Albert Barberan

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• Iñigo-Gámiz, G., Touceda-Suárez, M., Bustamante, E., Gornish, E. S., Martínez-Yrízar, A., Búrquez, A., & Barberán, A. (2025). Above and belowground effects of buffelgrass invasion in the Sonoran Desert. Biological Invasions, 27(Issue 9). doi:10.1007/s10530-025-03650-0
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  Invasive species pose a significant threat to biodiversity, particularly in arid ecosystems where extreme environmental conditions limit the capacity for rapid vegetation recovery. Buffelgrass (Cenchrus ciliaris), introduced from South Africa for livestock forage, has become one of the most detrimental invasive species throughout the Sonoran Desert. This species is known to begin its invasion process in native desertscrub beneath the canopy of trees, sometimes recognized as nurse plants. We investigated how buffelgrass invasion affects plant and soil microbial communities under contrasting desert conditions in central Sonora, Mexico. Specifically, we compared open areas (i.e., bare, with natives, and with buffelgrass) and areas beneath the canopy of three nurse tree species (i.e., mesquite, ironwood, and palo verde), with and without buffelgrass invasion, in two neighboring sites which differed in cover type: one, a deliberately planted buffelgrass pasture (transformed site) and the other, a desertscrub naturally invaded by buffelgrass (native site). Our results show that the transformed site exhibited higher plant species richness, along with a larger proportion of invasive and ruderal species. Cover type emerged as the primary factor influencing the richness and composition of soil microbial communities. Interestingly, our findings suggest that nurse trees (in particular, palo verde) may help mitigate the impact of buffelgrass in semi-arid ecosystems.
• Morris, M. L., Eastburn, D. J., Roche, L. M., Davy, J., Doran, M., Karle, B., Lile, D., Schohr, T., Snell, L., Macon, D., Woodmansee, G., Touceda-Suárez, M., & Barberán, A. (2025). Effects of grazing exclusion and pasture management on soil microbial communities in Californian irrigated pastures. Applied Soil Ecology, 215(Issue). doi:10.1016/j.apsoil.2025.106419
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  Grazing lands in California and across the globe are increasingly challenged to meet rising livestock product demands while simultaneously balancing diverse stakeholder and land management goals. An increasing focus on the soil health of grazed landscapes has enhanced our understanding of grazing impacts on sustainable agroecosystems. However, the scientific literature is limited on how the microbial community, as a component of soil health, responds to grazing, water, and soil nutrient management in irrigated pastures. We deployed a cross-sectional survey across 24 California irrigated pastures spanning multiple climate regimes and active management strategies. We established and maintained grazing exclosures for two years and collected soil samples from rested and grazed plots within each irrigated pasture. We used 16S rRNA and ITS amplicon sequencing to analyze soil bacteria and archaea, and soil fungi, respectively. Microbial diversity and community composition were not affected by grazing rest or management, but fungal Shannon diversity was significantly impacted by total nitrogen (TN; mixed linear effect model, p = 0.044). Bacterial/archaeal and fungal community compositions were significantly different between pastures (PERMANOVA; R2 = 0.78, p < 0.001 for 16S; R2 = 0.71, p < 0.001 for ITS). Soil properties were also significantly different between pastures (PERMANOVA, R2 = 0.98, p = 0.001) and differed to a lesser extent based on the level of grazing, irrigation, and nutrient management efforts (R2 = 0.022, p = 0.022). We found trends among microbial functional groups in response to grazing, but none of the impacts were statistically significant after accommodating false discovery errors. These results support a growing body of evidence that soil microorganisms are variably influenced by livestock grazing and are largely shaped by local vegetation and soil characteristics, both of which can vary based on geography and land management legacies.
• Touceda-Suárez, M., Ponsero, A. J., & Barberán, A. (2025). Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils. Applied and Environmental Microbiology, 91(Issue 8). doi:10.1128/aem.02124-24
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  Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.
• Chen, Y., Dierig, D. A., Wang, G. (., Elshikha, D. E., Ray, D. T., Barberán, A., Maier, R. M., & Neilson, J. W. (2024). Identifying critical microbes in guayule-microbe and microbe-microbe associations. Plant and Soil, 494(Issue 1-2). doi:10.1007/s11104-023-06269-z
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  Background: Plant-microbe associations play central roles in ecosystem functioning, with some critical microbes significantly influencing the growth and health of plants. Additionally, some microbes are highly associated with other microbes in either competitive or cooperative microbe-microbe associations. Here, we aimed to determine whether there is overlap between critical microbes in plant-microbe and microbe-microbe associations by using guayule (a rubber-producing crop) as a model plant. Methods: Using marker gene amplicon sequencing, we characterized the bacterial/archaeal and fungal communities in soil samples collected from a guayule agroecosystem at six time points that represent changes in guayule productivity and growth stage. The critical microbes in guayule-microbe associations were phylotypes whose relative abundances were positively (positive taxa) or negatively (negative taxa) associated with guayule productivity. Network analysis was used to identify the critical microbes in microbe-microbe associations. Results: Some positive taxa in guayule-microbe associations were ammonia-oxidizing archaea (AOA) and bacteria (AOB) and arbuscular mycorrhizal fungi (AMF), and negative taxa included some microbes resistant to aridity. Some of the critical microbes in microbe-microbe associations were fungal plant pathogens. There were 9 phylotypes representing the overlap between critical microbes in guayule-microbe and microbe-microbe associations. This overlap group included AOB, phototrophic bacteria, AMF, and saprotrophic fungi, along with unique taxa of unknown function. Conclusions: Our study highlighted the association of the soil microbiome with the growth and health of guayule. Our systematic approach narrowed down the immense number of microbial taxa to a ‘most wanted’ list that we define as critical to the entire guayule agroecosystem.
• Martinez, A., Schiro, G., & Barberán, A. (2024). Soil microbial communities along elevational gradients in the Madrean Sky Islands. Environmental Microbiology, 26(Issue 2). doi:10.1111/1462-2920.16596
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  The Madrean Sky Islands are mountain ranges isolated by a ‘desert sea’. This area is a biodiversity hotspot currently threatened by climate change. Here, we studied soil microbial communities along elevational gradients in eight Madrean Sky Islands in southeastern Arizona (USA). Our results showed that while elevational microbial richness gradients were weak and not consistent across different mountains, soil properties strongly influenced microbial community composition (overall composition and the abundance of key functional groups) along elevational gradients. In particular, warming is associated with a higher abundance of soil-borne fungal plant pathogens that concomitantly might facilitate upward elevational shifts of plant species released from negative plant–soil feedbacks. Furthermore, projected warming and drought in the area aggravated by anthropogenic nitrogen deposition on mountain tops (and thus, decreasing nitrogen limitation) can enhance a shift from ectomycorrhizal to arbuscular mycorrhizal fungi. Overall, these results indicate that climate change effects on plant–soil interactions might have profound ecosystem consequences.
• Rudolph, J., Gornish, E., & Barberán, A. (2024). Plant–plant and plant–soil interactions under drought and the presence of invasive buffelgrass (Cenchrus ciliaris). Biological Invasions, 26(4). doi:10.1007/s10530-023-03245-7
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  Soil microbiomes could mediate plant responses to interacting environmental changes such as drought and plant invasion. We used a greenhouse experiment to assess changes in soil bacterial/archaeal and fungal communities, and competition between buffelgrass (Cenchrus ciliaris; an African perennial C4 bunchgrass introduced in the Sonoran Desert) and two native Sonoran Desert plants (i.e., Aristida purpurea and Plantago patagonica) under experimental drought. We found that buffelgrass benefitted from growing in the vicinity of native plants, particularly in drier conditions, and that this effect might be mediated by higher bacterial richness and an increased proportion of putative nitrogen-fixing bacteria in surrounding soil. Overall, plant–soil interactions are key to understand the interactive effects of abiotic and biotic stressors, and thus, critical to the management and restoration of invaded ecosystems.
• Tegart, L., Schiro, G., Dickinson, J., Green, B., Marthick, J., Bissett, A., Johnston, F., Jones, P., & Barberán, A. (2024). Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis. Environmental Research, 243(Issue). doi:10.1016/j.envres.2023.117808
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  Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.
• Wang, X., Lin, J., Peng, X., Zhao, Y., Yu, H., Zhao, K., Kuzyakov, Y., Dai, Z., & Barberán, A. (2024). Microbial rrn copy number is associated with soil C: N ratio and pH under long-term fertilization. Science of the Total Environment, 954(Issue). doi:10.1016/j.scitotenv.2024.176675
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  Soil microbial life-history strategies, as indicated by rRNA operon (rrn) copy numbers, strongly influence agro-ecosystem functioning. Long-term N fertilization causes strong and lasting changes in soil properties, yet its impact on microbial strategies remains largely unexplored. Using long-term field experiments across three agro-ecosystems, we consistently found that N fertilization strongly decreased soil C: N ratio and pH, further increasing the community-level rrn copy number, including both average rrn copy number and total 16S rRNA copy number. Soil C: N stoichiometry balanced by N supplement favored the growth of N-dependent copiotrophic species containing high rrn copy numbers (an average of 2.5) and increased their network connections, predominantly contributing to community-level rrn copy number increase. Decreased soil pH caused by N fertilization also favored the growth of some species whose abundances negatively correlated with pH, partially contributing to the community-level rrn copy number increase. By examining the genomes of two dominant species, we found that microorganisms with a higher rrn copy number (6), e.g., Streptomyces scabiei, possessed more genes related to C and N transport and metabolism. In contrast, the Mycobacterium simiae with a lower rrn copy number (1) has more genes associated with secondary metabolite biosynthesis and lipid transport and metabolism. Our finding challenges the concept of microbial life-strategy regulation solely by nutrient availability, highlighting the important contributions of soil stoichiometric balance and pH to microbial strategies in agro-ecosystems under long-term N inputs.
• Yang, B., Spaeth, M., Parsons, L., & Barberán, A. (2024). Soil inoculation changed soil microbial communities, but did not accelerate the decomposition of European Beachgrass (Ammophila arenaria) in Point Reyes National Seashore. Restoration Ecology, 33(Issue 3). doi:10.1111/rec.14344
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  Legacy effects after the removal of invasive plants present significant challenges to restoration. The pivotal role of soil microbial communities in shaping these legacy effects is increasingly recognized, yet there is a lack of effective methods to mitigate altered microbial communities. In Point Reyes National Seashore (California), although the invaded European beachgrass (Ammophila arenaria [L.] Link) was successfully controlled by herbicide treatment, beachgrass litter remained undecomposed for over 5 years, leaving pronounced legacy effects on soil organic matter and microbial community composition. We hypothesized that soil inoculation from uninvaded dune scrub can accelerate the decomposition of beachgrass litter in herbicide-treated sites by restoring the soil microbial communities and the abundance of microbial decomposers. Three litterbags containing European beachgrass litter or litter from two common shrubs at dune scrub were deployed into each plot to assess the impact of soil inoculation on litter decomposition rates. Our results revealed that soil inoculation, regardless of the inoculation level, did not accelerate the decomposition of European beachgrass. Only the decomposition of bush lupine litter, which had the highest litter quality among three types of litter, was accelerated at the highest inoculation level (approximately 11,880 g/m2). Additionally, soil inoculation increased the richness and compositional homogeneity of soil microbial communities, along with the relative abundances of wood saprotrophic fungi, soil saprotrophic fungi, and lichenized fungi. Although these findings demonstrate the potential of soil inoculation, the cost-effectiveness of soil inoculation limits its feasibility in accelerating the delayed decomposition of European beachgrass litter in Point Reyes.
