Skip to main content
SpringerLink
Log in

Microbial Inhabitants of the Dark Ocean

  • Chapter
  • First Online:
The Marine Microbiome

Part of the book series: The Microbiomes of Humans, Animals, Plants, and the Environment ((MHAPE,volume 3))

  • 2210 Accesses

Abstract

The dark ocean refers to the oceanic water column deeper than 200 m, which includes the mesopelagic (200–1000 m), bathypelagic (1000–4000 m), abyssopelagic (4000–6000 m), and hadalpelagic (>6000 m) realms. This vast system is in terms of volume the largest habitat of the biosphere, harboring the largest reservoir of microbes in aquatic systems, and most of the heterotrophic microbial biomass and production of the global ocean. Despite its relevance, knowledge on the phylogenetic and functional diversity of the dark ocean’s microbes is rather limited compared to the euphotic waters. In this chapter, recent advances in our understanding of the dark ocean’s microbiome are summarized. The spatial and temporal heterogeneity of microbial communities and surface-deep ocean connectivity are described as well as their functional diversity. The chapter is concluding with a section summarizing the limited information available on the phylogenetic and functional microbial diversity of the abyssal and hadal realm. With this chapter, we hope to call the attention of the need to deepen our understanding on the dark ocean’s microbiome.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G (2019) Metabolic architecture of the deep ocean microbiome. bioRxiv: 635680

    Google Scholar 

  • Agogué H, Brink M, Dinasquet J, Herndl GJ (2008) Major gradients in putatively nitrifying and non-nitrifying archaea in the deep North Atlantic. Nature 456:788–791

    Article  PubMed  CAS  Google Scholar 

  • Agogué H, Lamy D, Neal PR, Sogin ML, Herndl GJ (2011) Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol Ecol 20:258–274

    Article  PubMed  Google Scholar 

  • Arístegui J, Gasol JM, Duarte CM, Herndl GJ (2009) Microbial oceanography of the dark ocean's pelagic realm. Limnol Oceanogr 54:1501–1529

    Article  Google Scholar 

  • Bach LT, Stange P, Taucher J, Achterberg EP, Algueró-Muñiz M, Horn H, Esposito M, Riebesell U (2019) The influence of plankton community structure on sinking velocity and remineralization rate of marine aggregates. Global Biogeochem Cycles 33:971–994

    Article  CAS  Google Scholar 

  • Baltar F, Arísstegui J, Gasol JM, Herndl GJ (2012) Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical Northeast Atlantic Ocean. Appl Environ Microbiol 78:3309–3316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baltar F, Arístegui J, Gasol JM, Hernández-León S, Herndl GJ (2007) Strong coast–ocean and surface–depth gradients in prokaryotic assemblage structure and activity in a coastal transition zone region. Aq Microb Ecol 50:63–74

    Article  Google Scholar 

  • Baltar F, Arístegui J, Gasol JM, Lekunberri I, Herndl GJ (2010a) Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean. ISME J 4:975–988

    Article  PubMed  Google Scholar 

  • Baltar F, Arístegui J, Gasol JM, Sintes E, van Aken HM, Herndl GJ (2010b) High dissolved extracellular enzymatic activity in the deep Central Atlantic Ocean. Aq Microb Ecol 58:287–302

    Article  Google Scholar 

  • Baltar F, Arístegui J, Gasol JM, Sintes E, Herndl GJ (2009) Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic. Limnol Oceanogr 54:182–193

    Article  CAS  Google Scholar 

  • Baltar F, Arístegui J, Gasol JM, Yokokawa T, Herndl GJ (2013) Bacterial versus archaeal origin of extracellular enzymatic activity in the Northeast Atlantic deep waters. Microb Ecol 65:277–288

    Article  CAS  PubMed  Google Scholar 

  • Baltar F, Arístegui J, Sintes E, Gasol JM, Reinthaler T, Herndl GJ (2010c) Significance of non-sinking particulate organic carbon and dark CO2 fixation to heterotrophic carbon demand in the mesopelagic Northeast Atlantic. Geophys Res Lett 37:L09602

    Article  CAS  Google Scholar 

  • Baltar F, Herndl GJ (2019) Ideas and perspectives: is dark carbon fixation relevant for oceanic primary production estimates? Biogeosciences 16:3793–3799

