Our papers are grouped by topic. If you're new to the lab's work, the five under "Start here" span the open ocean, soil, isotope geochemistry, the deep biosphere, and dormancy.

Start here

• Ocean physiology and Functional Genomics. SAR11 lipid renovation in response to phosphate starvation. Paul Carini, B.A.S. Van Mooy, J.C. Thrash, A.E. White, Y. Zhao, E.O. Campbell, H.F. Fredricks, and S.J. Giovannoni. 2015. PNAS. When phosphate runs out, SAR11 replaces the phospholipids in its membrane with lipids that contain no phosphorus.

• Soil microbial ecology. Relic DNA is abundant in soil and obscures estimates of microbial diversity. Paul Carini, P.J. Marsden, J.W. Leff, E.E. Morgan, M.S. Strickland, and N. Fierer. 2016. Nature Microbiology. Much of the DNA in soil is "relic DNA" from cells that are no longer alive, and it inflates estimates of microbial diversity.

• Isotope geochemistry. Microbial Methane From Methylphosphonate Isotopically Records Source. L. Taenzer, P. Carini, A.M. Masterson, B. Bourque, J.H. Gaube, and W.D. Leavitt. 2020. Geophysical Research Letters. Methane that marine bacteria make from methylphosphonate carries the isotopic signature of its source molecule.

• Deep biosphere and evolutionary genomics. Genome evolution in bacteria isolated from million-year-old subseafloor sediments. Orsi W.D., Magritsch T., Vargas S., Coskun O.K., Vuillemin A., Höhna S., Wörheide G., D’Hondt S., Shapiro B.J., and P. Carini. 2021. mBio. Bacteria cultured from million-year-old subseafloor sediments show how genomes evolve in cells that are perpetually starved.

• Dormancy and Functional Genomics. Transcriptional and metabolic stasis define desiccation-induced dormancy in a soil bacterium until water vapor initiates resuscitation. Carini, P, A Gomez-Buckley, CR Guerrero, MR Kridler, IA Viney, R AminiTabrizi, MM Tfaily, P Moma, LK Meredith, KB Louie, BP Bowen, TR Northen, OLO Snoeyenbos-West, and RP Bartelme. 2026. mSystems (Editor’s Pick). A desiccated soil bacterium halts transcription and metabolism, and stays halted until water vapor alone starts its recovery.

Perspectives and Commentary

• The Microbial Borg: New Allies Against Climate Change? Snoeyenbos-West, O., and P. Carini. 2022. GEN Biotechnology. (Views & News)

• Hazardous gases sustain microbes underfoot. Paul Carini. 2021. Nature Microbiology. (News & Views)

• A ‘cultural’ renaissance: Genomics breathes new life into an old craft. Paul Carini. 2019. mSystems.

• Microbial oxidation of DMS to DMSO: a biochemical surprise with geochemical implications. Paul Carini. 2016. Environmental Microbiology.

Microbial Cultivation

• Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers. Snoeyenbos-West O.L.O., Guerrero, C.R. Valencia, M., and P Carini. 2024. Microbiol Spectr 0:e03650-23. BioRxiv version.

• [Permanent preprint] Predicting microbial growth conditions from amino acid composition. Barnum, TP, A Crits-Christoph, M Molla, P Carini, HH Lee, N Ostrov. 2024. BioRxiv.

• The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation. Bartelme, R.P., J.M. Custer, C. Dupont, J.L. Espinoza, M. Torralba, B. Khalili and Paul Carini. 2020. mSphere. BioRxiv version.

• High proportions of bacteria and archaea across most biomes remain uncultured. Steen, A.D., A. Crits-Christoph, P. Carini, K.M. DeAngelis, N. Fierer, K.G. Lloyd and J.C. Thrash. 2019. The ISME Journal.

Desiccation and Dormancy

• Transcriptional and metabolic stasis define desiccation-induced dormancy in a soil bacterium until water vapor initiates resuscitation. Carini, P, A Gomez-Buckley, CR Guerrero, MR Kridler, IA Viney, R AminiTabrizi, MM Tfaily, P Moma, LK Meredith, KB Louie, BP Bowen, TR Northen, OLO Snoeyenbos-West, and RP Bartelme. 2026. mSystems (Editor’s Pick). BioRxiv version.

Deep Biosphere, Energy Limitation, and Genome Evolution

• Anergiobiosis: a testable framework for microbial life under extreme power limitation. Paul Carini, R. Hatzenpichler, and J. Biddle. 2026. EcoEvoRxiv. https://doi.org/10.32942/X2908F

• Genome evolution in bacteria isolated from million-year-old subseafloor sediments. Orsi W.D., Magritsch T., Vargas S., Coskun O.K., Vuillemin A., Höhna S., Wörheide G., D’Hondt S., Shapiro B.J., and P. Carini. 2021. mBio. BioRxiv version.

• Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus.’ T. Brewer, K. Handley, P. Carini, J. Gibert and N. Fierer. 2016. Nature Microbiology.

Relic DNA

New to relic DNA? See our Relic DNA FAQ.

• Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities. Paul Carini, M. Delgado-Baquerizo, E.S. Hinckley, H. Holland‐Moritz, T.E. Brewer, G. Rue, C. Vanderburgh, D. McKnight, and N. Fierer. 2020. mBio. BioRxiv version.

