann, J. (2022). Susceptibility of new soil organic carbon to mineralization during dry-wet cycling in soils from contrasting ends of a precipitation gradient. Soil Biology and Biochemistry, 169, 108681.
• Wilson, R. M., Hough, M. A., Verbeke, B. A., Hodgkins, S. B., Chanton, J. P., Saleska, S. D., Rich, V. I., Tfaily, M. M., & , I. C. (2022). Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. The Science of the total environment, 152757.
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  Peatlands are climate critical carbon (C) reservoirs that could become a C source under continued warming. A strong relationship between plant tissue chemistry and the soil organic matter (SOM) that fuels C gas emissions is inferred, but rarely examined at the molecular level. Here we compared Fourier transform infrared (FT-IR) spectroscopy measurements of solid phase functionalities in plants and SOM to ultra-high-resolution mass spectrometric analyses of plant and SOM water extracts across a palsa-bog-fen thaw and moisture gradient in an Arctic peatland. From these analyses we calculated the C oxidation state (NOSC), a measure which can be used to assess organic matter quality. Palsa plant extracts had the highest NOSC, indicating high quality, whereas extracts of Sphagnum, which dominated the bog, had the lowest NOSC. The percentage of plant compounds that are less bioavailable and accumulate in the peat, increases from palsa (25%) to fen (41%) to bog (47%), reflecting the pattern of percent Sphagnum cover. The pattern of NOSC in the plant extracts was consistent with the high number of consumed compounds in the palsa and low number of consumed compounds in the bog. However, in the FT-IR analysis of the solid phase bog peat, carbohydrate content was high implying high quality SOM. We explain this discrepancy as the result of low solubilization of bog SOM facilitated by the low pH in the bog which makes the solid phase carbohydrates less available to microbial decomposition. Plant-associated condensed aromatics, tannins, and lignin-like compounds declined in the unsaturated palsa peat indicating decomposition, but lignin-like compounds accumulated in the bog and fen peat where decomposition was presumably inhibited by the anaerobic conditions. A molecular-level comparison of the aboveground C sources and peat SOM demonstrates that climate-associated vegetation shifts in peatlands are important controls on the mechanisms underlying changing C gas emissions.
• Yang, Y. Y., Tfaily, M. M., Wilmoth, J. L., & Toor, G. S. (2022). Molecular characterization of dissolved organic nitrogen and phosphorus in agricultural runoff and surface waters. Water research, 219, 118533.
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  Agricultural runoff is a significant contributor to nitrogen (N) and phosphorus (P) pollution in water bodies. Limited information is available about the molecular characteristics of the dissolved organic N (DON) and P (DOP) species in the agricultural runoff and surface waters. We employed Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS) to investigate the changes in the molecular characteristics of DON and DOP at three watershed positions (upstream water, runoff from agricultural fields, and downstream waters). Across three watershed locations, more-bioavailable compounds (such as amino sugars, carbohydrates, lipids, and proteins) accounted for 95% of DON and 69-96% of DOP. Of the dissolved organic matter, runoff waters from agricultural fields contained the greatest proportion of DON formulas (20-25%) than upstream (18%) and downstream (13-14%) waters, indicating the presence of a greater diversity of DON species in the runoff. Various nutrient sources present in agricultural fields such as crop residues, soil organic matter, and transformed fertilizers likely contributed to the diverse composition of DON and DOP in the runoff, which were likely altered as the surface water traversed along the flow pathways in the watershed. The presence of more-bioavailable molecules detected in upstream compared to agricultural runoff and downstream waters suggests that photochemical and/or microbial processes likely altered the characteristics of DON and DOP compounds. The findings of this study increase our understanding of DON and DOP compounds lability and transformations in runoff and surface waters , which may be useful in quantifying the contribution of organic N and P sources to water quality impairment in aquatic ecosystems.
• Zhao, Q., Thompson, A. M., Callister, S. J., Tfaily, M. M., Bell, S. L., Hobbie, S. E., & Hofmockel, K. S. (2022). Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils. The Science of the total environment, 806(Pt 1), 150514.
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  Grassland soils store a substantial proportion of the global soil carbon (C) stock. The transformation of C in grassland soils with respect to chemical composition and persistence strongly regulate the predicted terrestrial-atmosphere C flux in global C biogeochemical cycling models. In addition, increasing atmospheric nitrogen (N) deposition alters C chemistry in grassland soils. However, there remains controversy about the importance of mineralogical versus biochemical preservation of soil C, as well as uncertainty regarding how grassland soil C chemistry responds to elevated N. This study used grassland soils with diverse soil organic matter (SOM) chemistries in an 8-month aerobic incubation experiment to evaluate whether the chemical composition of SOM converged across sites over time, and how SOM persistence responded to the N addition. This study demonstrates that over the course of incubation, the richness of labile compounds decreased in soils with less ferrihydrite content, whereas labile compounds were more persistent in ferrihydrite rich soils. In contrast, we found that the richness of more complex compounds increased over the incubation in most sites, independent of soil mineralogy. Moreover, we demonstrate the extent to which the diverse chemical composition of SOM converged among sites in response to microbial decomposition. N fertilization decreased soil respiration and inhibited the convergence of molecular composition across ecosystems by altering N demand for microbial metabolism and chemical interactions between minerals and organic molecules. This study provides original evidence that the decomposition and metabolism of labile organic molecules were largely regulated by soil mineralogy (physicochemical preservation), while the metabolism of more complex organic molecules was controlled by substrate complexity (biochemical preservation) independent to mineral-organic interactions. This study advanced our understanding of the dynamic biogeochemical cycling of C by unveiling that N addition dampened C respiration and diminished the convergence of SOM chemistry across diverse grassland ecosystems.
• Bahureksa, W., Tfaily, M. M., Boiteau, R. M., Young, R. B., Logan, M. N., McKenna, A. M., & Borch, T. (2021). Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation. Environmental science & technology, 55(14), 9637-9656.
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  The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.
• Buzzard, V., Gil-Loaiza, J., Graf Grachet, N., Talkington, H., Youngerman, C., Tfaily, M. M., & Meredith, L. K. (2021). Green infrastructure influences soil health: Biological divergence one year after installation. The Science of the total environment, 801, 149644.
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  Global threats to soils remain one of the greatest concerns and challenges of the 21st century. Built landscapes have profound local and global effects because they create urban heat islands, increase habitat fragmentation, and reduce biological diversity. Additionally, impervious surfaces alter natural watersheds and reduce infiltration increasing runoff that leads to erosion and soil degradation. To combat these effects, green infrastructure (GI) practices, like water harvesting rain gardens, are implemented in the Southwest United States to restore natural ecological function, yet little is known about how GI impacts soil health. Soil health can be measured using indicators that include physical, chemical, and biological characteristics that support ecosystem processes. This study aimed to evaluate changes in water holding capacity, bulk density, pH, electrical conductivity, Gibbs free energy, species richness and Shannon diversity in response to rain gardens that received different inputs (frequency and amount) and sources of harvested water (rain, municipal, greywater) one year after installation. We hypothesized that soil health indicators in GI diverge from the unaltered control treatment one year following installation. Although physical and chemical indicators were comparatively less sensitive to GI treatments than biological indicators, they varied within treatments after one year of GI management (pH increased: H = 36.37; p-value = 0.00; electrical conductivity decreased: H = 33.94; p-value = 0.00). Overall, we observed significantly higher soil microbial diversity (F = 4.29; p-value = 0.015) and richness (F = 4.02; p-value = 0.019) in surface soils in GI treatments after one year of management. Our findings suggest GI practices enhanced soil biological health which may lead to positive feedbacks that assist gradual changes in the abiotic environment thus enhancing soil health over time. These findings have broad implications for effectively assessing the success of GI management practices over short time periods using soil biological health indicators.
• Campbell, T. P., Ulrich, D. E., Toyoda, J., Thompson, J., Munsky, B., Albright, M. B., Bailey, V. L., Tfaily, M. M., & Dunbar, J. (2021). Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition. Frontiers in microbiology, 12, 799014.
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  Rapid microbial growth in the early phase of plant litter decomposition is viewed as an important component of soil organic matter (SOM) formation. However, the microbial taxa and chemical substrates that correlate with carbon storage are not well resolved. The complexity of microbial communities and diverse substrate chemistries that occur in natural soils make it difficult to identify links between community membership and decomposition processes in the soil environment. To identify potential relationships between microbes, soil organic matter, and their impact on carbon storage, we used sand microcosms to control for external environmental factors such as changes in temperature and moisture as well as the variability in available carbon that exist in soil cores. Using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) on microcosm samples from early phase litter decomposition, we found that protein- and tannin-like compounds exhibited the strongest correlation to dissolved organic carbon (DOC) concentration. Proteins correlated positively with DOC concentration, while tannins correlated negatively with DOC. Through random forest, neural network, and indicator species analyses, we identified 42 bacterial and 9 fungal taxa associated with DOC concentration. The majority of bacterial taxa (26 out of 42 taxa) belonged to the phylum Proteobacteria while all fungal taxa belonged to the phylum Ascomycota. Additionally, we identified significant connections between microorganisms and protein-like compounds and found that most taxa (12/14) correlated negatively with proteins indicating that microbial consumption of proteins is likely a significant driver of DOC concentration. This research links DOC concentration with microbial production and/or decomposition of specific metabolites to improve our understanding of microbial metabolism and carbon persistence.
• Fudyma, J. D., Chu, R. K., Graf, G. N., Stegen, J. C., & Tfaily, M. M. (2021). Coupled Biotic-Abiotic Processes Control Biogeochemical Cycling of Dissolved Organic Matter in the Columbia River Hyporheic Zone. Frontiers in Water, 2, 78.
• Fudyma, J. D., Toyoda, J. G., Chu, R. K., Weitz, K. K., Heyman, H. M., Eder, E., Hoyt, D. W., Gieschen, H., Graf, G. N., Wilson, R. M., & Tfaily, M. M. (2021). -Sequential abiotic-biotic processes drive organic carbon transformation in peat bogs. Journal of Geophysical Research: Biogeosciences, n/a(n/a), e2020JG006079.
• Honeker, L., Graves, K., Tfaily, M., Krechmer, J., & Meredith, L. (2021). The volatilome: a vital piece of the complete soil metabolome. Frontiers.
• Joshi, S. R., Morris, J. W., Tfaily, M. M., Young, R. P., & McNear, D. H. (2021). Low soil phosphorus availability triggers maize growth stage specific rhizosphere processes leading to mineralization of organic P. Plant and Soil.
• Li, H., Bölscher, T., Winnick, M., Tfaily, M. M., Cardon, Z. G., & Keiluweit, M. (2021). Correction to Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways. Environmental science & technology, 55(17), 12131.
• Li, H., Bölscher, T., Winnick, M., Tfaily, M. M., Cardon, Z. G., & Keiluweit, M. (2021). Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways. Environmental science & technology, 55(5), 3389-3398.
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  Most mineral-associated organic matter (MAOM) is protected against microbial attack, thereby contributing to long-term carbon storage in soils. However, the extent to which reactive compounds released by plants and microbes may destabilize MAOM and so enhance microbial access, as well as the underlying mechanisms, remain unclear. Here, we tested the ability of functionally distinct model exudates-ligands, reductants, and simple sugars-to promote microbial utilization of monomeric MAOM, bound via outer-sphere complexes to common iron and aluminum (hydr)oxide minerals. The strong ligand oxalic acid induced rapid MAOM mineralization, coinciding with greater sorption to and dissolution of minerals, suggestive of direct MAOM mobilization mechanisms. In contrast, the simple sugar glucose caused slower MAOM mineralization, but stimulated microbial activity and metabolite production, indicating an indirect microbially-mediated mechanism. Catechol, acting as reductant, promoted both mechanisms. While MAOM on ferrihydrite showed the greatest vulnerability to both direct and indirect mechanisms, MAOM on other (hydr)oxides was more susceptible to direct mechanisms. These findings suggest that MAOM persistence, and thus long-term carbon storage within a given soil, is not just a function of mineral reactivity but also depends on the capacity of plant roots and associated microbes to produce reactive compounds capable of triggering specific destabilization mechanisms.
• Lin, Y., Campbell, A., Bhattacharyya, A., DiDonato, N., Thompson, A., Tfaily, M., Nico, P., Silver, W., & Pett-Ridge, J. (2021). Differential effects of redox conditions on the decomposition of litter and soil organic matter. Biogeochemistry Letters.
• McGivern, B. B., Tfaily, M. M., Borton, M. A., Kosina, S. M., Daly, R. A., Nicora, C. D., Purvine, S. O., Wong, A. R., Lipton, M. S., Hoyt, D. W., Northen, T. R., Hagerman, A. E., & Wrighton, K. C. (2021). Decrypting bacterial polyphenol metabolism in an anoxic wetland soil. Nature communications, 12(1), 2466.
