Abstract
A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria–phage and bacteria–phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the microenvironments physically and compare the bacterial inhabitants from each. It remains poorly understood, however, which microenvironment primarily drives bacterioplankton evolution in the pelagic ocean. By applying a dilution cultivation approach to an undisturbed coastal water sample, we isolate a bacterial population affiliated with the globally dominant Roseobacter group. Although varying at just a few thousand nucleotide sites across the whole genomes, members of this clonal population are diverging into two genetically separated subspecies. Genes underlying speciation are not unique to subspecies but instead clustered at the shared regions that represent ~6% of the genomic DNA. They are primarily involved in vitamin synthesis, motility, oxidative defense, carbohydrate, and amino acid utilization, consistent with the known strategies that roseobacters take to interact with phytoplankton and particles. Physiological assays corroborate that one subspecies outcompetes the other in these traits. Our results indicate that the microenvironments in the pelagic ocean represented by phytoplankton and organic particles are likely important niches that drive the cryptic speciation of the Roseobacter population, though microhabitats contributed by other less abundant pelagic hosts cannot be ruled out.
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Data availability
Genomic sequences of the Roseobacter and Marinobacterium population are available at the NCBI GenBank database under the accession number WBXQ00000000-WBYV00000000.
Code availability
The scripts used for the population structure analyses, recombination history inference, SNP density plot and allelic replacements inference have been deposited in the online repository (https://github.com/Xiaojun928/Population-genomics).
References
Prgzelin BB, Alldredge AL. Primary production of marine snow during and after an upwelling event. Limnol Oceanogr. 1983;28:1156–67.
Shanks AL, Trent JD. Marine snow: microscale nutrient patches. Limnol Oceanogr. 1979;24:850–4.
Azam F, Malfatti F. Microbial structuring of marine ecosystems. Nat Rev Microbiol. 2007;5:782–91.
Moran MA. The global ocean microbiome. Science. 2015;350:aac8455.
Stocker R. Marine microbes see a sea of gradients. Science. 2012;338:628–33.
Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci USA. 2008;105:4209–14.
Stocker R, Seymour JR. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol Mol Biol Rev. 2012;76:792–812.
Rosenwasser S, Ziv C, Creveld SGvan, Vardi A. Virocell metabolism: metabolic innovations during host–virus interactions in the ocean. Trends Microbiol. 2016;24:821–32.
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.
Seymour JR, Amin SA, Raina J-B, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat Microbiol. 2017;2:1–12.
Smriga S, Fernandez VI, Mitchell JG, Stocker R. Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria. Proc Natl Acad Sci USA. 2016;113:1576–81.
Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S, et al. Ecological genomics of marine Roseobacters. Appl Environ Microbiol. 2007;73:4559–69.
Bischoff V, Bunk B, Meier-Kolthoff JP, Spröer C, Poehlein A, Dogs M, et al. Cobaviruses—a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J. 2019;13:1404–21.
Zhan Y, Chen F. Bacteriophages that infect marine roseobacters: genomics and ecology. Environ Microbiol. 2019;21:1885–95.
Ankrah NYD, May AL, Middleton JL, Jones DR, Hadden MK, Gooding JR, et al. Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. ISME J. 2014;8:1089–100.
Sonnenschein EC, Nielsen KF, D’Alvise P, Porsby CH, Melchiorsen J, Heilmann J, et al. Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis. ISME J. 2017;11:569–83.
Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev. 2014;78:573–87.
Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol. 2014;12:686–98.
Ramanan R, Kim B-H, Cho D-H, Oh H-M, Kim H-S. Algae–bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv. 2016;34:14–29.
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science. 2012;336:608–11.
Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84.
Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 2015;522:98–101.
Green DH, Echavarri-Bravo V, Brennan D, Hart MC. Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii. BioMed Res Int. https://www.hindawi.com/journals/bmri/2015/194540/. Accessed 28 May 2020.
González JM, Simó R, Massana R, Covert JS, Casamayor EO, Pedrós-Alió C, et al. Bacterial cmmunity structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol. 2000;66:4237–46.
Park BS, Guo R, Lim W-A, Ki J-S. Pyrosequencing reveals specific associations of bacterial clades Roseobacter and Flavobacterium with the harmful dinoflagellate Cochlodinium polykrikoides growing in culture. Mar Ecol. 2017;38:maec.12474.