    Article  CAS  Google Scholar 

  • Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, Pinhassi J (2016a) Prokaryotic responses to ammonium and organic carbon reveal alternative CO2 fixation pathways and importance of alkaline phosphatase in the mesopelagic North Atlantic. Front Microbiol 7:1670

    Article  PubMed  PubMed Central  Google Scholar 

  • Baltar F, Palovaara J, Unrein F, Catala P, Horňák K, Šimek K, Vaqué D, Massana R, Gasol JM, Pinhassi J (2016b) Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions. ISME J 10:568–581

    Article  PubMed  Google Scholar 

  • Bayer B, Saito MA, Mcilvin ME, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE (2021) Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. ISME J 15:1025–1039

    Article  CAS  PubMed  Google Scholar 

  • Beman JM, Popp BN, Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J 2:429–441

    Article  CAS  PubMed  Google Scholar 

  • Benner R (2002) Chemical composition and reactivity. In: Hansell DA, Carlson CA (eds) Biogeochemistry of marine dissolved organic matter. Elsevier Science, New York, pp 59–90

    Chapter  Google Scholar 

  • Bergauer K, Fernandez-Guerra A, Garcia JA, Sprenger RR, Stepanauskas R, Pachiadaki MG, Jensen ON, Herndl GJ (2017) Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc Natl Acad Sci 115:E400–E408

    PubMed  PubMed Central  Google Scholar 

  • Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P (2015) Tara oceans studies plankton at planetary scale. Science 348:873–873

    Article  CAS  PubMed  Google Scholar 

  • Boyd P, Newton P (1995) Evidence of the potential influence of planktonic community structure on the interannual variability of particulate organic carbon flux. Deep Sea Res I 42:619–639

    Article  Google Scholar 

  • Boyd PW, Claustre H, Levy M, Siegel DA, Weber T (2019) Multi-faceted particle pumps drive carbon sequestration in the ocean. Nature 568:327–335

    Article  CAS  PubMed  Google Scholar 

  • Bunse C, Bertos-Fortis M, Sassenhagen I, Sildever S, Sjöqvist C, Godhe A, Gross S, Kremp A, Lips I, Lundholm N (2016) Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom. Front Microbiol 7:517

    Article  PubMed  PubMed Central  Google Scholar 

  • Cho JC, Vergin KL, Morris RM, Giovannoni SJ (2004) Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae. Environ Microbiol 6:611–621

    Article  CAS  PubMed  Google Scholar 

  • Church MJ, DeLong EF, Ducklow HW, Karner MB, Preston CM, Karl DM (2003) Abundance and distribution of planktonic archaea and bacteria in the waters west of the Antarctic peninsula. Limnol Oceanogr 48:1893–1902

    Article  Google Scholar 

  • Cram JA, Chow C-ET, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA (2015a) Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J 9:563–580

    Article  PubMed  Google Scholar 

  • Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA (2015b) Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. ISME J 9:2573–2586

    Article  PubMed  PubMed Central  Google Scholar 

  • Crespo BG, Pommier T, Fernández-Gómez B, Pedrós-Alió C (2013) Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiol Open 2:541–552

    Article  CAS  Google Scholar 

  • DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311:496–503

    Article  CAS  PubMed  Google Scholar 

  • Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM (2008) Genomic insights into Mn (II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol 74:2646–2658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duret MT, Lampitt RS, Lam P (2019) Prokaryotic niche partitioning between suspended and sinking marine particles. Environ Microbiol Rep 11:386–400

    Article  CAS  PubMed  Google Scholar 

  • Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH (2011) Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environ Microbiol Rep 3:449–458

    Article  PubMed  Google Scholar 

  • Frank AH, Garcia JA, Herndl GJ, Reinthaler T (2016) Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic deep water. Environ Microbiol 18:2052–2063

    Article  PubMed  PubMed Central  Google Scholar 

  • Ghiglione J-F, Galand PE, Pommier T, Pedrós-Alió C, Maas EW, Bakker K, Bertilson S, Kirchman DL, Lovejoy C, Yager PL (2012) Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci 109:17633–17638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghiglione JF, Mevel G, Pujo-Pay M, Mousseau L, Lebaron P, Goutx M (2007) Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea. Microb Ecol 54:217–231

    Article  CAS  PubMed  Google Scholar 

  • Grossart HP, Levold F, Allgaier M, Simon M, Brinkhoff T (2005) Marine diatom species harbour distinct bacterial communities. Environ Microbiol 7:860–873