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  Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.
• Naughton, H., Keiluweit, M., Tfaily, M., Dynes, J., Regier, T., & Fendorf, S. (2021). Development of Energetic and Enzymatic Limitations on Microbial Carbon Cycling in Upland Soils. Biogeochemistry.
• Neurath, R. A., Pett-Ridge, J., Chu-Jacoby, I., Herman, D., Whitman, T., Nico, P. S., Lipton, A. S., Kyle, J., Tfaily, M. M., Thompson, A., & Firestone, M. K. (2021). Root Carbon Interaction with Soil Minerals Is Dynamic, Leaving a Legacy of Microbially Derived Residues. Environmental science & technology, 55(19), 13345-13355.
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  Minerals preserve the oldest, most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that roots, and differences in carbon source and microbial communities, influence mineral SOM associations over short timescales, we incubated permeable mineral bags in soil microcosms with and without plants, inside a CO labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or soil minerals isolated via density separation. Using C-nuclear magnetic resonance, Fourier transform ion cyclotron resonance mass spectrometry, and lipidomics, we traced carbon deposition onto minerals, characterizing total carbon, C enrichment, and SOM chemistry over three growth stages of . Carbon accumulation was rapid and mineral-dependent but slowed with time; the accumulated amount was not significantly affected by root presence. However, plant roots strongly shaped the chemistry of mineral-associated SOM. Minerals incubated in a plant rhizosphere were associated with a more diverse array of compounds (with different functional groups-carbonyl, aromatics, carbohydrates, and lipids) than minerals incubated in an unplanted bulk soil control. We also found that many of the lipids that sorbed to minerals were microbially derived, including many fungal lipids. Together, our data suggest that diverse rhizosphere-derived compounds may represent a transient fraction of mineral SOM, rapidly exchanging with mineral surfaces.
• Patel, K., Smith, P., Bond-Lamberty, B., Tfaily, M., Fansler, S., Bramer, L., Varga, T., & Bailey, V. (2021). Spatial access and resource limitations control carbon mineralization in soils. Soil Biology and Biochemistry.
• Rachel, R., Zayed, A., Crossen, K., Woodcroft, B., Tfaily, M., Raab, N., Hodgkins, S., Verbeke, B., Tyson, G., Crill, P., Saleska, S., Chanton, J., & Virginia, V. (2021). Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PloS ONE.
• Raczka, N. C., Piñeiro, J., Tfaily, M. M., Chu, R. K., Lipton, M. S., Pasa-Tolic, L., Morrissey, E., & Brzostek, E. (2021). Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil. Scientific reports, 11(1), 19320.
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  Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic capabilities, growth rates). Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater diversity of fungi and bacteria than ectomycorrhizal (ECM) soils. When incubated with C enriched substrates, substrate type drove shifts in which species were active decomposers and the abundance of metabolic products that were reduced or saturated in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and their ability to decompose and assimilate substrates. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.
• Sikder, M., Croteau, M., Poulin, B. A., & Baalousha, M. (2021). Effect of Nanoparticle Size and Natural Organic Matter Composition on the Bioavailability of Polyvinylpyrrolidone-Coated Platinum Nanoparticles to a Model Freshwater Invertebrate. Environmental Science & Technology.
• Waldo, N. B., Tfaily, M. M., Anderton, C., & Neumann, R. B. (2021). The importance of nutrients for microbial priming in a bog rhizosphere. Biogeochemistry.
• Webster, T., Wilhelm, R., Lynch, L., Schweizer, S., Inagaki, T., Tfaily, M., Kukkadapu, R., Hoeschen, C., Buckley, D., & Lehmann, J. (2021). Persistence of microbially-processed carbon in soils from contrasting ends of a precipitation gradient. Soil Biology and Biochemistry.
• Werner, C., Meredith, L. K., Ladd, S. N., Ingrisch, J., Kübert, A., van Haren, J., Bahn, M., Bailey, K., Bamberger, I., Beyer, M., Blomdahl, D., Byron, J., Daber, E., Deleeuw, J., Dippold, M. A., Fudyma, J., Gil-Loaiza, J., Honeker, L. K., Hu, J., , Huang, J., et al. (2021). Ecosystem fluxes during drought and recovery in an experimental forest. Science (New York, N.Y.), 374(6574), 1514-1518.
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  [Figure: see text].
• Werner, C., Meredith, L. K., Ladd, S. N., Ingrisch, J., Kübert, A., van, H. J., Bahn, M., Bailey, K., Bamberger, I., Beyer, M., Blomdahl, D., Byron, J., Daber, E., Deleeuw, J., Dippold, M. A., Fudyma, J., Gil-Loaiza, J., Honeker, L. K., Hu, J., , Huang, J., et al. (2021). Ecosystem fluxes during drought and recovery in an experimental forest. Science, 374(6574), 1514-1518.
• Wilson, R. M., Griffiths, N. A., Visser, A., McFarlane, K. J., Sebestyen, S. D., Oleheiser, K. C., Bosman, S., Hopple, A. M., Tfaily, M. M., Kolka, R. K., Hanson, P. J., Kostka, J. E., Bridgham, S. D., Keller, J. K., & Chanton, J. P. (2021). Radiocarbon Analyses Quantify Peat Carbon Losses With Increasing Temperature in a Whole Ecosystem Warming Experiment. Journal of Geophysical Research: Biogeosciences, 126(11), e2021JG006511.
• Wilson, R. M., Tfaily, M. M., Kolton, M., Johnston, E. R., Petro, C., Zalman, C. A., Hanson, P. J., Heyman, H. M., Kyle, J. E., Hoyt, D. W., Eder, E. K., Purvine, S. O., Kolka, R. K., Sebestyen, S. D., Griffiths, N. A., Schadt, C. W., Keller, J. K., Bridgham, S. D., Chanton, J. P., & Kostka, J. E. (2021). Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment. Proceedings of the National Academy of Sciences of the United States of America, 118(25).
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  In this study, a suite of complementary environmental geochemical analyses, including NMR and gas chromatography-mass spectrometry (GC-MS) analyses of central metabolites, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of secondary metabolites, and lipidomics, was used to investigate the influence of organic matter (OM) quality on the heterotrophic microbial mechanisms controlling peatland CO, CH, and CO:CH porewater production ratios in response to climate warming. Our investigations leverage the Spruce and Peatland Responses under Changing Environments (SPRUCE) experiment, where air and peat warming were combined in a whole-ecosystem warming treatment. We hypothesized that warming would enhance the production of plant-derived metabolites, resulting in increased labile OM inputs to the surface peat, thereby enhancing microbial activity and greenhouse gas production. Because shallow peat is most susceptible to enhanced warming, increases in labile OM inputs to the surface, in particular, are likely to result in significant changes to CO and CH dynamics and methanogenic pathways. In support of this hypothesis, significant correlations were observed between metabolites and temperature consistent with increased availability of labile substrates, which may stimulate more rapid turnover of microbial proteins. An increase in the abundance of methanogenic genes in response to the increase in the abundance of labile substrates was accompanied by a shift toward acetoclastic and methylotrophic methanogenesis. Our results suggest that as peatland vegetation trends toward increasing vascular plant cover with warming, we can expect a concomitant shift toward increasingly methanogenic conditions and amplified climate-peatland feedbacks.
• AminiTabrizi, R., Wilson, R. M., Fudyma, J. D., Hodgkins, S. B., Heyman, H. M., Rich, V. I., Saleska, S. R., Chanton, J. P., & Tfaily, M. M. (2020). Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas Emissions Across a Permafrost Thaw Gradient in Northern Sweden. Frontiers in Earth Science, 8, 381.
• Bolduc, B., Hodgkins, S., Varner, R., Crill, P., McCalley, C., Chanton, J., Tyson, G., Riley, W., Palace, M., Duhaime, M., Hough, M., Coordinators, I. P., (Malak Tfaily), I. T., Team, A. P., Saleska, S., Sullivan, M., & Rich, V. (2020). he IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ, 8:e9467. doi:https://doi.org/10.7717/peerj.9467
• Corbett, J. E., Tfaily, M., Ouni, S., & Peteel, D. (2019). Do shifts in vegetation affect dissolved organic carbon quality in a coastal marsh along the Hudson River Estuary, NY. Wetlands.
• Danczak, R. E., Chu, R. K., Fansler, S. J., Goldman, A. E., Graham, E. B., Tfaily, M. M., Toyoda, J., & Stegen, J. C. (2020). Using metacommunity ecology to understand environmental metabolomes. Nature communications, 11(1), 6369.
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  Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics 'meta-metabolome ecology' and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.
• LaCroix, R. E., Walpen, N., Sander, M., Tfaily, M. M., Blanchard, J. L., & Keiluweit, M. (2020). Long-Term Warming Decreases Redox Capacity of Soil Organic Matter. Environmental Science & Technology Letters.
• Lybrand, R. A., Fedenko, J., Tfaily, M., & Rao, S. (2020). Soil properties and biochemical composition of ground-dwelling bee nests in agricultural settings. Soil Science Society of America Journal, 84(4), 1139-1152.
• Rue, G. P., Darling, J. P., Graham, E., Tfaily, M., & McKnight, D. M. (2020). Dynamic changes in dissolved organic matter composition in a Mountain Lake under ice cover and relationships to changes in nutrient cycling and phytoplankton community composition. Aquat Sci, 82: 15. doi:https://doi.org/10.1007/s00027-019-0687-3
• Xu, J., Roley, S. S., Tfaily, M. M., Chu, R. K., & Tiedje, J. M. (2020). Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales. Soil Biology and Biochemistry, 150, 107986.
• Zhao, Q., Callister, S. J., Thompson, A. M., Kukkadapu, R. K., Tfaily, M. M., Bramer, L. M., Qafoku, N. P., Bell, S. L., Hobbie, S. E., Seabloom, E. W., Borer, E. T., & Hofmockel, K. S. (2020). Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites. Science of The Total Environment, 736, 137839.
• Zhao, Q., Callister, S. J., Thompson, A. M., Kukkadapu, R. K., Tfaily, M. M., Bramer, L. M., Qafoku, N. P., Bell, S. L., Hobbie, S. E., Seabloom, E. W., Borer, E. T., & Hofmockel, K. S. (2020). Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites. The Science of the total environment, 736, 137839.
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  Soil organic matter (SOM) dynamics are central to soil biogeochemistry and fertility. The retention of SOM is governed initially by interactions with minerals, which mediate the sorption of chemically diverse organic matter (OM) molecules via distinct surface areas and chemical functional group availabilities. Unifying principles of mineral-OM interactions remain elusive because of the multi-layered nature of biochemical-mineral interactions that contribute to soil aggregate formation and the heterogeneous nature of soils among ecosystems. This study sought to understand how soil mineralogy as well as nitrogen (N) enrichment regulate OM composition in grassland soils. Using a multi-site grassland experiment, we demonstrate that the composition of mineral-associated OM depended on the clay content and specific mineral composition in soils across the sites. With increasing abundance of ferrihydrite (Fh) across six different grassland locations, OM in the hydrophobic zone became more enriched in lipid- and protein-like compounds, whereas the kinetic zone OM became more enriched in lignin-like molecules. These relationships suggest that the persistence of various classes of OM in soils may depend on soil iron mineralogy and provide experimental evidence to support conceptual models of zonal mineral-OM associations. Experimental N addition disrupted the accumulation of protein-like molecules in the hydrophobic zone and the positive correlation of lignin-like molecules in the kinetic zone with Fh content, compared to unfertilized soils. These data suggest that mineralogy and clay content together influence the chemical composition not only of mineral-associated OM, but also of soluble compounds within the soil matrix. If these relationships are prevalent over larger spatial and temporal scales, they provide a foundation for understanding SOM cycling and persistence under a variety of environmental contexts.
• Arredondo, M. G., Lawrence, C. R., Schulz, M. S., Tfaily, M. M., Kukkadapu, R., Jones, M. E., Boye, K., & Keiluweit, M. (2019). Root-driven weathering impacts on mineral-organic associations in deep soils over pedogenic time scales. Geochimica et Cosmochimica Acta, 263, 68 - 84.
• Clair, G., Reehl, S., Stratton, K. G., Monroe, M. E., Tfaily, M. M., Ansong, C., & Kyle, J. E. (2019). Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data. Bioinformatics (Oxford, England), 35(21), 4507-4508.
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  Here we introduce Lipid Mini-On, an open-source tool that performs lipid enrichment analyses and visualizations of lipidomics data. Lipid Mini-On uses a text-mining process to bin individual lipid names into multiple lipid ontology groups based on the classification (e.g. LipidMaps) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches. Lipid classes can be added to customize the user's database and remain updated as new lipid classes are discovered. Visualization of results is available for all classification options (e.g. lipid subclass and individual fatty acid chains). Results are also visualized through an editable network of relationships between the individual lipids and their associated lipid ontology terms. The utility of the tool is demonstrated using biological (e.g. human lung endothelial cells) and environmental (e.g. peat soil) samples.
