Fuhrman JA, Campbell L. Marine ecology – microbial microdiversity. Nature. 1998;393:410–1.
Google Scholar
Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, Benoit J, et al. Genotypic diversity within a natural coastal bacterioplankton population. Science. 2005;307:1311–3.
Google Scholar
Oh S, Buddenborg S, Yoder-Himes DR, Tiedje JM, Konstantinidis KT. Genomic diversity of Escherichia isolates from diverse habitats. PLoS ONE. 2012;7:e47005.
Google Scholar
Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci USA. 2008;105:7774–8.
Google Scholar
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.
Google Scholar
Raes EJ, Bodrossy L, van de Kamp J, Bissett A, Ostrowski M, Brown MV, et al. Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean. Proc Natl Acad Sci USA. 2018;115:EB266–EB75.
Brown MV, Fuhrman JA. Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat Microb Ecol. 2005;41:15–23.
Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006;311:1737–40.
Google Scholar
Larkin AA, Blinebry SK, Howes C, Chandler J, Zinser ER, Johnson ZI. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific. ISME J. 2016;10:1555–67.
Google Scholar
Zinser ER, Johnson ZI, Coe A, Karaca E, Veneziano D, Chisholm SW. Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean. Limnol Oceanogr. 2007;52:2205–20.
Carlson M, Ribalet F, Maidanik I, Durham BP, Hulata Y, Ferrón S, et al. Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nat Microbiol. 2022;7:570–80.
Google Scholar
Follett CL, Dutkiewicz S, Ribalet F, Zakem E, Caron D, Armbrust EV, et al. Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proc Natl Acad Sci USA. 2022;119:e2110993118.
Google Scholar
Moore LR, Rocap G, Chisholm SW. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature. 1998;393:464–7.
Google Scholar
Zwirglmaier K, Jardillier L, Ostrowski M, Mazard S, Garczarek L, Vaulot D, et al. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol. 2008;10:147–61.
Google Scholar
Carlson CA, Morris R, Parsons R, Treusch AH, Giovannoni SJ, Vergin K. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 2009;3:283–95.
Google Scholar
Ribalet F, Swalwell J, Clayton S, Jimenez V, Sudek S, Lin YJ, et al. Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre. Proc Natl Acad Sci USA. 2015;112:8008–12.
Google Scholar
Pernthaler A, Pernthaler J, Schattenhofer M, Amann R. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microbiol. 2002;68:5728–36.
Google Scholar
Del Giorgio PA, Gasol JM. Physiological structure and single-cell activity in marine bacterioplankton. In: Kirchman DL, editor. Microbial ecology of the oceans. 2nd ed. New Jersey:John Wiley & Sons, Inc.; 2008. p. 243–298.
Lin Y, Gazsi K, Lance VP, Larkin A, Chandler J, Zinser ER, et al. In situ activity of a dominant Prochlorococcus ecotype (eHL-II) from rRNA content and cell size. Environ Microbiol. 2013;15:2736–47.
Google Scholar
Kirchman DL. Growth rates of microbes in the oceans. Annu Rev Mar Sci. 2016;8:285–309.
Landry MR, Selph KE, Yang EJ. Decoupled phytoplankton growth and microzooplankton grazing in the deep euphotic zone of the eastern equatorial Pacific. Mar Ecol Prog Ser. 2011;421:13–24.
Selph KE, Landry MR, Taylor AG, Yang E-J, Measures CI, Yang J, et al. Spatially-resolved taxon-specific phytoplankton production and grazing dynamics in relation to iron distributions in the Equatorial Pacific between 110 and 140 degrees W. Deep Sea Res Part II Top Stud Oceanogr. 2011;58:358–77.
Google Scholar
Hunt DE, Lin Y, Church MJ, Karl DM, Tringe SG, Izzo LK, et al. Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters. Appl Environ Microbiol. 2013;79:177–84.
Google Scholar
Sintes E, Herndl GJ. Quantifying substrate uptake by individual cells of marine bacterioplankton by catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography. Appl Environ Microbiol. 2006;72:7022–8.
Google Scholar
Hall E, Maixner F, Franklin O, Daims H, Richter A, Battin T. Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches. Ecosystems. 2011;14:261–73.
Musat N, Foster R, Vagner T, Adam B, Kuypers MM. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev. 2012;36:486–511.
Google Scholar
Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol. 2014;16:2568–90.
Google Scholar
Sebastián M, Gasol JM. Visualization is crucial for understanding microbial processes in the ocean. Philos Trans R Soc Lond B. 2019;374:20190083.
Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015;349:1101–6.
Google Scholar
Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotech. 2016;34:1256–63.
Google Scholar
Gao Y, Li H. Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. Nat Methods. 2018;15:1041–4.
Google Scholar
Emiola A, Zhou W, Oh J. Metagenomic growth rate inferences of strains in situ. Sci Adv. 2020;6:eaaz2299.
Google Scholar
Long ANM, Hou SW, Ignacio-Espinoza JC, Fuhrman JA. Benchmarking microbial growth rate predictions from metagenomes. ISME J. 2020;15:183–195.
Google Scholar
Carroll J, Van Oostende N, Ward BB. Evaluation of genomic sequence-based growth rate methods for synchronized Synechococcus cultures. Appl Environ Microbiol. 2021;01743-21.
Vaulot D, Marie D. Diel variability of photosynthetic picoplankton in the equatorial Pacific. J Geophys Res Oceans. 1999;104:3297–310.
Google Scholar
Hunter-Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. Limnol Oceanogr. 2020;65:1085–102.
