Paul Carini

Interests

Teaching

Environmental Microbiology -physiology, cellular evolution, cellular survival mechanisms, and nutrient cycling

Research

Environmental Microbiology -physiology, cellular evolution, cellular survival mechanisms, and nutrient cycling

Courses

Scholarly Contributions

Journals/Publications

• Snoeyenbos-West, O. L., Guerrero, C. R., Valencia, M., & Carini, P. (2023). Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers. bioRxiv : the preprint server for biology.
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  Anaerobic microbes play crucial roles in environmental processes, industry, and human health. Traditional methods for monitoring the growth of anaerobes, including plate counts or subsampling broth cultures for optical density measurements, are time and resource intensive. The advent of microplate readers revolutionized bacterial growth studies by enabling high-throughput and real-time monitoring of microbial growth kinetics but their use in anaerobic microbiology has remained limited. Here, we present a workflow for using small-footprint microplate readers and the Growthcurver R package to analyze the kinetic growth metrics of anaerobic bacteria. We benchmarked the small-footprint Cerillo Stratus microplate reader against a BioTek Synergy HTX microplate reader in aerobic conditions using DSM 28618 cultures. The growth rates and carrying capacities obtained from the two readers were statistically indistinguishable. However, the area under the logistic curve was significantly higher in cultures monitored by the Stratus reader. We used the Stratus to quantify the growth responses of anaerobically grown and DSM 29485 to different doses of the toxin sodium arsenite. The growth of and was sensitive to arsenite doses of 1.3 μM and 0.4 μM, respectively. Complete inhibition of growth was achieved at 38 μM arsenite for , and 338 μM in . These results show that the Stratus performs similarly to a leading brand of microplate reader and can be reliably used in anaerobic conditions. We discuss the advantages of the small format microplate readers and our experiences with the Stratus.
• Carini, P., & Snoeyenbos-West, O. (2022). The Microbial Borg: New Allies Against Climate Change?. GEN Biotechnology, 1(6), 485-486. doi:10.1089/genbio.2022.29067.osw
• Carini, P., & Snoeyenbos-West, O. (2022). The Microbial Borg: New Allies Against Climate Change?. GEN Biotechnology. doi:10.1089/genbio.2022.29067.osw
• Carini, P. (2021). Hazardous gases sustain microbes underfoot.. Nature microbiology, 6(2), 145-146. doi:10.1038/s41564-020-00855-y
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  Most soil microorganisms can use the trace gases carbon monoxide, hydrogen and methane — and potentially other inorganic compounds — to supplement their cellular energetic needs.
• Emerson, D., Yarza, P., Whitman, W. B., Wang, F., Wagner, M., Venter, S. N., Vandamme, P., Tiedje, J. M., Thrash, J. C., Sutcliffe, I. C., Stott, M. B., Stewart, F. J., Steenkamp, E. T., Steen, A. D., Spang, A., Smits, T. H., Santos, P. E., Rossello-mora, R., Rios, M. A., , Reysenbach, A., et al. (2021). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.. Nature microbiology, 6(1), 136. doi:10.1038/s41564-020-00827-2
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  In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online.
• Orsi, W. D., Magritsch, T., Vargas, S., Coskun, Ö. K., Vuillemin, A., Höhna, S., Wörheide, G., D'Hondt, S., Shapiro, B. J., & Carini, P. (2021). Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment. mBio, 12(4), e0115021.
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  Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of , in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of that have accumulated mutations in their genomes over millions of years.
• Bartelme, R. P., Custer, J. M., Dupont, C. L., Espinoza, J. L., Torralba, M., Khalili, B., & Carini, P. (2020). Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation. mSphere, 5(1).
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  The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here, we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted cells extracted from soil into one of two custom-designed defined growth media that differed by 100-fold in the concentration of amino acids and organic carbon. Across the two media, we isolated a total of 133 pure cultures, all of which were classified as or The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of We isolated cultures that were representative of the most abundant phylotype in the soil microbial community ( spp.) and representatives of five of the top 10 most abundant phylotypes, including spp., spp., and several other phylogenetically divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and that the concentration of substrates in culture medium influences the culturability of specific microbial lineages. Isolating environmental microbes and studying their physiology under controlled conditions are essential aspects of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities-the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.
• Carini, P. (2020). Microbial Methane from Methylphosphonate Isotopically Records Source. Geophysical Research Letters.
• Carini, P., Delgado-Baquerizo, M., Hinckley, E. S., Holland-Moritz, H., Brewer, T. E., Rue, G., Vanderburgh, C., McKnight, D., & Fierer, N. (2020). Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities. mBio, 11(1).
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  Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.
• Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., , Armengaud, J., et al. (2020). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology.
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  An amendment to this paper has been published and can be accessed via a link at the top of the paper.
• Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., , Armengaud, J., et al. (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology, 5(8), 987-994.
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  The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
• Carini, P. (2019). A "Cultural" Renaissance: Genomics Breathes New Life into an Old Craft. MSYSTEMS, 4(3).
• Steen, A. D., Crits-Christoph, A., Carini, P., DeAngelis, K. M., Fierer, N., Lloyd, K. G., & Thrash, J. C. (2019). High proportions of bacteria and archaea across most biomes remain uncultured. ISME JOURNAL, 13(12), 3126-3130.
• Becker, K. W., Collins, J. R., Durham, B. P., Groussman, R. D., White, A. E., Fredricks, H. F., Ossolinski, J. E., Repeta, D. J., Carini, P., Armbrust, E. V., & Van, M. (2018). Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. NATURE COMMUNICATIONS, 9.
• Carini, P., Becker, K. W., Collins, J. R., Durham, B. R., Groussman, R. D., White, A. E., Fredricks, H. F., Ossolinski, J. E., Repeta, D. J., Armbrust, E. V., & Van Mooy, B. A. (2018). Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean.. Nature Communications. doi:https://doi.org/10.1038/s41467-018-07346-z
• Carini, P., Dupont, C. L., & Santoro, A. E. (2018). Patterns of thaumarchaeal gene expression in culture and diverse marine environments. ENVIRONMENTAL MICROBIOLOGY, 20(6), 2112-2124.
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  Preprint of this paper is availible here: https://www.biorxiv.org/content/early/2018/03/19/175141
• Brewer, T. E., Handley, K. M., Carini, P., Gilbert, J. A., & Fierer, N. (2017). Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'. NATURE MICROBIOLOGY, 2(2).
• Carini, P., Marsden, P. J., Leff, J., Morgan, E. E., Strickland, M. S., & Fierer, N. (2017). Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. NATURE MICROBIOLOGY, 2(3).
• Carini, P. (2016). Microbial oxidation of DMS to DMSO: a biochemical surprise with geochemical implications. ENVIRONMENTAL MICROBIOLOGY, 18(8), 2302-2304.
• Handley, K. M., Gilbert, J. A., Fierer, N., Carini, P., & Brewer, T. E. (2016). Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'.. Nature microbiology, 2(2), 16198. doi:10.1038/nmicrobiol.2016.198
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  Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Candidatus Udaeobacter copiosus'. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.
• Smith, D. P., Nicora, C. D., Carini, P., Lipton, M. S., Norbeck, A. D., Smith, R. D., & Giovannoni, S. J. (2016). Proteome Remodeling in Response to Sulfur Limitation in "Candidatus Pelagibacter ubique". MSYSTEMS, 1(4).
• Strickland, M. S., Morgan, E. E., Marsden, P. J., Leff, J. W., Fierer, N., & Carini, P. (2016). Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.. Nature microbiology, 2(3), 16242. doi:10.1038/nmicrobiol.2016.242
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  Extracellular DNA from dead microorganisms can persist in soil for weeks to years1-3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide4. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.
• Carini, P., Van, M., Thrash, J. C., White, A., Zhao, Y., Campbell, E. O., Fredricks, H. F., & Giovannoni, S. J. (2015). SAR11 lipid renovation in response to phosphate starvation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(25), 7767-7772.
• Orsi, W. D., Smith, J. M., Wilcox, H. M., Swalwell, J. E., Carini, P., Worden, A. Z., & Santoro, A. E. (2015). Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME JOURNAL, 9(8), 1747-1763.
• Santoro, A. E., Dupont, C. L., Richter, R. A., Craig, M. T., Carini, P., McIlvin, M. R., Yang, Y., Orsi, W. D., Moran, D. M., & Saito, M. A. (2015). Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": An ammonia-oxidizing archaeon from the open ocean. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(4), 1173-1178.
• Carini, P., Campbell, E. O., Morre, J., Sanudo-Wilhelmy, S. A., Thrash, J. C., Bennett, S. E., Temperton, B., Begley, T., & Giovannoni, S. J. (2014). Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea. ISME JOURNAL, 8(8), 1727-1738.
• Carini, P., White, A. E., Campbell, E. O., & Giovannoni, S. J. (2014). Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. NATURE COMMUNICATIONS, 5.
• Carini, P., Steindler, L., Beszteri, S., & Giovannoni, S. J. (2013). Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium. ISME JOURNAL, 7(3), 592-602.
• Smith, D. P., Thrash, J. C., Nicora, C. D., Lipton, M. S., Burnum-Johnson, K. E., Carini, P., Smith, R. D., & Giovannoni, S. J. (2013). Proteomic and Transcriptomic Analyses of "Candidatus Pelagibacter ubique" Describe the First P-II-Independent Response to Nitrogen Limitation in a Free-Living Alphaproteobacterium. MBIO, 4(6).
• Grote, J., Thrash, J. C., Huggett, M. J., Landry, Z. C., Carini, P., Giovannoni, S. J., & Rappe, M. S. (2012). Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade. MBIO, 3(5).
• Thrash, J. C., Boyd, A., Huggett, M. J., Grote, J., Carini, P., Yoder, R. J., Robbertse, B., Spatafora, J. W., Rappe, M. S., & Giovannoni, S. J. (2011). Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. SCIENTIFIC REPORTS, 1.
• Kraetzer, C., Carini, P., Hovey, R., & Deppenmeier, U. (2009). Transcriptional Profiling of Methyltransferase Genes during Growth of Methanosarcina mazei on Trimethylamine. JOURNAL OF BACTERIOLOGY, 191(16), 5108-5115.