• Fudyma, J. D., Lyon, J., AminiTabrizi, R., Gieschen, H., Chu, R. K., Hoyt, D. W., Kyle, J. E., Toyoda, J., Tolic, N., Heyman, H. M., Hess, N. J., Metz, T. O., & Tfaily, M. M. (2019). Untargeted metabolomic profiling of reveals novel antimicrobial metabolites. Plant direct, 3(11), e00179.
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  mosses dominate peatlands by employing harsh ecosystem tactics to prevent vascular plant growth and microbial degradation of these large carbon stores. Knowledge about -produced metabolites, their structure and their function, is important to better understand the mechanisms, underlying this carbon sequestration phenomenon in the face of climate variability. It is currently unclear which compounds are responsible for inhibition of organic matter decomposition and the mechanisms by which this inhibition occurs. Metabolite profiling of was performed using two types of mass spectrometry (MS) systems and H nuclear magnetic resonance spectroscopy (H NMR). Lipidome profiling was performed using LC-MS/MS. A total of 655 metabolites, including one hundred fifty-two lipids, were detected by NMR and LC-MS/MS-329 of which were novel metabolites (31 unknown lipids). metabolite profile was composed mainly of acid-like and flavonoid glycoside compounds, that could be acting as potent antimicrobial compounds, allowing to control its environment. metabolite composition comparison against previously known antimicrobial plant metabolites confirmed this trend, with seventeen antimicrobial compounds discovered to be present in , the majority of which were acids and glycosides. Biological activity of these compounds needs to be further tested to confirm antimicrobial qualities. Three fungal metabolites were identified providing insights into fungal colonization that may benefit . Characterizing the metabolite profile of provided a baseline to understand the mechanisms in which acts on its environment, its relation to carbon sequestration in peatlands, and provide key biomarkers to predict peatland C store changes (sequestration, emissions) as climate shifts.
• Hopple, A., Pfeifer-Meister, L., Zalmar, C., Keller, J., Tfaily, M., WIilson, R., Chanton, J., & bridgham, S. (2019). Does dissolved organic matter or solid peat fuel anaerobic respiration in peatlands?. Geoderma.
• Kane, E. S., Veverica, T. J., Tfaily, M. M., Lilleskov, E. A., Meingast, K. M., Kolka, R. K., Daniels, A. L., & Chimner, R. A. (2019). Reduction-Oxidation Potential and Dissolved Organic Matter Composition in Northern Peat Soil: Interactive Controls of Water Table Position and Plant Functional Groups. Journal of Geophysical Research: Biogeosciences, 124(11), 3600-3617.
• LaCroix, R. E., Tfaily, M. M., McCreight, M., Jones, M. E., Spokas, L., & Keiluweit, M. (2019). Shifting mineral and redox controls on carbon cycling in seasonally flooded mineral soils. Biogeosciences, 16(13), 2573--2589.
• Nuñez, J. R., Colby, S. M., Thomas, D. G., Tfaily, M. M., Tolic, N., Ulrich, E. M., Sobus, J. R., Metz, T. O., Teeguarden, J. G., & Renslow, R. S. (2019). Evaluation of Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. Journal of chemical information and modeling, 59(9), 4052-4060.
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  The current gold standard for unambiguous molecular identification in metabolomics analysis is comparing two or more orthogonal properties from the analysis of authentic reference materials (standards) to experimental data acquired in the same laboratory with the same analytical methods. This represents a significant limitation for comprehensive chemical identification of small molecules in complex samples. The process is time consuming and costly, and the majority of molecules are not yet represented by standards. Thus, there is a need to assemble evidence for the presence of small molecules in complex samples through the use of libraries containing calculated chemical properties. To address this need, we developed a Multi-Attribute Matching Engine (MAME) and a library derived in part from our chemical library engine (ISiCLE). Here, we describe an initial evaluation of these methods in a blinded analysis of synthetic chemical mixtures as part of the U.S. Environmental Protection Agency's (EPA) Non-Targeted Analysis Collaborative Trial (ENTACT, Phase 1). For molecules in all mixtures, the initial blinded false negative rate (FNR), false discovery rate (FDR), and accuracy were 57%, 77%, and 91%, respectively. For high evidence scores, the FDR was 35%. After unblinding of the sample compositions, we optimized the scoring parameters to better exploit the available evidence and increased the accuracy for molecules suspected as present. The final FNR, FDR, and accuracy were 67%, 53%, and 96%, respectively. For high evidence scores, the FDR was 10%. This study demonstrates that multiattribute matching methods in conjunction with libraries may one day enable reduced reliance on experimentally derived libraries for building evidence for the presence of molecules in complex samples.
• Nuñez, J., Colby, S., thomas, D., Tfaily, M., Tolic, N., Ulrich, E., Sobus, J., Metz, T., Teeguarden, J., & Renslow, R. (2019). Advancing Standards-Free Methods for the Identification of Small Molecules in Complex Samples. Analytical Chemistry.
• Rivas-Ubach, A., Liu, Y., Steiner, A. L., Sardans, J., Tfaily, M. M., Kulkarni, G., Kim, Y. M., Bourrianne, E., Paša-Tolić, L., Peñuelas, J., & Guenther, A. (2019). Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research. Environmental monitoring and assessment, 191(2), 78.
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  Aerosol particles play important roles in processes controlling the composition of the atmosphere and function of ecosystems. A better understanding of the composition of aerosol particles is beginning to be recognized as critical for ecological research to further comprehend the link between aerosols and ecosystems. While chemical characterization of aerosols has been practiced in the atmospheric science community, detailed methodology tailored to the needs of ecological research does not exist yet. In this study, we describe an efficient methodology (atmo-ecometabolomics), in step-by-step details, from the sampling to the data analyses, to characterize the chemical composition of aerosol particles, namely atmo-metabolome. This method employs mass spectrometry platforms such as liquid and gas chromatography mass spectrometries (MS) and Fourier transform ion cyclotron resonance MS (FT-ICR-MS). For methodology evaluation, we analyzed aerosol particles collected during two different seasons (spring and summer) in a low-biological-activity ecosystem. Additionally, to further validate our methodology, we analyzed aerosol particles collected in a more biologically active ecosystem during the pollination peaks of three different representative tree species. Our statistical results showed that our sampling and extraction methods are suitable for characterizing the atmo-ecometabolomes in these two distinct ecosystems with any of the analytical platforms. Datasets obtained from each mass spectrometry instrument showed overall significant differences of the atmo-ecometabolomes between spring and summer as well as between the three pollination peak periods. Furthermore, we have identified several metabolites that can be attributed to pollen and other plant-related aerosol particles. We additionally provide a basic guide of the potential use ecometabolomic techniques on different mass spectrometry platforms to accurately analyze the atmo-ecometabolomes for ecological studies. Our method represents an advanced novel approach for future studies in the impact of aerosol particle chemical compositions on ecosystem structure and function and biogeochemistry.
• Saup, C. M., Bryant, S. R., Nelson, A. R., Harris, K. D., Sawyer, A. H., Christensen, J. N., Tfaily, M. M., Williams, K. H., & Wilkins, M. J. (2019). Hyporheic Zone Microbiome Assembly Is Linked to Dynamic Water Mixing Patterns in Snowmelt-Dominated Headwater Catchments. Journal of Geophysical Research: Biogeosciences, 124(11), 3269-3280.
• Sengupta, A., Indivero, J., Gunn, C., Tfaily, M. M., Chu, R. K., Toyoda, J., Bailey, V. L., Ward, N. D., & Stegen, J. C. (2019). Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities. Biogeosciences, 16(19), 3911--3928.
• Shen, Y., Zhao, R., Tolić, N., Tfaily, M. M., Robinson, E. W., Boiteau, R., Paša-Tolić, L., & Hess, N. J. (2019). Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter. Faraday discussions, 218(0), 157-171.
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  We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil. For example, in a single experiment, >6000 molecular formulas can be assigned based upon FTICR MS data from 1-50 μL of soil samples (roughly 1-50 mg of soil, dependent on soil density), nearly twice that typically obtained from direct infusion liquid solvent extraction (LSE) from an order of magnitude larger volume of the same soil. The detected species consisted predominately of lipid-like, lignin-like and protein-like compounds, based on their O/C and H/C ratios, with predominantly CHO and CHONP molecular compositions. These results clearly demonstrate that SFE has the potential to effectively extract a variety of molecular species and could become an important member of a suite of extraction methods for studying SOM and other natural organic matter. This is especially true when comprehensive coverage, minimal sample volumes, and high sensitivity are required, or when the presence of organic solvent residue in residual soil is problematic. The SFE based extraction protocol could potentially enable spatially resolved characterization of organic matter in soil with a resolution of ∼1 mm3 to facilitate studies probing the spatial heterogeneity of soil.
• Tfaily, M. M., Wilson, R. M., Brewer, H. M., Chu, R. K., Heyman, H. M., Hoyt, D. W., Kyle, J. E., & Purvine, S. O. (2019). Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures. Journal of visualized experiments : JoVE.
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  Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO2] and methane [CH4]) production resulting from the decomposition of NOM, a molecular-level characterization coupled with microbial proteome analyses is necessary. Further, climate and environmental changes are expected to perturb natural ecosystems, potentially upsetting complex interactions that influence both the supply of organic matter substrates and the microorganisms performing the transformations. A detailed molecular characterization of the organic matter, microbial proteomics, and the pathways and transformations by which organic matter is decomposed will be necessary to predict the direction and magnitude of the effects of environmental changes. This article describes a methodological throughput for comprehensive metabolite characterization in a single sample by direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography mass spectrometry (LC-MS), and proteomics analysis. This approach results in a fully-paired dataset which improves statistical confidence for inferring pathways of organic matter decomposition, the resulting CO2 and CH4 production rates, and their responses to environmental perturbation. Herein we present results of applying this method to NOM samples collected from peatlands; however, the protocol is applicable to any NOM sample (e.g., peat, forested soils, marine sediments, etc.).
• Tfaily, M., Clair, G., Reehl, S., Stratton, K., Monroa, M., Ansong, C., & Kyle, J. (2019). Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data. Bioinformatics.
• Tfaily, M., Rivas-Ubach, A., Liu, Y., Steiner, A., Sardans, J., Kulkarni, G., Kim, Y., Bourrianne, E., Paša-Tolić, L., Peñuelas, J., & Guenther, A. (2019). Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research. Environmental Monitoring and Assessment, 191(78). doi:https://doi.org/10.1007/s10661-019-7205-x
• Tfaily, M., Wilson, R., Brewer, H., Chu, R., Heino, H., Hoyt, D., Kyle, J., & Purvine, S. (2019). Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures. J. Vis. Exp, 143, e59035. doi:10.3791/59035
• Zhou, C., Liu, Y., Liu, C., Liu, Y., & Tfaily, M. M. (2019). Compositional changes of dissolved organic carbon during its dynamic desorption from hyporheic zone sediments. Science of The Total Environment, 658, 16 - 23.
• Bhattacharyya, A., Campbell, A. N., Tfaily, M. M., Lin, Y., Kukkadapu, R. K., Silver, W., Nico, P. S., & Pett-Ridge, J. (2018). Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils. Environmental science & technology.
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  Oscillating redox conditions are a common feature of humid tropical forest soils, driven by an ample supply and dynamics of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. However, the net result of variable soil redox regimes on iron (Fe) mineral dynamics and associated carbon (C) forms and fluxes is poorly understood in tropical soils. Using a 44-day redox incubation experiment with humid tropical forest soils from Puerto Rico, we examined patterns in Fe and C transformations under four redox regimes: static anoxic, 'flux 4-day' (4d oxic, 4d anoxic), 'flux 8-day' (8d oxic, 4d anoxic) and static oxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides, and led to an increase in soluble Fe(II) and amorphous Fe oxide pools. Preferential dissolution of the less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic C, presumably due to acidification or direct release of organic matter (OM) from dissolving Fe(III) mineral phases. The average nominal oxidation state of water-soluble C was lowest under persistent anoxic conditions, suggesting that more reduced organic compounds were metabolically unavailable for microbial consumption under reducing conditions. Anoxic soil compounds had high H/C values (and were similar to lignin-like compounds) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic C was highest in static oxic soils. These results show how Fe minerals and Fe-OM interactions in tropical soils are highly sensitive to variable redox effects. Shifting soil oxygen availability rapidly impacted exchanges between mineral-sorbed and aqueous C pools, increased the dissolved organic C pool under anoxic conditions implying that the periodicity of low-redox events may control the fate of C in wet tropical soils.
• Bottos, E. M., Kennedy, D. W., Romero, E. B., Fansler, S. J., Brown, J. M., Bramer, L. M., Chu, R. K., Tfaily, M. M., Jansson, J. K., & Stegen, J. C. (2018). Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. FEMS microbiology ecology, 94(8).