• Cleavenger, S., Chen, Y., & Barberán, A. (2023). Mesquite-associated soil and phyllosphere microbial communities differ across land-use types in drylands. Elementa, 11(1). doi:10.1525/elementa.2023.00026
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  Plant-associated microbiomes play prominent roles in maintaining plant health and productivity. Here, we characterized the soil and phyllosphere microbiomes associated with mesquite trees in grazing and urban areas compared to natural areas in the arid Southwestern United States. Our results showed that grazing areas were associated with higher phyllosphere fungal richness, while urban areas had higher phyllosphere richness for both fungi and bacteria/archaea, and additionally, urban soils had lower fungal richness. Specifically, grazing areas were characterized by larger proportions of nitrogen-fixing bacteria in the soil and fungal plant pathogens in the phyllosphere, while urban areas presented higher proportions of fungal plant pathogens in both the soil and phyllosphere as well as nitrifying and denitrifying bacteria in the phyllosphere, but a lower proportion of cellulolytic bacteria in the soil. Furthermore, in urban areas, more phyllosphere microorganisms were sourced from the soil. Collectively, these results suggest that plantassociated microbiomes change significantly across land-use types, and these patterns are different between aboveground and belowground parts of plants, as well as between bacteria/archaea and fungi. These changes in plant-associated microbiomes across land-use types might have important implications for nutrient cycling, plant health, and ecosystem restoration.
• Cowan, D., Rockey, E., Barberán, A., & Touceda-Suárez, M. (2023). Effects of historical agricultural crops on the soil microbiome of a living agricultural museum in the Sonoran Desert. Agronomy Journal, 115(6). doi:10.1002/agj2.21456
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  Although soil has been a central piece in agricultural knowledge for most of recorded history, introductions of exotic plant assemblages can produce loss of soil quality, especially in more fragile ecosystems such as drylands. Here, we investigate the impact of indigenous and introduced plant assemblages associated with ethno-agricultural traditions of Tucson, AZ, on soil microbial communities using 16S rRNA gene (bacteria and archaea) and internal transcribed spacer region (fungi) metabarcoding. We found differences in soil microbial community diversity and composition across plant assemblages associated with ethno-agricultural traditions. However, we found the largest community structure differences between managed cultivated plots and not cultivated desert soils. Managed cultivated plots were characterized by higher diversity (23% increment for bacteria/archaea, and 40% for fungi) and a higher abundance of nitrifying bacteria (19% higher) and cellulolytic bacteria (39% higher) relative to minimally disturbed plots, suggesting higher rates of decomposition and nitrogen cycling. Given the observed influence of management on soil microbial communities, we conclude that efforts to build arid-specific sustainable agricultural solutions would benefit from the use of adapted plants that require minimal management.
• Demergasso, C., Neilson, J., Tebes-Cayo, C., Ayma, D., Laubitz, D., Maier, R., Barberán, A., Chong-Díaz, G., & Véliz, R. (2023). Corrigendum: Hyperarid soil microbial community response to simulated rainfall (Frontiers in Microbiology, (2023), 14, (1202266), 10.3389/fmicb.2023.1202266). Frontiers in Microbiology, 14(Issue). doi:10.3389/fmicb.2023.1327998
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  In the published article, there was an error regarding the affiliation for Diego Ayma. Instead of “Steele Steele Children's Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States,” it should be “Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile.” The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.
• Auladell, A., Logares, R., Gasol, J., Ferrera, I., Barberán, A., & Garcés, E. (2022). Seasonal niche differentiation among closely related marine bacteria. ISME Journal, 16(1). doi:10.1038/s41396-021-01053-2
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  Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
• Barberan, A., Blankinship, J., Chen, Y., & Schiro, G. (2022). Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape. ENVIRONMENTAL MICROBIOLOGY, N/A.
• Barberan, A., Gornish, E., & Williams, J. (2021). Effects of buffelgrass removal and nitrogen addition on soil microbial communities during an extreme drought in the Sonoran Desert. Restoration Ecology, NA.
• Barberan, A., Gornish, E., Munson, S., Laushman, K., Butterfield, B., Balazs, K., & Yang, B. (2022). Does restoration of plant diversity trigger concomitant soil microbiome changes in dryland     ecosystems? . Journal of Applied Ecology.
• Gornish, E., Kline, A., Yang, B., Miller, M., Blankinship, J., Barberan, A., & Martyn, T. (2022). Rock structures improve seedling establishment, litter catchment, fungal richness, and soil moisture in the first year after installation. ENVIRONMENTAL MANAGEMENT, N/A.
• Kiela, P. R., Barberan, A., Ghishan, F. K., Zhang, D. D., Dodson, M., Liu, P., & Schiro, G. (2022). Interactions between arsenic exposure, high-fat diet and NRF2 shape the complex responses in the murine gut microbiome and hepatic metabolism. Frontiers in Microbiomes. doi:https://doi.org/10.3389/frmbi.2022.1041188
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  Inorganic arsenic (iAs) exposure has been associated to various detrimental effects such as development of metabolic syndrome and type 2 diabetes via oxidative stress and induced prolonged activation of the NRF2 transcription factor. Such effects can be aggravated by poor dietary habits. The role of gut microbiota in promoting metabolic changes in response to arsenic has yet to be precisely defined. To address the complexity of the interactions between diet, NFE2L2/NRF2, and gut microbiota, we studied the chronic effects of iAs exposure in wild-type (WT) and Nrf2-/- mice fed normal (ND) vs. high-fat diet (HFD), on the gut microbial community in the context of hepatic metabolism. We demonstrate that all treatments and interactions influenced bacteria and metabolic profiles, with dietary differences causing a strong overlap of responses between the datasets. By identifying five metabolites of known microbial origin and following their fate across treatments, we provide examples on how gut microbial products can participate in the development of iAs and HFD-induced metabolic disease. Overall, our results underline the importance of the microbial community in driving gut-liver-cross talk during iAs and HFD exposure.
• Liu, L., Gao, C., Zhang, Z., Wang, M., Wurzburger, N., Wang, X., Zhang, R., Li, J., Zhang, J., & Barberán, A. (2022). Impact of urbanization on soil microbial diversity and composition in the megacity of Shanghai. Land Degradation and Development, 33(2). doi:10.1002/ldr.4145
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  Urbanization alters the physicochemical environment on an unprecedented scale and strongly affects biodiversity. How urbanization affects the biodiversity of soil microbial communities, especially in large cities, however, is poorly known. We investigated soil microbial communities from 258 sites covering a variety of environmental gradients in the megacity of Shanghai, China, to determine the impact of urbanization on soil microbial biodiversity. Using the distance to city centre, urbanized land cover, and road density as three proxies to characterize the levels of urbanization, we revealed that increased urbanization was associated with slightly homogenized communities of prokaryotes, total fungi, and arbuscular mycorrhizal fungi but not ectomycorrhizal fungi. The richness of soil prokaryotes and total fungi was weakly but positively related to urbanization as well. For the abundance of microbial phylotypes along urban gradients, we observed synchronous increases and decreases of many phylotypes at relatively high and low urbanization levels, respectively. Further, urbanization explained an independent part of microbial variances in richness and community composition, although the contribution of soil properties in explaining the variances was generally larger than that of urbanization. Together, this work provides evidence for the influences of urbanization on the biodiversity of soil microbes and highlights the importance of considering taxa and the level of urbanization to assess the impacts of urbanization on biodiversity.
• Martyn, T. E., Barberán, A., Blankinship, J. C., Miller, M., Yang, B., Kline, A., & Gornish, E. S. (2022). Rock structures improve seedling establishment, litter catchment, fungal richness, and soil moisture in the first year after installation. Environmental Management, 70(Issue 1). doi:10.1007/s00267-022-01651-6
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  Grasslands are essential natural and agricultural ecosystems that encompass over one-third of global lands. However, land conversion and poor management have caused losses of these systems which contributed to a 10% reduction of net primary production, a 4% increase in carbon emissions, and a potential loss of US $42 billion a year. It is, therefore, important to restore, enhance and conserve these grasslands to sustain natural plant communities and the livelihoods of those that rely on them. We installed low cost rock structures (media lunas) to assess their ability to restore grasslands by slowing water flow, reducing erosion and improving plant establishment. Our treatments included sites with small and large rock structures that were seeded with a native seed mix as well as sites with no seed or rock and sites with only seed addition. We collected summer percent cover for plants, litter, and rock and spring seedling count data. We also collected soil for nutrient, moisture, and microbial analysis. Within the first year, we found no change in plant cover between rock structures of two rock sizes. We did find, however, an increase in soil moisture, litter, fungal richness, and spring seedling germination within the rock structures, despite a historic drought. This work demonstrates that rock structures can positively impact plants and soils of grasslands even within the first year. Our results suggest that managers should seriously consider employing these low-cost structures to increase short-term plant establishment and possibly, soil health, in grasslands.
• Menéndez-Serra, M., Ontiveros, V. J., Barberán, A., & Casamayor, E. O. (2022). Absence of stress-promoted facilitation coupled with a competition decrease in the microbiome of ephemeral saline lakes. Ecology, 103(Issue 12). doi:10.1002/ecy.3834
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  Salinity fluctuations constitute a well-known high stress factor strongly shaping global biological distributions and abundances. However, there is a knowledge gap regarding how increasing saline stress affects microbial biological interactions. We applied the combination of a probabilistic method for estimating significant co-occurrences/exclusions and a conceptual framework for filtering out associations potentially linked to environmental and/or spatial factors, in a series of connected ephemeral (hyper) saline lakes. We carried out a network analysis over the full aquatic microbiome—bacteria, eukarya, and archaea—under severe salinity fluctuations. Most of the observed co-occurrences/exclusions were potentially explained by environmental niche and/or dispersal limitation. Co-occurrences assigned to potential biological interactions remained stable, suggesting that the salt gradient was not promoting interspecific facilitation processes. Conversely, co-exclusions assigned to potential biological interactions decreased along the gradient both in number and network complexity, pointing to a decrease of interspecies competition as salinity increased. Overall, higher saline stress reduced microbial co-exclusions while co-occurrences remained stable suggesting decreasing competition coupled with lack of stress-gradient promoted facilitation in the microbiome of ephemeral saline lakes.
• Ontiveros, V., Alonso, D., Casamayor, E., Barberán, A., Capitán, J., & Ortiz-Álvarez, R. (2022). Biological Microbial Interactions from Cooccurrence Networks in a High Mountain Lacustrine District. mSphere, 7(3). doi:10.1128/msphere.00918-21
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  A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed coexisting. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, where biotic interactions might be required to make the most of an extreme environment. We studied a high-throughput gene data set of alpine lakes (.220 Pyrenean lakes) with cooccurrence network analysis to infer potential biotic interactions, using the combination of a probabilistic method for determining significant cooccurrences and coexclusions between pairs of species and a conceptual framework for classifying the nature of the observed cooccurrences and coexclusions. This computational approach (i) determined and quantified the importance of environmental variables and spatial distribution and (ii) defined potential interacting microbial assemblages. We determined the properties and relationships between these assemblages by examining node properties at the taxonomic level, indicating associations with their potential habitat sources (i.e., aquatic versus terrestrial) and their functional strategies (i.e., parasitic versus mixotrophic). Environmental variables explained fewer pairs in bacteria than in microbial eukaryotes for the alpine data set, with pH alone explaining the highest proportion of bacterial pairs. Nutrient composition was also relevant for explaining association pairs, particularly in microeukaryotes. We identified a reduced subset of pairs with the highest probability of species interactions (“interacting guilds”) that significantly reached higher occupancies and lower mean relative abundances in agreement with the carrying capacity hypothesis. The interacting bacterial guilds could be more related to habitat and microdispersal processes (i.e., aquatic versus soil microbes), whereas for microeukaryotes trophic roles (osmotrophs, mixotrophs, and parasitics) could potentially play a major role. Overall, our approach may add helpful information to guide further efforts for a mechanistic understanding of microbial interactions in situ.