Li S, Chen M, Chen Y, Tong J, Wang L, Xu Y, et al. Epibiotic bacterial community composition in red-tide dinoflagellate Akashiwo sanguinea culture under various growth conditions. FEMS Microbiol Ecol. 2019;95:fiz057.
Bell W, Mitchell R. Chemotactic and growth responses of marine bacteria to algal extracellular products. Biol Bull. 1972;143:265–77.
Cole JJ. Interactions between bacteria and algae in aquatic ecosystems. Annu Rev Ecol Syst. 1982;13:291–314.
Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 2004;432:910–3.
Durham BP, Dearth SP, Sharma S, Amin SA, Smith CB, Campagna SR, et al. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environ Microbiol. 2017;19:3500–13.
Barak-Gavish N, Frada MJ, Ku C, Lee PA, DiTullio GR, Malitsky S, et al. Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. Sci Adv. 2018;4:eaau5716.
Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, et al. Dynamic metabolic exchange governs a marine algal-bacterial interaction. Elife. 2016;5:e17473.
Darling AE, Mau B, Perna NT. Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5:e11147.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol. 2015;11:e1004041.
Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012;8:e1002453.
Sun Y, Luo H. Homologous recombination in core genomes facilitates marine bacterial adaptation. Appl Environ Microbiol. 2018;84:e02545–17.
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, et al. Population genomics of early events in the ecological differentiation of bacteria. Science. 2012;336:48–51.
Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol. 2008;62:53–70.
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet. 2008;40:987–93.
Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet. 2010;42:1140–3.
Achtman M. Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philos Trans R Soc Lond B Biol Sci. 2012;367:860–7.
Didelot X, Maiden MCJ. Impact of recombination on bacterial evolution. Trends Microbiol. 2010;18:315–22.
Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 2009;3:199–208.
Hanage WP. Not so simple after all: bacteria, their population genetics, and recombination. Cold Spring Harb Perspect Biol. 2016;8:a018069.
Fraser C, Hanage WP, Spratt BG. Recombination and the nature of bacterial speciation. Science. 2007;315:476–80.
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008;6:e311.
Holt KE, Baker S, Weill F-X, Holmes EC, Kitchen A, Yu J, et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet. 2012;44:1056–9.
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet. 2012;44:1215–21.
Zhi X-Y, Zhao W, Li W-J, Zhao G-P. Prokaryotic systematics in the genomics era. Antonie Van Leeuwenhoek. 2012;101:21–34.
Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol. 2013;30:1454–64.
Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, et al. Patterns of gene flow define species of thermophilic Archaea. PLoS Biol. 2012;10:e1001265.
Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SGE. Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet. 2013;9:e1003381.
Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ, et al. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. ISME J. 2016;10:2468–77.
Hoetzinger M, Hahn MW. Genomic divergence and cohesion in a species of pelagic freshwater bacteria. BMC Genom. 2017;18:794.
Arevalo P, VanInsberghe D, Elsherbini J, Gore J, Polz MF. A reverse ecology approach based on a biological definition of microbial populations. Cell. 2019;178:820–34.
Bobay L-M, Ochman H. Biological species are universal across life’s domains. Genome Biol Evol. 2017;9:491–501.
Engel P, Stepanauskas R, Moran NA. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genet. 2014;10:e1004596.
Hughes AL, French JO. Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene. 2007;387:31–7.
Hughes AL, Friedman R. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. J Bacteriol. 2005;187:2698–704.
Charrad M, Ghazzali N, Boiteau V, Niknafs A. NbClust: an R package for determining the relevant number of clusters in a data set. J Stat Softw. 2014;61:1–36.
Raina J-B, Fernandez V, Lambert B, Stocker R, Seymour JR. The role of microbial motility and chemotaxis in symbiosis. Nat Rev Microbiol. 2019;17:284–94.
Hünken M, Harder J, Kirst GO. Epiphytic bacteria on the Antarctic ice diatom Amphiprora kufferathii Manguin cleave hydrogen peroxide produced during algal photosynthesis. Plant Biol. 2008;10:519–26.
Morris JJ, Kirkegaard R, Szul MJ, Johnson ZI, Zinser ER. Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by “helper” heterotrophic bacteria. Appl Environ Microbiol. 2008;74:4530–4.