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  Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw. We hypothesize that permafrost communities are shaped by physical constraints imposed by prolonged freezing, and exhibit spatial distributions that reflect dispersal limitation and selective pressures associated with these physical constraints. To test this, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16) and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2 = 0.14, P = 0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings suggest that the dominant processes shaping microbial communities in permafrost result from the stability of the permafrost environment, which imposes dispersal and thermodynamic constraints.
• Boye, K., Herrmann, A., Schaefer, M., Tfaily, M., & Fendorf, S. (2018). Discerning Microbially Mediated Processes During Redox Transitions in Flooded Soils Using Carbon and Energy Balances. Front. Environ. Sci..
• Davis, J., Heckman, K., Fox, P., Nico, P., & Tfaily, M. (2018). Characterization of Natural Organic Matter in Low-Carbon Sediments.. ESS-DIVE, Watershed Function SFA. doi:doi:10.21952/WTR/1470442
• Graham, E. B., Crump, A. R., Kennedy, D. W., Arntzen, E., Fansler, S., Purvine, S. O., Nicora, C. D., Nelson, W., Tfaily, M. M., & Stegen, J. C. (2018). Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone. The Science of the total environment, 642, 742-753.
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  Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C or N content only (explaining 67% vs. 42% and 37% of variation respectively), and bulk C and N did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.
• Li, L., He, Z. L., Tfaily, M. M., Inglett, P., & Stoffella, P. J. (2018). Spatial-temporal variations of dissolved organic nitrogen molecular composition in agricultural runoff water. Water research, 137, 375-383.
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  Leaching of dissolved organic nitrogen (DON) has been reported as a pathway of N loss from agriculture, but the molecular composition of DON in agricultural water is poorly understood. Runoff water samples were collected from citrus grove furrows (CGF), ditches (CGD) and pasture ditches (PD) in four seasons. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) was used to investigate molecular composition of DON. Chemodiversity index of DON had spatiotemporal variations, while the molecular composition of total DON showed minimal variations, except for PD in November. Lignin derivatives constituted 61% of the total DON compounds. Relative abundance of aliphatic compounds, char and condensed aromatics of unique DON compounds varied spatiotemporally and had a significant correlation with DON concentration. Aromaticity index decreased from CGF to connected CGD, implying that photodegradation is possibly the dominant process that alters molecular composition of aquatic DON during the transport. Significant differences in unique DON composition between CGD and PD indicates that fertilization and land use affect DON composition. The information on molecular characterization of DON should be useful for tracking DON source and developing technologies to remove DON in the agricultural runoff water.
• Orton, D. J., Tfaily, M. M., Moore, R. J., LaMarche, B. L., Zheng, X., Fillmore, T. L., Chu, R. K., Weitz, K. K., Monroe, M. E., Kelly, R. T., Smith, R. D., & Baker, E. S. (2018). A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements. Analytical chemistry, 90(1), 737-744.
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  To better understand disease conditions and environmental perturbations, multiomic studies combining proteomic, lipidomic, and metabolomic analyses are vastly increasing in popularity. In a multiomic study, a single sample is typically extracted in multiple ways, and various analyses are performed using different instruments, most often based upon mass spectrometry (MS). Thus, one sample becomes many measurements, making high throughput and reproducible evaluations a necessity. One way to address the numerous samples and varying instrumental conditions is to utilize a flow injection analysis (FIA) system for rapid sample injections. While some FIA systems have been created to address these challenges, many have limitations such as costly consumables, low pressure capabilities, limited pressure monitoring, and fixed flow rates. To address these limitations, we created an automated, customizable FIA system capable of operating at a range of flow rates (∼50 nL/min to 500 μL/min) to accommodate both low- and high-flow MS ionization sources. This system also functions at varying analytical throughputs from 24 to 1200 samples per day to enable different MS analysis approaches. Applications ranging from native protein analyses to molecular library construction were performed using the FIA system, and results showed a highly robust and reproducible platform capable of providing consistent performance over many days without carryover, as long as washing buffers specific to each molecular analysis were utilized.
• Reynolds, L. L., Lajtha, K., Bowden, R. D., Tfaily, M. M., Johnson, B. R., & Bridgham, S. D. (2018). The Path From Litter to Soil: Insights Into Soil C Cycling From Long-Term Input Manipulation and High-Resolution Mass Spectrometry. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 123(5), 1486-1497.
• Stegen, J. C., Johnson, T., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Fansler, S. J., Graham, E. B., Kennedy, D. W., Resch, C. T., Tfaily, M., & Zachara, J. (2018). Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology. Nature communications, 9(1), 585.
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  The hyporheic corridor (HC) encompasses the river-groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology-biochemistry-microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW-RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.
• Stegen, J. C., Johnson, T., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Fansler, S. J., Graham, E. B., Kennedy, D. W., Resch, C. T., Tfaily, M., & Zachara, J. (2018). Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology. Nature communications, 9(1), 1034.
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  The original version of this Article contained an error in Fig. 6e, in which the text in the legend was omitted. This has been corrected in both the PDF and HTML versions of the article.
• Tfaily, M. M., Hess, N. J., Koyama, A., & Evans, R. D. (2018). Elevated [CO2] changes soil organic matter composition and substrate diversity in an arid ecosystem. GEODERMA, 330, 1-8.
• Tfaily, M. M., Wilson, R. M., Cooper, W. T., Kostka, J. E., Hanson, P., & Chanton, J. P. (2018). Vertical Stratification of Peat Pore Water Dissolved Organic Matter Composition in a Peat Bog in Northern Minnesota. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 123(2), 479-494.
• Tfaily, M., Stegen, J., Goldman, A., Blackburn, S., Chu, R., Danczak, R., Garayburu-Caruso, V., Graham, E., Grieshauber, C., Lin, X., & Morad, J. (2018). WHONDRS Surface Water Sampling for Metabolite Biogeography. Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS).. ESS-DIVE. doi:doi:10.15485/1484811
• Wilson, R. M., & Tfaily, M. M. (2018). Advanced Molecular Techniques Provide New Rigorous Tools for Characterizing Organic Matter Quality in Complex Systems. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 123(6), 1790-1795.
• Yao, Q., Li, Z., Song, Y., Wright, S. J., Guo, X., Tringe, S. G., Tfaily, M. M., Paša-Tolić, L., Hazen, T. C., Turner, B. L., Mayes, M. A., & Pan, C. (2018). Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nature ecology & evolution, 2(3), 499-509.
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  Phosphorus is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient soils. In contrast, microbial communities in the phosphorus-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.
• Zalman, C., Keller, J. K., Tfaily, M., Kolton, M., Pfeifer-Meister, L., Wilson, R. M., Lin, X., Chanton, J., Kostka, J. E., Gill, A., Finzi, A. C., Hopple, A. M., Bohannan, B., & Bridgham, S. D. (2018). Small differences in ombrotrophy control regional-scale variation in methane cycling among Sphagnum-dominated peatlands. BIOGEOCHEMISTRY, 139(2), 155-177.
• Bailey, V. L., Smith, A. P., Tfaily, M., Fansler, S. J., & Bond-Lamberty, B. (2017). Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains. SOIL BIOLOGY & BIOCHEMISTRY, 107, 133-143.
• Boye, K., Noel, V., Tfaily, M. M., Bone, S. E., Williams, K. H., Bargar, J. R., & Fendorf, S. (2017). Thermodynamically controlled preservation of organic carbon in floodplains. NATURE GEOSCIENCE, 10(6), 415-+.
• Dalcin Martins, P., Hoyt, D. W., Bansal, S., Mills, C. T., Tfaily, M., Tangen, B. A., Finocchiaro, R. G., Johnston, M. D., McAdams, B. C., Solensky, M. J., Smith, G. J., Chin, Y. P., & Wilkins, M. J. (2017). Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands. Global change biology, 23(8), 3107-3120.
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  Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co-occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate-reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions.
• Graham, E. B., Tfaily, M. M., Crump, A. R., Goldman, A. E., Bramer, L. M., Arntzen, E., Romero, E., Resch, C. T., Kennedy, D. W., & Stegen, J. C. (2017). Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 122(12), 3188-3205.
• Smith, A. P., Bond-Lamberty, B., Benscoter, B. W., Tfaily, M. M., Hinkle, C. R., Liu, C., & Bailey, V. L. (2017). Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. NATURE COMMUNICATIONS, 8.
• Smith, A. P., Bond-Lamberty, B., Benscoter, B. W., Tfaily, M. M., Hinkle, C. R., Liu, C., & Bailey, V. L. (2017). Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature communications, 8(1), 1335.
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  Droughts and other extreme precipitation events are predicted to increase in intensity, duration, and extent, with uncertain implications for terrestrial carbon (C) sequestration. Soil wetting from above (precipitation) results in a characteristically different pattern of pore-filling than wetting from below (groundwater), with larger, well-connected pores filling before finer pore spaces, unlike groundwater rise in which capillary forces saturate the finest pores first. Here we demonstrate that pore-scale wetting patterns interact with antecedent soil moisture conditions to alter pore-scale, core-scale, and field-scale C dynamics. Drought legacy and wetting direction are perhaps more important determinants of short-term C mineralization than current soil moisture content in these soils. Our results highlight that microbial access to C is not solely limited by physical protection, but also by drought or wetting-induced shifts in hydrologic connectivity. We argue that models should treat soil moisture within a three-dimensional framework emphasizing hydrologic conduits for C and resource diffusion.
• Staley, C., Ferrieri, A. P., Tfaily, M. M., Cui, Y., Chu, R. K., Wang, P., Shaw, J. B., Ansong, C. K., Brewer, H., Norbeck, A. D., Markillie, M., do Amaral, F., Tuleski, T., Pellizzaro, T., Agtuca, B., Ferrieri, R., Tringe, S. G., Paša-Tolić, L., Stacey, G., & Sadowsky, M. J. (2017). Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome, 5(1), 65.
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  The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.
• Tfaily, M. M., Chu, R. K., Toyoda, J., Tolic, N., Robinson, E. W., Pasa-Tolic, L., & Hess, N. J. (2017). Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry. ANALYTICA CHIMICA ACTA, 972, 54-61.
• Tfaily, M. M., Chu, R. K., Toyoda, J., Tolić, N., Robinson, E. W., Paša-Tolić, L., & Hess, N. J. (2017). Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry. Analytica chimica acta, 972, 54-61.
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  A vast number of organic compounds are present in soil organic matter (SOM) and play an important role in the terrestrial carbon cycle, facilitate interactions between organisms, and represent a sink for atmospheric CO. The diversity of different SOM compounds and their molecular characteristics is a function of the organic source material and biogeochemical history. By understanding how SOM composition changes with sources and the processes by which it is biogeochemically altered in different terrestrial ecosystems, it may be possible to predict nutrient and carbon cycling, response to system perturbations, and impact of climate change will have on SOM composition. In this study, a sequential chemical extraction procedure was developed to reveal the diversity of organic matter (OM) in different ecosystems and was compared to the previously published protocol using parallel solvent extraction (PSE). We compared six extraction methods using three sample types, peat soil, spruce forest soil and river sediment, so as to select the best method for extracting a representative fraction of organic matter from soils and sediments from a wide range of ecosystems. We estimated the extraction yield of dissolved organic carbon (DOC) by total organic carbon analysis, and measured the composition of extracted OM using high resolution mass spectrometry. This study showed that OM composition depends primarily on soil and sediment characteristics. Two sequential extraction protocols, progressing from polar to non-polar solvents, were found to provide the highest number and diversity of organic compounds extracted from the soil and sediments. Water (HO) is the first solvent used for both protocols followed by either co-extraction with methanol-chloroform (MeOH-CHCl) mixture, or acetonitrile (ACN) and CHCl sequentially. The sequential extraction protocol developed in this study offers improved sensitivity, and requires less sample compared to the PSE workflow where a new sample is used for each solvent type. Furthermore, a comparison of SOM composition from the different sample types revealed that our sequential protocol allows for ecosystem comparisons based on the diversity of compounds present, which in turn could provide new insights about source and processing of organic compounds in different soil and sediment types.
• Tolić, N., Liu, Y., Liyu, A., Shen, Y., Tfaily, M. M., Kujawinski, E. B., Longnecker, K., Kuo, L. J., Robinson, E. W., Paša-Tolić, L., & Hess, N. J. (2017). Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. Analytical chemistry, 89(23), 12659-12665.
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  Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.
• Walker, L. R., Tfaily, M. M., Shaw, J. B., Hess, N. J., Paša-Tolić, L., & Koppenaal, D. W. (2017). Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry. Metallomics : integrated biometal science, 9(1), 82-92.