• Reitstetter, R., Yang, B., Tews, A. D., & Barberán, A. (2022). Soil microbial communities and nitrogen associated with cheatgrass invasion in a sagebrush shrubland. Plant and Soil, 479(Issue 1-2). doi:10.1007/s11104-022-05523-0
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  Purpose: Cheatgrass invasion of Intermountain sagebrush steppe in the western United States poses increasing challenges to the function and survival of this native ecosystem. The invasive success and persistence of cheatgrass has been attributed to the increasing soil total nitrogen, but mechanisms behind remain inconclusive. We hypothesized that soil microorganisms play a role in soil nitrogen associated with cheatgrass invasion. Methods: We collected soil samples from the root zone of cheatgrass, native bunchgrass, and sagebrush at two depths and from two adjacent sites in April. We examined soil chemical properties (pH, moisture content, and NH4+ and NO3− concentration) and soil microbial communities. Results: We found that cheatgrass invasion was associated with different soil microbial community composition compared to native bunchgrass and sagebrush. In particular, we observed higher relative abundances of N2 fixers and ureolytic bacteria and lower relative abundance of denitrifiers providing a potential mechanistic belowground explanation of raising soil nitrogen. Conclusions: Overall, our results indicate the importance of soil microorganisms in the dominance and persistence of invasive species. Targeted microbiome interventions should be considered to control cheatgrass invasion.
• Schiro, G., Chen, Y., Blankinship, J. C., & Barberán, A. (2022). Ride the dust: linking dust dispersal and spatial distribution of microorganisms across an arid landscape. Environmental Microbiology, 24(Issue 9). doi:10.1111/1462-2920.15998
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  In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbour a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems.
• Schiro, G., Liu, P., Dodson, M., Zhang, D. D., Ghishan, F. K., Barberán, A., & Kiela, P. R. (2022). Interactions between arsenic exposure, high-fat diet and NRF2 shape the complex responses in the murine gut microbiome and hepatic metabolism. Frontiers in Microbiomes, 1(Issue). doi:10.3389/frmbi.2022.1041188
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  Inorganic arsenic (iAs) exposure has been associated to various detrimental effects such as development of metabolic syndrome and type 2 diabetes via oxidative stress and induced prolonged activation of the NRF2 transcription factor. Such effects can be aggravated by poor dietary habits. The role of gut microbiota in promoting metabolic changes in response to arsenic has yet to be precisely defined. To address the complexity of the interactions between diet, NFE2L2/NRF2, and gut microbiota, we studied the chronic effects of iAs exposure in wild-type (WT) and Nrf2-/- mice fed normal (ND) vs. high-fat diet (HFD), on the gut microbial community in the context of hepatic metabolism. We demonstrate that all treatments and interactions influenced bacteria and metabolic profiles, with dietary differences causing a strong overlap of responses between the datasets. By identifying five metabolites of known microbial origin and following their fate across treatments, we provide examples on how gut microbial products can participate in the development of iAs and HFD-induced metabolic disease. Overall, our results underline the importance of the microbial community in driving gut-liver-cross talk during iAs and HFD exposure.
• Vanni, C., Schechter, M., Acinas, S., Buttigieg, P., Casamayor, E., Delmont, T., Duarte, C., Eren, A., Finn, R., Kottmann, R., Mitchell, A., Sanchez, P., Siren, K., Steinegger, M., Fernandez-Guerra, A., Barberán, A., & Glöckner, F. (2022). Unifying the known and unknown microbial coding sequence space. eLife, 11(Issue). doi:10.7554/elife.67667
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  Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40%-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.
• Williams, J. P., Gornish, E. S., & Barberán, A. (2022). Effects of buffelgrass removal and nitrogen addition on soil microbial communities during an extreme drought in the Sonoran Desert. Restoration Ecology, 30(Issue 2). doi:10.1111/rec.13570
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  Buffelgrass (Cenchrus ciliaris), an invasive perennial grass in arid regions of the United States, has drastically modified natural ecosystems. Understanding the aboveground–belowground links between buffelgrass invasion and soil microbial communities will be critical for developing a comprehensive understanding of arid ecosystems and for deploying successful control strategies. In a randomized block-field experiment located in Tucson, AZ, U.S.A., we investigated the effects of buffelgrass removal via hand pulling and nitrogen addition (and their interaction) on soil microbial communities during an extreme drought (summer 2020). We found that experimental treatments did not significantly impact bacterial and archaeal community diversity and composition, while plant removal affected fungal community diversity and composition. In addition, the removal treatment increased the proportion of putative chitinolytic bacteria (genus Lysobacter) and decreased the proportion of putative fungal endophytes (genus Darksidea). Buffelgrass manual removal appeared to favor fungal endophyte death around and inside of leftover intact roots, which may result in an increase of chitinolytic bacteria thriving on the degradation of fungal cell walls. Overall, our results suggest that hand removal—which is a common type of buffelgrass control—can alter soil fungal communities and the proportion of certain microbial functional groups. As these changes could subsequently affect native plants, more research is needed to develop a comprehensive understanding of the effect of buffelgrass control efforts on target plants as well as surrounding ecosystem dynamics.
• Yang, B., Balazs, K. R., Butterfield, B. J., Laushman, K. M., Munson, S. M., Gornish, E. S., & Barberán, A. (2022). Does restoration of plant diversity trigger concomitant soil microbiome changes in dryland ecosystems?. Journal of Applied Ecology, 59(Issue 2). doi:10.1111/1365-2664.14074
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  Drylands are highly vulnerable to land degradation, and despite increasing efforts, restoration success remains low. Although often ignored in the design and deployment of management strategies, soil microbial communities might be critical for dryland restoration due to their central role in promoting soil stability, nutrient cycling and plant establishment. We collected soil samples from eight dryland restoration sites within RestoreNet, a restoration field trial network, and determined their soil microbiome using 16S rRNA (bacteria and archaea) and ITS (fungi) amplicon sequencing. Each previously degraded site was treated with monoculture (single species) and polyculture (multiple species) seedling plantings. Contrary to our initial expectations, we found that these different revegetation interventions did not trigger changes in microbial diversity, composition or relative abundance of functional groups across sites after 1 year of revegetation. Synthesis and applications. Considering the crucial role of soil micro-organisms in dryland ecosystem functions, our results suggest that site-specific targeted microbiome restoration should be considered to accelerate the establishment of desired microbial communities. Plant community-based restoration practices such as revegetation have a limited impact on soil micro-organisms in the short term.
• Barberan, A. (2021). Changes in soil microbial communities across an urbanization gradient: a local-scale temporal study in the arid Southwestern USA. Microorganisms.
• Barberan, A. (2021). Contrasting community assembly forces drive microbial structural and potential functional responses to precipitation in an incipient soil system. Frontiers Microbiology.
• Barberan, A. (2021). Dynamics and complexity of dark fermentation microbial communities producing hydrogen from sugar beet molasses in continuously operating packed bed reactors. Frontiers Microbiology.
• Barberan, A. (2021). Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. Microbiome.
• Barberan, A. (2021). Dynamics of gut microbiota recovery after antibiotic exposure in young and old mice (a pilot study). Microorganisms.
• Barberan, A. (2021). Global patterns and climatic controls of dust-associated microbial communities.. Microbiology Spectrum.
• Barberan, A. (2021). Life-history strategies of soil microbial communities in an arid ecosystem. The ISME Journal.
• Barberan, A. (2021). Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences. Environmental Microbiology.
• Barberan, A., Fernandez-guerra, A., Glockner, F. O., & Pereira-flores, E. (2021). Mg-Traits pipeline: advancing functional trait-based approaches in metagenomics. ARPHA Conference Abstracts, 4. doi:10.3897/aca.4.e64908
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  Microorganisms comprise an immense phylogenetic and metabolic diversity, inhabit every conceivable niche on earth, and play a fundamental role in global biogeochemical processes. Among others, their study is highly relevant to develop biotechnological applications, understand ecosystem processes and monitor environmental systems. Functional traits (FTs) (i.e., measurable properties of an organism that influence its fitness (McGill et al. 2006)) provide complementary information to the taxonomic composition to improve the characterization of microbial communities and study their ecology (Martiny et al. 2012). The application of FT-based approaches can be particularly enhanced when coupled with metagenomics, which as a culture-independent method, allows us to obtain the genetic material of microorganisms from the environment: Metagenomic data can be used to compute functional traits at the genome level from a random sample of individuals in a microbial community, irrespective of their taxonomic affiliation (Fierer et al. 2014). Previous works using FT-based approaches in metagenomics include the study of community assembly processes (Burke et al. 2011) and responses to environmental change (Leff et al. 2015), and ecosystem functioning (Babilonia et al. 2018). In this work, we present the Metagenomic Traits pipeline: Mg-Traits. Mg-Traits is dedicated to the computation of 25 (and counting) functional traits in short-read metagenomic data, ranging from GC content and amino acid composition to functional diversity and average genome size (see Fig. 1). As an example application, we used the Mg-Traits pipeline to process the 139 prokaryotic metagenomes of the TARA Oceans data set (Sunagawa et al. 2015). In this analysis, we observed that the computed metagenomic traits track community changes along the water column, which denote microorganisms’ environmental adaptations. Mg-Traits allows the systematic computation of a comprehensive set of metagenomic functional traits, which can be used to generate a functional and taxonomic fingerprint and reveal the predominant life-history strategies and ecological processes in a microbial community. Mg-Traits contributes to improving the exploitation of metagenomic data and facilitates comparative and quantitative studies. Considering the high genomic plasticity of microorganisms and their capacity to rapidly adapt to changing environmental conditions, Mg-Traits constitutes a valuable tool to monitor environmental systems. The Mg-Traits pipeline is available at https://github.com/pereiramemo/metagenomic_pipelines. It is programmed in AWK, BASH, and R, and it was devised using a modular design to facilitate the integration of new metagenomic traits.
• Chen, Y., Gebert, M. J., Faith, S. A., Dunn, R. R., Fierer, N., & Barberán, A. (2021). Global patterns and climatic controls of dust-associated microbial communities. Microbiology Spectrum, 9(Issue 2). doi:10.1128/spectrum.01447-21
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  The ubiquity and long-range transport of the microorganisms inhabiting dust can pose a serious risk to human, animal, and plant health. The well-recognized importance of dust-associated microorganisms contrasts starkly with our limited understanding of the factors determining the variation in the composition of these communities at the global scale. Here, we provide the first insight into the global determinants of dust-associated microorganisms by quantifying the environmental factors shaping bacterial and fungal community composition in 467 outdoor settled dust samples collected from 33 countries and 6 continents. Our results show that the global variation in dust-associated bacterial and fungal community composition was, to some degree, predictable from mean annual precipitation and temperature. Notably, our results show that the fungal genera Alternaria and Aspergillus, which contain many species that can serve as triggers of allergenic disease in humans and as plant pathogens, were more abundant in drier regions. Collectively, these results highlight the key influence of climate on the global distribution of dust-associated microorganisms and provide the baseline information needed to build a more comprehensive understanding of how microbial exposures vary across the globe and in response to climate change.
• Chen, Y., Martinez, A., Cleavenger, S., Rudolph, J., & Barberán, A. (2021). Changes in soil microbial communities across an urbanization gradient: A local-scale temporal study in the arid southwestern usa. Microorganisms, 9(Issue 7). doi:10.3390/microorganisms9071470
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  Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited non-significant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.
• Chen, Y., Neilson, J. W., Kushwaha, P., Maier, R. M., & Barberán, A. (2021). Life-history strategies of soil microbial communities in an arid ecosystem. ISME Journal, 15(Issue 3). doi:10.1038/s41396-020-00803-y
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  The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.
