Giovannoni, S. J., Thrash, J. C. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).
McCutcheon, J. P. & Moran, N. A. Extreme genome reduction in symbiotic bacteria. Nat. Rev. Microbiol. 10, 13–26 (2011).
Morris, R. M. et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420, 806–810 (2002).
Schattenhofer, M. et al. Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environ. Microbiol. 11, 2078–2093 (2009).
Giovannoni, S. J. SAR11 Bacteria: the most abundant plankton in the oceans. Ann. Rev. Mar. Sci. 9, 231–255 (2017).
Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).
Grote, J. et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3, e00252-12 (2012).
Noell, S. E. & Giovannoni, S. J. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ. Microbiol. 21, 2559–2575 (2019).
Clifton, B. E., Alcolombri, U., Uechi, G.-I., Jackson, C. J. & Laurino, P. The ultra-high affinity transport proteins of ubiquitous marine bacteria. Nature 634, 721–728 (2024).
Grzymski, J. J. & Dussaq, A. M. The significance of nitrogen cost minimization in proteomes of marine microorganisms. ISME J. 6, 71–80 (2012).
Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).
Lachance, J.-C., Rodrigue, S. & Palsson, B. O. Minimal cells, maximal knowledge. eLife 8, e45379 (2019).
Moger-Reischer, R. Z. et al. Evolution of a minimal cell. Nature 620, 122–127 (2023).
Cottrell, M. T. & Kirchman, D. L. Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes. Appl. Environ. Microbiol. 82, 6010–6018 (2016).
Noell, S. E., Hellweger, F. L., Temperton, B. & Giovannoni, S. J. A reduction of transcriptional regulation in aquatic oligotrophic microorganisms enhances fitness in nutrient-poor environments. Microbiol. Mol. Biol. Rev. 87, e0012422 (2023).
Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008).
Tripp, H. J. et al. Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ. Microbiol. 11, 230–238 (2009).
Carini, P., Steindler, L., Beszteri, S. & Giovannoni, S. J. Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. ISME J. 7, 592–602 (2013).
Carlson, C. A. et al. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 3, 283–295 (2009).
Becker, J. W., Hogle, S. L., Rosendo, K. & Chisholm, S. W. Co-culture and biogeography of Prochlorococcus and SAR11. ISME J. 13, 1506–1519 (2019).
Dethlefsen, L. & Schmidt, T. M. Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol. 189, 3237–3245 (2007).
Roller, B. R. K., Stoddard, S. F. & Schmidt, T. M. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat. Microbiol. 1, 16160 (2016).
Schwalbach, M. S., Tripp, H. J., Steindler, L., Smith, D. P. & Giovannoni, S. J. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. Environ. Microbiol. 12, 490–500 (2010).
Carini, P., White, A. E., Campbell, E. O. & Giovannoni, S. J. Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nat. Commun. 5, 4346 (2014).
Lankiewicz, T. S., Cottrell, M. T. & Kirchman, D. L. Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary. ISME J. 10, 823–832 (2016).
Henson, M. W., Lanclos, V. C., Faircloth, B. C. & Thrash, J. C. Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. ISME J. 12, 1846–1860 (2018).
Lanclos, V. C. et al. Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. ISME J. 17, 620–629 (2023).
Willis, L. & Huang, K. C. Sizing up the bacterial cell cycle. Nat. Rev. Microbiol. 15, 606–620 (2017).
Olsson, J. A., Nordström, K., Hjort, K. & Dasgupta, S. Eclipse–synchrony relationship in Escherichia coli strains with mutations affecting sequestration, initiation of replication and superhelicity of the bacterial chromosome. J. Mol. Biol. 334, 919–931 (2003).
Levin, P. A., Shim, J. J. & Grossman, A. D. Effect of minCD on FtsZ ring position and polar septation in Bacillus subtilis. J. Bacteriol. 180, 6048–6051 (1998).
Sundararajan, K. et al. The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction. Nat. Commun. 6, 7281 (2015).
Dubarry, N., Willis, C. R., Ball, G., Lesterlin, C. & Armitage, J. P. In vivo imaging of the segregation of the 2 chromosomes and the cell division proteins of Rhodobacter sphaeroides reveals an unexpected role for MipZ. mBio 10, e02515-18 (2019).
Pelletier, J. F. et al. Genetic requirements for cell division in a genomically minimal cell. Cell 184, 2430–2440.e16 (2021).
Fujikawa, N. et al. Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Res. 32, 82–92 (2004).
Boye, E. & Løbner-Olesen, A. The role of dam methyltransferase in the control of DNA replication in E. coli. Cell 62, 981–989 (1990).
Blair, J. A. et al. Branched signal wiring of an essential bacterial cell-cycle phosphotransfer protein. Structure 21, 1590–1601 (2013).
