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A Sea of Microbes: What’s So Special about Marine Microbiology

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The Marine Microbiome

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

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Abstract

This chapter investigates what justifies marine microbiology as a discipline in its own right. Do marine microorganisms really exist? And if so, what distinguishes them from freshwater- or terrestrial microorganisms, or from microorganisms living in any other specialized habitat? The marine environment—particularly the ocean—is the largest continuous habitat on Earth. This makes the ocean different in terms of scale and sharing space and nutrients, as well as in terms of the distribution, dispersal, and encounters of microorganisms that inhabit it. The ocean comprises a large variety of confined sub-habitats. It has an impact on the function of the planet Earth as a whole. A critical property of seawater is that it contains a large amount of salt and that this requires microorganisms that live in it are able to adjust their osmotic pressure. The marine microbiome is composed of the three domains of life: bacteria, archaea, and eukarya, as well as viruses, all of which in dazzling numbers and diversity. All of the known microbial lineages are represented and many are exclusively found in the ocean and there is little doubt that life originated in the ocean.

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References

  • Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nature Rev Microbiol 6:431–440

    Article  CAS  Google Scholar 

  • Amaral-Zettler L, Artigas LF, Baross J, Bharathi PAL, Boetius A, Chandramohan D, Herndl G, Kogure K, Neal P, Pedrós-Alió C, Ramette A, Schouten S, Stal L, Thessen A, de Leeuw J, Sogin M (2010) A global census of marine microbes. In: McIntyre AD (ed) Life in the World’s Oceans. Blackwell, Oxford, pp 223–245

    Google Scholar 

  • Arrieta JM, Mayol E, Hansman RL, Herndl GJ, Dittmar T, Duarte CM (2015) Dilution limits dissolved organic carbon utilization in the deep ocean. Science 348:331–333

    Article  CAS  PubMed  Google Scholar 

  • Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F (1983) The ecological role of water-column microbes in the sea. Mar Ecol Progr Ser 10:257–263

    Article  Google Scholar 

  • Baas Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. WP van Stockum & Zoon NV, Den Haag, p 263

    Google Scholar 

  • Barker HA (1939) Studies upon the methane fermentation. IV. The isolation and culture of Methanobacterium omelianskii. Ant Leeuwenhoek 6:201–220

    Article  Google Scholar 

  • Behrenfeld MJ, Falkowski PG (1997) Photosynthetic rates derived from satellite-based chlorophyll concentration. Limnol Oceanogr 42:1–20

    Article  CAS  Google Scholar 

  • Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902–1906

    Article  PubMed  Google Scholar 

  • Bergh Ø, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467–468

    Article  CAS  PubMed  Google Scholar 

  • Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ (2013) Trichodesmium – a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol Rev 37:286–302

    Google Scholar 

  • Birch J (2018) Collecting and processing samples in remote and dangerous places: the environmental sample processor as a case study. Pure Appl Chem 90:1625–1630

    Article  CAS  Google Scholar 

  • Blomqvist S, Gunnars A, Elmgren R (2005) Why the limiting nutrient differs between temperate coastal seas and freshwater lakes: a matter of salt. Limnol Oceanogr 49:2236–2241

    Article  Google Scholar 

  • Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O (2000) Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities. Nature 407:623–626

    Article  CAS  PubMed  Google Scholar 

  • Bolhuis H, Severin I, Confurius-Guns V, Wollenzien UIA, Stal LJ (2010) Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes. ISME J 4:121–130

    Article  CAS  PubMed  Google Scholar 

  • Bremer E, Krämer R (2019) Responses of microorganisms to osmotic stress. Ann Rev Microbiol 73:313–334

    Article  CAS  Google Scholar 

  • Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Rev Microbiol 6:245–252

    Article  CAS  Google Scholar 

  • Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch Mikrobiol 59:20–31

    Google Scholar 

  • Canfield DE (2015) Baas Becking’s Geobiology – or introduction to environmental science. Wiley Blackwell, Oxford, p 152

    Google Scholar 

  • Canfield DE, Glazer AN, Falkowski PG (2010) The evolution and future of Earth’s nitrogen cycle. Science 330:192–196