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  Under iron-limiting conditions, bacteria produce low molecular mass Fe(iii) binding molecules known as siderophores to sequester the Fe(iii), along with other elements, increasing their bioavailability. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized by use of a newly developed 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization. This technique allowed for the rapid detection of synechobactins from Synechococcus sp. PCC 7002 as well as amphibactins from Vibrio cyclitrophicus 1F53 based on high mass accuracy and resolution allowing for observation of specific Fe isotopes and isotopic fine structure enabling highly confident identification of these siderophores. When combined with molecular network analysis two new amphibactins were discovered and verified by tandem MS. These results show that high-field FTICR MS is a powerful technique that will greatly improve the ability to rapidly identify and discover metal binding species in the environment.
• Hodgkins, S. B., Tfaily, M. M., Podgorski, D. C., McCalley, C. K., Saleska, S. R., Crill, P. M., Rich, V. I., Chanton, J. P., & Cooper, W. T. (2016). Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland. GEOCHIMICA ET COSMOCHIMICA ACTA, 187, 123-140.
• Stegen, J. C., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Danczak, R. E., Fansler, S. J., Kennedy, D. W., Resch, C. T., & Tfaily, M. (2016). Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. NATURE COMMUNICATIONS, 7.
• Stegen, J. C., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Danczak, R. E., Fansler, S. J., Kennedy, D. W., Resch, C. T., & Tfaily, M. (2016). Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nature communications, 7, 11237.
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  Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.
• Stegen, J. C., Hurlbert, A. H., Bond-Lamberty, B., Chen, X., Anderson, C. G., Chu, R. K., Dini-Andreote, F., Fansler, S. J., Hess, N. J., & Tfaily, M. (2016). Aligning the Measurement of Microbial Diversity with Macroecological Theory. FRONTIERS IN MICROBIOLOGY, 7.
• Stegen, J. C., Hurlbert, A. H., Bond-Lamberty, B., Chen, X., Anderson, C. G., Chu, R. K., Dini-Andreote, F., Fansler, S. J., Hess, N. J., & Tfaily, M. (2016). Aligning the Measurement of Microbial Diversity with Macroecological Theory. Frontiers in microbiology, 7, 1487.
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  The number of microbial operational taxonomic units (OTUs) within a community is akin to species richness within plant/animal ("macrobial") systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study's outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we () propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, () use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and () show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts), we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.
• Wilson, R. M., Hopple, A. M., Tfaily, M. M., Sebestyen, S. D., Schadt, C. W., Pfeifer-Meister, L., Medvedeff, C., McFarlane, K. J., Kostka, J. E., Kolton, M., Kolka, R. K., Kluber, L. A., Keller, J. K., Guilderson, T. P., Griffiths, N. A., Chanton, J. P., Bridgham, S. D., & Hanson, P. J. (2016). Stability of peatland carbon to rising temperatures. NATURE COMMUNICATIONS, 7.
• Wilson, R. M., Hopple, A. M., Tfaily, M. M., Sebestyen, S. D., Schadt, C. W., Pfeifer-Meister, L., Medvedeff, C., McFarlane, K. J., Kostka, J. E., Kolton, M., Kolka, R. K., Kluber, L. A., Keller, J. K., Guilderson, T. P., Griffiths, N. A., Chanton, J. P., Bridgham, S. D., & Hanson, P. J. (2016). Stability of peatland carbon to rising temperatures. Nature communications, 7, 13723.
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  Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH and CO are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.
• Corbett, J. E., Tfaily, M. M., Burdige, D. J., Glaser, P. H., & Chanton, J. P. (2015). The relative importance of methanogenesis in the decomposition of organic matter in northern peatlands. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 120(2), 280-293.
• Holmes, M. E., Chanton, J. P., Tfaily, M. M., & Ogram, A. (2015). CO2 and CH4 isotope compositions and production pathways in a tropical peatland. GLOBAL BIOGEOCHEMICAL CYCLES, 29(1), 1-18.
• Tfaily, M. M., Chu, R. K., Tolic, N., Roscioli, K. M., Anderton, C. R., Pasa-Tolic, L., Robinson, E. W., & Hess, N. J. (2015). Advanced Solvent Based Methods for Molecular Characterization of Soil Organic Matter by High-Resolution Mass Spectrometry. ANALYTICAL CHEMISTRY, 87(10), 5206-5215.
• Tfaily, M. M., Chu, R. K., Tolić, N., Roscioli, K. M., Anderton, C. R., Paša-Tolić, L., Robinson, E. W., & Hess, N. J. (2015). Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry. Analytical chemistry, 87(10), 5206-15.
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  Soil organic matter (SOM), a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and accurately predict how terrestrial carbon fluxes will respond to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soils with a wide range of C content. Our use of electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O/C ratios ( 0.5; methanol (MeOH) has higher selectivity toward compounds characterized with low O/C < 0.5; and hexane, MeOH, ACN, and H2O solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils. We present the first comparative study of the molecular composition of SOM from different ecosystems using ultra high-resolution mass spectrometry.
• Tfaily, M. M., Corbett, J. E., Wilson, R., Chanton, J. P., Glaser, P. H., Cawley, K. M., Jaffe, R., & Cooper, W. T. (2015). Utilization of PARAFAC-Modeled Excitation-Emission Matrix (EEM) Fluorescence Spectroscopy to Identify Biogeochemical Processing of Dissolved Organic Matter in a Northern Peatland. PHOTOCHEMISTRY AND PHOTOBIOLOGY, 91(3), 684-695.
• Tfaily, M. M., Corbett, J. E., Wilson, R., Chanton, J. P., Glaser, P. H., Cawley, K. M., Jaffé, R., & Cooper, W. T. (2015). Utilization of PARAFAC-Modeled Excitation-Emission Matrix (EEM) Fluorescence Spectroscopy to Identify Biogeochemical Processing of Dissolved Organic Matter in a Northern Peatland. Photochemistry and photobiology, 91(3), 684-95.
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  In this study, we contrast the fluorescent properties of dissolved organic matter (DOM) in fens and bogs in a Northern Minnesota peatland using excitation emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC). EEM-PARAFAC identified four humic-like components and one protein-like component and the dynamics of each were evaluated based on their distribution with depth as well as across sites differing in hydrology and major biological species. The PARAFAC-EEM experiments were supported by dissolved organic carbon measurements (DOC), optical spectroscopy (UV-Vis), and compositional characterization by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS). The FT-ICR MS data indicate that metabolism in peatlands reduces the molecular weights of individual components of DOM, and oxygen-rich less aromatic molecules are selectively biodegraded. Our data suggest that different hydrologic and biological conditions within the larger peat ecosystem drive molecular changes in DOM, resulting in distinctly different chemical compositions and unique fluorescent fingerprints. PARAFAC modeling of EEM data coupled with ultrahigh resolution FT-ICR MS has the potential to provide significant molecular-based information on DOM composition that will support efforts to better understand the composition, sources, and diagenetic status of DOM from different terrestrial and aquatic systems.
• Hodgkins, S. B., Tfaily, M. M., McCalley, C. K., Logan, T. A., Crill, P. M., Saleska, S. R., Rich, V. I., & Chanton, J. P. (2014). Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(16), 5819-5824.
• Lin, X., Tfaily, M. M., Green, S. J., Steinweg, J. M., Chanton, P., Imvittaya, A., Chanton, J. P., Cooper, W., Schadt, C., & Kostka, J. E. (2014). Microbial Metabolic Potential for Carbon Degradation and Nutrient (Nitrogen and Phosphorus) Acquisition in an Ombrotrophic Peatland. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(11), 3531-3540.
• Lin, X., Tfaily, M. M., Green, S. J., Steinweg, J. M., Chanton, P., Imvittaya, A., Chanton, J. P., Cooper, W., Schadt, C., & Kostka, J. E. (2014). Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland. Applied and environmental microbiology, 80(11), 3531-40.
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  This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland.
• Lin, X., Tfaily, M. M., Steinweg, J. M., Chanton, P., Esson, K., Yang, Z. K., Chanton, J. P., Cooper, W., Schadt, C. W., & Kostka, J. E. (2014). Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA. Applied and environmental microbiology, 80(11), 3518-30.
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  This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub, Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.
• Lin, X., Tfaily, M. M., Steinweg, M., Chanton, P., Esson, K., Yang, Z. K., Chanton, J. P., Cooper, W., Schadt, C. W., & Kostka, J. E. (2014). Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(11), 3518-3530.
• Tfaily, M. M., Cooper, W. T., Kostka, J. E., Chanton, P. R., Schadt, C. W., Hanson, P. J., Iversen, C. M., & Chanton, J. P. (2014). Organic matter transformation in the peat column at Marcell Experimental Forest: Humification and vertical stratification. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 119(4), 661-675.
• Corbett, J. E., Burdige, D. J., Tfaily, M. M., Dial, A. R., Cooper, W. T., Glaser, P. H., & Chanton, J. P. (2013). Surface production fuels deep heterotrophic respiration in northern peatlands. GLOBAL BIOGEOCHEMICAL CYCLES, 27(4), 1163-1174.
• Corbett, J. E., Tfaily, M. M., Burdige, D. J., Cooper, W. T., Glaser, P. H., & Chanton, J. P. (2013). Partitioning pathways of CO2 production in peatlands with stable carbon isotopes. BIOGEOCHEMISTRY, 114(1-3), 327-340.
• Tfaily, M. M., Hamdan, R., Corbett, J. E., Chanton, J. P., Glaser, P. H., & Cooper, W. T. (2013). Investigating dissolved organic matter decomposition in northern peatlands using complimentary analytical techniques. GEOCHIMICA ET COSMOCHIMICA ACTA, 112, 116-129.
• Lin, X., Green, S., Tfaily, M. M., Prakash, O., Konstantinidis, K. T., Corbett, J. E., Chanton, J. P., Cooper, W. T., & Kostka, J. E. (2012). Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78(19), 7023-7031.
• Lin, X., Green, S., Tfaily, M. M., Prakash, O., Konstantinidis, K. T., Corbett, J. E., Chanton, J. P., Cooper, W. T., & Kostka, J. E. (2012). Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland. Applied and environmental microbiology, 78(19), 7023-31.
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  The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.
• Tfaily, M. M., Hodgkins, S., Podgorski, D. C., Chanton, J. P., & Cooper, W. T. (2012). Comparison of dialysis and solid-phase extraction for isolation and concentration of dissolved organic matter prior to Fourier transform ion cyclotron resonance mass spectrometry. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 404(2), 447-457.
• Tfaily, M. M., Podgorski, D. C., Corbett, J. E., Chanton, J. P., & Cooper, W. T. (2011). Influence of acidification on the optical properties and molecular composition of dissolved organic matter. ANALYTICA CHIMICA ACTA, 706(2), 261-267.

Presentations

• Arredondo, M. G., Tfaily, M., & Keiluweit, M. (2022). Nutrient and Water Availability Modulate the Destabilization of Mineral-Associated Organic Matter in the Rhizosphere. AGU.
• Ayala-Ortiz, C., & Tfaily, M. (2022). Unraveling the responses of soil bacteria and fungal communities to changes in resource availability in a desert ecosystem. The University of Arizona, BRIDGES Ecosystem Genomics Convergence Institute.
• Ellenbogen, J., Tfaily, M., & Wrighton, K. (2022). Methylotrophic Metabolism in the Mire: Unearthing Direct and Indirect Routes for Methane Production in a Model Permafrost Thaw Peatland. AGU.
• Freire Zapata, V., & Tfaily, M. (2022). Differential microbial and metabolite assembly forces drive ecosystem function across a thaw gradient in Northern Sweden. The University of Arizona, BRIDGES Ecosystem Genomics Convergence Institute.
• Freire Zapata, V., Ayala-Ortiz, C., & Tfaily, M. (2022). Unraveling the Responses of Soil Bacterial and Fungal Communities to Changes in Resource Availability in a Desert Ecosystem. AGU.
• Guo, B., Cao, Z., Du, J., Wang, Y., Niu, G., Dontsova, K. M., Hitzelberger, M., Chen, L., Troch, P. A., & Chorover, J. D. (2022, December 2022). Reactive transport modeling of basalt weathering and early soil formation within a highly-controlled, sloping lysimeter.
  . American Geophysical Union Fall Meeting. Chicago, IL: American Geophysical Union.
• Honeker, L., Tfaily, M., & Meredith, L. (2022). Soil carbon and volatile organic compound (VOC) cycling patterns during drought and rewet in an artificial tropical rainforest: Do microbes play a role?. AGU.
• Leewis, M., & Tfaily, M. (2022). Climate, Time, and Soil Development Interact to Shape the Depth Distribution and Structure of Microbial Communities. AGU.
• Nickerson, M., Tfaily, M., & U'Ren, J. (2022). Multi-omics investigation of boreal and arctic moss microbial community diversity and ecosystem function. The University of Arizona, BRIDGES Ecosystem Genomics Convergence Institute.