    Article  CAS  PubMed  Google Scholar 

  • Gruber N, Friedlingstein P, Field CB, Valentini R, Heimann M, Richey JE, Romero-Lankao P, Schulze D, Chenille C-TA (2004) The vulnerability of the carbon cycle in the 21st century: an assessment of carbon-climate-human interactions. In: Field CB, Raupach MR (eds) The global carbon cycle: integrating humans, climate, and the natural world. Island Press, Washington, DC, pp 45–76

    Google Scholar 

  • Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR (2016) Plankton networks driving carbon export in the oligotrophic ocean. Nature 532:465–470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamdan LJ, Coffin RB, Sikaroodi M, Greinert J, Treude T, Gillevet PM (2013) Ocean currents shape the microbiome of Arctic marine sediments. ISME J 7:685–696

    Article  CAS  PubMed  Google Scholar 

  • Hansell DA, Carlson CA (1998) Deep-ocean gradients of dissolved organic carbon. Nature 395:263–266

    Article  CAS  Google Scholar 

  • Hansman RL, Griffin S, Watson JT, Druffel ERM, Ingalls AE (2009) The radiocarbon signature of microorganisms in the mesopelagic ocean. Proc Natl Acad Sci 106:6513–6518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herndl GJ, Reinthaler T (2013) Microbial control of the dark end of the biological pump. Nat Geosci 6:718–724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herndl GJ, Reinthaler T, Teira E, Hv A, Veth C, Pernthaler A, Pernthaler J (2005) Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol 71:2303–2309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hewson I, Steele JA, Capone DG, Fuhrman JA (2006) Remarkable heterogeneity in meso- and bathypelagic bacterioplantkon assemblage composition. Limnol Oceanogr 51:1274–1283

    Article  Google Scholar 

  • Hügler M, Sievert SM (2011) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annu Rev Mar Sci 3:261–289

    Article  Google Scholar 

  • Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM, Pearson A (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci 103:6442–6447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ivars-Martínez E, Martín-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F (2008) Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J 2:1194–1212

    Article  PubMed  CAS  Google Scholar 

  • Jensen PR, Lauro FM (2008) An assessment of actinobacterial diversity in the marine environment. Ant Leeuwenhoek 94:51–62

    Article  CAS  Google Scholar 

  • Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442–453

    Article  CAS  PubMed  Google Scholar 

  • Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510

    Article  CAS  PubMed  Google Scholar 

  • Kirchman DL (2002) The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91–100

    CAS  PubMed  Google Scholar 

  • Kirchman DL, Ducklow HW (1993) Estimating conversion factors for thymidine and leucine methods for measuring bacterial production. In: Kemp PF, Sherr BF, Sherr EB, Cole JJ (eds) Handbook of methods in aquatic microbial ecology. Lewis Publishers, Boca Raton, pp 513–517

    Google Scholar 

  • Kirchman DL, Elifantz H, Dittel AI, Malmstrom RR, Cottrell MT (2007) Standing stock and activity of archaea and bacteria in the western Arctic Ocean. Limnol Oceanogr 52:495–507

    Article  CAS  Google Scholar 

  • Könneke M, Bernhard AE, JRDL T, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546

    Article  PubMed  CAS  Google Scholar 

  • 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:e00413–e00417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lauro F, Bartlett DH (2008) Prokaryotic lifestyles in deep sea habitats. Extremophiles 12:15–25

    Article  PubMed  Google Scholar 

  • Libes SM (1992) An introduction to marine biogeochemistry. Wiley, New York

    Google Scholar 

  • Longhurst A (1998) Ecological geography of the sea. Academic Press, San Diego

    Google Scholar 

  • Maas AE, Liu S, Bolaños LM, Widner B, Parsons RJ, Kujawinski EB, Blanco Bercial L, Carlson CA (2020) Migratory zooplankton excreta and its influence on prokaryotic communities. Front Mar Sci 7:1014

    Article  Google Scholar 

  • Maixner F, Wagner M, Lücker S, Pelletier E, Schmitz-Esser S, Hace K, Spieck E, Konrat R, Le Paslier D, Daims H (2008) Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ‘Candidatus Nitrospira defluvii’. Environ Microbiol 10:3043–3056