    Article  CAS  PubMed  Google Scholar 

  • Chapra SC, Dove A, Warren GJ (2012) Long-term trends of Great Lakes major ion chemistry. J Great Lakes Res 38:550–560

    Article  CAS  Google Scholar 

  • Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA (1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340–343

    Article  Google Scholar 

  • Claustre H, Johnson KS, Takeshita Y (2020) Observing the global ocean with biogeochemical-Argo. Annu Rev Mar Sci 12:23–48

    Article  Google Scholar 

  • Cohen Y, Krumbein WE, Goldberg M, Shilo M (1977) Solar Lake (Sinai). 1. Physical and chemical limnology. Limnol Oceanogr 22:597–608

    Article  CAS  Google Scholar 

  • Coles VJ, Wilson C, Hood RR (2004) Remote sensing of new production fuelled by nitrogen fixation. Geophys Res Lett 31:L06301

    Article  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Monte S, Soccodato A, Alvain S, d’Ovidio F (2013) Can we detect oceanic biodiversity hotspots from space? ISME J 7:2054–2056

    Article  PubMed  PubMed Central  Google Scholar 

  • De Wit R, Bouvier T (2006) ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Env Microbiol 8:755–758

    Article  Google Scholar 

  • del Giorgio PA, Cole JJ, Cimbleris A (1997) Respiration rates in bacteria exceed phytoplankton production in unproductive aquatic systems. Nature 385:148–151

    Article  Google Scholar 

  • Dubos R (1974) Pasteur’s dilemma – the road not taken. ASM News 40:703–709

    Google Scholar 

  • Ducklow HW (1983) Production and fate of bacteria in the oceans. BioSciences 33:494–501

    Article  Google Scholar 

  • Dugdale RC, Menzel DW, Ryther JH (1961) Nitrogen fixation in the Sargasso Sea. Deep-Sea Res 7:297–300

    CAS  Google Scholar 

  • Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Zeigler Allen L, Ekman M, Lucas AJ, Hagström A, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B (2014) Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One 9(2):e89549

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73:25–33

    Article  CAS  PubMed  Google Scholar 

  • Edgcomb VP, Bernhard JM, Summons RE, Orsi W, Beaudoin D, Visscher PT (2014) Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia. ISME J 8:418–429

    Article  CAS  PubMed  Google Scholar 

  • Falkowski PG (1997) Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature 387:272–274

    Article  CAS  Google Scholar 

  • Falkowski PG, Davis CS (2004) Natural proportions. Redfield ratios: the uniformity of elemental ratios in the oceans and the life they contain underpins our understanding of marine biogeochemistry. Nature 431:131

    Article  CAS  PubMed  Google Scholar 

  • Farnelid H, Andersson AF, Bertilsson S, Al-Soud WA, Hansen LH, Sørensen S, Steward GF, Hagström A, Riemann L (2011) Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS One 6(4):e19223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240

    Article  CAS  PubMed  Google Scholar 

  • Fischer B (1894) Die Bakterien des Meeres. Verlag von Lipsius & Tischer, Kiel und Leipzig, p 82

    Google Scholar 

  • Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, Karl DM, Li WKW, Lomas MW, Veneziano D, Vera CS, Vrugt JA, Martiny AC (2013) Present and future global distributions of the marine cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci U S A 110:9824–9829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Foster RA, Zehr JP (2019) Diversity, genomics, and distribution of phytoplankton-cyanobacterium single-cell symbiotic associations. Ann Rev Microbiol 73:435–456

    Article  CAS  Google Scholar 

  • Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149

    Article  CAS  PubMed  Google Scholar 

  • Gaucher EA, Thomson JM, Burgan MF, Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425:285–288

    Article  CAS  PubMed  Google Scholar 

  • Geider RJ (1997) Photosynthesis or planktonic respiration? Nature 388:132–133

    Article  CAS  Google Scholar 

  • Ghai R, Megumi Mizuno C, Picazo A, Camacho A, Rodriguez-Valera F (2013) Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Sci Rep 3:2471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D (2012) Defining seasonal marine microbial community dynamics. ISME J 6:298–308