Google Scholar
Baer SE, Rauschenberg S, Garcia CA, Garcia NS, Martiny AC, Twining BS, et al. Carbon and nitrogen productivity during spring in the oligotrophic Indian Ocean along the GO-SHIP IO9N transect. Deep Sea Res Part II Top Stud Oceanogr. 2019;161:81–91.
Google Scholar
Larkin AA, Garcia CA, Ingoglia KA, Garcia NS, Baer SE, Twining BS, et al. Subtle biogeochemical regimes in the Indian Ocean revealed by spatial and diel frequency of Prochlorococcus haplotypes. Limnol Oceanogr. 2020;65:S220–S32.
Google Scholar
Larkin AA, Garcia CA, Garcia N, Brock ML, Lee JA, Ustick LJ, et al. High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects. Sci Data. 2021;8:1–6.
Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE. 2015;10:e0128036.
Google Scholar
Wandro S, Oliver A, Gallagher T, Weihe C, England W, Martiny JBH, et al. Predictable molecular adaptation of coevolving Enterococcus faecium and lytic phage EfV12-phi1. Front Microbiol. 2019;9:3192.
Google Scholar
Oliver A, LaMere B, Weihe C, Wandro S, Lindsay KL, Wadhwa PD, et al. Cervicovaginal microbiome composition is associated with metabolic profiles in healthy pregnancy. mBio. 2020;11:e01851–20.
Google Scholar
Eren AM, Esen OC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. In: van Helden J, Toussaint A, Thieffry D, editors. Bacterial molecular networks: methods and protocol. New Jersey:Humana Totowa; 2012. p. 281–295.
Bergeron A, Mixtacki J, Stoye J. A unifying view of genome rearrangements. In: Proceeding of the International Workshop on Algorithms in Bioinformatics. Berlin, Heidelberg: Springer; 2006. p. 163–73.
Hilker R, Sickinger C, Pedersen CNS, Stoye J. UniMoG-a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics. 2012;28:2509–11.
Google Scholar
Gelman A, Carlin JB, Stern HS, Dunson D, Vehtari A, Rubin DB. Bayesian data analysis: 3rd ed. Boca Raton:Chapman and Hall/CRC; 2013.
Martiny AC, Ustick L, Garcia CA, Lomas MW. Genomic adaptation of marine phytoplankton populations regulates phosphate uptake. Limnol Oceanogr. 2020;65:S340–S50.
Google Scholar
Garcia CA, Hagstrom GI, Larkin AA, Ustick LJ, Levin SA, Lomas MW, et al. Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry. Philos Trans R Soc Lond, B. 2020;375:20190254.
Google Scholar
Ustick LJ, Larkin AA, Garcia CA, Garcia NS, Brock ML, Lee JA, et al. Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation. Science. 2021;372:287–291.
Google Scholar
Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 2018;6:e4320.
Google Scholar
Worden AZ, Binder BJ. Application of dilution experiments for measuring growth and mortality rates among Prochlorococcus and Synechococcus populations in oligotrophic environments. Aquat Microb Ecol. 2003;30:159–74.
Casey JR, Boiteau RM, Engqvist MKM, Finkel ZV, Li G, Liefer J, et al. Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology. Sci Adv. 2022;8:eabl4930.
Google Scholar
Berube PM, Rasmussen A, Braakman R, Stepanauskas R, Chisholm SW. Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus. Elife. 2019;8:e41043.
Google Scholar
Luo HW, Benner R, Long RA, Hu JJ. Subcellular localization of marine bacterial alkaline phosphatases. Proc Natl Acad Sci USA. 2009;106:21219–23.
Google Scholar
Schapiro JM, Libby SJ, Fang FC. Inhibition of bacterial DNA replication by zinc mobilization during nitrosative stress. Proc Natl Acad Sci USA. 2003;100:8496–501.
Google Scholar
Hantke K. Bacterial zinc uptake and regulators. Curr Opin Microbiol. 2005;8:196–202.
Google Scholar
Glass JB, Axler RP, Chandra S, Goldman CR. Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures. Front Microbiol. 2012;3:331.
Google Scholar
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77.
Google Scholar
Noell SE, Barrell GE, Suffridge C, Morré J, Gable KP, Graff JR, et al. SAR11 cells rely on enzyme multifunctionality to transport and metabolize a range of polyamine compounds. 2021. https://www.biorxiv.org/content/10.1101/2021.05.13.444117v1.
Binder BJ, Chisholm SW. Cell-cycle regulation in marine Synechcococcus sp strains. Appl Environ Microbiol. 1995;61:708–17.
Google Scholar
Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, et al. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus. PLoS ONE. 2009;4:e5135.
Google Scholar
Hynes AM, Rhodes KL, Binder BJ. Assessing cell cycle-based methods of measuring Prochlorococcus division rates using an individual-based model. Limnol Oceanogr-Meth. 2015;13:640–50.
Vieira-Silva S, Rocha EP. The systemic imprint of growth and its uses in ecological (meta) genomics. PLoS Genet. 2010;6:e1000808.
Google Scholar
Weissman JL, Hou SW, Fuhrman JA. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proc Natl Acad Sci USA. 2021;118:e2016810118.
Google Scholar
Chase AB, Karaoz U, Brodie EL, Gomez-Lunar Z, Martiny AC, Martiny JB. Microdiversity of an abundant terrestrial bacterium encompasses extensive variation in ecologically relevant traits. mBio. 2017;8:e01809–17.
Google Scholar
Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol. 2021;39:727–36.
Google Scholar
Flombaum P, Gallegos JL, Gordillo RA, Rincon J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA. 2013;110:9824–9.
Google Scholar
Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, et al. Global biogeography of SAR11 marine bacteria. Mol Sys Biol. 2012;8:595.
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