• Portman, T., Tfaily, M., & Arnold, A. E. (2022). Litter decomposition dynamics of the invasive grass Eragrostis lehmanniana. The University of Arizona, BRIDGES Ecosystem Genomics Convergence Institute.
• Tfaily, M. (2022). Unraveling the responses of soil bacterial and fungal communities to changes in resource availability in a desert ecosystem using a multi-omics approach . Society for Industrial Microbiology and Biotechnology.
• AminiTabrizi, R., & Tfaily, M. (2021). A systems biology approach to understanding the stability of peatland carbon pools under climate change. ACS Geoscience.
• AminiTabrizi, R., & Tfaily, M. (2021). “Coupled Metabolomics and Transcriptomics Analyses Reveal Active Dynamics of Infection in Virocells. The University of Arizona Graduate and Professional Student Council (GPSC) Showcase.
• Andrews, H., & Tfaily, M. (2021). Microbial controls of nitrous oxide pulses in rewetted forest soils: An integrated -omic and isotopic approach. AGU meeting.
• Ayala-Ortiz, C., & Tfaily, M. (2021). Stable isotope labeling to trace litter degradation pathways: A view into the carbon cycling processes occurring in a peat bog. American Geophysical Union (AGU) Meeting.
• Ayala-Ortiz, C., & Tfaily, M. (2021). The role that Sphagnum litter plays in the biogeochemical cycling of carbon in a peat bog. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Blankinship, J., Rathke, S., Babst-Kostecka, A., Gornish, E., Barberan, A., Field, J., Saez, A. E., Rasmussen, C., & Tfaily, M. (2021). Mitigating dust pollution for climate-resilience development in arid regions. Arizona Institutes for Resilience.
• Blankinship, J., Rathke, S., Babst-Kostecka, A., Gornish, E., Barberan, A., Field, J., Saez, A. E., Rasmussen, C., & Tfaily, M. (2021). Mitigating dust pollution for climate-resilient development in arid regions. Arizona Institutes for Resilience Symposium.
• Freire Zapata, V., & Tfaily, M. (2021). hawing permafrost alters soil metabolic profile and microbial decomposition pathways in Stordalen Mire, Sweden. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Garcia Arredondo, M., & Tfaily, M. (2021). Sticky Roots Change Rhizodeposition Quality and Quantity Leading to Variable Disruption of Mineral-Organic Associations. AGU meeting.
• Hildebrand, G., & Tfaily, M. (2021). Microbial Community and Metabolomic Response to Drought and Ecological Stress at the Biosphere 2 Tropical Rainforest. American Geophysical Union (AGU) Meeting.
• Hildebrand, G., & Tfaily, M. (2021). The metabolomic response to drought: a peek into the roots of the tropical rainforest. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Honeker, L., & Tfaily, M. (2021). Effect of drought on soil microbial metabolisms driving carbon allocation and volatile organic compound cycling in the tropical rainforest at Biosphere 2. AGU meeting.
• Narrowe, A., & Tfaily, M. (2021). A Deep, Diverse Reservoir of Methane-Cycling Microorganisms Resists Hydrologic Perturbation to Sustain Metabolic Activity in Freshwater Wetland Soils. AGU meeting.
• Oliverio, A., & Tfaily, M. (2021). Elucidating the ecological dynamics of microbial systems in freshwater wetlands with an integrative ‘omics approach across time and space. AGU meeting.
• Petro, C., & Tfaily, M. (2021). Whole-Ecosystem Warming of a Boreal Peatland Decreases Microbial Diversity and Stimulates Methane Production from Plant Metabolites. AGU meeting.
• Tfaily, M. (2021). Invited Speaker and Participant, Inspire Session: "Connecting Evolutionary and Ecological Perspectives to Find What Matters in Microbial Responses to Change. Ecological Society of America, August 2, 2021.
• Tfaily, M. (2021). Invited Speaker and Participant, Panel, Session: “Harnessing the Power of Multi–Omics Capabilities in the Life Sciences for Applications Related to Climate Change and the Environment”. National Academies of Sciences, Engineering, and Medicine’s (NASEM) Board on Life Sciences (BLS). National Academies of Sciences, Engineering, and Medicine’s (NASEM) Board on Life Sciences (BLS).
• Tfaily, M. (2021). Invited Speaker and Participant, “Session: Physical, Chemical, and Biological Processes Controlling Solute Transport and Remediation of Contaminants in Soils" through the Soils and Environmental Quality Division. ASA-CSSA-SSSA International Annual Meeting; Salt Lake City, Utah (November 7-10).
• Tfaily, M. (2021). Keynote Speaker and Participant, International Humic Substances Society (IHSS), “Session: Stabilization mechanisms of soil organic matter. International Humic Substances Society (IHSS).
• Tfaily, M., Rasmussen, C., Saez, A. E., Field, J., Barberan, A., Gornish, E., Babst-Kostecka, A., Rathke, S., Blankinship, J., Tfaily, M., Rasmussen, C., Saez, A. E., Field, J., Barberan, A., Gornish, E., Babst-Kostecka, A., Rathke, S., & Blankinship, J. (2021). Mitigating dust pollution for climate-resilient development in arid regions. Symposium on Resilience Research for Global Development ChallengesArizona Institutes for Environment.
• Zhao, Q., & Tfaily, M. (2021). Dynamics of Organic Matter Molecular Composition under Aerobic Decomposition and Their Response to the Nitrogen Addition in Grassland Soils. AGU meeting.
• Graf Grachet, N., Rodshagen, T., Jones, A., Reichman, H., & Tfaily, M. (2020, Fall 2020). Temperature controls organic matter bioavailability, greenhouse gas production, and microbial community in a peat bog. 2020-VIRTUAL, Nov. 9-13 -Recordings available February 15, 2021.
• Tfaily, M. (2020, Fall 2020). Unifying meta-genomic and -transcriptomic data with metabolomics to help infer ecosystem processes in a thawing permafrost. AGU Fall meeting 2020 (virtual).
• Tfaily, M. (2020, Spring 2020). Invited Speaker and Participant, DOE Virocell Workshop, Ohio State University, Columbus, OH (February). DOE Virocell Workshop.
• Tfaily, M. (2020, Summer 2020). Invited Speaker and Participant, Watershed Community Workshop, Pacific Northwest National laboratory, Richland, WA (September). Watershed Community Workshop. Virtual.
• Wilson, R., & Tfaily, M. (2020, Fall 2020). Plant Exudate-Soil Interactions Linked to Delayed Mineralization of Subsurface C Stores After 3 Years of Experimental Warming.. AGU Fall 2020.
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  Monday, 7 December 2020: 10:54VirtualRachel Wilson1, Anya Hopple2, Malak M Tfaily3, Cassandra Zalman4, Eric Johnston5, Caitlin Petro6, Max Kolton7, Tianze Song8, Karis J McFarlane9, Stephen Sebestyen10, Natalie Griffiths11, Randall K Kolka12, Christopher W Schadt11, Paul J Hanson13, Jason Keller4, Scott D Bridgham14, Jeff Chanton1 and Joel E Kostka15, (1)Florida State University, Tallahassee, FL, United States, (2)Smithsonian Environmental Research Center, Edgewater, MD, United States, (3)University of Arizona, Tucson, AZ, United States, (4)Chapman University, Orange, CA, United States, (5)Bloomington, IN, United States, (6)Georgia Institute of Technology Main Campus, Atlanta, United States, (7)Georgia Institute of Technology Main Campus, Atlanta, GA, United States, (8)Georgia Institute of Technology, Atlanta, United States, (9)Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, United States, (10)USDA Forest Service Northern Research Station, Grand Rapids, MN, United States, (11)Oak Ridge National Laboratory, Oak Ridge, TN, United States, (12)USDA Forest Service, Grand Rapids, United States, (13)Oak Ridge National Laboratory, Climate Change Science Institute and Environmental Sciences Division, Oak Ridge, TN, United States, (14)University of Oregon, Eugene, OR, United States, (15)Do Not Wish to Give out, Atlanta, GA, United StatesRecorded PresentationAbstract:Following one year of experimental deep peat warming at the Spruce and Peatland Response Under Changing Environments (SPRUCE) project within the Marcell Experimental Forest (Minnesota, USA), we observed changes in shallow subsurface methane production, but no response of CO2. The shift towards increasingly methanogenic conditions was itself concerning because methane is a much more potent greenhouse gas than CO2 and could accelerate climate-peatland feedbacks to warming. However, at that time, we found little evidence that the vast majority of stored C in the peatland was vulnerable to rising temperatures. Three years after introduction of whole ecosystem warming (WEW), however, we find radiocarbon evidence that enhanced production of both CH4 and CO2 with warming is fueled by mobilization of the ancient buried peat that had previously been shown to be stable. Tandem radiocarbon (14C) and stable isotope (13C) mass balance modeling indicates that up to 30% of current DIC production originates from the mineralization of peat up to 2m depth. Using a combination of complementary ultra-high resolution geochemical and microbial analyses, we find evidence that increasing plant root exudates to the subsurface may be providing the necessary substrates to stimulate this decomposition of buried peat (“priming”). Although acetoclasty and hydrogentrophy have traditionally been considered the dominant pathways for methane production in peatlands, using our complementary approach we find multiple lines of evidence for methylotrophic methanogenesis including (1) correlations between peat temperature and porewater methanol concentrations, (2) all of the necessary enzymes involved in the methylotrophic methanogenesis pathway, and (3) SSU rRNA gene amplicon and metagenomic evidence for known methylotrophic methanogens in the higher temperature treatments suggesting that, as the peat warms, new pathways of methane production become increasingly favorable with the potential to further lower CO2:CH4 production ratios. Accumulation of plant-derived lignin decomposition products, including methanol, has increased with warming providing a compelling link between above-ground production and changing soil dynamics.
• Tfaily, M. (2019, Fall). Microbial controls on biogeochemical cycling of carbon using stable isotope labeling and other novel techniques. HAS. University of Ariozna: HAS department.
• Tfaily, M. (2019, Fall). Quantification of abiotic controls on dissolved organic matter in watersheds. SFA Watershed Community WorkshopPNNL.
• Tfaily, M. (2019, Fall). Quantifying biotic and abiotic controls on dissolved organic matter dynamics in natural systems using complementary analytical techniques. AGU.
• Tfaily, M. (2019, Fall). Towards a Better Understanding of Microbial-Organo-Mineral Interactions Using High Resolution Mass Spectrometry. SSSA.
• Tfaily, M. (2019, January 2019). Molecular-Level Investigation into the Fractionation of Dissolved Organic Carbon during Co-Precipitation with Ferrihydrite. SSSA 2019.
• Tfaily, M. (2019, January 2019). Soil Pore Architecture Drives SOC Transformations with Drought. SSSA 2019.
• Tfaily, M. (2019, January 2019). The Nexus of Water, Physical Structure, and Microbial Communities in Soil: Unpredictable Soil Biogeochemistry in a Changing Earth System. SSSA 2019.
• Tfaily, M. (2019, January 2019). The Persistence of Mineral Associated Organic Matter Among Nutrient Network Grasslands.. SSSA 2019.
• Tfaily, M. (2019, January 2019). Twenty Years of Dirt: Detrital Influences on Soil Carbon Dynamics. SSSA 2019.
• Tfaily, M. (2019, Jnauary 2019). Riparian Carbon Inputs and Sediment Metabolomes, but Not Metagenomes or Metaproteomes, Correspond to Enhanced Water-Soluble C Oxidation and Bound C Protection in the Hyporheic Zone.. SSSA 2019.
• Tfaily, M., & Cardon, Z. (2019, Fall). Beyond the “lollipop” – roots as dynamic participants in root-microbe-mineral interactions. AGU.
• Tfaily, M., & Lybrand, R. (2019, Fall). Soil Geophysical Properties Influence Nest-Site Selection By Ground Nesting Bees in Agricultural Settings. SSSA.
• Tfaily, M., & Lybrand, R. (2019, Fall). dentifying the organic and inorganic products of incipient weathering in natural environments. AGU.
• Tfaily, M., & Lynch, L. (2019, Spring). Moving beyond stoichiometry: Simple substrates do not fully capture complex pathways of root exudate decomposition. Vol. 21, EGU2019-10603, 2019.
• Tfaily, M., & Neurath, R. (2019, Fall). Dynamic carbon association with minerals in the rhizosphere and detritosphere. AGU.
• Tfaily, M., & Sorensen, P. (2019, Fall). Snowmelt mediates microbial metabolic potential and soil metabolite profiles in a high altitude watershed. AGU.
• Tfaily, M., Chanton, J., Tfaily, M., & Pierson1, D. (2019, Fall). Isotopic and high resolution analytical techniques to investigate the stability of peat soils across gradients in latitude and altitude. AGU.
• Tfaily, M. (2018, December 2018). Metabolomic and metagenomic insights into drought- and flood-induced greenhouse gas emissions in soils. AGU 2018.