    Article  CAS  PubMed  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    Article  CAS  PubMed  Google Scholar 

  • Grasshoff K, Voipio A (1981) Chemical oceanography. In: Voipio A (ed) The Baltic Sea. Elsevier Scientific Publishing Company, Amsterdam, pp 183–218. 418 pp

    Chapter  Google Scholar 

  • Grimes DJ (2006) Koch’s postulates – then and now. Microbe 1:223–228

    Google Scholar 

  • Gruber N, Sarmiento JL (1997) Global patterns of marine nitrogen fixation and denitrification. Glob Biogeochem Cyc 11:235–266

    Article  CAS  Google Scholar 

  • Hagström Å, Azam F, Wikner J, Rassoulzadegan F (1988) Microbial loop in an oligotrophic pelagic marine ecosystem: possible roles of cyanobacteria and nanoflagellates in the organic fluxes. Mar Ecol Progr Ser 49:171–178

    Article  Google Scholar 

  • Hagström Å, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Env Microbiol 68:3628–3633

    Article  CAS  Google Scholar 

  • Harris HMB, Hill C (2021) A place for viruses on the tree of life. Front Microbiol 11:604048

    Article  PubMed  PubMed Central  Google Scholar 

  • Haverkamp THA, Schouten D, Doeleman M, Wollenzien U, Huisman J, Stal LJ (2009) Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea. The ISME J 3:397–408

    Article  CAS  PubMed  Google Scholar 

  • Hecky RE, Campbell P, Hendzel LL (1993) The stoichiometry of carbon, nitrogen, and phosphorus in particulate matter of lakes and oceans. Limnol Oceanogr 38:709–724

    Article  CAS  Google Scholar 

  • Heip CHR, Goosen NK, Herman PMJ, Kromkamp J, Middelburg JJ, Soetaert K (1995) Production and consumption of biological particles in temperate tidal estuaries. Oceanogr Mar Biol Ann Rev 33:1–149

    Google Scholar 

  • Henderson LJ (1913) The fitness of the environment. An inquiry into the biological significance of the properties of matter. MacMillan, New York, p 317

    Google Scholar 

  • Herbert D, Elsworth R, Telling RC (1956) The continuous culture of bacteria; a theoretical and experimental study. J Gen Microbiol 14:601–622

    Article  CAS  PubMed  Google Scholar 

  • Hobbie JE, Daley RJ, Jasper S (1977) Use of nucleopore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33:1225–1228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howarth RW, Cole JJ (1985) Molybdenum availability, nitrogen limitation and phytoplankton growth in natural waters. Science 229:653–655

    Article  CAS  PubMed  Google Scholar 

  • Hutchinson GE (1961) The paradox of the plankton. Am Nat 95:137–145

    Article  Google Scholar 

  • Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K (2020) Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577:519–525

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jannasch HW, Jones A (1959) Bacterial populations in sea water as determined by different methods of enumeration. Limnol Oceanogr 4:128–139

    Article  Google Scholar 

  • Jetten MSM, Sliekers O, Kuypers M, Dalsgaard T, van Niftrik L, Cirpus I, van de Pas-Schoonen K, Lavik G, Thamdrup B, Le Paslier D, Op den Camp HJM, Hulth S, Nielsen LP, Abma W, Third K, Engström J, Kuenen JG, Jørgensen BB, Canfield DE, Sinninghe Damsté JS, Revsbech NP, Fuerst J, Weissenbach J, Wagner M, Schmidt I, Schmid M, Strous M (2003) Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria. Appl Microbiol Biotechnol 63:107–114

    Article  CAS  PubMed  Google Scholar 

  • Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PLOS Biol 5(3):e17

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Karl DM (2001) A sea of microbes. Trends Microbiol 9:44–45

    Article  CAS  Google Scholar 

  • Karl DM, Proctor LM (2007) Foundations of microbial oceanography. Oceanography 20:16–27

    Article  Google Scholar 

  • Kirchman DL (2000) Microbial ecology of the oceans. Wiley-Liss, Hoboken, NJ, p 542