• Relic DNA is abundant in soil and obscures estimates of microbial diversity. Paul Carini, P.J. Marsden, J.W. Leff, E.E. Morgan, M.S. Strickland, and N. Fierer. 2016. Nature Microbiology.

Microbes and Geochemistry

• Microbial Methane From Methylphosphonate Isotopically Records Source. L. Taenzer, P. Carini, A.M. Masterson, B. Bourque, J.H. Gaube, and W.D. Leavitt. 2020. Geophysical Research Letters.

• Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. Becker K.W., J.R. Collins, B.P. Durham, R.D. Groussman, A.E. White, H.F. Fredricks, J.E. Ossolinski, D.J. Repeta, P. Carini, E.V. Armbrust, and B.A.S. Van Mooy. 2018. Nature Communications.

Pelagibacter ubique/SAR11

• Proteome Remodeling in Response to Sulfur Limitation in ‘Candidatus Pelagibacter ubique.’ D.P. Smith, C.D. Nicora, P. Carini, M.S. Lipton, A.D. Norbeck, R.D. Smith, S.J. Giovannoni. 2016. mSystems.

• SAR11 lipid renovation in response to phosphate starvation. Paul Carini, B.A.S. Van Mooy, J.C. Thrash, A.E. White, Y. Zhao, E.O. Campbell, H.F. Fredricks, and S.J. Giovannoni. 2015. PNAS.

• Methane production by phosphate starved SAR11 chemoheterotrophic marine bacteria. Paul Carini, A.E. White, E.O. Campbell, and S.J. Giovannoni. 2014. Nature Communications.

• Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea. Paul Carini, E.O. Campbell, J. Morré, S.A. Sañudo-Wilhelmy, J.C. Thrash, S.E. Bennett, B. Temperton, T. Begley and S.J. Giovannoni. (2014). ISME J.

• Proteomic and Transcriptomic Analyses of “Candidatus Pelagibacter ubique” Describe the First PII-Independent Response to Nitrogen Limitation in a Free-Living Alphaproteobacterium. Smith, D.P., J.C. Thrash, C.D. Nicora, M.S. Lipton, K.E. Burnum-Johnson, P. Carini, R.D. Smith, S.J. Giovannoni. 2013. mBio.

• Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. Paul Carini, L. Steindler, S. Beszteri and S.J. Giovannoni. 2013. ISME J.

• Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade. Grote J., J.C. Thrash, M.J. Huggett, Z.C. Landry, P. Carini, S.J. Giovannoni, et al. 2012. mBio.

• Phylogenomic Evidence for a Common Ancestor of Mitochondria and the SAR11 Clade. Thrash, J.C., A. Boyd, M. Huggett, J. Grote, P. Carini, R.J. Yoder, B. Robbertse, J.W. Spatafora, M.S. Rappé and S.J. Giovannoni. 2011. Sci. Rep.

Archaea

• Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Paul Carini, C. Dupont and A.E. Santoro. 2018. Environmental Microbiology.

• Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. Orsi, W.D., J.M. Smith, H.M. Wilcox, J.E. Swalwell, P. Carini, A.Z. Worden, and A.E. Santoro. 2015. ISME J.

• Genomic and proteomic characterization of ‘Candidatus Nitrosopelagicus brevis’: an ammonia-oxidizing archaeon from the open ocean. Santoro, A.E., C.L. Dupont, R.A. Richter, M.T. Craig, P. Carini, M.R. McIlvin, Y. Yang, W. Orsi, D. Moran and M.A. Saito. 2015. PNAS.

• Transcriptional Profiling of Methyltransferase Genes during Growth of Methanosarcina mazei on Trimethylamine. Kratzer, C., P. Carini, R. Hovey and U. Deppenmeier. 2009. Journal of Bacteriology.

Microbial Taxonomy

• A roadmap for naming the uncultivated majority. Murray, AE, J Freudenstein, S Gribaldo, R Hatzenpichler, P Hugenholtz, P Kämpfer, KT Konstantinidis, CE Lane, RT Papke, DH Parks, T Rossello-Mora, MB Stott, IC Sutcliffe, JC Thrash, SN Venter, WB Whitman, SG Acinas, RI Amann, K Anantharaman, J Armengaud, BJ Baker, RA Barco, HB Bode, ES Boyd, CL Brady, P Carini, PSG Chain, DR Colman, KM DeAngelis, M Asuncion de los Rios, P Estrada de los Santos, CA Dunlap, JA Eisen, D Emerson, TJG Ettema, D Eveillard, PR Girguis, U Hentschel, JT Hollibaugh, LA Hug, WP Inskeep, EP Ivanova, H Klenk, W Li, KG Lloyd, FE Löffler, T Makhalanyane, D Moser, T Nunoura, M Palmer, V Parro, C Pedrós-Alió, AJ Probst, THM Smits, AD Steen, ET Steenkamp, A Spang, FJ Stewart, JM Tiedje, P Vandamme, M Wagner, F Wang, BP Hedlund, A Reysenbach. 2020. Nature Microbiology.

Genome Announcements

• Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona. Kridler, M, IA Viney, JM Custer, B Schlottman, R Bartelme, and Paul Carini. 2024. Microbiology Resource Announcements.

• High-quality PacBio draft genome sequences of 17 free-living Bradyrhizobium and four related Nitrobacteraceae strains isolated from arid soils in the Santa Catalina Mountains of Southern Arizona. Kridler, MA, A Howe, JA Legins, C Guerrero, RP Bartelme, B Taylor, and P Carini. 2024. Access Microbiology.