• Dai, Z., Zang, H., Chen, J., Fu, Y., Wang, X., Liu, H., Shen, C., Wang, J., Kuzyakov, Y., Becker, J. N., Hemp, A., Barberán, A., Gunina, A., Chen, H., Luo, Y., & Xu, J. (2021). Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences. Environmental Microbiology, 23(Issue 8). doi:10.1111/1462-2920.15655
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  Diversity and community composition of soil microorganisms along the elevation climosequences have been widely studied, while the microbial metabolic potential, particularly in regard to carbon (C) cycling, remains unclear. Here, a metagenomic analysis of C related genes along five elevations ranging from 767 to 4190 m at Mount Kilimanjaro was analysed to evaluate the microbial organic C transformation capacities in various ecosystems. The highest gene abundances for decomposition of moderate mineralizable compounds, i.e. carbohydrate esters, chitin and pectin were found at the mid-elevations with hump-shaped pattern, where the genes for decompositions of recalcitrant C (i.e. lignin) and easily mineralizable C (i.e. starch) showed the opposite trend (i.e. U-shaped pattern), due to high soil pH and seasonality in both low and high elevations. Notably, the gene abundances for the decompositions of starch, carbohydrate esters, chitin and lignin had positive relationships with corresponding C compounds, indicating the consistent responses of microbial functional profiles and metabolites to elevation climosequences. Understanding of adaptation of microbial communities, potential function and metabolites to elevation climosequences and their influencing factors provided a new insight for the regulation of terrestrial C storage.
• Detman, A., Laubitz, D., Chojnacka, A., Kiela, P. R., Salamon, A., Barberán, A., Chen, Y., Yang, F., Błaszczyk, M. K., & Sikora, A. (2021). Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. Microbiome, 9(Issue 1). doi:10.1186/s40168-021-01105-x
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  Background: This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation. Results: MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0–6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes. Conclusions: Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. [MediaObject not available: see fulltext.]
• Kushwaha, P., Neilson, J. W., Barberán, A., Chen, Y., Fontana, C. G., Butterfield, B. J., & Maier, R. M. (2021). Arid Ecosystem Vegetation Canopy-Gap Dichotomy: Influence on Soil Microbial Composition and Nutrient Cycling Functional Potential. Applied and Environmental Microbiology, 87(Issue 5). doi:10.1128/aem.02780-20
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  Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity vary between the vegetated canopy and gap soils. The specific aim of this study was to characterize canopy versus gap microsite effect on soil microbial diversity, the capacity of gap soils to serve as a canopy soil microbial reservoir, nitrogen (N)-mineralization genetic potential (ureC gene abundance) and urease enzyme activity, and microbial-nutrient pool associations in four arid-hyperarid geolocations of the western Sonoran Desert, Arizona, United States. Microsite combined with geolocation explained 57% and 45.8% of the observed variation in bacterial/archaeal and fungal community composition, respectively. A core microbiome of amplicon sequence variants was shared between the canopy and gap soil communities; however, canopy soils included abundant taxa that were not present in associated gap communities, thereby suggesting that these taxa cannot be sourced from the associated gap soils. Linear mixed-effects models showed that canopy soils have significantly higher microbial richness, nutrient content, and organic N-mineralization genetic and functional capacity. Furthermore, ureC gene abundance was detected in all samples, suggesting that ureC is a relevant indicator of N mineralization in deserts. Additionally, novel phylogenetic associations were observed for ureC, with the majority belonging to Actinobacteria and uncharacterized bacteria. Thus, key N-mineralization functional capacity is associated with a dominant desert phylum. Overall, these results suggest that lower microbial diversity and functional capacity in gap soils may impact ecosystem sustainability as aridity drives openspace expansion in deserts.
• Laubitz, D., Typpo, K., Midura-Kiela, M., Brown, C., Barberán, A., Ghishan, F. K., & Kiela, P. R. (2021). Dynamics of gut microbiota recovery after antibiotic exposure in young and old mice (A pilot study). Microorganisms, 9(Issue 3). doi:10.3390/microorganisms9030647
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  Antibiotics have improved survival from previously deadly infectious diseases. Antibiotics alter the microbial composition of the gut microbiota, and these changes are associated with diminished innate immunity and decline in cognitive function in older adults. The composition of the human microbiota changes with age over the human lifespan. In this pilot study, we sought to identify if age is associated with differential recovery of the microbiota after antibiotic exposure. Using 16S rRNA gene sequencing, we compared recovery of the gut microbiota after the 10-day broad-spectrum antibiotic treatment in wild-type C57BL/six young and older mice. Immediately after antibiotic cessation, as expected, the number of ASVs, representing taxonomic richness, in both young and older mice significantly declined from the baseline. Mice were followed up to 6 months after cessation of the single 10-day antibiotic regimen. The Bray-Curtis index recovered within 20 days after antibiotic cessation in young mice, whereas in older mice the microbiota did not fully recover during the 6-months of follow-up. Bifidobacterium, Dubosiella, Lachnospiraceae_NK4A136_group became dominant in older mice, whereas in young mice, the bacteria were more evenly distributed, with only one dominant genus of Anaeroplasma. From 45 genera that became extinct after antibiotic treatment in young mice, 31 (68.9%) did not recover by the end of the study. In older mice, from 36 extinct genera, 27 (75%) did not recover. The majority of the genera that became extinct and never recovered belonged to Firmicutes phylum and Clostridiales family. In our study, age was a factor associated with the long-term recovery of the gut microbiota after the 10-day antibiotic treatment.
• Maier, R. M., Butterfield, B. J., Fontana, C. G., Chen, Y., Barberan, A., Neilson, J. W., & Kushwaha, P. (2021). Arid ecosystem vegetation canopy-gap dichotomy: influence on soil microbial composition and nutrient cycling functional potential. Applied and Environmental Microbiology. doi:10.1128/AEM.02780-20
• Sengupta, A., Volkmann, T. H., Danczak, R. E., Stegen, J. C., Dontsova, K. M., Abramson, N., Bugaj, A. S., Volk, M. J., Matos, K. A., Meira-Neto, A. A., Barberan, A., Neilson, J. W., Maier, R. M., Chorover, J. D., Troch, P. A., & Meredith, L. (2021). Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System.. Frontiers in Microbiology, 12(3414).
• Sengupta, A., Volkmann, T. H., Danczak, R. E., Stegen, J. C., Dontsova, K., Abramson, N., Bugaj, A. S., Volk, M. J., Matos, K. A., Meira-Neto, A. A., Barberán, A., Neilson, J. W., Maier, R. M., Chorover, J., Troch, P. A., & Meredith, L. K. (2021). Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. Frontiers in Microbiology, 12(Issue). doi:10.3389/fmicb.2021.754698
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  Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.
• Yang, F., Zhang, Z., Barberan, A., Yang, Y., Ju, S., & Gu0, H. (2021). Nitrogen-induced acidification plays a vital role driving ecosystem functions: Insights from a 6-year nitrogen enrichment experiment in a Tibetan alpine meadow. Soil Biology and Biochemistry.
• Yang, F., Zhang, Z., Barberán, A., Yang, Y., Hu, S., & Guo, H. (2021). Nitrogen-induced acidification plays a vital role driving ecosystem functions: Insights from a 6-year nitrogen enrichment experiment in a Tibetan alpine meadow. Soil Biology and Biochemistry, 153(Issue). doi:10.1016/j.soilbio.2020.108107
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  Anthropogenic nitrogen (N) input has overtaken natural N fixation as the leading source of reactive N, and can profoundly alter the structure and functions of terrestrial ecosystems. N input impacts ecosystem functions through altering abiotic (e.g., soil nutrients and pH) and biotic (e.g., biological community composition) properties, but the relative importance of these abiotic and biotic effects remains largely unknown. We conducted a 6-year experiment of N manipulations (0, 5, 10, and 20 g N m−2 yr−1) in a Tibetan alpine meadow to assess N-induced abiotic and biotic effects on ecosystem functions. A complementary experiment with acid additions (0, 0.66, 2.65, 4.63, and 7.28 mol H+ m−2 yr−1) was also carried out to examine the direct impact of acidification. We found that N enrichment significantly increased plant productivity but decreased soil microbial respiration. While the increased productivity was associated with increased N availability, the reduction in soil microbial respiration was mainly explained by the decreased soil pH. In the acid addition experiment, enhanced soil acidity due to the increased proton concentration significantly reduced soil microbial respiration. These results indicate that N-induced changes in soil pH represent an important mechanism driving the ecosystem functions, suggesting that N-induced acidification should receive more attention for understanding and predicting ecosystem services under future N-enrichment scenarios.
• Barberan, A., Blaszczyk, M. K., Chen, Y., Chojnacka, A., Detman, A., Kazmierczak, W., Laubitz, D., Lupikasza, E., Piotrowski, J., Salamon, A., Sikora, A., Wiktorowska-sowa, E., & Yang, F. (2020). Dynamics and Complexity of Dark Fermentation Microbial Communities Producing Hydrogen From Sugar Beet Molasses in Continuously Operating Packed Bed Reactors.. Frontiers in microbiology, 11(Issue), 612344. doi:10.3389/fmicb.2020.612344
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  This study describes the dynamics and complexity of microbial communities producing hydrogen-rich fermentation gas from sugar-beet molasses in five packed-bed reactors (PBRs). The bioreactors constitute a part of a system producing hydrogen from the by-products of the sugar-beet industry that has been operating continuously in one of the Polish sugar factories. PBRs with different working volumes, packing materials, construction and inocula were tested. This study focused on analysis (based on 16S rRNA profiling and shotgun metagenomics sequencing) of the microbial communities selected in the PBRs under the conditions of high (>100 cm3/g COD of molasses) and low (
• Barberan, A., Maier, R. M., Kushwaha, P., Neilson, J. W., & Chen, Y. (2020). Life history strategies of soil microbial communities is an arid ecosystem. ISME Journal, online journal, doi.org/10.1038/s41396-020-00803-y. doi:doi.org/10.1038/s41396-020-00803-y
• Barberan, A., Rowe, J., Franklin, K., & Gornish, E. (2020). Buffelgrass invasion and glyphosate effects on desert soil microbiome communities. Biological Invasions.
• Chen, Y., Kuang, J., Wang, P., Shu, W., & Barberan, A. (2020). Associations between human impacts and forest soil microbial communities. Elementa.
• Farrell, H. L., Barberán, A., Danielson, R. E., Fehmi, J. S., & Gornish, E. S. (2020). Disturbance is more important than seeding or grazing in determining soil microbial communities in a semiarid grassland. Restoration Ecology, 28(Issue 4). doi:10.1111/rec.13156
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  A primary goal of ecological restoration is often to return processes and functions to degraded ecosystems. Soil, while often ignored in restoration, supports diverse communities of organisms and is a fundamental actor in providing ecosystem processes and services. We investigated the impact of seeding and livestock grazing on plant communities, soil microorganisms, and soil fertility 3 years after the restoration of a disturbed pipeline corridor in southeastern Arizona. The initial soil disturbance and topsoil treatment, regardless of seeding or grazing, was the most influential factor in determining differences in both plant and microbial communities. Compared with the control, the disturbed and restored sites had greater plant species richness, greater total herbaceous plant cover, greater soil organic matter, higher pH, and differed in soil nutrients. Bacteria and fungi appeared to generally correlate with micro-environment and soil physiochemical properties rather than specific plant species. The undisturbed control had a smaller proportion of bacterial functional groups associated with the breakdown of plant biomass (polysaccharide decomposition) and a smaller proportion of arbuscular mycorrhizal fungi (AMF) compared with disturbed and restored sites. The ability of the unseeded disturbed site to recover robust vegetation may be due in part to the high presence of AMF. These differences show selection for soil microorganisms that thrive in disturbed and restored sites and may contribute to increased plant productivity. Restoration of specific plant species or ecological processes and services would both benefit from better understanding of the impacts of disturbance on soil microorganisms and soil fertility.