    Google Scholar 

  • Kirchman DL (2008) Microbial ecology of the oceans. Wiley-Liss, Hoboken, NJ, p 593

    Book  Google Scholar 

  • Kirsch F, Klähn S, Hagemann M (2019) Salt-regulated accumulation of the compatible solutes sucrose and glucosylglycerol in cyanobacteria and its biotechnological potential. Front Microbiol 10:2139

    Article  PubMed  PubMed Central  Google Scholar 

  • Knauth LP (2005) Temperature and salinity history of the Precambrian Ocean: implications for the course of microbial evolution. Palaeogr Palaeoclimat Palaeoecol 219:53–69

    Article  Google Scholar 

  • Koch R (1884) Die Aetiologie der Tuberkulose. Mitt Kaiserl Ges 2:1–88

    Google Scholar 

  • Koeve W, Kähler P (2010) Balancing Ocean nitrogen. Nat Geosci 3:383–384

    Article  CAS  Google Scholar 

  • Kolber ZS, Plumley FG, Lang AS, Beatty JT, Blankenship RE, VanDover CL, Vetriani C, Koblizek M, Rathgeber C, Falkowski PG (2001) Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492–2495

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Kopf A et al (2015) The ocean sampling day consortium. GigaScience 4:27

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Paul D, Bhushan B, Wakchaure GC, Meena KK, Shouche Y (2020) Traversing the “Omic” landscape of microbial halotolerance for key molecular processes and new insights. Crit Rev Microbiol 46:631–653

    Article  CAS  PubMed  Google Scholar 

  • Kuypers MMM, Sliekers AO, Lavik G, Schmid M, Jørgensen BB, Kuenen JG, Sinninghe Damste JS, Strous M, Jetten MSM (2003) Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608–611

    Article  CAS  PubMed  Google Scholar 

  • Langlois RJ, Mills MM, Ridame C, Croot P, LaRoche J (2012) Diazotrophic bacteria respond to Saharan dust additions. Mar Ecol Progr Ser 470:1–14

    Article  CAS  Google Scholar 

  • Langlois RJ, Großkopf T, Mills M, Takeda S, LaRoche J (2015) Widespread distribution and expression of gamma a (UMB), an uncultured, diazotrophic, γ-proteobacterial nifH phylotype. PLoS One 10(6):e0128912

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee SH, Malone C, Kemp PF (1993) Use of multiple 16S rRNA-targeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria. Mar Ecol Progr Ser 101:193–201

    Article  CAS  Google Scholar 

  • Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K (2009) Infrequent marine–freshwater transitions in the microbial world. Trends Microbiol 17:414–422

    Article  CAS  PubMed  Google Scholar 

  • Logares R, Deutschmann IM, Junger PC, Giner CR, Krabberød AK, Schmidt TSB, Rubinat-Ripoll L, Mestre M, Salazar G, Ruiz-González C, Sebastián M, de Vargas C, Acinas SG, Duarte CM, Gasol JM, Massana R (2020) Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome 8:55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacLeod RA (1965) The question of the existence of specific marine bacteria. Bact Rev 29:9–23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacLeod RA (1985) Marine microbiology far from the sea. Ann Rev Microbiol 39:1–20

    Article  CAS  Google Scholar 

  • MacLeod RA (1986) Salt requirements for membrane transport and solute retention in some moderate halophiles. FEMS Microbiol Rev 39:109–113

    Article  CAS  Google Scholar 

  • Margulis L (1992) Biodiversity: molecular biological domains, symbiosis and kingdom origins. Biosystems 27:39–51

    Article  CAS  PubMed  Google Scholar 

  • Martiny AC, Pham CTA, Primeau FW, Vrugt JA, Moore JK, Levin SA, Lomas MW (2013) Strong latitudinal patterns in the elemental ratios of marine plankton and organic matter. Nat Geosci 6:279–283

    Article  CAS  Google Scholar 

  • Massana R, Guillou L, Díez B, Pedrós-Alió C (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Env Microbiol 68:4554–4558