• Tfaily, M. (2018, December 2018). Subsurface carbon signatures in a coastal watershed experiencing tidal inundation. AGU 2018.
• Tfaily, M. (2018, December 2018). TOWARD THE PREDICTIVE UNDERSTANDING OF GREENHOUSE GAS PRODUCTION IN HIGH LATITUDE. AGU 2018.
• Tfaily, M. (2018, December 2018). Tracking the Fate of new C in Northern Peatlands by a Compound-Specific Stable Isotope-Labeling Approach coupled with multiple analytical techniques and gas fluxes analysis. AGU 2018.
• Tfaily, M., Graham, E., Crump, A., Bramer, L., Fransler, S., Purvine, S., Nicora, C., Artzen, E., Resch, T., Neslon, W., Goldman, A., Kennedy, D., & Stegen, J. (2018, December 2018). Riparian carbon inputs and sediment metabolomes, but not metagenomes or metaproteomes, correspond to enhanced water-soluble C oxidation and bound C protection in the hyporheic zone. AGU 2018.
• Tfaily, M., Stegen, J., & Graham, E. (2018, December 2018). Merging Ecological Theory with Organic Geochemistry and Environmental Metabolomics. AGU 2018.
• Yang, Y., Adhikari, D., Hess, N., Tfaily, M., Kukkadapu, R., Zhao, Q., Chu, R., & Graham, T. (2018, December 2018). Molecular-level investigation into the fractionation of dissolved organic carbon during co-precipitation with ferrihydrite. AGU 2018.

Poster Presentations

• Dontsova, K. M., Cortes, L., Makke, G., Tfaily, M., Garcia, J., Sengupta, A., Arnold, A. E., Chorover, J. D., & Saleska, S. R. (2023, July). Effects of biocrust formation and moss colonization on biogeochemical properties of basaltic tephra.. Goldschmidt conference. Lyon, France.
• Makke, G., Bugaj, A., Dontsova, K. M., Chorover, J. D., Arnold, A. E., Saleska, S. R., & Tfaily, M. (2023, July). FTICR-Based Metabolomics Reveals the Dynamics of Soil Metabolic Complexity of Primary Succession at the Landscape Evolutionary Observatory at Biosphere 2, AZ, USA. Goldschmidt conference. Lyon, France.
• Tfaily, M. (2022). MetaboDirect: An analytical pipeline for FT-ICR mass spectrometry data. Genomic Science Program for the Department of Energy.
• AminiTabrizi, R., & Tfaily, M. (2022). Nutrient Limitation Drives Dynamics of Host-virus Interactions

   . Genomic Science Program for the Department of Energy.

• Andrews, H., Tfaily, M., & Meredith, L. (2022). Nitrogen competition in the rhizosphere: Using multi-omic and isotopic tools to trace belowground fates of nitrogenous fertilizers in a sorghum field. AGU.
• Ayala-Ortiz, C., & Tfaily, M. (2022). Metabotandem And Metabodirect: Software Pipelines for the Analysis of High Throughput Metabolomics Data for Complex Environmental Samples. AGU.
• Clark, M., Meredith, L., & Tfaily, M. (2022). Understanding Temporal, Spatial and Metabolomic Effects of Hydrogen Hotspots in Soil. AGU.
• Makke, G., & Tfaily, M. (2022). Changes in soil metabolic complexity driven by plant succession at the Landscape Evolutionary Observatory at Biosphere 2. NSF-NRT annual Meeting.
• Makke, G., & Tfaily, M. (2022). Growing a New Science of Landscape Terraformation. The University of Arizona, BRIDGES Ecosystem Genomics Convergence Institute.
• Makke, G., & Tfaily, M. (2022). Substrate addition primes soil organic matter decomposition in a peat bog. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Makke, G., & Tfaily, M. (2022). Changes in the Soil Metabolic Complexity Driven by Plant Succession at the Landscape Evolutionary Observatory at Biosphere2. AGU.
• Nickerson, M., & Tfaily, M. (2022). Characterization of the chemical environment of phylogenetically diverse Alaskan mosses: does Sphagnum harbor a unique metabolome?. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Portman, T., Elizabeth Arnold, A. E., & Tfaily, M. (2022). ungal symbionts associated with an invasive grass decrease seed germination and litter degradation of native species, with distinctive metabolites as a likely mechanism. ESA.
• Tfaily, M., Nickerson, M., & U'Ren, J. (2022). Characterization of Sphagnum Metabolome and Microbiome with Depth in an Arctic Ecosystem. AGU.
• Tfaily, M., Saleska, S. R., Arnold, A. E., Chorover, J. D., Sengupta, A., Dontsova, K. M., Bugaj, A., & Makke, G. (2022, December 2022). Changes in the Soil Metabolic Complexity Driven by Plant Succession at the Landscape Evolutionary Observatory at Biosphere 2
  . American Geophysical Union Fall Meeting. Chicago, IL: American Geophysical Union.
• Valencia Meza Sr, S. A., & Tfaily, M. (2022). Metabolite analysis using FTICR (Fourier transform ion cyclotron resonance mass spectrometry) spectrometry in LEO with methanol extraction. AGU.
• AminiTabrizi, R., & Tfaily, M. (2021). Coupled Metabolomics and Transcriptomics Analyses Reveal Active Dynamics of Infection in Virocells. DOE-GSP PI meeting.
• AminiTabrizi, R., & Tfaily, M. (2021). Coupled Metabolomics and Transcriptomics Analyses Reveal Active Dynamics of Infection in Virocells. The University of Arizona EarthWeek (ENViSion) Student Research Presentation.
• Brodie, E., & Tfaily, M. (2021). Uncovering microbial metabolic trajectories during the snowmelt period in mountainous watersheds. AGU meeting.
• Castro, S., & Tfaily, M. (2021). Sticky Roots: Plants and microbes poised to attack mineral-associated organic matter. AGU meeting.
• Fansler, S., & Tfaily, M. (2021). Organic matter biochemical transformation diversity is higher in surface water than in hyporheic zone sediments across global river corridors. AGU meeting.
• Freire Zapata, V., & Tfaily, M. (2021). Exploring ecometabolomics and metabolomic diversity in response to permafrost thaw in northern Sweden. American Geophysical Union (AGU) Meeting.
• Graf-Grachet, N., & Tfaily, M. (2021). Untargeted metabolomics by high resolution LC-MS/MS revealed different metabolic profiles of oaks. DOE-GSP PI meeting.
• Graves, K., & Tfaily, M. (2021). Microbial Volatile Organic Compounds: Important but Undetected. AGU meeting.
• Hildebrand, G., & Tfaily, M. (2021). Spatial metabolic profiling in roots reveals plant specific responses to drought. Environmental Molecular Sciences Laboratory (EMSL) Meeting.
• Ronan, T., & Tfaily, M. (2021). Predicting volatile organic compound (VOC) production and uptake locations using depth-resolved concentrations for a better understanding of the soil metabolome. AGU meeting.
• Tfaily, M. (2021). Spatial metabolic profiling in roots reveals plant specific responses to drought at the Biosphere 2 tropical rainforest. AGU meeting.
• Tfaily, M., & AminiTabrizi, R. (2021). Community Response to Changing Environmental Conditions Among Contrasting Ecosystems. American Geophysical Union (AGU) Meeting.
• Tfaily, M., & Makke, G. (2021). Substrate addition primes soil organic matter decomposition in a peat bog. AGU21 Fall Meeting.
• AminiTabrizi, R., & Tfaily, M. (2020, Fall 2020). A systems Biology Approach to Understanding the Stability of Peatland Carbon Pools under Climate Change. Abstract for 2020 ASA-CSSA-SSSA International Annual Meeting November 8-11 | Phoenix, Arizona (VIRTUAL).
• Anderson, C., & Tfaily, M. (2020, Fall 2020). Spatiotemporal redox dynamics regulate mineral and metabolic constraints on carbon export from floodplain soils. AGU Fall meeting 2020 (Virtual).
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  Carolyn Anderson1, Christian Dewey2, Malak M Tfaily3, Ravi K Kukkadapu4, Kew William5, Peter S Nico6, Patricia M Fox6, Scott E Fendorf2 and Marco Keiluweit1, (1)University of Massachusetts Amherst, Amherst, MA, United States, (2)Stanford University, Department of Earth System Science, Stanford, CA, United States, (3)University of Arizona, Tucson, AZ, United States, (4)Pacific Northwest National Lab, Richland, WA, United States, (5)Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, United States, (6)Lawrence Berkeley National Lab, Berkeley, CA, United StatesAbstract:Floodplain soils are large and dynamic reservoirs of carbon (C), where seasonal flooding regulates both C storage and export downstream. Timing and frequency of flooding events are altered by climate change, increasingly subjecting floodplain soils to extreme flooding or droughts. These shifts have profound implications on greenhouse gas emissions and dissolved organic carbon (DOC) export. Yet, the underlying (hydro)biogeochemical controls on C retention and export in floodplain soils are poorly constrained, limiting our ability to predict responses to climate change. Here we aimed to determine how seasonal flooding, and associated spatiotemporal variations in redox conditions, impact the dominant controls on microbial soil C cycling. Using in-field monitoring and advanced analytical and molecular tools, we examined how changes in mineral interactions and microbial metabolism during flooding and subsequent drainage affected C export from floodplain soils of the mountainous East River watershed (Gothic, Colorado).Our results show the abundance of reactive iron (Fe) mineral phases varies with soil depth and is a significant control on C concentrations across floodplain soils, and that these mineral associations are sensitive to seasonal redox dynamics. Specifically, we find that reducing conditions during flooded periods caused reductive dissolution of Fe (hydr)oxides, leading to redox-driven mobilization of mineral-associated organic matter and enhancing DOC export. At the same time, flooding decreased CO2 production and selectively preserved chemically-reduced organic matter, likely due to metabolic constraints on microbial respiration. Upon drainage and re-oxygenation of floodplain soils, CO2 production increased, partly due to the oxidation of reduced organic compounds, but was limited by the concurrent entrapment of DOC by newly precipitated Fe (hydr)oxides.Combined, our results reveal that spatiotemporal redox variations during seasonal flooding shift the relative and interactive effects of mineral and metabolic constraints on CO2 and DOC export from floodplain soils. These findings provide a mechanistic framework for understanding how changes in the intensity and timing of flooding may alter predominant pathways, rates, and controls of C export from floodplain soils.
• Meredith, L., & Tfaily, M. (2020, Fall 2020). Exploring the role of volatile organic compounds in the rhizosphere interactome. AGU Fall 2020 meeting.
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  Tuesday, 15 December 2020PosterLaura K Meredith1, Jordan E. Krechmer2, Juliana Gil-Loaiza1, Joseph R Roscioli3, Joanne H Shorter2, Megan Claflin2, Lars Erik Daber4, Jane Fudyma5, Johannes Ingrisch6, Kathiravan Meeran6, Giovanni Pugliese7, Thomas Kluepfel7, Eva Y Pfannerstill8, Jonathan Williams8, Linnea K Honeker9, Malak M Tfaily9, S. Nemiah Ladd10, Christiane Werner4 and Water, Atmosphere and Life Dynamics (WALD), (1)University of Arizona, School of Natural Resources and the Environment, Tucson, AZ, United States, (2)Aerodyne Research Inc., Billerica, MA, United States, (3)Aerodyne Research Inc, Billerica, MA, United States, (4)University of Freiburg, Freiburg, Germany, (5)University of Arizona, Environmental Science, Tucson, United States, (6)University of Innsbruck, Institute of Ecology, Innsbruck, Austria, (7)Max Planck Institute for Chemistry, Mainz, Germany, (8)Max Planck Institute for Chemistry, Atmospheric Chemistry Department, Mainz, Germany, (9)University of Arizona, Tucson, AZ, United States, (10)ETH Swiss Federal Institute of Technology Zurich, Earth Science, Zurich, SwitzerlandAbstract:Roots and microbes interact through gas-phase metabolites and signaling molecules including volatile organic compounds (VOCs). VOCs show potential as biomarkers for specific processes and interactions belowground, individually, or as the volatile subset of the comprehensive metabolome of an organism or ecosystem—coined the volatilome. Recently, we developed a non-invasive, online soil gas sampling approach to measure subsurface VOCs in real time. Here, we present an intercomparison of VOC measurements from three soil perspectives—subsurface, surface, and isolated roots—to explore the role of VOCs in the belowground during a controlled, whole ecosystem drought.As part of the Water, Atmosphere, and Life Dynamics (WALD) drought campaign in the Biosphere 2 Tropical Rainforest, we measured subsurface VOC concentrations during mid-drought from the following locations: 1) triplicate probes buried across a 15-30 cm depth range in a rhizosphere dense location within 0.5 m of a sugar palm (Arenga pinnata) and a control location 2.0 m away; and 2) probes installed in a soil pit at 20, 50, 150, 200, and 300 cm depths. Soil probes were sampled over four days with a Vocus proton transfer reaction time of flight mass spectrometer (PTR-TOF-MS) resulting in a time series data for a set of 64 identified VOC masses.In this presentation, we will compare the subsurface soil VOC data set to 1) root VOC emission profiles measured by the Vocus and 2) soil-atmosphere fluxes measured during pre-drought and drought periods by a separate PTR-TOF-MS auto-chamber system. With these data, we look through a new window into the biochemical nature and spatiotemporal dynamics of subsurface soil interactions mediated by VOCs.