• Gornish, E. S., Franklin, K., Rowe, J., & Barberán, A. (2020). Buffelgrass invasion and glyphosate effects on desert soil microbiome communities. Biological Invasions, 22(Issue 8). doi:10.1007/s10530-020-02268-8
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  Buffelgrass (Cenchus ciliaris) is a drought-tolerant invasive grass in the Americas and Australia that significantly impacts native plant communities and ecosystems. Despite the clear need to develop a comprehensive understanding of how buffelgrass is able to invade and rapidly establish in arid ecosystems, there is still a lack of knowledge as to if and how this weed might change the soil microbiome in a way that affects its dominance in the presence of management. We investigated the effect of buffelgrass on soil microbial communities in areas that have either been exposed to or not exposed to glyphosate in Saguaro National Park, Arizona USA. We found that buffelgrass roots in invaded areas are surrounded by a distinct soil community that includes a greater number of nitrifiers than in uninvaded soil. We also observed increases in arbuscular mycorrhizal fungi, ectomycorrhizal fungi and methanotrophs with buffelgrass invasion compared to uninvaded soil. Finally, we found no evidence of glyphosate effects on the soil microbiome. Overall, our study results suggest that buffelgrass can escape the limitation of nutrient availability in arid ecosystems by directly or indirectly modifying the soil microbiome. The competitive dominance of buffelgrass in arid systems might be indirectly enhanced by nitrifiers and fungal symbionts, which are often involved in rapid biomass accumulation. This work highlights the importance of soil microbiome considerations in weed science research.
• Gornish, E., Fehmi, J. S., Danielson, R., Barberan, A., & Farrell, H. (2020). Disturbance is more important than seeding or grazing in determining soil microbial communities in a semi-arid grassland. Restoration Ecology.
• Parsons, L. S., Sayre, J., Ender, C., Rodrigues, J. L., & Barberán, A. (2020). Soil microbial communities in restored and unrestored coastal dune ecosystems in California. Restoration Ecology, 28(Issue 4). doi:10.1111/rec.13101
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  Most restoration projects involving invasive plant eradication tend to focus on plant removal with little consideration given to how these invasives change soil microbial communities. However, soil microorganisms can determine invasibility of habitats and, in turn, be altered by invasives once established, potentially inhibiting native plant establishment. We studied soil microbial communities in coastal dunes with varying invasion intensity and different restoration approaches (herbicide, mechanical excavation) at Point Reyes National Seashore. Overall, we found evidence of a strong link between bacterial and fungal soil communities and the presence of invasives and restoration approach. Heavily invaded sites were characterized by a lower abundance of putatively identified nitrifiers, fermentative bacteria, fungal parasites, and fungal dung saprotrophs and a higher abundance of cellulolytic bacteria and a class of arbuscular mycorrhizal fungi (Archaeosporomycetes). Changes in soil microbiota did not fully dissipate following removal of invasives using herbicide, with exception of reductions in cellulolytic bacteria and Archaeosporomycetes abundance. Mechanical restoration effectively removed both invasives and soil legacy effects by inverting or “flipping” rhizome-contaminated surface soils with soils from below and may have inadvertently induced other adverse effects on soils that impeded reestablishment of native dune plants. Land managers should consider additional measures to counteract lingering legacy effects and/or focus restoration efforts in areas where legacy effects are less pronounced.
• Parsons, L. S., Sayre, J., Ender, C., Rodrigues, J., & Barberan, A. (2020). Soil microbial communities in restored and unrestored coastal dune ecosystems in California. RESTORATION ECOLOGY.
• Aanderud, Z. T., Adams, B. J., Ball, B. A., Barberan, A., Barrett, J. E., Griffin, N. A., Muscarella, M. E., Saurey, S., Virginia, R. A., & Wall, D. H. (2019). Corrigendum: Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages.. Frontiers in microbiology, 10(Issue), 391. doi:10.3389/fmicb.2019.00391
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  [This corrects the article DOI: 10.3389/fmicb.2018.01401.].
• Aanderud, Z. T., Saurey, S., Ball, B. A., Wall, D. H., Barrett, J. E., Muscarella, M. E., Griffin, N. A., Virginia, R. A., Barberan, A., & Adams, B. J. (2019). Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages (vol 9, 1401, 2018). FRONTIERS IN MICROBIOLOGY, 10.
• Angadi, S. S., Barberan, A., Brown, C., Gaesser, G. A., Laubitz, D., Ortega-santos, C. P., Tucker, W. J., & Whisner, C. M. (2019). The Impact of Exercise on Gut Microbiota Diversity During a Period of Increased Caloric Intake Characteristic of the Winter Holiday Period (P21-029-19). Current Developments in Nutrition, 3(Supplement_1). doi:10.1093/cdn/nzz041.p21-029-19
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  Abstract Objectives The winter holiday period is associated with weight gain from overconsumption of calories from fat and sugar. Such short-term lifestyle change has the ability to decrease diversity of the gut microbiome and enhance the harvest of energy from the hosts’ diet, both of which are relevant factors in obesity. Exercise may influence gut microbial diversity and prevent diet induced obesity related health outcomes. The study aim to determine the impact of exercise on taxonomic diversity of the gut microbiota (GM) and cardiometabolic health parameters after four weeks of consuming a fat-sugar supplemented diet. Methods Healthy overweight/obese (BMI 29.8 ± 3.5 kg/m2, age 29 ± 7 yrs, waist circumference (WC) 99.8 ± 10 cm) males (n = 18) supplemented their diet with 2 donuts per day (606 kcal, 50% fat, 46% carbs, 4% protein), 6 days/week, for 4 weeks. Subjects were randomized to sedentary control (n = 4) or 1000 kcal/week on a cycle ergometer 4 days/week of supervised exercise (n = 14). We measured WC (cm), flow mediated dilation (FMD, %) and insulin resistance (HOMA-IR). GM diversity was analyzed, in stool samples collected pre- and post-intervention, with DADA2 and vegan, and visualized with ggplot in R. SILVA v.132 was used for taxonomic assignment. Differences in GM alpha (Shannon Index) and beta (Bray-Curtis) diversity were evaluated with Mann-Whitney U and Permutational Multivariate Analysis of Variance (PERMANOVA) tests. Results Microbial diversity analysis revealed no significant (P > 0.05) alpha (Shannon Index) or beta diversity (Bray-Curtis) differences between the control and exercise group after 4 weeks intervention. GM alpha and beta diversity also did not differ (P > 0.05) by HOMA-IR and FMD categories. We did observe that participants with a lower WC ( 110 cm. Conclusions In this study, exercise training during 4 weeks of consuming a fat-sugar supplemented diet did not appear to influence GM diversity. However, beta-diversity was heterogeneous across WC classes suggesting a potential link between central adiposity and GM community structure. Further studies with a larger sample size should be done to confirm these findings. Funding Sources This study was partially funded by the Arizona State University Graduate and Professional Student Association Research Program.
• Angel, F. M., dos, S., Moreno-Paz, M., Gallardo-Carreno, I., Blanco, Y., Warren-Rhodes, K., Garcia-Villadangos, M., Ruiz-Bermejo, M., Barberan, A., Wettergreen, D., Cabrol, N., & Parro, V. (2019). Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period. FRONTIERS IN MICROBIOLOGY, 10.
• Barberan, A., Bohannan, B. J., Khan, M. A., Nusslein, K., Parlade, E., Rodrigues, J. L., Tiedje, J. M., & Tringe, S. G. (2019). Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils.. FEMS microbiology ecology, 95(2). doi:10.1093/femsec/fiy230
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  Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.
• Dietzel, K., Valle, D., Fierer, N., U'Ren, J. M., & Barberan, A. (2019). Geographical Distribution of Fungal Plant Pathogens in Dust Across the United States. FRONTIERS IN ECOLOGY AND EVOLUTION, 7.
• Dietzel, K., Valle, D., Fierer, N., U’ren, J. M., & Barberán, A. (2019). Geographical distribution of fungal plant pathogens in dust across the united states. Frontiers in Ecology and Evolution, 7(Issue). doi:10.3389/fevo.2019.00304
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  As the world’s population grows, global food production will need to increase. While food production efficiency has increased in recent decades through pathogen control, climate change poses new challenges in crop protection against pathogens. Understanding the natural geographical distribution and dispersal likelihood of fungal plant pathogens is essential for forecasting disease plant spread. Here we used cultivation-independent techniques to identify fungal plant pathogens in 1,289 near-surface dust samples collected across the United States. We found that overall fungal pathogen community composition is more related to environmental conditions (in particular soil pH, precipitation and frost) than to agricultural hosts and practices. We also delimited five susceptibility geographical areas in the United States where different sets of pathogens tend to occur.
• Fernández-Martínez, M. Á., Dos Santos Severino, R., Moreno-Paz, M., Gallardo-Carreño, I., Blanco, Y., Warren-Rhodes, K., García-Villadangos, M., Ruiz-Bermejo, M., Barberán, A., Wettergreen, D., Cabrol, N., & Parro, V. (2019). Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period. Frontiers in Microbiology, 10(Issue). doi:10.3389/fmicb.2019.01641
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  The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13–1,125; 168–10,109; and 9,904–30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.
• Aanderud, Z. T., Adams, B. J., Ball, B. A., Barberan, A., Barrett, J. E., Griffin, N. A., Muscarella, M. E., Saurey, S., Virginia, R. A., & Wall, D. H. (2018). Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages.. Frontiers in microbiology, 9, 1401. doi:10.3389/fmicb.2018.01401
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  Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH4+ and NO3-, and P as Na3PO4) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After 6 years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an Arthrobacter species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant [e.g., nitrite oxidizing Nitrospira species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium]. Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.
• Choudoir, M. J., Barberan, A., Menninger, H. L., Dunn, R. R., & Fierer, N. (2018). Variation in range size and dispersal capabilities of microbial taxa. ECOLOGY, 99(2), 322-334.
• Choudoir, M. J., Barberán, A., Menninger, H. L., Dunn, R. R., & Fierer, N. (2018). Variation in range size and dispersal capabilities of microbial taxa. Ecology, 99(Issue 2). doi:10.1002/ecy.2094
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  Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.
• Dai, Z., Su, W., Chen, H., Barberan, A., Zhao, H., Yu, M., Yu, L. u., Brookes, P. C., Schadt, C. W., Chang, S. X., & Xu, J. (2018). Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe. GLOBAL CHANGE BIOLOGY, 24(8), 3452-3461.
• Dai, Z., Su, W., Chen, H., Barberán, A., Zhao, H., Yu, M., Yu, L., Brookes, P. C., Schadt, C. W., Chang, S. X., & Xu, J. (2018). Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe. Global Change Biology, 24(Issue 8). doi:10.1111/gcb.14163
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  Long-term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro-ecosystems worldwide.
• Ortiz-Alvarez, R., Fierer, N., de, l., Casamayor, E. O., & Barberan, A. (2018). Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME JOURNAL, 12(7), 1658-1667.
• Ortiz-Álvarez, R., Fierer, N., De Los Ríos, A., Casamayor, E. O., & Barberán, A. (2018). Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME Journal, 12(Issue 7). doi:10.1038/s41396-018-0076-2
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  Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.
• Sederholm, M. R., Schmitz, B. W., Barberan, A., & Pepper, I. L. (2018). Effects of metam sodium fumigation on the abundance, activity, and diversity of soil bacterial communities. APPLIED SOIL ECOLOGY, 124, 27-33.