Krupka, M., Sobrinos-Sanguino, M., Jiménez, M., Rivas, G. & Margolin, W. Escherichia coli ZipA organizes FtsZ polymers into dynamic ring-like protofilament structures. mBio 9, e01008-18 (2018).
Pichoff, S., Du, S. & Lutkenhaus, J. Roles of FtsEX in cell division. Res. Microbiol. 170, 374–380 (2019).
Corrales-Guerrero, L. et al. MipZ caps the plus-end of FtsZ polymers to promote their rapid disassembly. Proc. Natl Acad. Sci. USA 119, e2208227119 (2022).
Letzkus, M., Trela, C. & Mera, P. E. Three factors ParA, TipN, and DnaA-mediated chromosome replication initiation are contributors of centromere segregation in Caulobacter crescentus. Mol. Biol. Cell 35, ar68 (2024).
Freel, K. C. et al. New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales. Nat. Commun. 17, 328 (2025).
Oren, A. A plea for linguistic accuracy – also for Candidatus taxa. Int. J. Syst. Evol. Microbiol. 67, 1085–1094 (2017).
Cooper, S. & Helmstetter, C. E. Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 31, 519–540 (1968).
Jun, S., Si, F., Pugatch, R. & Scott, M. Fundamental principles in bacterial physiology—history, recent progress, and the future with focus on cell size control: a review. Rep. Prog. Phys. 81, 056601 (2018).
Skarstad, K., Steen, H. B. & Boye, E. Escherichia coli DNA distributions measured by flow cytometry and compared with theoretical computer simulations. J. Bacteriol. 163, 661–668 (1985).
Fu, H., Uchimiya, M., Gore, J. & Moran, M. A. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proc. Natl Acad. Sci. USA.117, 3656–3662 (2020).
Amin, S. A. et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522, 98–101 (2015).
Daniel, R. M. & Danson, M. J. Temperature and the catalytic activity of enzymes: a fresh understanding. FEBS Lett. 587, 2738–2743 (2013).
Løbner-Olesen, A., Skarstad, K., Hansen, F. G., von Meyenburg, K. & Boye, E. The DnaA protein determines the initiation mass of Escherichia coli K-12. Cell 57, 881–889 (1989).
Bremer, H. & Churchward, G. Deoxyribonucleic acid synthesis after inhibition of initiation of rounds of replication in Escherichia coli B/r. J. Bacteriol. 130, 692–697 (1977).
Dai, K. & Lutkenhaus, J. The proper ratio of FtsZ to FtsA is required for cell division to occur in Escherichia coli. J. Bacteriol. 174, 6145–6151 (1992).
Luo, H., Csűros, M., Hughes, A. L. & Moran, M. A. Evolution of divergent life history strategies in marine Alphaproteobacteria. mBio 4, e00373-13 (2013).
Smith, D. P. et al. Proteomic and transcriptomic analyses of ‘Candidatus Pelagibacter ubique’ describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. mBio 4, e00133–12 (2013).
Zheng, H. et al. General quantitative relations linking cell growth and the cell cycle in Escherichia coli. Nat. Microbiol. 5, 995–1001 (2020).
Lee, C. Characterizing Growth Promoters and Inhibitors of SAR11 Pelagibacter sp. HTCC7211. BSc thesis, Oregon State Univ. (2013).
Braakman, R. et al. Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes. Sci. Adv. 11, eadp1949 (2025).
Monod, J. The growth of bacterial cultures. Annu. Rev. Microbiol. 3, 371–394 (1949).
Held, N. A. et al. Nutrient colimitation is a quantitative, dynamic property of microbial populations. Proc. Natl Acad. Sci. USA 121, e2400304121 (2024).
Schaechter, M., MaalØe, O. & Kjeldgaard, N. O. Dependency on medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium. Microbiology 19, 592–606 (1958).
Si, F. et al. Mechanistic origin of cell-size control and homeostasis in bacteria. Curr. Biol. 29, 1760–1770.e7 (2019).
Guo, X. et al. Automated determination of ammonium at nanomolar levels in seawater by coupling lab-in-syringe with highly sensitive light-emitting-diode-induced fluorescence detection. Molecules 30, 1288 (2025).
Moran, M. A. et al. The ocean’s labile DOC supply chain. Limnol. Oceanogr. 67, 1007–1021 (2022).
Seymour, J. R., Amin, S. A., Raina, J.-B. & Stocker, R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat. Microbiol. 2, 17065 (2017).
Paerl, H. W. Why does N-limitation persist in the world’s marine waters? Mar. Chem. 206, 1–6 (2018).
Sarmento, H. & Gasol, J. M. Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton: use of phytoplankton-derived DOC by bacterioplankton. Environ. Microbiol. 14, 2348–2360 (2012).
Brüwer, J. D. et al. In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls. mSystems 8, e0128722 (2023).
