BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm3), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date. RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters. CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.

Center of Excellence for Science and Technology Integration of Mediterranean Region Zagreb Croatia

Centre for Limnology Estonian University of Life Sciences 6117 Vehendi Tartu County Estonia

Centre for Systems Biology Biodiversity and Bioresources Babeș Bolyai University 5 7 Clinicilor Street Cluj Napoca 400006 Romania

Department of Fisheries Oceanography and Marine Ecology National Marine Fisheries Research Institute Gdynia 81 332 Poland

Department of Hydrobiology Faculty of Biology Institute of Ecology Biological and Chemical Research Centre University of Warsaw Zwirki 1 Wigury 101 Warsaw 02 089 Poland

Department of Molecular Biology and Biotechnology Faculty of Biology and Geology Babeş Bolyai University 5 7 Clinicilor Street Cluj Napoca 400006 Romania

Department of Plankton and Microbial Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries Zur Alten Fischerhuette 2 Stechlin 16775 Germany

Division of Materials Chemistry Ruder Bošković Institute Bijenička Cesta 54 Zagreb 10000 Croatia

Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic

Hydrobiological Station Faculty of Biology University of Warsaw Pilchy 5 Pisz 12 200 Poland

Institute for Chemical Research Kyoto University Kyoto Japan

Institute of Biochemistry and Biology Potsdam University Maulbeerallee 2 Potsdam 14469 Germany

Institute of Hydrobiology Biology Centre CAS Ceske Budejovice Czech Republic

Laboratoire Microorganismes Génome Et Environnement CNRS Université Clermont Auvergne Clermont Ferrand 63000 France

Lake and Glacier Ecology Research Group Department of Ecology Universität Innsbruck Innsbruck 6020 Austria

Leibniz Institute for Baltic Sea Research Warnemünde Seestrasse 15 Rostock 18119 Germany

Research Department for Limnology Mondsee University of Innsbruck Mondsee 5310 Austria

Universität Innsbruck Department of Ecology Innsbruck Austria

University of Montenegro Cetinjski Put 2 Podgorica 81000 Montenegro

Water Research Institute National Research Council Largo Tonolli 50 Verbania 28922 Italy

Zobrazit více v PubMed

Giovannoni SJ, Cameron Thrash J, Temperton B. Implications of streamlining theory for microbial ecology. ISME J. 2014;8:1553–65. PubMed DOI PMC

Luo H, Thompson LR, Stingl U, Hughes AL. Selection maintains low genomic GC content in marine SAR11 lineages. Mol Biol Evol. 2015;32:2738–48. PubMed DOI

Neuenschwander SM, Ghai R, Pernthaler J, Salcher MM. Microdiversification in genome-streamlined ubiquitous freshwater actinobacteria. ISME J. 2018;12:185–98. PubMed DOI PMC

Chiriac M-C, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol. 2023;25:606–41. PubMed DOI

Morris JJ, Lenski RE, Zinser ER. The black queen hypothesis: evolution of dependencies through adaptive gene loss. MBio. 2012. 10.1128/mbio.00036-12. PubMed DOI PMC

Warnecke F, Amann R, Pernthaler J. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ Microbiol. 2004;6:242–53. PubMed DOI

Zwart G, et al. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol. 1998;21:546–56. PubMed DOI

Hugerth LW, et al. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol. 2015;16:279. PubMed DOI PMC

Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome reconstruction from metagenomic data sets reveals novel microbes in the brackish waters of the Caspian Sea. Appl Environ Microbiol. 2016;82:1599–612. PubMed DOI PMC

Salka I, et al. Distribution of acI-actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters. Environ Microbiol. 2014;16:586–97. PubMed DOI

Newton R, Jones S, Helmus M, Mcmahon K. Phylogenetic ecology of the freshwater actinobacteria PubMed DOI PMC

Glöckner FO, et al. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol. 2000;66:5053–65. PubMed DOI PMC

Warnecke F, Sommaruga R, Sekar R, Hofer JS, Pernthaler J. Abundances, identity, and growth state of actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol. 2005;71:5551–9. PubMed DOI PMC

Allgaier M, Grossart H-P. Diversity and seasonal dynamics of actinobacteria populations in four lakes in northeastern Germany. Appl Environ Microbiol. 2006;72:3489–97. PubMed DOI PMC

Salcher MM, Pernthaler J, Posch T. Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. Limnol Oceanogr. 2010;55:846–56. DOI

Salcher MM, Posch T, Pernthaler J. In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake. ISME J. 2013;7:896–907. PubMed DOI PMC

