Abstract
The ocean harbors an enormous diversity of bacteria and archaea whose metabolic activities have global biogeochemical impacts. Evolutionary genomic studies play an important role in marine microbiology by providing insights into the selective pressures that influence the diversity and functioning of marine microbial lineages, shedding light on their niche specialization, and helping to define their broader ecological roles. The scope of evolutionary genomic studies in the ocean has dramatically expanded in recent years owing to advances in sequencing technology, metagenomics, and single-cell sequencing. Historically the collection of sequenced genomes has been composed of a small number of cultured microbes, but recent advances have opened a window into the genomics of a broad diversity of lineages throughout the biosphere. This broad genomic representation of lineages across the tree of life has enabled comparative genomic analyses that help to identify the ecological and evolutionary forces that drive the diversification of microorganisms in the ocean. In this chapter, we review some of the salient themes that have emerged in the last few decades of these studies. We discuss the main findings of these evolutionary genomic studies and their implications for our understanding of the diversity and functioning of microbial life in the ocean.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA (2019) Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J 13:618–631
Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ (2014) Sulfur oxidation genes in diverse deep-sea viruses. Science 344:757–760. https://doi.org/10.1126/science.1252229
Arístegui J, Gasol JM, Duarte CM, Herndl GJ (2009) Microbial oceanography of the dark ocean’s pelagic realm. Limnol Oceanogr 54:1501–1529. https://doi.org/10.4319/lo.2009.54.5.1501
Arrigo KR (2005) Marine microorganisms and global nutrient cycles. Nature 437:349–355
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474:604–608
Aylward FO, Boeuf D, Mende DR, Wood-Charlson EM, Vislova A, Eppley JM, Romano AE, DeLong EF (2017) Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone. Proc Natl Acad Sci U S A 114:11446–11451. https://doi.org/10.1073/pnas.1714821114
Aylward FO, Santoro AE (2020) Heterotrophic Thaumarchaea with small genomes are widespread in the dark ocean. mSystems 5:1–20. https://doi.org/10.1128/mSystems.00415-20
Azam F (2004) Oceaonography: microbes, molecules, and marine ecosystems. Science 303:1622–1624. https://doi.org/10.1126/science.1093892
Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5:782–791
Bach W, Edwards KJ, Hayes JM, Sievert S, Huber JA, Sogin ML (2006) Energy in the dark: fuel for life in the deep ocean and beyond. Eos 87:73–79. https://doi.org/10.1029/2006eo070002
Bansal MS, Banay G, Peter Gogarten J, Shamir R (2011) Detecting highways of horizontal gene transfer. J Comput Biol 18:1087–1114. https://doi.org/10.1089/cmb.2011.0066
Batut B, Knibbe C, Marais G, Daubin V (2014) Reductive genome evolution at both ends of the bacterial population size spectrum. Nat Rev Microbiol 12:841–850
Beja O (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906. https://doi.org/10.1126/science.289.5486.1902
Berube P, Biller S, Hackl T et al (2018) Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Sci Data 5:1–11. https://doi.org/10.1038/sdata.2018.154
Biller SJ, McDaniel LD, Breitbart M, Rogers E, Paul JH, Chisholm SW (2017) Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates. ISME J 11:394–404
Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW (2014) Bacterial vesicles in marine ecosystems. Science 343:183–186
Bobay LM, Ochman H (2017) The evolution of bacterial genome architecture. Front Genet 8:1–6. https://doi.org/10.3389/fgene.2017.00072
Bock E, Wagner M (2006) Oxidation of inorganic nitrogen compounds as an energy source. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, pp 457–495. https://doi.org/10.1007/0-387-30742-7_16
Bondy-Denomy J, Davidson AR (2014) When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol 52:235–242. https://doi.org/10.1007/s12275-014-4083-3
Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL (2016) Prophages mediate defense against phage infection through diverse mechanisms. ISME J 10:2854–2866. https://doi.org/10.1038/ismej.2016.79
Bragg JG, Hyder CL (2004) Nitrogen versus carbon use in prokaryotic genomes and proteomes. Proc R Soc Lond B Biol Sci 271:374–377
Breitbart M (2012) Marine viruses: truth or dare. Annu Rev Mar Sci 4:425–448. https://doi.org/10.1146/annurev-marine-120709-142805
Breitbart M, Bonnain C, Malki K, Sawaya NA (2018) Phage puppet masters of the marine microbial realm. Nat Microbiol 3:754–766
Breitbart M, Miyake JH, Rohwer F (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236:249–256
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13:278–284
Breitbart M, Thompson L, Suttle C, Sullivan M (2007) Exploring the vast diversity of marine viruses. Oceanography 20:135–139. https://doi.org/10.5670/oceanog.2007.58
Brochier-Armanet C, Deschamps P, López-García P, Zivanovic Y, Rodríguez-Valera F, Moreira D (2011) Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. ISME J 5:1291–1302
Brockhurst MA, Harrison E, Hall JPJ, Richards T, McNally A, MacLean C (2019) The ecology and evolution of pangenomes. Curr Biol 29:1094–1103
Brown MV, Ostrowski M, Grzymski JJ, Lauro FM (2014) A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades. Mar Genomics 15:17–28
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G et al (2015) Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science 348:1261498
Bunse C, Pinhassi J (2017) Marine bacterioplankton seasonal succession dynamics. Trends Microbiol 25:494–505
Cao H, Dong C, Bougouffa S, Li J, Zhang W, Shao Z, Bajic VB, Qian PY (2016) Delta-proteobacterial SAR324 group in hydrothermal plumes on the south mid-Atlantic ridge. Sci Rep 6:1–9
Cohan FM (2006) Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Phil Trans R Soc Lond B Biol Sci 361:1985–1996
Cohan FM, Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17:373–386
Cordero OX, Polz MF (2014) Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol 12:263–273
Corinaldesi C (2015) New perspectives in benthic deep-sea microbial ecology. Front Mar Sci 2:1–12. https://doi.org/10.3389/fmars.2015.00017
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504–509
Deatherage BL, Cookson BT (2012) Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life. Infect Immun 80:1948–1957
DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89:5685–5689
DeLong EF (1997) Marine microbial diversity: the tip of the iceberg. Trends Biotechnol 15:203–207
DeLong EF (2006) Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311:496–503. https://doi.org/10.1126/science.1120250
DeLong EF, Béjà O (2010) The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol 8:e1000359
Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P (2014) Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota. Genome Biol Evol 6:1549–1563
Dick GJ (2019) The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol 17:271–283
Dupont CL, Rusch DB, Yooseph S et al (2012) Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 6:1186–1199
Eguíluz VM, Salazar G, Fernández-Gracia J, Pearman JK, Gasol JM, Acinas SG, Sunagawa S, Irigoien X, Duarte CM (2019) Scaling of species distribution explains the vast potential marine prokaryote diversity. Sci Rep 9:1–8
Falkowski PG (1998) Biogeochemical controls and feedbacks on ocean primary production. Science 281:200–206
Falkowski PG, Fenchel T, DeLong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039
Feil EJ (2004) Small change: keeping pace with microevolution. Nat Rev Microbiol 2:483–495
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci U S A 102:14683–14688
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741–746
Fridman S, Flores-Uribe J, Larom S et al (2017) A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol 2:1350–1357
Frigaard NU, Martinez A, Mincer TJ, DeLong EF (2006) Proteorhodopsin lateral gene transfer between marine planktonic bacteria and archaea. Nature 439:847–850
Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548
Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149
Futuyma DJ (1986) Evolutionary biology, 2nd edn. Sinauer Associates Inc.