    Article  CAS  Google Scholar 

  • Mayol E, Arrieta JM, Jiménez MA, Martínez-Asensio A, Garcias-Bonet N, Dachs J, González-Gaya B, Royer S-J, Benítez-Barrios VM, Fraile-Nuez E, Duarte CM (2017) Long-range transport of airborne microbes over the global tropical and subtropical ocean. Nature Comm 8:201

    Article  CAS  Google Scholar 

  • Merlino G, Barozzi A, Michoud G, Ngugi DK, Daffonchio D (2018) Microbial ecology of deep-sea hypersaline anoxic basins. FEMS Microbiol Ecol 94:fiy085

    Article  CAS  Google Scholar 

  • Middelburg JJ, Levin LA (2009) Coastal hypoxia and sediment biogeochemistry. Biohgeosciences 6:1273–1293

    Article  CAS  Google Scholar 

  • Millero FJ, Feistel R, Wright DG, McDougall TJ (2008) The composition of standard seawater and the definition of the reference-composition salinity scale. Deep-Sea Res I 55:50–72

    Article  Google Scholar 

  • Mills MM, Arrigo KR (2010) Magnitude of oceanic nitrogen fixation influenced by the nutrient uptake ratio of phytoplankton. Nat Geosci 3:412–416

    Article  CAS  Google Scholar 

  • Moisander PH, Beinart RA, Hewson I, White AE, Johnson KS, Carlson DJ, Montoya JP, Zehr JP (2010) Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327:1512–1514

    Article  CAS  PubMed  Google Scholar 

  • Moisander PH, Serros TRC, Paerl RW, Beinart RA, Zehr JP (2014) Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean. ISME J 8:1962–1973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394

    Article  CAS  Google Scholar 

  • Moran MA (2015) The global ocean microbiome. Science 350:aac8455

    Article  PubMed  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 

  • Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C (2013) Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 37:384–406

    Article  CAS  PubMed  Google Scholar 

  • Nissenbaum A (1975) The microbiology and biogeochemistry of the Dead Sea. Microb Ecol 2:139–161

    Article  CAS  PubMed  Google Scholar 

  • Oren A (2009) Saltern evaporation ponds as model systems for the study of primary production processes under hypersaline conditions. Aq Microb Ecol 56:193–204

    Article  Google Scholar 

  • Ottensen EA, Young CR, Eppley JM, Ryan JP, Chavez FP, Scholin CA, DeLong EF (2013) Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci 110:E488–E497

    Google Scholar 

  • Overmann J, van Gemerden H (2000) Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities. FEMS Microbiol Rev 24:591–599

    Article  CAS  PubMed  Google Scholar 

  • Pace NR (2006) Time for a change. Nature 441:289–289

    Article  CAS  PubMed  Google Scholar 

  • Pace NR (2009) It’s time to retire the prokaryote. Microbiol Today 5:85–87

    Google Scholar 

  • Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J (2003) The genome of a motile marine Synechococcus. Nature 424:1037–1042

    Article  CAS  PubMed  Google Scholar 

  • Paul J, Scholin C, van den Engh G, Perry MJ (2007) In situ instrumentation. Oceanography 20:70–78

    Article  Google Scholar 

  • Paulmier A, Ruiz-Pino D (2009) Oxygen minimum zones (OMZs) in the modern ocean. Progr Oceanogr 80:113–128

    Article  Google Scholar 

  • Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257–263

    Article  PubMed  CAS  Google Scholar 

  • Planavsky NJ (2014) The elements of marine life. Nat Geosci 7:855–856

    Article  CAS  Google Scholar 

  • Platt T, Subba Rao DV, Irwin B (1983) Photosynthesis of picoplankton in the oligotrophic ocean. Nature 301:702–704

    Article  CAS  Google Scholar 

  • Pomeroy LR (1974) The ocean’s food web, a changing paradigm. Bioscience 24:499–504

    Article  Google Scholar 

  • Proctor LM, Karl DM (2007) A sea of microbes. Introduction Oceanography 20:14–15

    Google Scholar 

  • Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  PubMed  CAS  Google Scholar 