• Sederholm, M. R., Schmitz, B. W., Barberán, A., & Pepper, I. L. (2018). Effects of metam sodium fumigation on the abundance, activity, and diversity of soil bacterial communities. Applied Soil Ecology, 124(Issue). doi:10.1016/j.apsoil.2017.10.012
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  Metam sodium is a fumigant used as a crop pretreatment in agriculture to control a wide array of pests, and soil borne diseases that may adversely affect plant quantity and quality. This present study utilized control and treated field plots to examine the effects of metam sodium on indigenous soil microbes in terms of numbers, activity, and diversity. Following metam sodium application, culturable heterotrophic counts in all soils increased significantly for 24 h, but quickly returned back to original levels. Application resulted in decreased microbial activity, detected by ATP-based assays, that was significantly lower in treated soils than control plots, but recovered quickly. High-throughput sequencing of the 16S rRNA gene showed that treated plots contained significantly lower numbers of observed OTUs, particularly 14, 21, and 28 days after treatment. Soil bacterial communities were significantly altered by MS-treatment due to increased relative abundances of Actinomycetales, Bacilli, and Chloroflexi, as well as decreased Acidobacteria. These dominant taxa observed in MS-treated plots are major contributors to biological activity in various healthy soils and rhizospheres. Therefore, the increase in relative abundance of these biologically productive phyla coupled with abundant ATP production suggests that soil health recovered following MS-treatment and remained functionally intact.
• Valle, D., Albuquerque, P., Zhao, Q., Barberan, A., & Fletcher Jr., R. J. (2018). Extending the Latent Dirichlet Allocation model to presence/absence data: A case study on North American breeding birds and biogeographical shifts expected from climate change. GLOBAL CHANGE BIOLOGY, 24(11), 5560-5572.
• Valle, D., Albuquerque, P., Zhao, Q., Barberan, A., & Fletcher, R. J. (2018). Extending the Latent Dirichlet Allocation model to presence/absence data: A case study on North American breeding birds and biogeographical shifts expected from climate change. Global Change Biology, 24(Issue 11). doi:10.1111/gcb.14412
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  Understanding how species composition varies across space and time is fundamental to ecology. While multiple methods having been created to characterize this variation through the identification of groups of species that tend to co-occur, most of these methods unfortunately are not able to represent gradual variation in species composition. The Latent Dirichlet Allocation (LDA) model is a mixed-membership method that can represent gradual changes in community structure by delineating overlapping groups of species, but its use has been limited because it requires abundance data and requires users to a priori set the number of groups. We substantially extend LDA to accommodate widely available presence/absence data and to simultaneously determine the optimal number of groups. Using simulated data, we show that this model is able to accurately determine the true number of groups, estimate the underlying parameters, and fit with the data. We illustrate this method with data from the North American Breeding Bird Survey (BBS). Overall, our model identified 18 main bird groups, revealing striking spatial patterns for each group, many of which were closely associated with temperature and precipitation gradients. Furthermore, by comparing the estimated proportion of each group for two time periods (1997–2002 and 2010–2015), our results indicate that nine (of 18) breeding bird groups exhibited an expansion northward and contraction southward of their ranges, revealing subtle but important community-level biodiversity changes at a continental scale that are consistent with those expected under climate change. Our proposed method is likely to find multiple uses in ecology, being a valuable addition to the toolkit of ecologists.
• Zhang, X., Johnston, E. R., Barberan, A., Ren, Y. i., Wang, Z., & Han, X. (2018). Effect of intermediate disturbance on soil microbial functional diversity depends on the amount of effective resources. ENVIRONMENTAL MICROBIOLOGY, 20(10), 3862-3875.
• Zhang, X., Johnston, E. R., Barberán, A., Ren, Y., Wang, Z., & Han, X. (2018). Effect of intermediate disturbance on soil microbial functional diversity depends on the amount of effective resources. Environmental Microbiology, 20(Issue 10). doi:10.1111/1462-2920.14407
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  Many anthropogenic environmental changes are leading to a rapid decline in soil microbial functional diversity. However, ecological mechanisms that can serve to counteract/resist the diversity loss remain largely underexplored. In particular, although intermediate disturbance and increased amount of effective resources can promote the diversity of higher organisms, the potential role of these factors, and their combination, in maintaining microbial functional diversity is poorly studied. We conducted a 5-year experiment in a Eurasian steppe, manipulating mowing, nitrogen addition, phosphorus addition and their combinations. Nitrogen addition decreased soil pH by ~0.6 and bacterial abundance by ~19.5%, causing a disturbance effect. Phosphorus addition significantly decreased the effective amount of soil carbon-, nitrogen-, phosphorus- and water-relevant resources. Across all nitrogen-addition treatments subject to intermediate disturbance, there was a significant positive correlation between soil effective resource amount and microbial gene richness (r > 0.6, p < 0.01), which was elevated, in part, due to the increased fungal abundance. In contrast, significant correlations between gene richness and resource amount were not found under low-disturbance conditions. Overall, gene richness was greatest under conditions of both intermediate disturbance and ample effective resources, suggesting that the two factors could be manipulated in combination for the maintenance of microbial functional diversity.
• Barberan, A., Velazquez, H. C., Jones, S., & Fierer, N. (2017). Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. MSPHERE, 2(4).
• Barberán, A., Velazquez, H. C., Jones, S., & Fierer, N. (2017). Hiding in plain sight: Mining bacterial species records for phenotypic trait information. mSphere, 2(Issue 4). doi:10.1128/msphere.00237-17
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  Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for > 5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants. Most of the routinely measured traits tended to show a significant phylogenetic signal, although this signal was weak for environmental preferences. We demonstrated how this database could be used to link genomic attributes to differences in pH and salinity optima. We found that adaptations to high salinity or high-pH conditions are related to cell surface transporter genes, along with previously uncharacterized genes that might play a role in regulating environmental tolerances. Together, this work highlights the utility of this database for associating bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and emphasizes the need for more comprehensive and consistent measurements of traits across a broader diversity of bacteria.
• Connor, N., Barberan, A., & Clauset, A. (2017). Using null models to infer microbial co-occurrence networks. PLOS ONE, 12(5).
• Connor, N., Barberán, A., & Clauset, A. (2017). Using null models to infer microbial cooccurrence networks. PLoS ONE, 12(Issue 5). doi:10.1371/journal.pone.0176751
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  Although microbial communities are ubiquitous in nature, relatively little is known about the structural and functional roles of their constituent organisms' underlying interactions. A common approach to study such questions begins with extracting a network of statistically significant pairwise co-occurrences from a matrix of observed operational taxonomic unit (OTU) abundances across sites. The structure of this network is assumed to encode information about ecological interactions and processes, resistance to perturbation, and the identity of keystone species. However, common methods for identifying these pairwise interactions can contaminate the network with spurious patterns that obscure true ecological signals. Here, we describe this problem in detail and develop a solution that incorporates null models to distinguish ecological signals from statistical noise. We apply these methods to the initial OTU abundance matrix and to the extracted network. We demonstrate this approach by applying it to a large soil microbiome data set and show that many previously reported patterns for these data are statistical artifacts. In contrast, we find the frequency of three-way interactions among microbial OTUs to be highly statistically significant. These results demonstrate the importance of using appropriate null models when studying observational microbiome data, and suggest that extracting and characterizing three-way interactions among OTUs is a promising direction for unraveling the structure and function of microbial ecosystems.
• Craine, J. M., Barberan, A., Lynch, R. C., Menninger, H. L., Dunn, R. R., & Fierer, N. (2017). Molecular analysis of environmental plant DNA in house dust across the United States. AEROBIOLOGIA, 33(1), 71-86.
• Craine, J. M., Barberán, A., Lynch, R. C., Menninger, H. L., Dunn, R. R., & Fierer, N. (2017). Molecular analysis of environmental plant DNA in house dust across the United States. Aerobiologia, 33(Issue 1). doi:10.1007/s10453-016-9451-5
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  Despite the prevalence and costs of allergic diseases caused by pollen, we know little about the distributions of allergenic and non-allergenic pollen inside and outside homes at the continental scale. To better understand patterns in potential pollen diversity across the United States, we used DNA sequencing of a chloroplast marker gene to identify the plant DNA found in settled dust collected on indoor and outdoor surfaces across 459 homes. House location was the best predictor of the relative abundance of plant taxa found in outdoor dust samples. Urban, southern houses in hotter climates that were further from the coast were more likely to have more DNA from grass and moss species, while rural houses in northern, cooler climates closer to the coast were more likely to have higher relative abundances of DNA from Pinus and Cedrus species. In general, those plant taxa that were more abundant outdoors were also more abundant indoors, but indoor dust had uniquely high abundances of DNA from food plants and plants associated with lawns. Approximately 14 % of the plant DNA sequences found outside were from plant taxa that are known to have allergenic pollen compared to just 8 % inside. There was little geographic pattern in the total relative abundance of these allergens highlighting the difficulties associated with trying to predict allergen exposures based on geographic location alone. Together, this work demonstrates the utility of using environmental DNA sequencing to reconstruct the distributions of plant DNA inside and outside buildings, an approach that could prove useful for better understanding and predicting plant allergen exposures.
• Dai, Z., Barberan, A., Li, Y., Brookes, P. C., & Xu, J. (2017). Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment. MSPHERE, 2(2).
• Dai, Z., Barberán, A., Li, Y., Brookes, P. C., & Xu, J. (2017). Bacterial community composition associated with pyrogenic organic matter (biochar) varies with pyrolysis temperature and colonization environment. mSphere, 2(Issue 2). doi:10.1128/msphere.00085-17
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  Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysistemperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in highpyrolysis- temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content.
• Luongo, J. C., Barberan, A., Hacker-Cary, R., Morgan, E. E., Miller, S. L., & Fierer, N. (2017). Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants. INDOOR AIR, 27(2), 338-344.
• Zhang, X., Johnston, E. R., Barberan, A., Ren, Y. i., Lu, X., & Han, X. (2017). Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity. GLOBAL CHANGE BIOLOGY, 23(10), 4318-4332.
• Zhang, X., Johnston, E. R., Barberán, A., Ren, Y., Lü, X., & Han, X. (2017). Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity. Global Change Biology, 23(Issue 10). doi:10.1111/gcb.13783
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  Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0–3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.
• Barberan, A., Hammer, T. J., Madden, A. A., & Fierer, N. (2016). Microbes Should Be Central to Ecological Education and Outreach. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION, 23-28. doi:http://dx.doi.org/10.1128/jmbe.v17i1.984
• Gornish, E. S., Fierer, N., & Barberan, A. (2016). Associations between an Invasive Plant (Taeniatherum caput-medusae, Medusahead) and Soil Microbial Communities. PLOS ONE, 11(9).
• Gornish, E. S., Fierer, N., & Barberán, A. (2016). Associations between an invasive plant (Taeniatherum caput-medusae, medusahead) and soil microbial communities. PLoS ONE, 11(Issue 9). doi:10.1371/journal.pone.0163930
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  Understanding plant-microbe relationships can be important for developing management strategies for invasive plants, particularly when these relationships interact with underlying variables, such as habitat type and seedbank density, to mediate control efforts. In a field study located in California, USA, we investigated how soil microbial communities differ across the invasion front of Taeniatherum caput-medusae (medusahead), an annual grass that has rapidly invaded most of the western USA. Plots were installed in habitats where medusahead invasion is typically successful (open grassland) and typically not successful (oak woodland). Medusahead was seeded into plots at a range of densities (from 0-50,000 seeds/m2) to simulate different levels of invasion. We found that bacterial and fungal soil community composition were significantly different between oak woodland and open grassland habitats. Specifically, ectomycorrhizal fungi were more abundant in oak woodlands while arbuscular mycorrhizal fungi and plant pathogens were more abundant in open grasslands. We did not find a direct effect of medusahead density on soil microbial communities across the simulated invasion front two seasons after medusahead were seeded into plots. Our results suggest that future medusahead management initiatives might consider plantmicrobe interactions.
• Madden, A. A., Barberan, A., Bertone, M. A., Menninger, H. L., Dunn, R. R., & Fierer, N. (2016). The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. MOLECULAR ECOLOGY, 25(24), 6214-6224.