Ghai R, McMahon KD, Rodriguez-Valera F. Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environ Microbiol Rep. 2012;4:29–35. PubMed DOI

Garcia SL, et al. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J. 2013;7:137–47. PubMed DOI PMC

Hamilton JJ, et al. Metabolic network analysis and metatranscriptomics reveal auxotrophies and nutrient sources of the cosmopolitan freshwater microbial lineage acI. mSystems. 2017;2:e00091–17. PubMed DOI PMC

Ghai R, et al. Metagenomics of the water column in the pristine upper course of the Amazon River. PLoS ONE. 2011;6:e23785. PubMed DOI PMC

Partensky F, Hoepffner N, Li WKW, Ulloa O, Vaulot D. Photoacclimation of PubMed DOI PMC

Rappé MS, Connon SA, Vergin KL, Giovannoni SJ. Cultivation of the ubiquitous PubMed DOI

Kang I, Kim S, Islam MR, Cho J-C. The first complete genome sequences of the acI lineage, the most abundant freshwater actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures. Sci Rep. 2017;7:42252. PubMed DOI PMC

Kim S, Kang I, Seo J-H, Cho J-C. Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase. ISME J. 2019;13:2252–63. PubMed DOI PMC

Kim S, Park MS, Song J, Kang I, Cho J-C. High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang. J Microbiol. 2020;58:893–905. PubMed DOI

Kim S, et al. Heme auxotrophy in abundant aquatic microbial lineages. Proc Natl Acad Sci U S A. 2021;118:e2102750118. PubMed DOI PMC

Salcher M, Šimek K. Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology. Aquat Microb Ecol. 2016;77:183–96. DOI

Salcher MM, et al. Bringing the uncultivated microbial majority of freshwater ecosystems into culture. Nat Commun. 2025;16:7971. PubMed DOI PMC

Fernandes C, et al. Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus PubMed DOI

Paul Layoun et al PubMed PMC

Porter KG, Feig YS. The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr. 1980;25:943–8. DOI

Salcher MM, Schaefle D, Kaspar M, Neuenschwander SM, Ghai R. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. ISME J. 2019;13:2764–77. PubMed DOI PMC

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics. 2020;70:e102. PubMed DOI

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. PubMed DOI

Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010;11:431. PubMed DOI PMC

Blum M, et al. Interpro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025;53:D444–56. PubMed DOI PMC

Tatusov RL. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001;29:22–8. PubMed DOI PMC

Haft DH. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001;29:41–3. PubMed DOI PMC

Mistry J, Bateman A, Finn RD. Predicting active site residue annotations in the Pfam database. BMC Bioinformatics. 2007;8:298. PubMed DOI PMC

Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726. PubMed DOI

Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29. PubMed DOI PMC

Yin Y, et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:W445–51. PubMed DOI PMC

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043. PubMed DOI PMC

Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2020;36:1925–7. PubMed DOI PMC

Goris J, et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57:81–91. PubMed DOI

Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol. 2020;70:2937–48. PubMed DOI

Olm MR, Brown CT, Brooks B, Banfield JF. DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8. PubMed DOI PMC

Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8. PubMed DOI

Parks DH, et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2022;50:D785–94. PubMed DOI PMC

Löytynoja A. Phylogeny-aware alignment with PRANK. Methods Mol Biol. 2014;1079:155–70. PubMed DOI

Criscuolo A, Gribaldo S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10:210. PubMed DOI PMC

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9. PubMed DOI PMC

Minh BQ, et al. Iq-tree 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4. PubMed DOI PMC

Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29-37. PubMed DOI PMC

Bulzu P-A, Kavagutti VS, Andrei A-S, Ghai R. The evolutionary kaleidoscope of rhodopsins. mSystems. 2022;7:e00405-e422. PubMed DOI PMC

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. PubMed DOI PMC

Käll L, Krogh A, Sonnhammer ELL. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics. 2005;21(Suppl 1):i251-257. PubMed DOI

Ernst OP, et al. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev. 2014;114:126–63. PubMed DOI PMC

Mirarab S, et al. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J Comput Biol. 2015;22:377–86. PubMed DOI PMC

Bushnell B, Rood J, Singer E. Bbmerge – accurate paired shotgun read merging via overlap. PLoS ONE. 2017;12:e0185056. PubMed DOI PMC

Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng Des Sel. 1996;9:1063–5. PubMed DOI

Kille B, et al. Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics. 2024;40:btae311. PubMed DOI PMC

