- Assistant Professor, Soil / Subsurface Microbial Ecology
- Assistant Professor, BIO5 Institute
- Assistant Professor, Genetics - GIDP
- Assistant Professor, School of Plant Sciences
- Ph.D. Microbiology
- Oregon State University, Corvallis, Oregon, United States
- Genome-enabled investigation of the minimal growth requirements and phosphate metabolism for Pelagibacter marine bacteria
- M.S. Biology
- University of Wisconsin - Milwaukee, Milwaukee, Wisconsin, United States
- Sequence Diversity of the Lux Operon and Related Genes in Geographically Distinct Vibrio Harveyi-like Bacteria
- B.S. Biology
- University of Wisconsin- Milwaukee, Milwaukee, Wisconsin, United States
- University of Arizona, Tucson, Arizona (2017 - Ongoing)
- University of Colorado Boulder (2015 - 2017)
- Horn Point Laboratory (2013 - 2015)
- Cooperative Institute for Research in Environmental Science (CIRES) Postdoctoral Visiting Fellowship
- Cooperative Institute for Research in Environmental Science at the University of Colorado Boulder., Summer 2015
- Linus Pauling Distinguished Postdoctoral Fellowship
- Pacific Northwest National Laboratory, Spring 2015
Environmental Microbiology -physiology, cellular evolution, cellular survival mechanisms, and nutrient cycling
Environmental Microbiology -physiology, cellular evolution, cellular survival mechanisms, and nutrient cycling
Directed ResearchMCB 792 (Spring 2021)
ResearchMIC 900 (Spring 2021)
Envir MicrobiologyENVS 425 (Fall 2020)
Envir MicrobiologyENVS 525 (Fall 2020)
Envir MicrobiologyMIC 425 (Fall 2020)
ThesisENVS 910 (Spring 2020)
Envir MicrobiologyENVS 425 (Fall 2019)
Envir MicrobiologyENVS 525 (Fall 2019)
Envir MicrobiologyMIC 425 (Fall 2019)
ThesisENVS 910 (Fall 2019)
DissertationENVS 920 (Spring 2019)
Honors ThesisENVS 498H (Spring 2019)
DissertationENVS 920 (Fall 2018)
Envir MicrobiologyENVS 425 (Fall 2018)
Envir MicrobiologyENVS 525 (Fall 2018)
Envir MicrobiologyIMB 525 (Fall 2018)
Envir MicrobiologyMIC 425 (Fall 2018)
Honors ThesisENVS 498H (Fall 2018)
DissertationENVS 920 (Spring 2018)
Independent StudyENVS 399 (Spring 2018)
Independent StudyMIC 399 (Spring 2018)
Directed ResearchENVS 492 (Fall 2017)
Envir MicrobiologyENVS 425 (Fall 2017)
Envir MicrobiologyENVS 525 (Fall 2017)
Envir MicrobiologyMIC 425 (Fall 2017)
Honors Independent StudyENVS 399H (Fall 2017)
Independent StudyENVS 399 (Fall 2017)
Independent StudyMIC 399 (Fall 2017)
Senior CapstoneBIOC 498 (Fall 2017)
- 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).More infoThe 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).More infoFew 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.More infoAn 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.More infoThe 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.More infoPreprint 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.
- 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).
- 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.
- 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.
- 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-schoolMore infoBlog 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