Durham BP, Sharma S, Luo H, Smith CB, Amin SA, Bender SJ, et al. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Natl Acad Sci USA. 2015;112:453–7.
Cooper MB, Kazamia E, Helliwell KE, Kudahl UJ, Sayer A, Wheeler GL, et al. Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. ISME J. 2019;13:334–45.
Tang YZ, Koch F, Gobler CJ. Most harmful algal bloom species are vitamin B1 and B12 auxotrophs. Proc Natl Acad Sci USA. 2010;107:20756–61.
Helliwell KE. The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects. New Phytol. 2017;216:62–8.
Gao R, Krysciak D, Petersen K, Utpatel C, Knapp A, Schmeisser C, et al. Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain. Appl Environ Microbiol. 2015;81:7993–8007.
Ng VH, Cox JS, Sousa AO, MacMicking JD, McKinney JD. Role of KatG catalase-peroxidase in mycobacterial pathogenesis: countering the phagocyte oxidative burst. Mol Microbiol. 2004;52:1291–302.
Ivanova A, Miller C, Glinsky G, Eisenstark A. Role of rpoS (katF) in oxyR-independent regulation of hydroperoxidase I in Escherichia coli. Mol Microbiol. 1994;12:571–8.
Amábile-Cuevas CF, Demple B. Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon. Nucleic Acids Res. 1991;19:4479–84.
Landfald B, Strøm AR. Choline-glycine betaine pathway confers a high level of osmotic tolerance in Escherichia coli. J Bacteriol. 1986;165:849–55.
Lidbury I, Kimberley G, Scanlan DJ, Murrell JC, Chen Y. Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Mol Microbiol. 2015;17:5048–62.
Bochner BR, Gadzinski P, Panomitros E. Phenotype microArrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 2001;11:1246–55.
Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk H-P, et al. opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics. 2013;29:1823–4.
Mou X, Vila-Costa M, Sun S, Zhao W, Sharma S, Moran MA. Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton. Environ Microbiol Rep. 2011;3:798–806.
Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic. Mesorhizobium ISME J. 2017;11:248–62.
Andam CP, Gogarten JP. Biased gene transfer in microbial evolution. Nat Rev Microbiol. 2011;9:543–55.
Boucher Y, Cordero OX, Takemura A. Endemicity within global Vibrio cholerae populations. mBio. 2011;2:1–8.
Coleman ML, Chisholm SW. Ecosystem-specific selection pressures revealed through comparative population genomics. Proc Natl Acad Sci USA. 2010;107:18634–9.
Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013;29:170–5.
Cordero OX, Polz MF. Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol. 2014;12:263–73.
Hoetzinger M, Schmidt J, Jezberová J, Koll U, Hahn MW. Microdiversification of a pelagic Polynucleobacter species Is mainly driven by acquisition of genomic islands from a partially interspecific gene pool. Appl Environ Microbiol. 2017;83:e02266–16.
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, et al. Deciphering ocean carbon in a changing world. Proc Natl Acad Sci USA. 2016;113:3143–51.
Christie-Oleza JA, Sousoni D, Lloyd M, Armengaud J, Scanlan DJ. Nutrient recycling facilitates long-term stability of marine microbial phototroph-heterotroph interactions. Nat Microbiol. 2017;2:17100.
Acknowledgements
We thank Ying Sun for sharing her bioinformatics pipeline, Xiaoyuan Feng for his helpful discussion, Kan Zhu for his assistance in the access to the OmniLOG instrument, and Leon Zou (BiOLOG Inc.) for his helpful suggestions on the Biolog experiments. This work was supported by the National Key R&D Program of China (2018YFC0309800), the National Natural Science Foundation of China (41776129), the National Key R&D Program of China (2016YFA0601400 to YZ), the Shenzhen City Knowledge Innovation Plan (JCYJ20160530174441706 to AY), the Hong Kong Research Grants Council General Research Fund (14163917), the Hong Kong Environment and Conservation Fund (15/2016), the Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M-403/16), and the Direct Grant of CUHK (4053257 & 3132809).
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Wang, X., Zhang, Y., Ren, M. et al. Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. ISME J 14, 3106–3119 (2020). https://doi.org/10.1038/s41396-020-00743-7
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DOI: https://doi.org/10.1038/s41396-020-00743-7
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