• Madden, A. A., Barberán, A., Bertone, M. A., Menninger, H. L., Dunn, R. R., & Fierer, N. (2016). The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. Molecular Ecology, 25(Issue 24). doi:10.1111/mec.13900
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  We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well-being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. As previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification, we used a DNA-based method for investigating the arthropod diversity in homes via high-throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental-scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods – from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants and surrounding land use, were more useful than climate parameters in predicting arthropod diversity in homes. These noninvasive, scalable tools and resultant findings not only provide the first continental-scale maps of household arthropod diversity, but our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes.
• Stopnisek, N., Zuehlke, D., Carlier, A., Barberan, A., Fierer, N., Becher, D., Riedel, K., Eberl, L., & Weisskopf, L. (2016). Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME JOURNAL, 10(1), 253-264.
• Stopnisek, N., Zuhlke, D., Carlier, A., Barberan, A., Fierer, N., Becher, D., Riedel, K., Eberl, L., & Weisskopf, L. (2016). Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME Journal, 10(Issue 1). doi:10.1038/ismej.2015.73
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  Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.
• Tripp, E. A., Lendemer, J. C., Barberan, A., Dunn, R. R., & Fierer, N. (2016). Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States. JOURNAL OF BIOGEOGRAPHY, 43(8), 1667-1678.
• Barberan, A., Dunn, R. R., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., Morton, J. M., Henley, J. B., Leff, J. W., Miller, S. L., & Fierer, N. (2015). The ecology of microscopic life in household dust. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 282(1814), 212-220.
• Barberan, A., Ladau, J., Leff, J. W., Pollard, K. S., Menninger, H. L., Dunn, R. R., & Fierer, N. (2015). Continental-scale distributions of dust-associated bacteria and fungi. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(18), 5756-5761.
• Barberan, A., McGuire, K. L., Wolf, J. A., Jones, F. A., Wright, S. J., Turner, B. L., Essene, A., Hubbell, S. P., Faircloth, B. C., & Fierer, N. (2015). Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest. ECOLOGY LETTERS, 18(12), 1397-1405.
• Barberán, A., Dunn, R. R., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., Morton, J. M., Henley, J. B., Leff, J. W., Miller, S. L., & Fierer, N. (2015). The ecology of microscopic life in household dust. Proceedings of the Royal Society B: Biological Sciences, 282(Issue 1814). doi:10.1098/rspb.2015.1139
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  We spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predict ablyacross climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female: male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home.
• Barberán, A., Ladau, J., Leff, J. W., Pollard, K. S., Menninger, H. L., Dunn, R. R., & Fierer, N. (2015). Continental-scale distributions of dust-associated bacteria and fungi. Proceedings of the National Academy of Sciences of the United States of America, 112(Issue 18). doi:10.1073/pnas.1420815112
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  It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continen-tal- scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans.
• Barberán, A., Mcguire, K. L., Wolf, J. A., Jones, F. A., Wright, S. J., Turner, B. L., Essene, A., Hubbell, S. P., Faircloth, B. C., & Fierer, N. (2015). Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest. Ecology Letters, 18(Issue 12). doi:10.1111/ele.12536
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  The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley
• Grantham, N. S., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., Henley, J. B., Barberan, A., Leff, J. W., Fierer, N., & Dunn, R. R. (2015). Fungi Identify the Geographic Origin of Dust Samples. PLOS ONE, 10(4).
• Grantham, N. S., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., Henley, J. B., Barberán, A., Leff, J. W., Fierer, N., & Dunn, R. R. (2015). Fungi identify the geographic origin of dust samples. PLoS ONE, 10(Issue 4). doi:10.1371/journal.pone.0122605
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  There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.
• Leff, J. W., Jones, S. E., Prober, S. M., Barberan, A., Borer, E. T., Firn, J. L., Harpole, W. S., Hobbie, S. E., Hofmockel, K. S., Knops, J., McCulley, R. L., La, P. K., Risch, A. C., Seabloom, E. W., Schuetz, M., Steenbock, C., Stevens, C. J., & Fierer, N. (2015). Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(35), 10967-10972.
• Leff, J. W., Jones, S. E., Prober, S. M., Barberán, A., Borer, E. T., Firn, J. L., Harpole, W. S., Hobbie, S. E., Hofmockel, K. S., Knops, J. M., McCulley, R. L., La Pierre, K., Risch, A. C., Seabloom, E. W., Schütz, M., Steenbock, C., Stevens, C. J., & Fierer, N. (2015). Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proceedings of the National Academy of Sciences of the United States of America, 112(Issue 35). doi:10.1073/pnas.1508382112
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  Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of fastergrowing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.
• Barberan, A., & Casamayor, E. O. (2014). A phylogenetic perspective on species diversity, beta-diversity and biogeography for the microbial world. MOLECULAR ECOLOGY, 23(23), 5868-5876.
• Barberan, A., Casamayor, E. O., & Fierer, N. (2014). The microbial contribution to macroecology. FRONTIERS IN MICROBIOLOGY, 5.
• Barberan, A., Henley, J., Fierer, N., & Casamayor, E. O. (2014). Structure, inter-annual recurrence, and global-scale connectivity of airborne microbial communities. SCIENCE OF THE TOTAL ENVIRONMENT, 487, 187-195.
• Barberan, A., Ramirez, K. S., Leff, J. W., Bradford, M. A., Wall, D. H., & Fierer, N. (2014). Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. ECOLOGY LETTERS, 17(7), 794-802.
• Barberán, A., & Casamayor, E. O. (2014). A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world. Molecular Ecology, 23(Issue 23). doi:10.1111/mec.12971
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  There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-Altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-Altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.
• Barberán, A., Henley, J., Fierer, N., & Casamayor, E. O. (2014). Structure, inter-annual recurrence, and global-scale connectivity of airborne microbial communities. Science of the Total Environment, 487(Issue 1). doi:10.1016/j.scitotenv.2014.04.030
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  Dust coming from the large deserts on Earth, such as the Sahara, can travel long distances and be dispersed over thousands of square kilometers. Remote dust deposition rates are increasing as a consequence of global change and may represent a mechanism for intercontinental microbial dispersal. Remote oligotrophic alpine lakes are particularly sensitive to dust inputs and can serve as sentinels of airborne microbial transport and the ecological consequences of accelerated intercontinental microbial migration. In this study, we applied high-throughput sequencing techniques (16S rRNA amplicon pyrosequencing) to characterize the microbial communities of atmospheric deposition collected in the Central Pyrenees (NE Spain) along three years. Additionally, bacteria from soils in Mauritania and from the air-water interface of high altitude Pyrenean lakes were also examined. Communities in aerosol deposition varied in time with a strong seasonal component of interannual similarity. Communities from the same season tended to resemble more each other than those from different seasons. Samples from disparate dates, in turn, slightly tended to have more dissimilar microbial assemblages (i.e., temporal distance decay), overall suggesting that atmospheric deposition may influence sink habitats in a temporally predictable manner. The three habitats examined (soil, deposition, and air-water interface) harbored distinct microbial communities, although airborne samples collected in the Pyrenees during Saharan dust outbreaks were closer to Mauritian soil samples than those collected during no Saharan dust episodes. The three habitats shared c.a. 1.4% of the total number of microbial sequences in the dataset. Such successful immigrants were spread in different bacterial classes. Overall, this study suggests that local and regional features may generate global trends in the dynamics and distribution of airborne microbial assemblages, and that the diversity of viable cells in the high atmosphere is likely higher than previously expected. © 2014 Elsevier B.V.
• Barberán, A., Ramirez, K. S., Leff, J. W., Bradford, M. A., Wall, D. H., & Fierer, N. (2014). Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecology Letters, 17(Issue 7). doi:10.1111/ele.12282
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  Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non-existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km2 area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait-based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait-based predictions of the biogeographical patterns exhibited by microbes. © 2014 John Wiley & Sons Ltd/CNRS.
• Bates, S., Casamayor, E., Fierer, N., & Barberán, A. (2014). Erratum: Using network analysis to explore co-occurrencepatterns in soil microbial communitie (ISME Journal (2014) 8 (952) DOI:10.1038/ismej.2013.236). ISME Journal, 8(4). doi:10.1038/ismej.2013.236
• Fierer, N., Barberan, A., & Laughlin, D. C. (2014). Seeing the forest for the genes: using rnetagenomics to infer the aggregated traits of microbial communities. FRONTIERS IN MICROBIOLOGY, 5.
• Fierer, N., Barberán, A., & Laughlin, D. C. (2014). Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities. Frontiers in Microbiology, 5(Issue). doi:10.3389/fmicb.2014.00614
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  Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.
• Ramirez, K. S., Leff, J. W., Barberan, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Shaw, E. A., Steenbock, C., Bradford, M. A., Wall, D. H., & Fierer, N. (2014). Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 281(1795).
• Ramirez, K. S., Leff, J. W., Barberán, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Ashley Shaw, E., Steenbock, C., Bradford, M. A., Wall, D. H., & Fierer, N. (2014). Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proceedings of the Royal Society B: Biological Sciences, 281(Issue 1795). doi:10.1098/rspb.2014.1988
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  Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents.
• Zhang, X., Barberan, A., Zhu, X., Zhang, G., & Han, X. (2014). Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem. PLOS ONE, 9(12).
• Zhang, X., Barberán, A., Zhu, X., Zhang, G., & Han, X. (2014). Water content differences have stronger effects than plant functional groups on soil bacteria in a steppe ecosystem. PLoS ONE, 9(Issue 12). doi:10.1371/journal.pone.0115798
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  Many investigations across natural and artificial plant diversity gradients have reported that both soil physicochemical factors and plant community composition affect soil microbial communities. To test the effect of plant diversity loss on soil bacterial communities, we conducted a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia (China). We found that the number and composition type of plant functional groups had no effect on bacterial diversity and community composition, or on the relative abundance of major taxa. In contrast, bacterial community patterns were significantly structured by soil water content differences among plots. Our results support researches that suggest that water availability is the key factor structuring soil bacterial communities in this semi-arid ecosystem.
• Gornish, E. S., Hamilton, J. A., Barberán, A., Benito, B. M., Binzer, A., Demeester, J. E., Gruwez, R., Moreira, B., Taheri, S., Tomiolo, S., Vinagre, C., Vuarin, P., & Weaver, J. (2013). Interdisciplinary climate change collaborations are essential for early-career scientists. Eos, 94(Issue 16). doi:10.1002/2013eo160003
• Gornish, E., Hamilton, J., Barberan, A., & Benito, B. (2013). Interdisciplinary climate change collaborations are essential for early-career scientists. EOS, Transactions American Geophysical Union, 94, 151.
• Rodriguez-Lanetty, M., Granados-Cifuentes, C., Barberan, A., Bellantuono, A. J., & Bastidas, C. (2013). Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides. MOLECULAR ECOLOGY, 22(16), 4349-4362.
• Rodriguez-Lanetty, M., Granados-Cifuentes, C., Barberan, A., Bellantuono, A. J., & Bastidas, C. (2013). Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides. Molecular Ecology, 22(Issue 16). doi:10.1111/mec.12392
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  The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont. © 2013 John Wiley & Sons Ltd.
• Vila-Costa, M., Barberan, A., Auguet, J. C., Sharma, S., Moran, M. A., & Casamayor, E. O. (2013). Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS Microbiology Ecology, 84(Issue 2). doi:10.1111/1574-6941.12068
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  Bacteria and Archaea of the air-water surface microlayer (neuston) and plankton from three high mountain lakes (Limnological Observatory of the Pyrenees, Spain) were analysed by 16S rRNA gene 454 pyrosequencing (V6 region) in two dates with different atmospheric aerosol loading conditions: (1) under a Saharan dust plume driven by southern winds; and (2) under northern winds with oceanic influence. In general, bacterial communities were richer than archaea, with estimated total richness of c. 2500 OTUs for Bacteria and c. 900 OTUs for Archaea equivalent to a sequencing effort of c. 250 000 and c. 20 000 sequences, respectively. The dominant bacterial OTU was affiliated to Actinobacteria. Archaea were one to two orders of magnitude less abundant than bacteria but were more evenly distributed. Apparently, Bacteroidetes and Thaumarchaeota sequences were preferentially found at the neuston, but no consistent pattern in either total microbial abundance or richness was found in any sample. However, we observed more marked changes in microbial relative abundances between neuston and plankton in the dust-influenced scenario. Higher community dissimilarities between neuston and plankton were also found during the Saharan dust episode, and such differences were higher for Bacteria than for Archaea. Nonetheless, relatively few (< 0.05%) of the neuston sequences matched previously identified airborne microorganisms, and none became important in the dates analysed. © 2013 Federation of European Microbiological Societies.