Drost H-G, Gabel A, Grosse I, Quint M. Evidence for active maintenance of phylotranscriptomic hourglass patterns in animal and plant embryogenesis. Mol Biol Evol. 2015;32:1221–31. PubMed DOI PMC

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. PubMed DOI

Hedlund BP, et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol. 2022;7:1702–8. PubMed PMC

Cho BC, Hardies SC, Jang GI, Hwang CY. Complete genome of streamlined marine actinobacterium PubMed DOI PMC

Mehrshad M, et al. Hidden in plain sight—highly abundant and diverse planktonic freshwater chloroflexi. Microbiome. 2018;6:176. PubMed DOI PMC

Kavagutti VS, Andrei A-Ş, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome. 2019;7:135. PubMed DOI PMC

Kavagutti VS, et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome. 2023;11:15. PubMed DOI PMC

Krinos AI, et al. Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake. Microbiome. 2024;12:133. PubMed DOI PMC

Cronan JE, Thomas J. Bacterial fatty acid synthesis and its relationships with polyketide synthetic pathways. Methods Enzymol. 2009;459:395–433. PubMed DOI PMC

Ghylin TW, et al. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI actinobacteria lineage. ISME J. 2014;8:2503–16. PubMed DOI PMC

Escalante-Semerena JC. Conversion of cobinamide into adenosylcobamide in bacteria and archaea. J Bacteriol. 2007;189:4555–60. PubMed DOI PMC

Beale J, Lee SY, Iwata S, Beis K. Structure of the aliphatic sulfonate-binding protein SsuA from PubMed DOI PMC

Tanaka Y, et al. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Sci Adv. 2020;6:eaba7637. PubMed DOI PMC

White D. The physiology and biochemistry of prokaryotes

Takeuchi N, Fullmer MS, Maddock DJ, Poole AM. The constructive black queen hypothesis: new functions can evolve under conditions favouring gene loss. ISME J. 2024;18:wrae011. PubMed DOI PMC

Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1991;280(Pt 2):309–16. PubMed DOI PMC

Li X-L, Spániková S, de Vries RP, Biely P. Identification of genes encoding microbial glucuronoyl esterases. FEBS Lett. 2007;581:4029–35. PubMed DOI

Molina-Henares, A. J., Krell, T., Eugenia Guazzaroni, M., Segura, A. & Ramos, J. L. Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol Rev 30, 157–186 (2006). PubMed

Catara G, Caggiano R, Palazzo L. The DarT/DarG toxin-antitoxin ADP-ribosylation system as a novel target for a rational design of innovative antimicrobial strategies. Pathogens. 2023;12(2):240. PubMed DOI PMC

Cebrián-Sastre E, Martín-Blecua I, Gullón S, Blázquez J, Castañeda-García A. Control of genome stability by EndoMS/NucS-mediated non-canonical mismatch repair. Cells. 2021;10:1314. PubMed DOI PMC

Poindexter, J. S. Oligotrophy. in

Gómez-Consarnau L, et al. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Sci Adv. 2019;5:eaaw8855. PubMed DOI PMC

Béjà O, et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000;289:1902–6. PubMed DOI

Pinhassi J, DeLong EF, Béjà O, González JM, Pedrós-Alió C. Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology. Microbiol Mol Biol Rev. 2016;80:929–54. PubMed DOI PMC

Dwulit-Smith JR, et al. A PubMed DOI PMC

Nakajima Y, PubMed PMC

Chazan A, et al. Diverse heliorhodopsins detected via functional metagenomics in freshwater actinobacteria, Chloroflexi and archaea. Environ Microbiol. 2022;24:110–21. PubMed DOI

Cho S-G, et al. Heliorhodopsin binds and regulates glutamine synthetase activity. PLoS Biol. 2022;20:e3001817. PubMed DOI PMC

Bulzu, P.-A. PubMed PMC

Burkert U, Warnecke F, Babenzien D, Zwirnmann E, Pernthaler J. Members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake. Appl Environ Microbiol. 2003;69:6550–9. PubMed DOI PMC

Eckert EM, Salcher MM, Posch T, Eugster B, Pernthaler J. Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. Environ Microbiol. 2012;14:794–806. PubMed DOI

Buck U, Grossart H-P, Amann R, Pernthaler J. Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environ Microbiol. 2009;11:1854–65. PubMed DOI

Beier S, Bertilsson S. Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton. Limnol Oceanogr. 2011;56:1179–88. DOI

Taipale S, Jones RI, Tiirola M. Vertical diversity of bacteria in an oxygen-stratified humic lake, evaluated using DNA and phospholipid analyses. Aquat Microb Ecol. 2009;55:1–16. DOI