Getz EW, Tithi SS, Zhang L, Aylward FO (2018) Parallel evolution of genome streamlining and cellular bioenergetics across the marine radiation of a bacterial phylum. mBio 9:1–14. https://doi.org/10.1128/mBio.01089-18
Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F (2013) Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Sci Rep 3:1–8. https://doi.org/10.1038/srep02471
Giovannoni SJ (2017) SAR11 bacteria: the most abundant plankton in the oceans. Annu Rev Mar Sci 9:231–255
Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, Rappé MS, Laney S, Wilhelm LJ, Tripp HJ, Mathur EJ, Barofsky DF (2005) Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438:82–85
Giovannoni SJ, Cameron Thrash J, Temperton B (2014) Implications of streamlining theory for microbial ecology. ISME J 8:1553–1565
Giovannoni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437:343–348. https://doi.org/10.1038/nature04158
Giovannoni SJ, Vergin KL (2012) Seasonality in ocean microbial communities. Science 335:671–676
Gogarten JP, Peter Gogarten J, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687. https://doi.org/10.1038/nrmicro1204
Gómez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, González JM, Pinhassi J (2010) Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol 8:e1000358. https://doi.org/10.1371/journal.pbio.1000358
Gómez-Consarnau L, González JM, Coll-Lladó M, Gourdon P, Pascher T, Neutze R, Pedrós-Alió C, Pinhassi J (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445:210–213. https://doi.org/10.1038/nature05381
Graham ED, Tully BJ (2020) Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. ISME J 15:1248–1256. https://doi.org/10.1038/s41396-020-00834-5
Grzymski JJ, Dussaq AM (2012) The significance of nitrogen cost minimization in proteomes of marine microorganisms. ISME J 6:71–80
Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4:e95
Heidelberg KB, Gilbert JA, Joint I (2010) Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol 3:531–543
Hevroni G, Flores-Uribe J, Béjà O, Philosof A (2020) Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. Proc Natl Acad Sci U S A 117:29738–29747
Hu J, Blanchard JL (2009) Environmental sequence data from the Sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus are not a harbinger for an escalation in genetic drift. Mol Biol Evol 26:1191–1191. https://doi.org/10.1093/molbev/msn299
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320:1081–1085
Hurwitz BL, Hallam SJ, Sullivan MB (2013) Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol 14:1–14
Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA (2020) Long-term stability and red queen-like strain dynamics in marine viruses. Nat Microbiol 5:265–271
Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510
Kashtan N, Roggensack SE, Rodrigue S et al (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416–420
Kasting JF (2002) Life and the evolution of Earth’s atmosphere. Science 296:1066–1068. https://doi.org/10.1126/science.1071184
Kettler GC, Martiny AC, Huang K et al (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 3:e231
Kirchberger PC, Schmidt M, Ochman H (2020) The ingenuity of bacterial genomes. Ann Rev Microbiol 74:815–834. https://doi.org/10.1146/annurev-micro-020518-115822
Klieve AV, Yokoyama MT, Forster RJ, Ouwerkerk D, Bain PA, Mawhinney EL (2005) Naturally occurring DNA transfer system associated with membrane vesicles in cellulolytic Ruminococcus spp. of ruminal origin. Appl Environ Microbiol 71:4248–4253
Konstantinidis KT, Braff J, Karl DM, DeLong EF (2009) Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol 75:5345–5355. https://doi.org/10.1128/aem.00473-09
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Ann Rev Microbiol 55:709–742
Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13:1589–1594
Kuo CH, Ochman H (2009) The fate of new bacterial genes. FEMS Microbiol Rev 33:38–43. https://doi.org/10.1111/j.1574-6976.2008.00140.x
Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ (2017) SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. mBio 8:1–19. https://doi.org/10.1128/mBio.00413-17
Lang AS, Westbye AB, Beatty JT (2017) The distribution, evolution, and roles of gene transfer agents in prokaryotic genetic exchange. Ann Rev Virol 4:87–104
Lasken RS, McLean JS (2014) Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15:577–584
Lauro FM, Bartlett DH (2008) Prokaryotic lifestyles in deep sea habitats. Extremophiles 12:15–25
Lauro FM, McDougald D, Thomas T et al (2009) The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A 106:15527–15533
Lindell D, Jaffe JD, Coleman ML et al (2007) Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449:83–86
Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci U S A 101:11013–11018
López-Pérez M, Gonzaga A, Ivanova EP, Rodriguez-Valera F (2014) Genomes of Alteromonas australica, a world apart. BMC Genomics 15:1–13
López-Pérez M, Haro-Moreno JM, Coutinho FH, Martinez-Garcia M, Rodriguez-Valera F (2020) The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5:1–13. https://doi.org/10.1128/mSystems.00605-20
López-Pérez M, Rodriguez-Valera F (2016) Pangenome evolution in the marine bacterium Alteromonas. Genome Biol Evol 8:1556–1570
Lücker S, Nowka B, Rattei T, Spieck E, Daims H (2013) The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol 4:1–17. https://doi.org/10.3389/fmicb.2013.00027
Luo H, Huang Y, Stepanauskas R, Tang J (2017) Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nat Microbiol 2:1–9
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA (2014a) Comparing effective population sizes of dominant marine alphaproteobacteria lineages. Environ Microbiol Rep 6:167–172
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA (2014b) Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. ISME J 8:1428–1439
Luo H, Thompson LR, Stingl U, Hughes AL (2015) Selection maintains low genomic GC content in marine SAR11 lineages. Mol Biol Evol 32:2738–2748
Luo H, Tolar BB, Swan BK, Zhang CL, Stepanauskas R, Ann Moran M, Hollibaugh JT (2014) Single-cell genomics shedding light on marine Thaumarchaeota diversification. ISME J 8:732–736
Lynch M (2007) The origins of genome architecture, 1st edn. Sinauer Associates Inc.
Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW (2013) Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J 7:184–198. https://doi.org/10.1038/ismej.2012.89
Marston MF, Martiny JBH (2016) Genomic diversification of marine cyanophages into stable ecotypes. Environ Microbiol 18:4240–4253
Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F (2015) A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME J 9:1619–1634
Martinez-Gutierrez CA, Aylward FO (2019) Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biol Evol 11:2887–2894
Martiny AC, Tai APK, Veneziano D, Primeau F, Chisholm SW (2009) Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11:823–832
Mas A, Jamshidi S, Lagadeuc Y, Eveillard D, Vandenkoornhuyse P (2016) Beyond the black queen hypothesis. ISME J 10:2085–2091
McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH (2010) High frequency of horizontal gene transfer in the oceans. Science 330:50
Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R (2018) The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J 12:655–668
Mende DR, Bryant JA, Aylward FO, Eppley JM, Nielsen T, Karl DM, DeLong EF (2017) Environmental drivers of a microbial genomic transition zone in the ocean’s interior. Nat Microbiol 2:1367–1373. https://doi.org/10.1038/s41564-017-0008-3
Middelboe M, Holmfeldt K, Riemann L, Nybroe O, Haaber J (2009) Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environ Microbiol 11:1971–1982. https://doi.org/10.1111/j.1462-2920.2009.01920.x
Mira A, Ochman H, Moran NA (2001) Deletional bias and the evolution of bacterial genomes. Trends Genet 17:589–596
Moore LR, Goericke R, Chisholm SW (1995) Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties. Mar Ecol Prog Ser 116:259–275. https://doi.org/10.3354/meps116259
Moran MA (2008) Genomics and metagenomics of marine prokaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans, 2nd edn. Wiley, pp 91–129
Moran MA, Miller WL (2007) Resourceful heterotrophs make the most of light in the coastal ocean. Nat Rev Microbiol 5:792–800. https://doi.org/10.1038/nrmicro1746
Moran NA (1996) Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A 93:2873–2878. https://doi.org/10.1073/pnas.93.7.2873
Morris JJ, Lenski RE, Zinser ER (2012) The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3:1–7. https://doi.org/10.1128/mBio.00036-12
Morris RM, Cain KR, Hvorecny KL, Kollman JM (2020) Lysogenic host-virus interactions in SAR11 marine bacteria. Nat Microbiol 5:1011–1015. https://doi.org/10.1038/s41564-020-0725-x
Nicol GW, Leininger S, Schleper C (2014) Distribution and activity of ammonia-oxidizing archaea in natural environments. In: Ward B, Arp D, Klotz M (eds) Nitrification. ASM Press, pp. 157–178 doi:https://doi.org/10.1128/9781555817145.ch7
Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ (2011) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75:361–422. https://doi.org/10.1128/mmbr.00039-10
Orellana LH, Ben Francis T, Krüger K, Teeling H, Müller MC, Fuchs BM, Konstantinidis KT, Amann RI (2019) Niche differentiation among annually recurrent coastal marine group II Euryarchaeota. ISME J 13:3024–3036
Orsi WD (2018) Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol 16:671–683
Pachiadaki MG, Sintes E, Bergauer K et al (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358:1046–1051
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004
Partensky F, Garczarek L (2010) Prochlorococcus: advantages and limits of minimalism. Annu Rev Mar Sci 2:305–331
Paul JH (2008) Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J 2:579–589. https://doi.org/10.1038/ismej.2008.35
Paul S, Dutta A, Bag SK, Das S, Dutta C (2010) Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus. BMC Genomics 11:2–15
Pinhassi J, DeLong EF, Béjà O, González JM, Pedrós-Alió C (2016) Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology. Microbiol Mol Biol Rev 80:929–954. https://doi.org/10.1128/mmbr.00003-16
Pomeroy L, Williams PL, Azam F, Hobbie J (2007) The microbial loop. Oceanography 20:28–33. https://doi.org/10.5670/oceanog.2007.45
Price MN, Arkin AP (2015) Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes. mBio 6:e01302–e01315
Qin W, Zheng Y, Zhao F et al (2020) Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME J 14:2595–2609. https://doi.org/10.1038/s41396-020-0710-7