• Vila-Costa, M., Barberan, A., Auguet, J., Sharma, S., Moran, M. A., & Casamayor, E. O. (2013). Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS MICROBIOLOGY ECOLOGY, 84(2), 387-397.
• Barberan, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012). Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME JOURNAL, 6(2), 343-351.
• Barberan, A., Fernandez-Guerra, A., Bohannan, B., & Casamayor, E. O. (2012). Exploration of community traits as ecological markers in microbial metagenomes. MOLECULAR ECOLOGY, 21(8), 1909-1917.
• Barberán, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012). Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME Journal, 6(Issue 2). doi:10.1038/ismej.2011.119
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  Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly. © 2012 International Society for Microbial Ecology All rights reserved.
• Barberán, A., Fernández-Guerra, A., Bohannan, B. J., & Casamayor, E. O. (2012). Exploration of community traits as ecological markers in microbial metagenomes. Molecular Ecology, 21(Issue 8). doi:10.1111/j.1365-294x.2011.05383.x
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  The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait-based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework. © 2011 Blackwell Publishing Ltd.
• Casamayor, E. O., Lliros, M., Picazo, A., Barberan, A., Borrego, C. M., & Camacho, A. (2012). Contribution of deep dark fixation processes to overall CO2 incorporation and large vertical changes of microbial populations in stratified karstic lakes. AQUATIC SCIENCES, 74(1), 61-75.
• Casamayor, E. O., Llirós, M., Picazo, A., Barberán, A., Borrego, C. M., & Camacho, A. (2012). Contribution of deep dark fixation processes to overall CO2 incorporation and large vertical changes of microbial populations in stratified karstic lakes. Aquatic Sciences, 74(Issue 1). doi:10.1007/s00027-011-0196-5
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  We carried out a detailed study in five stratified lakes in the karstic regions of NE Spain along a redox gradient combining vertical profiles of inorganic carbon dioxide fixation and analysis of microbial (bacteria and archaea) community composition determined by 16S rRNA gene fingerprinting (DGGE), microscopic counts, and pigment analysis. High rates of non-photosynthetic (i.e., "dark") inorganic carbon incorporation were detected mostly at deeper layers after short-term in situ incubations at noon. Significant contribution of dark CO2 incorporation was observed at the whole lake level for the single time sampling, ranging between 4 and 19% of total carbon fixation measured, and up to 31% in the case of a meromictic basin. Good agreement was found between vertical patterns in redox conditions and the different microbial diversity descriptors (DGGE band sequencing, microscopic analysis, and pigment data), showing large vertical changes in microbial community composition covering a wide range of phylogenetic diversity. Cyanobacteria, Alpha and Beta-Proteobacteria, Actinobacteria, Flavobacteria and Flectobacillaceae were the most frequently recovered groups in the DGGE from oxygenated water masses. In anoxic waters, we found Beta-Proteobacteria mostly of the Rhodoferax group, Gamma-Proteobacteria (Chromatiaceae), Delta-Proteobacteria related to different sulfate reducing bacteria, Chlorobiaceae, and anaerobic Bacteroidetes spread among the Bacteroidales, Flavobacteriales and Saprospiraceae. However, as a whole, we did not find any significant correlation between dark fixation rates and either nutrient distribution and microbial community composition in the study lakes. All of this suggests that (1) different physiologies and ecologies are simultaneously contributing to the process (2) more sensitive methods are needed and more specific compounds measured and (3) some of the non-specialist microbial populations detected may carry out carbon dioxide assimilation in the dark under in situ conditions. © 2011 Springer Basel AG.
• Barberan, A., & Casamayor, E. O. (2011). Euxinic Freshwater Hypolimnia Promote Bacterial Endemicity in Continental Areas. MICROBIAL ECOLOGY, 61(2), 465-472.
• Barberan, A., Fernandez-Guerra, A., Auguet, J., Galand, P. E., & Casamayor, E. O. (2011). Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. MOLECULAR ECOLOGY, 20(9), 1988-1996.
• Barberán, A., & Casamayor, E. O. (2011). Euxinic Freshwater Hypolimnia Promote Bacterial Endemicity in Continental Areas. Microbial Ecology, 61(Issue 2). doi:10.1007/s00248-010-9775-6
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  Bacteria and archaea represent the vast majority of biodiversity on Earth. The ways that dynamic ecological and evolutionary processes interact in the microbial world are, however, poorly known. Here, we have explored community patterns of planktonic freshwater bacteria inhabiting stratified lakes with oxic/anoxic interfaces and euxinic (anoxic and sulfurous) water masses. The interface separates a well-oxygenated upper water mass (epilimnion) from a lower anoxic water compartment (hypolimnion). We assessed whether or not the vertical zonation of lakes promoted endemism in deeper layers by analyzing bacterial 16S rRNA gene sequences from the water column of worldwide distributed stratified lakes and applying a community ecology approach. Community similarity based on the phylogenetic relatedness showed that bacterial assemblages from the same water layer were more similar across lakes than to communities from different layer within lakes and that anoxic hypolimnia presented greater β-diversity than oxic epilimnia. Higher β-diversity values are attributable to low dispersal and small connectivity between community patches. In addition, surface waters had significant spatial but non-significant environmental components controlling phylogenetic β-diversity patterns, respectively. Conversely, the bottom layers were significantly correlated with environment but not with geographic distance. Thus, we observed different ecological mechanisms simultaneously acting on the same water body. Overall, bacterial endemicity is probably more common than previously thought, particularly in isolated and environmentally heterogeneous freshwater habitats. We argue for a microbial diversity conservation perspective still lacking in the global and local biodiversity preservation policies. © 2010 Springer Science+Business Media, LLC.
• Barberán, A., Fernández-Guerra, A., Auguet, J. C., Galand, P. E., & Casamayor, E. O. (2011). Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Molecular Ecology, 20(Issue 9). doi:10.1111/j.1365-294x.2011.05057.x
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  Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world. © 2011 Blackwell Publishing Ltd.
• Auguet, J. C., Barberan, A., & Casamayor, E. O. (2010). Global ecological patterns in uncultured Archaea. ISME Journal, 4(Issue 2). doi:10.1038/ismej.2009.109
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  We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.
• Auguet, J., Barberan, A., & Casamayor, E. O. (2010). Global ecological patterns in uncultured Archaea. ISME JOURNAL, 4(2), 182-190.
• Barberan, A., & Casamayor, E. O. (2010). Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. AQUATIC MICROBIAL ECOLOGY, 59(1), 1-10.
• Barberán, A., & Casamayor, E. O. (2010). Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities. Aquatic Microbial Ecology, 59(Issue 1). doi:10.3354/ame01389
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  We aimed to identify phylogenetic community patterns in abundant planktonic bacteria (Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes) from a worldwide range of surface waters (lakes and seas-34 sites and ca. 4500 16S rRNA gene sequences). At each site we assessed the number of observed bacterial groups and the genetic relatedness of the most abundant groups through a community phylogenetic metaanalysis approach in order to (1) explore which potential ecological processes were consistent with the observed phylogenetic patterns in community assembly and (2) disentangle the effects of space and environment in β-diversity patterns for the different bacterial groups. Inland waters had significantly more bacterial groups and were more diverse than marine waters. Marine habitats showed a higher percentage of clustered sites than lakes, and bacterial communities were more closely related than expected by chance. Phylogenetic β-diversity analyses revealed different patterns to both salt composition (marine vs. inland salt lakes) and salt concentration for the dominant bacteria. We observed that while â-diversity patterns for Bacteroidetes were mostly shaped by salinity concentration, patterns in Alphaproteobacteria and Gammaproteobacteria were controlled by salt composition. Actinobacteria, Betaproteobacteria and Sphingobacteria were largely absent from marine habitats and from saline continental sites. In general and despite the lack of contextual metadata, environmental similarity was more relevant than spatial distribution for bacterial β-diversity patterns. However, we detected a geographic signal for some inland waters' groups (i.e. Actinobacteria, Beta-, and Gammaproteobacteria). Overall, the analyses indicated differences among phylogenetic groups and reflected patterns upon which further exploration of community assembly theory could be based. © Inter-Research 2010.

Presentations

• Barberan, A., & Gornish, E. (2021). Ecological restoration for soil health research and development lab. Dean's Research Advisory Council meeting.
• 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-resilience development in arid regions. Arizona Institutes for Resilience.
• 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.
• Chen, Y., Neilson, J. W., Kushwaha, P., Maier, R. M., & Barberan, A. (2020, August). Microbial life history strategies in arid soils. Ecology Society of America Annual Meeting. Virtual: Ecology Society of America.
• Butterfield, B. J., Maier, R. M., Barberan, A., Kushwaha, P., & Neilson, J. W. (2019, June). Linking Microbial Phylogenetics and Genetics of N-cycling Potential in Arid Soils. ASM Microbe. San Francisco, CA: American Society of Microbiology.
• Farrell, H., Barberan, A., & Gornish, E. (2019, September). How does restoration impact the soil organisms and properties of a disturbed semi-arid grassland?. Society for Ecological Restoration Southwest Chapter Annual Meeting.

Poster Presentations

• Gornish, E., Barberan, A., & Spaeth, M. (2024). Down with the richness: varied disturbance effects on coastal dune soil microbial communities
  
  . ALVSCE Research Poster Showcase.
• Gornish, E., Barberan, A., & Spaeth, M. (2024). Down with the richness: varied disturbance effects on coastal dune soil microbial communities
  
  . SEES Earth Week Poster Showcase.
• Barberan, A., Gornish, E., & Yang, B. (2023). Adding microbial innoculants into seedpellets: one stone, two birds? . Society for Ecological Restoration Southwest Chapter Annual Meeting.
• Gornish, E., Miller, T., Barberan, A., & Spaeth, M. (2023). Soil microbial community patterns across successional dune habitats of a barrier island.. Ecological Society of American Conference.
• Gornish, E., Roche, L., Funk, J., Barberan, A., & Spaeth, M. (2023). Belowground resilience: impacts of   grazing and controlled burns on soil microbial communitie. Society for Ecological Restoration Southwest Chapter Annual Meeting.
• Barberan, A., Martinez-Yrizar, A., Burquez, A., Gornish, E., Touceda-Suarez, M., & Inigo, G. (2022). Influence of buffelgrass invasion on the soil microbiome under native trees in the Sonoran          Desert. Connections Across Borders.
• Meredith, L., Troch, P. A., Maier, R. M., Chorover, J. D., Neilson, J. W., Dontsova, K. M., Volkmann, T., Stegen, J., Barberan, A., & Sengupta, A. (2019, January). Structural and Functional Response of Microbial Community in an Oligotrophic Basalt Soil System to Shifts in Rainfall Regimes. Soil Science Society of America (SSSA) International Soils Meeting “Soils Across Latitudes”. San Diego, CA: Soil Science Society of America.
• Sengupta, A., Barberan, A., Stegen, J., Volkmann, T., Dontsova, K. M., Neilson, J. W., Chorover, J. D., Maier, R. M., Troch, P. A., & Meredith, L. (2018, August). Structural and functional response of incipient basaltic microbial community to shifts in soil moisture regime. Goldschmidt. Boston, MA.