Margolin, W. FtsZ and the division of prokaryotic cells and organelles. Nat. Rev. Mol. Cell Biol. 6, 862–871 (2005).
Barrows, J. M., Sundararajan, K., Bhargava, A. & Goley, E. D. FtsA regulates Z-ring morphology and cell wall metabolism in an FtsZ C-terminal linker-dependent manner in Caulobacter crescentus. J. Bacteriol. 202, e00693-19 (2020).
Wu, K. J. et al. Characterization of conserved and novel septal factors in Mycobacterium smegmatis. J. Bacteriol. 200, e00649-17 (2018).
Oh, H.-M. et al. Complete genome sequence of ‘Candidatus Puniceispirillum marinum’ IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J. Bacteriol. 192, 3240–3241 (2010).
Coelho, J. T. et al. Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning. ISME J. 19, wraf124 (2025).
Cho, J.-C. & Giovannoni, S. J. Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 53, 1031–1036 (2003).
Dang, H., Li, T., Chen, M. & Huang, G. Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl. Environ. Microbiol. 74, 52–60 (2008).
Follows, M. J., Dutkiewicz, S., Grant, S. & Chisholm, S. W. Emergent biogeography of microbial communities in a model ocean. Science 315, 1843–1846 (2007).
Aumont, O., Ethé, C., Tagliabue, A., Bopp, L. & Gehlen, M. PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies. Geosci. Model Dev. 8, 2465–2513 (2015).
Stock, C. A. et al. Ocean biogeochemistry in GFDL’s Earth System Model 4.1 and its response to increasing atmospheric CO2. J. Adv. Model. Earth Syst. 12, e2019MS002043 (2020).
Ross, A. C. et al. A high-resolution physical–biogeochemical model for marine resource applications in the northwest Atlantic (MOM6-COBALT-NWA12 v1.0). Geosci. Model Dev. 16, 6943–6985 (2023).
Martinez-Gutierrez, C. A., Uyeda, J. C. & Aylward, F. O. A timeline of bacterial and archaeal diversification in the ocean. Elife 12, RP88268 (2023).
Hyun, J. C. & Palsson, B. O. Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome. Genome Biol. 24, 183 (2023).
Staley, J. T. & Konopka, A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39, 321–346 (1985).
Henson, M. W. et al. Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large-scale dilution-to-extinction cultivation. Appl. Environ. Microbiol. 86, e00943-20 (2020).
Paysan-Lafosse, T. et al. InterPro in 2022. Nucleic Acids Res. 51, D418–D427 (2023).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Thrash, C. Pangenomic analyses files. figshare https://doi.org/10.6084/M9.FIGSHARE.30087295.V1 (2025).
UniProt Consortium. UniProt: the universal protein knowledgebase in 2025. Nucleic Acids Res. 53, D609–D617 (2025).
Ahmad, S. et al. The UniProt website API: facilitating programmatic access to protein knowledge. Nucleic Acids Res. 53, W547–W553 (2025).
Rappé, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002).
Henson, M. W. et al. Artificial seawater media facilitate cultivating members of the microbial majority from the Gulf of Mexico. mSphere 1, e00028-16 (2016).
Sodium phosphate. Cold Spring Harb. Protoc. 2006, db.rec8303 (2006).
Cheng, C. & Thrash, J. C. sparse-growth-curve: a computational pipeline for parsing cellular growth curves with low temporal resolution. Microbiol. Resour. Announc. 10, e00296-21 (2021).
Lanclos, V. C. et al. New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage. ISME Commun. 5, ycaf068 (2025).
Cheng, C. Thrash-lab/SAR11_cell_cycle: V1.0.0. Zenodo https://doi.org/10.5281/ZENODO.17703344 (2025).
Stokke, C., Flåtten, I. & Skarstad, K. An easy-to-use simulation program demonstrates variations in bacterial cell cycle parameters depending on medium and temperature. PLoS ONE 7, e30981 (2012).
Michelsen, O., Teixeira de Mattos, M. J., Jensen, P. R. & Hansen, F. G. Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r. Microbiology 149, 1001–1010 (2003).
Thrash, C. Epimicroscopy images of SAR11. figshare https://doi.org/10.6084/M9.FIGSHARE.29396375.V1 (2025).
Messer, W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 26, 355–374 (2002).
Katayama, T., Ozaki, S., Keyamura, K. & Fujimitsu, K. Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat. Rev. Microbiol. 8, 163–170 (2010).
Boye, E. & Løbner-Olesen, A. Bacterial growth control studied by flow cytometry. Res. Microbiol. 142, 131–135 (1991).
Stokke, C., Waldminghaus, T. & Skarstad, K. Replication patterns and organization of replication forks in Vibrio cholerae. Microbiology 157, 695–708 (2011).
Read more about this post…
Credits: Source
Disclaimer




Serving