Presentations

• Carini, P. (2021). Surviving a dry spell: using microbial culture collections to understand the complex phenotype of actinobacterial dehydration-rehydration tolerance.. University of Innsbruck Online seminar series. Innsbruck, Austria.
• Carini, P. (2019, June). High Throughput Cultivation of Bacteria from Shallow Subsurface Soils. ASM Microbe. San Francisco.
• Carini, P. (2020, April). Leveraging microbial cultivation to identify core principles in soil microbial ecology and evolution. MicroSeminar. Live & archived on YouTube: MicroSeminar Series.
• Carini, P. (2020, Fall). Developing microbial culture collections to understand the complex phenotype of actinobacterial desiccation (and rehydration!) tolerance. Invited Seminar; University of California Riverside Plant Pathology Seminar Series. Virtual from my garage in Tucson: University of California Riverside.
• Carini, P. (2020, February). Leveraging microbial cultivation to identify core principles in soil microbial ecology and evolution. Invited Seminar; Department of Plant, Soil, and Microbial Sciences. Michigan State University.
• Carini, P. (2020, November). High-throughput dilution-to-extinction cultivation of bacterial from soil microbiomes. Invited Seminar; International Union of Microbiological Societies Congress (IUMS). South Korea/Virtual: International Union of Microbiological Societies Congress (IUMS).
• Carini, P. (2020, September). High-throughput dilution-to-extinction cultivation of bacterial from soil microbiomes. Invited Seminar; Microbiome Center Arizona State University. Virtual Seminar: Arizona State university Microbiome Center.

Others

• Carini, P. (2017, February). Hindsight 20/20: What I really learned in graduate school. Nature Microbiology Community. https://naturemicrobiologycommunity.nature.com/users/15756-paul-carini/posts/14799-hindsight-20-20-what-i-really-learned-in-graduate-school
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  Blog Post on Nature Microbiology Community Website
• Carini, P. (2016, December). A census of the dead: the story behind microbial relic DNA in soil.. Nature microbiology Community. https://naturemicrobiologycommunity.nature.com/users/15756-paul-carini/posts/14107-a-census-of-the-dead-the-story-behind-relic-dna-in-soil