Read RW, Berube PM, Biller SJ, Neveux I, Cubillos-Ruiz A, Chisholm SW, Grzymski JJ (2017) Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells. ISME J 11:2267–2278
Reji L, Francis CA (2020) Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME J 14:2105–2115
Renelli M, Matias V, Lo RY, Beveridge TJ (2004) DNA-containing membrane vesicles of Pseudomonas aeruginosa PAO1 and their genetic transformation potential. Microbiology 150:2161–2169
Ren M, Feng X, Huang Y et al (2019) Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J 13:2150–2161
Rinke C, Rubino F, Messer LF et al (2019) A phylogenomic and ecological analysis of the globally abundant marine group II archaea (ca. Poseidoniales Ord. Nov.). ISME J 13:663–675
Rocap G, Larimer FW, Lamerdin J et al (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047
Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasić L, Thingstad TF, Rohwer F, Mira A (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7:828–836
Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
Roux S, Brum JR, Dutilh BE et al (2016) Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537:689–693
Salazar G, Sunagawa S (2017) Marine microbial diversity. Curr Biol 27:489–494
Salcher MM, Schaefle D, Kaspar M, Neuenschwander SM, Ghai R (2019) Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. ISME J 13:2764–2777
Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM (2019) Insights into the evolution of picocyanobacteria and phycoerythrin genes (mpeBA and cpeBA). Front Microbiol 10:1–17. https://doi.org/10.3389/fmicb.2019.00045
Sanchez-Perez G, Mira A, Nyiro G, Pasić L, Rodriguez-Valera F (2008) Adapting to environmental changes using specialized paralogs. Trends Genet 24:154–158
Sandaa RA (2008) Burden or benefit? Virus-host interactions in the marine environment. Res Microbiol 159:374–381. https://doi.org/10.1016/j.resmic.2008.04.013
Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, Yang Y, Orsi WD, Moran DM, Saito MA (2015) Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: an ammonia-oxidizing archaeon from the open ocean. Proc Natl Acad Sci U S A 112:1173–1178
Santoro AE, Richter RA, Dupont CL (2019) Planktonic marine archaea. Annu Rev Mar Sci 11:131–158
Saw JHW, Nunoura T, Hirai M, Takaki Y, Parsons R, Michelsen M, Longnecker K, Kujawinski EB, Stepanauskas R, Landry Z, Carlson CA, Giovannoni SJ (2020) Pangenomics analysis reveals diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria. mBio 11:1–18. https://doi.org/10.1128/mBio.02975-19
Shakya M, Soucy SM, Zhaxybayeva O (2017) Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 3:1–13
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ (2012) Population genomics of early events in the ecological differentiation of bacteria. Science 336:48–51
Sharon I, Banfield JF (2013) Genomes from metagenomics. Science 342:1057–1058. https://doi.org/10.1126/science.1247023
Sheik CS, Jain S, Dick GJ (2014) Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environ Microbiol 16:304–317
Sherr E, Sherr B (2008) Understanding roles of microbes in marine pelagic food webs: a brief history. In: Kirchman DL (ed) Microbial ecology of the oceans, 2nd edn. Wiley, pp 27–44. https://doi.org/10.1002/9780470281840.ch2
Short CM, Suttle CA (2005) Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71:480–486
Snel B, Bork P, Huynen MA (2002) Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res 12:17–25
Sobecky PA, Hazen TH (2009) Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol Biol 532:435–453
Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346
Stern A, Sorek R (2011) The phage-host arms race: shaping the evolution of microbes. BioEssays 33:43–51
Sullivan MB, Huang KH, Ignacio-Espinoza JC et al (2010) Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol 12:3035–3056
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 4:1344–1357. https://doi.org/10.1371/journal.pbio.0040234
Sun X, Kop LFM, Lau MCY, Frank J, Jayakumar A, Lücker S, Ward BB (2019) Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. ISME J 13:2391–2402
Sun Z, Blanchard JL (2014) Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PLoS One 9:1–15. https://doi.org/10.1371/journal.pone.0088837
Suttle CA (2007) Marine viruses — major players in the global ecosystem. Nat Rev Microbiol 5:801–812. https://doi.org/10.1038/nrmicro1750
