Microbial Cultivation

• [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.

• 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.

• 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. BioRxiv version. mSphere.

• 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.

  Relic DNA

• 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. 

• 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.

  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

  Commentaries

• 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.

  Genome Evolution

• 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. 

  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.

  Pelagibacter ubique/SAR11

• 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. Ossolinsi, D.J. repeta, P. Carini, E.V. Armbrust, and B.A.S. Van Mooy. 2018. Nature Communications. 

• 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.

• 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.