[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 Microbial Borg: New Allies Against Climate Change?

Snoeyenbos-West, O., and P. Carini. 2022. GEN Biotechnology. (Views & News)

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.

 
 
 

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.

Hazardous gases sustain microbes underfoot

Paul Carini. 2021. Nature Microbiology. (News & Views)

 
 
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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.

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.

 
 
 
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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.

 
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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.

 
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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. 

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Paul Carini, C. Dupont and A.E. Santoro. 2018. Environmental Microbiology.

 
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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.

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. 

 
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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. 

 
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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.

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.

 
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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.

Methane production by phosphate starved SAR11 chemoheterotrophic marine bacteria

Paul Carini, A.E. White, E.O. Campbell, and S.J. Giovannoni. 2014. Nature Communications. 

 
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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. 

 
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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.