• Quiñonez-González, K., & Tfaily, M. (2020, Fall 2020). Molecular Composition and Stability of Soil Organic Matter in Tropical Soils- A Belowground View to Afforestation Through Payment for Ecosystem Services in Costa Rica. AGU Fall meeting 2020 (virtual).
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  Tuesday, 15 December 2020PosterKatherine Quiñonez-González, Texas A&M University College Station, College Station, United States, Andreas Khechfe, Humboldt State University, Arcata, CA, United States, Malak M Tfaily, University of Arizona, Tucson, AZ, United States, Jane Fudyma, University of Arizona, Environmental Science, Tucson, United States, Eugenio Gonzalez, Texas A&M University, Soltis Center for Research and Education, San Juan, Costa Rica and A. Peyton Smith, Texas A&M University College Station, Soil and Crop Sciences, College Station, TX, United StatesAbstract:Shifts in the molecular composition of organic matter has the potential to regulate the persistence and stability of carbon (C) in soils. Soils, which act as the largest terrestrial sink of C, are not well recognized in atmospheric C mitigation strategies in the tropics; this is especially valid in Payment for Ecosystem Service (PES) programs that focus on C sequestration in aboveground biomass. The objective of this research was to identify the potential of soils to store persistent C under PES and non-PES land uses in Northeastern Costa Rica, a country that leads the world in managing for carbon neutrality. We used a space-for-time approach to characterize the quality (i.e., FT-ICR-MS molecular composition) and quantity of soil organic matter under PES plantations, PES-contracted conservation forests, and at adjacent non-PES agricultural plot that represented pre-plantation land uses at several different sites (i.e., land owners). Our results show that a principal components analysis of the molecular composition of organic matter differed among PES land cover, but not between PES and non-PES land uses (PCA axis 1; P = 0.0007, N = 72). Soil depth (0-5 vs. 5-10 cm) also influenced the variation seen in the molecular composition of soil organic matter (PCA axis 1; P = 0.013). More specifically, PES-conservation forests were relatively enriched in protein- and unsaturated hydrocarbon-like compounds, and relatively depleted in lignin-like compounds compared to PES-plantation forests. We also observed an effect of PES-plantation tree species on the relative abundance of condensed hydrocarbon-like compounds, highlighting that more PES forest type is important in shaping soil C composition. Furthermore, aromatic compounds were highest in 0-5 cm soils from PES-conservation forests compared to PES plantations and non-PES agricultural land uses, suggesting that the increase in aromatic compounds accumulate, as more labile carbon is preferentially degraded. This was also reflected in the lower active-to-total C ratio seen in PES-conservation forests relative to non-PES agricultural land uses. The quantity of soil C followed a similar trajectory, emphasizing that PES-conservation forests have more persistent (i.e., molecularly complex) organic matter compared to PES-plantations or non-PES agricultural land uses.
• Sutfin, N., & Tfaily, M. (2020, Fall 2020). Floodplain hydrogeomorphic connectivity of abandoned channels regulates the content and diversity of dissolved organic matter within sediment Wednesday, 9 December 2020. AGU Fall 2020.
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  Wednesday, 9 December 2020PosterNicholas A Sutfin, Case Western Reserve University, Earth, Environmental, and Planetary Sciences, Cleveland, OH, United States, Joel C Rowland, Los Alamos National Laboratory, Los Alamos, NM, United States, Meghan King, Oregon State University, Corvallis, OR, United States, Kenneth Hurst Williams, Earth and Environment Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States and Malak M Tfaily, University of Arizona, Tucson, AZ, United StatesAbstract:Retention and transformation of organic matter within floodplains has strong implications for carbon budgets, food webs, and the fate and transport of contaminants. Carbon content does not appear to vary greatly across the floodplain on the East River, Colorado, USA, nor does it contain significant trends with distance from the channel. However, carbon content decreases with depth, as expected, and does appear to vary in relation to the degree of hydrologic connectivity with the river channel. Using the relative elevation and distance from the channel as a proxy for connectivity, the quality and diversity of organic matter appears to be associated with hydrologic connectivity of geomorphic surfaces. Results from FT ICR MS indicate that drier geomorphic surfaces like elevated cutbanks retain more OM compounds with increasing depth, compared to more frequently wetted point bars that exhibit a greater loss of OM compounds with increasing depth. Additionally, cutbanks have a lower ratio of protein to lignin than more frequently wetted features like gravel bars, point bars, and abandoned channels, suggesting transformation and mineralization of OM. The composition of OM compounds in abandoned channels and oxbow lakes, however, vary in their (1) age since abandonment, (2) rate of abandoned channel sedimentation, and the (3) relative degree of hydrologic connectivity. Abandoned channels that are partially connected to the floodplain and much more likely to experience frequent wetting-and-drying periods exhibit a significant loss in OM compound abundance and diversity. Less hydrologically connected abandoned channels that may experience anoxic conditions periodically throughout each year exhibit substantially high diversity and abundance of OM compounds. This abundance in OM compounds decreases only minimally with increasing depth in older disconnected abandoned channels.Retention and transformation of organic matter within floodplains has strong implications for carbon budgets, food webs, and the fate and transport of contaminants. Carbon content does not appear to vary greatly across the floodplain on the East River, Colorado, USA, nor does it contain significant trends with distance from the channel. However, carbon content decreases with depth, as expected, and does appear to vary in relation to the degree of hydrologic connectivity with the river channel. Using the relative elevation and distance from the channel as a proxy for connectivity, the quality and diversity of organic matter appears to be associated with hydrologic connectivity of geomorphic surfaces. Results from FT ICR MS indicate that drier geomorphic surfaces like elevated cutbanks retain more OM compounds with increasing depth, compared to more frequently wetted point bars that exhibit a greater loss of OM compounds with increasing depth. Additionally, cutbanks have a lower ratio of protein to lignin than more frequently wetted features like gravel bars, point bars, and abandoned channels, suggesting transformation and mineralization of OM. The composition of OM compounds in abandoned channels and oxbow lakes, however, vary in their (1) age since abandonment, (2) rate of abandoned channel sedimentation, and the (3) relative degree of hydrologic connectivity. Abandoned channels that are partially connected to the floodplain and much more likely to experience frequent wetting-and-drying periods exhibit a significant loss in OM compound abundance and diversity. Less hydrologically connected abandoned channels that may experience anoxic conditions periodically throughout each year exhibit substantially high diversity and abundance of OM compounds. This abundance in OM compounds decreases only minimally with increasing depth in older disconnected abandoned channels.
• Tfaily, M., & AminiTabrizi, R. (2020, Summer 2020). A systems Biology Approach to Understanding the Stability of Peatland Carbon Pools under Climate Change. 2nd annual MANA conference, U Michigan / online -virtual, September 14-16, 2020.
• Zhao, Q., & Tfaily, M. (2020, Fall 2020). Mineral-mediated persistence of soil organic matter and its chemical dynamics in response to nitrogen fertilization in grassland soils. AGU Fall 2020.
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  Tuesday, 15 December 2020PosterQian Zhao1, Stephen Callister2, Allison Thompson1, Ravi K Kukkadapu3, Malak M Tfaily4, Lisa Bramer1, Nikolla P Qafoku1, Sheryl L Bell1, Sarah E Hobbie5, Eric W. Seabloom6, Elizabeth T. Borer7 and Kirsten S Hofmockel8, (1)Pacific Northwest National Laboratory, Richland, WA, United States, (2)Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA, United States, (3)Pacific Northwest National Lab, Richland, WA, United States, (4)University of Arizona, Tucson, AZ, United States, (5)University of Minnesota Twin Cities, Ecology, Evolution, and Behavior, Saint Paul, MN, United States, (6)University of Minnesota Twin Cities, Minneapolis, United States, (7)University of Minnesota Twin Cities, Minneapolis, MN, United States, (8)Pacific Northwest National Laboratory, Earth and Biological Sciences, Richland, WA, United StatesAbstract:Biogeochemical cycling of carbon (C) in grassland soils is crucial to global terrestrial-atmosphere C flux in C cycling models. The retention of soil organic matter (OM) is governed by interactions with minerals, which mediate the sorption of chemically diverse OM molecules via distinct surface areas and chemical functional group availabilities. A quantitative and mechanistic understanding of how mineralogy influences OM persistence remains challenging due to the multi-layered nature of biochemical-mineral interactions that contribute to soil C persistence. In addition, human impacts on grassland soils, such as increased nitrogen (N) deposition, can influence C biogeochemical cycling by altering OM chemistry and mineral-OM associations. Therefore, soil management to enhance the formation and persistence of soil OM is increasingly needed.This study sought to understand how soil mineralogy as well as N enrichment regulate OM persistence in grassland soils and how the chemical composition of OM is altered during microbial decomposition. Using a multi-site grassland experiment, the Nutrient Network, we found that with increasing abundance of ferrihydrite (Fh), the mineral-associated, hydrophobic fraction of OM became more enriched in lipid- and protein-like compounds, whereas the water-extractable organic carbon (WEOC) became more enriched in lignin-like molecules. Nitrogen addition disrupted the accumulation of protein-like molecules in the mineral-associated hydrophobic fraction. Microorganisms preferentially decomposed energetically favorable compounds, such as amino sugars, carbohydrates, proteins, and lipids in most soils; however, these molecules were preserved in soils with high Fh content. The microbial decomposition resulted in an increased richness of lignin and tannin derivatives. Moreover, the chemical composition of OM across different soils was similar after 8-months of microbial decomposition. The changes in chemical composition of OM were not as pronounced with N addition. This study provides an advanced understanding of mineral-dependent OM persistence, OM chemical composition during the microbial decomposition and altered mineral-OM interactions in response to N inputs.
• Meredith, L., & Tfaily, M. (2019, Fall). Soil Genomics into the Study of Biosphere-Atmosphere Trace Gas Fluxes. AGU. SF.
• Tfaily, M. (2019, Fall). Microbial controls on biogeochemical cycling of carbon using stable isotope labeling and other novel techniques. AGU. SF.
• Tfaily, M., & AminiTabrizi, R. (2019, Fall). Controls on organic matter degradation in thawing permafrost peatlands and subsequent greenhouse gas emissions. AGU. SF.
• Tfaily, M., & Anderson, C. (2019, fall). Seasonal flooding impacts on mineral-organic associations regulate carbon export from subalpine floodplains. AGU. SF.
• Tfaily, M., & Chee, T. (2019, Fall). Comparison of Soil Organic Matter (SOM) Composition in the soil column at the Biosphere 2 Tropical Rainforest. AGU. SF.
• Tfaily, M., & Cruz Pérez, R. (2019, Fall). Journey from Roots to Bulk Soil: Organic Matter Characterization in the Biosphere 2 Tropical Rainforest. AGU. SF.
• Tfaily, M., & Dontsova, K. M. (2019, Fall). Spatial differences and temporal change in organic matter composition across artificial hillslope during incipient soil formation. AGU. SF.
• Tfaily, M., & Fudyma, J. (2019, Fall). Untargeted metabolic profiling of Sphagnum fallax from boreal peatlands identifies antimicrobial compounds and novel metabolites. AGU. SF.
• Tfaily, M., & Kelly-Slatten, M. (2019, Fall). Plant Genotype Impacts on Soil Biochemical Profiles and Implications for Soil Carbon Stabilization. AGU. SF.
• Tfaily, M., & Khechfe, A. (2019, Fall). Do payments for ecosystem services promote soil carbon sequestration in the tropics?. AGU. SF.
• Tfaily, M., & Toyoda, J. (2019, Fall). Extraction efficiency and molecular characterization of organic matter from soils and sediments using high resolution mass spectrometry. AGU. SF.
• Tfaily, M., & Wan, J. (2019, Fall). Hydrological controls on subsurface shale bedrock-nitrogen release and export from a mountainous watershed hillslope. AGU.
• Tfaily, M., & Zhao, Q. (2019, Fall). Coupled dynamics of carbon geochemistry and microbial communities in grassland soils. AGU. SF.

Creative Productions

• Tfaily, M. (2019. What Does The Future Hold For Our Arid And Semi-Arid Ecosystems?. Science trends. https://sciencetrends.com/?p=50080&preview=1&_ppp=635059e085