    Article  CAS  PubMed  Google Scholar 

  • Martín-Cuadrado AB, López-García R, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodriguez-Valera F (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One 2:e914

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • 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. Nature Microbiol 2:1367–1373

    Article  CAS  Google Scholar 

  • Mestre M, Höfer J, Sala MM, Gasol JM (2020) Seasonal variation of bacterial diversity along the marine particulate matter continuum. Front Microbiol 11:1590

    Article  PubMed  PubMed Central  Google Scholar 

  • Mestre M, Ruiz-González C, Logares R, Duarte CM, Gasol JM, Sala MM (2018) Sinking particles promote vertical connectivity in the ocean microbiome. Proc Natl Acad Sci 115:E6799–E6807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miki T, Yokokawa T, Nagata T, Yamamura N (2008) Immigration of prokaryotes to local environments enhances remineralization efficiency of sinking particles: a metacommunity model. Mar Ecol Progr Ser 366:1–14

    Article  CAS  Google Scholar 

  • Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806–810

    Article  CAS  PubMed  Google Scholar 

  • Nagata T, Tamburini C, Arístegui J, Baltar F, Bochdansky AB, Fonda-Umani S, Fukuda H, Gogou A, Hansell DA, Hansman RL (2010) Emerging concepts on microbial processes in the bathypelagic ocean–ecology, biogeochemistry, and genomics. Deep Sea Res Pt II: Top Stud Oceanogr 57:1519–1536

    Article  CAS  Google Scholar 

  • Needham DM, Fuhrman JA (2016) Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nature Microbiol 1:1–7

    Article  CAS  Google Scholar 

  • Nunoura T, Takaki Y, Hirai M, Shimamura S, Makabe A, Koide O, Kikuchi T, Miyazaki J, Koba K, Yoshida N (2015) Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on earth. Proc Natl Acad Sci 112:E1230–E1236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Onyenwoke RU, Brill JA, Farahi K, Wiegel J (2004) Sporulation genes in members of the low G+C gram-type-positive phylogenetic branch (Firmicutes). Arch Microbiol 182:182–192

    Article  CAS  PubMed  Google Scholar 

  • Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358:1046–1051

    Article  CAS  PubMed  Google Scholar 

  • Parada AE, Fuhrman JA (2017) Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. ISME J 11:2510–2525

    Article  PubMed  PubMed Central  Google Scholar 

  • Poff KE, Leu AO, Eppley JM, Karl DM, DeLong EF (2021) Microbial dynamics of elevated carbon flux in the open ocean’s abyss. Proc Natl Acad Sci 118:E2018269118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quince C, Curtis TP, Sloan WT (2008) The rational exploration of microbial diversity. ISME J 2:997–1006

    Article  CAS  PubMed  Google Scholar 

  • Reinthaler T, van Aken HM, Herndl GJ (2010) Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic's interior. Deep Sea Res Pt II: Top Stud Oceanogr 57:1572–1580

    Article  CAS  Google Scholar 

  • Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Genome Biol 5:R90

    Article  PubMed  PubMed Central  Google Scholar 

  • Ruiz-González C, Mestre M, Estrada M, Sebastián M, Salazar G, Agustí S, Moreno-Ostos E, Reche I, Álvarez-Salgado XA, Morán XAG (2020) Major imprint of surface plankton on deep ocean prokaryotic structure and activity. Mol Ecol 29:1820–1838

    Article  PubMed  CAS  Google Scholar 

  • Salazar G, Cornejo-Castillo FM, Benítez-Barrios V, Fraile-Nuez E, Álvarez-Salgado XA, Duarte CM, Gasol JM, Acinas SG (2016) Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME J 10:596–608

    Article  PubMed  Google Scholar 

  • Salazar G, Cornejo-Castillo FM, Borrull E, Díez-Vives C, Lara E, Vaqué D, Arrieta JM, Duarte CM, Gasol JM, Acinas SG (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol 24:5692–5706

    Article  PubMed  Google Scholar 

  • Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H-J, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S (2019) Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179:1068–1083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santoro AE, Richter RA, Dupont CL (2019) Planktonic marine archaea. Annu Rev Mar Sci 11:131–158

    Article  Google Scholar 

  • Sintes E, Bergauer K, De Corte D, Yokokawa T, Herndl GJ (2013) Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean. Environ Microbiol 15:1647–1658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sintes E, De Corte D, Haberleitner E, Herndl GJ (2016) Geographic distribution of archaeal ammonia oxidizing ecotypes in the Atlantic Ocean. Front Microbiol 7:77