Swan BK, Chaffin MD, Martinez-Garcia M et al (2014) Genomic and metabolic diversity of marine group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One 9:1–9. https://doi.org/10.1371/journal.pone.0095380
Swan BK, Martinez-Garcia M, Preston CM et al (2011) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300
Swan BK, Tupper B, Sczyrba A et al (2013) Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci U S A 110:11463–11468
Thingstad TF, Våge S, Storesund JE, Sandaa RA, Giske J (2014) A theoretical analysis of how strain-specific viruses can control microbial species diversity. Proc Natl Acad Sci U S A 111:7813–7818
Ting CS, Rocap G, King J, Chisholm SW (2002) Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol 10:134–142
Torre JR, Christianson LM, Beja O, Suzuki MT, Karl DM, Heidelberg J, DeLong EF (2003) Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc Natl Acad Sci U S A 100:12830–12835. https://doi.org/10.1073/pnas.2133554100
Touchon M, Moura de Sousa JA, Rocha EP (2017) Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr Opin Microbiol 38:66–73
Treangen TJ, Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7:1–12. https://doi.org/10.1371/journal.pgen.1001284
Tringe SG, Hugenholtz P (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11:442–446
Tully BJ (2019) Metabolic diversity within the globally abundant marine group II Euryarchaea offers insight into ecological patterns. Nat Commun 10:1–12
van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MSM, Lücker S (2015) Complete nitrification by a single microorganism. Nature 528:555–559
Wang B, Qin W, Ren Y et al (2019) Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME J 13:3067–3079
Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ (2007) Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol Direct 2:1–19
Williams HTP (2013) Phage-induced diversification improves host evolvability. BMC Evol Biol 13:1–17
Witzel KP (1990) Approaches to bacterial population dynamics. In: Overbeck J, Chróst RJ (eds) Aquatic microbial ecology: biochemical and molecular approaches. Springer, pp 96–128. https://doi.org/10.1007/978-1-4612-3382-4_5
Wolf YI, Koonin EV (2013) Genome reduction as the dominant mode of evolution. BioEssays 35:829–837
Wommack KE, Eric Wommack K, Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64:69–114. https://doi.org/10.1128/mmbr.64.1.69-114.2000
Yaron S, Kolling GL, Simon L, Matthews KR (2000) Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl Environ Microbiol 66:4414–4420
Yilmaz P, Yarza P, Rapp JZ, Glöckner FO (2015) Expanding the world of marine bacterial and archaeal clades. Front Microbiol 6:1–29
Yutin N, Koonin EV (2012) Proteorhodopsin genes in giant viruses. Biol Direct 7:1–6. https://doi.org/10.1186/1745-6150-7-34
Zhang CL, Xie W, Martin-Cuadrado AB, Rodriguez-Valera F (2015) Marine group II archaea, potentially important players in the global ocean carbon cycle. Front Microbiol 6:1–9
Zhang H, Yoshizawa S, Sun Y, Huang Y, Chu X, González JM, Pinhassi J, Luo H (2019) Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats. Environ Microbiol 21:648–666
Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, Du S, Rensing C (2019) Pelagiphages in the Podoviridae family integrate into host genomes. Environ Microbiol 21:1989–2001
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML (2020) Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 18:21–34
Zwirglmaier K, Jardillier L, Ostrowski M, Mazard S, Garczarek L, Vaulot D, Not F, Massana R, Ulloa O, Scanlan DJ (2008) Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol 10:147–161
Acknowledgments
Given the broad scope of topics discussed in this chapter, it is inevitable that many important studies could not be discussed, and we apologize to all colleagues whose important work could not be included in this chapter. This work was supported by a Simons Foundation Early Career Award in Marine Microbial Ecology and Evolution to FOA.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
Martinez-Gutierrez, C.A., Aylward, F.O. (2022). Evolutionary Genomics of Marine Bacteria and Archaea. In: Stal, L.J., Cretoiu, M.S. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham. https://doi.org/10.1007/978-3-030-90383-1_7
Download citation
DOI: https://doi.org/10.1007/978-3-030-90383-1_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-90382-4
Online ISBN: 978-3-030-90383-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)