Hoetzinger, M. PubMed PMC

Okazaki Y, Nishikawa Y, Wagatsuma R, Takeyama H, Nakano S. Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria. ISME Commun. 2025;5:ycaf086. PubMed DOI PMC

Eckert EM, Baumgartner M, Huber IM, Pernthaler J. Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon. Environ Microbiol. 2013;15:2019–30. PubMed DOI

Pernthaler J, et al. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol. 2001;67:2145–55. PubMed DOI PMC

Šimek K, et al. Differential freshwater flagellate community response to bacterial food quality with a focus on PubMed DOI PMC

Tarao M, Jezbera J, Hahn MW. Involvement of cell surface structures in size-independent grazing resistance of freshwater actinobacteria. Appl Environ Microbiol. 2009;75:4720–6. PubMed DOI PMC

Ferris JA, Lehman JT. Interannual variation in diatom bloom dynamics: roles of hydrology, nutrient limitation, sinking, and whole lake manipulation. Water Res. 2007;41:2551–62. PubMed DOI

Kovářová J, Barrett MP. The pentose phosphate pathway in parasitic trypanosomatids. Trends Parasitol. 2016;32:622–34. PubMed DOI

Lam HM, Winkler ME. Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in PubMed DOI PMC

Zhao J, Baba T, Mori H, Shimizu K. Global metabolic response of PubMed DOI

Schwalbach MS, Tripp HJ, Steindler L, Smith DP, Giovannoni SJ. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. Environ Microbiol. 2010;12:490–500. PubMed DOI

Spaans SK, Weusthuis RA, Van Der Oost J, Kengen SW. NADPH-generating systems in bacteria and archaea. Front Microbiol PubMed PMC

Szebenyi DME, Musayev FN, di Salvo ML, Safo MK, Schirch V. Serine hydroxymethyltransferase: role of glu75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry. 2004;43:6865–76. PubMed DOI

Qin Z, Yan Q, Ma Q, Jiang Z. Crystal structure and characterization of a novel L-serine ammonia-lyase from PubMed DOI

Hu H, Mylon SE, Benoit G. Distribution of the thiols glutathione and 3-mercaptopropionic acid in Connecticut lakes. Limnol Oceanogr. 2006;51:2763–74. DOI

Bachhawat AK, Thakur A, Kaur J, Zulkifli M. Glutathione transporters. Biochimica et Biophysica Acta (BBA) - General Subjects. 2013;1830:3154–64. PubMed DOI

Suzuki H, Koyanagi T, Izuka S, Onishi A, Kumagai H. The yliA, -B, -C, and -D genes of PubMed DOI PMC

Mondav, R. PubMed PMC

Kettler GC, et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 2007;3:e231. PubMed DOI PMC

Rodriguez-Valera F, Molina-Pardines C. On the biological meaning of the population pangenome. Trends Microbiol. 2025. 10.1016/j.tim.2025.07.004. PubMed DOI

Hahn J, Inamine G, Kozlov Y, Dubnau D. Characterization of comE, a late competence operon of PubMed DOI

Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F. Key roles for freshwater actinobacteria revealed by deep metagenomic sequencing. Mol Ecol. 2014;23:6073–90. PubMed DOI

Okazaki, Y., Nishikawa, Y., Wagatsuma, R., Takeyama, H. & Nakano, S. Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria. 2024.07.24.604879 Preprint at 10.1101/2024.07.24.604879 (2024). PubMed PMC

Kavagutti VS, Chiriac M-C, Ghai R, Salcher MM, Haber M. Isolation of phages infecting the abundant freshwater Actinobacteriota order ‘Ca. Nanopelagicales.’ ISME J. 2023;17:943–6. PubMed DOI PMC

Chen L-X, et al. Wide distribution of phage that infect freshwater SAR11 bacteria. mSystems. 2019;4:e00410–19. PubMed DOI PMC

Giovannoni S, Temperton B, Zhao Y, et al. Giovannoni et al. reply. Nature. 2013;499:E4–5. PubMed DOI

Drula E, et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 2022;50:D571–7. PubMed DOI PMC

Tada Y, Grossart H-P. Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method. ISME J. 2014;8:441–54. PubMed DOI PMC

Ceccaldi P, et al. Reductive activation of PubMed DOI

Rodriguez-Valera F, et al. Explaining microbial population genomics through phage predation. Nat Prec. 2009. 10.1038/npre.2009.3489.1. PubMed DOI