    Article  PubMed  PubMed Central  Google Scholar 

  • Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the under-explored "rare biosphere". Proc Natl Acad Sci 103:12115–12120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sorokin DY (2003) Oxidation of inorganic sulfur compounds by obligately organotrophic bacteria. Microbiology 72:641–653

    Article  CAS  Google Scholar 

  • Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, Rockhold ML, Konopka A (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7:2069–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Stegen JC, Lin X, Konopka AE, Fredrickson JK (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6:1653–1664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steiner PA, Betel J, Fadeev E, Obiol A, Sintes E, Rattei T, Herndl GJ (2020) Functional seasonality of free-living and particle-associated prokaryotic communities in the coastal Adriatic Sea. Front Microbiol 11:2875

    Article  Google Scholar 

  • Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F (2020) Tara oceans: towards global ocean ecosystems biology. Nature Rev Microbiol 18:428–445

    Article  CAS  Google Scholar 

  • Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A (2015) Structure and function of the global ocean microbiome. Science 348:1261359

    Article  PubMed  CAS  Google Scholar 

  • Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R (2011) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300

    Article  CAS  PubMed  Google Scholar 

  • Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW (2013) Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci 110:11463–11468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teira E, Lebaron P, Hv A, Herndl GJ (2006) Distribution and activity of bacteria and archaea in the deep water masses of the North Atlantic. Limnol Oceanogr 51:2131–2144

    Article  CAS  Google Scholar 

  • Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ (2014) Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J 8:1440–1451

    Article  PubMed  CAS  Google Scholar 

  • Varela M, van Aken HM, Sintes E, Herndl GJ (2008) Latitudinal trends of Crenarchaeota and bacteria in the meso- and bathypelagic water masses of the eastern North Atlantic. Environ Microbiol 10:110–124

    CAS  PubMed  Google Scholar 

  • Wagner M, Horn M (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17:241–249

    Article  CAS  PubMed  Google Scholar 

  • Wenley J, Currie K, Lockwood S, Thomson B, Baltar F, Morales SE (2021) Seasonal prokaryotic community linkages between surface and deep ocean water. Front Mar Sci 659641

    Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95:6578–6583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilkins D, Van Sebille E, Rintoul SR, Lauro FM, Cavicchioli R (2013) Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects. Nature Comm 4:1–7

    Article  CAS  Google Scholar 

  • Woebken D, Teeling H, Wecker P, Dumitriu A, Kostadinov I, DeLong EF, Amann R, Glöckner FO (2007) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J 1:419–435

    Article  CAS  PubMed  Google Scholar 

  • Wuchter C, Herfort L, Coolen MJL, Abbas B, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Damsté JSS (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci 103:12317–12322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. J Med Microbiol 53:1155–1163

    CAS  Google Scholar 

  • Zhang Y, Qin W, Hou L, Zakem EJ, Wan X, Zhao Z, Liu L, Hunt KA, Jiao N, Kao S-J (2020) Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proc Natl Acad Sci 117:4823–4830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao Z, Baltar F, Herndl GJ (2020) Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Sci Adv 6:eaaz4354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

GJH was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21), the projects I486-B09 and P23234-B11, and by the European Research Council (ERC) under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 268595 (MEDEA project). FB was supported by the Austrian Science Fund (FWF) project OCEANIDES (P34304-B), by a University of Otago Research Grant and a Rutherford Discovery Fellowship (Royal Society of New Zealand).

Author information

Authors and Affiliations

  1. Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria

    Federico Baltar & Gerhard J. Herndl

  2. NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Texel, The Netherlands

    Gerhard J. Herndl

Authors
  1. Federico Baltar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gerhard J. Herndl
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Federico Baltar .

Editor information

Editors and Affiliations

  1. Department of Freshwater and Marine Ecology – IBED, University of Amsterdam, Amsterdam, The Netherlands

    Lucas J. Stal

  2. University of Utrecht, Utrecht, The Netherlands

    Mariana Silvia Cretoiu

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Baltar, F., Herndl, G.J. (2022). Microbial Inhabitants of the Dark Ocean. 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_10

Download citation

Publish with us

Policies and ethics

Search

Navigation