  • Rathgeber C, Beatty JT, Yurkov V (2004) Aerobic phototrophic bacteria: new evidence for the diversity, ecological importance and applied potential of this previously overlooked group. Photosynthesis Res 81:113–128

    Article  CAS  Google Scholar 

  • Redfield AC (1934) On the proportions of organic derivatives in sea water and their relation to the composition of plankton. In: James Johnstone memorial volume. University Press of Liverpool, Liverpool, pp 176–192

    Google Scholar 

  • Redfield AC (1958) The biological control of chemical factors in the environment. Am Sci 46:205–221

    CAS  Google Scholar 

  • Rijkenberg MJA, Powell CF, Dall’Osto D, Nielsdottir MC, Patey MD, Hill PG, Baker AR, Jickells TD, Harrison RM, Achterberg EP (2008) Changes in iron speciation following a Saharan dust event in the tropical North Atlantic Ocean. Mar Chem 110:56–67

    Article  CAS  Google Scholar 

  • Riley MA, Lizotte-Waniewski M (2009) Population genomics and the bacterial species concept. Meth Mol Biol 532:367–377

    Article  CAS  Google Scholar 

  • Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  PubMed  Google Scholar 

  • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers Y-H, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The sorcerer II global ocean sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLOS Biol 5(3):e77

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bact 173:4371–4378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schreiber UC, Mayer C (2020) The first cell. Springer, Cham, Switzerland, p 178

    Book  Google Scholar 

  • Schulz HN, Jørgensen BB (2001) Big bacteria. Ann Rev Microbiol 55:105–137

    Article  CAS  Google Scholar 

  • Schunck H, Lavik G, Desai DK, Großkopf T, Kalvelage T, Löscher CR, Paulmier A, Contreras S, Siegel H, Holtappels M, Rosenstiel P, Schilhabel MB, Graco M, Schmitz RA, Kuypers MMM, LaRoche J (2013) Giant hydrogen sulfide plume in the oxygen minimum zone off Peru supports chemolithoautotrophy. PLoS One 8(8):e68661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schut F, Jansen M, Gomes TMP, Gottschal JC, Harder W, Prins RA (1995) Substrate uptake and utilization by a marine ultramicrobacterium. Microbiology 141:351–361

    Article  CAS  PubMed  Google Scholar 

  • Severin I, Stal LJ (2008) Light dependency of nitrogen fixation in a coastal cyanobacterial mat. ISME J 2:1077–1088

    Article  CAS  PubMed  Google Scholar 

  • Shanks AL, Reeder ML (1993) Reducing microzones and sulfide production in marine snow. Mar Ecol Progr Ser 96:43–47

    Article  Google Scholar 

  • Sherr EB, Sherr BF (1996) Temporal offset in oceanic production and respiration processes implied by seasonal changes in atmospheric oxygen: the role of heterotrophic microbes. Aq Microb Ecol 11:91–100

    Article  Google Scholar 

  • Smith RC, Baker KS (1982) Oceanic chlorophyll concentrations as determined by satellite (Nimbus-7 coastal zone color scanner). Mar Biol 66:269–279

    Article  Google Scholar 

  • Smriga S, Fernandez VI, Mitchell JG, Stocker R (2016) Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria. Proc Natl Acad Sci U S A 113:1576–1581

    Article  CAS  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 underexplored “rare biosphere”. Proc Natl Acad Sci U S A 193:12115–12120

    Article  CAS  Google Scholar 

  • Staal M, Meysman FJR, Stal LJ (2003) Temperature excludes N2-fixing heterocystous cyanobacteria in the tropical oceans. Nature 425:504–507

    Article  CAS  PubMed  Google Scholar 

  • Staal M, te Lintel HS, Brummer GJ, Veldhuis M, Sikkens C, Persijn S, Stal LJ (2007) Nitrogen fixation along a north-south transect in the eastern Atlantic Ocean. Limnol Oceanogr 52:1305–1316

    Article  CAS  Google Scholar 

  • Stal LJ (2009) Is the distribution of nitrogen-fixing cyanobacteria in the oceans related to temperature? Env Microbiol 11:1632–1645

    Article  CAS  Google Scholar 

  • Stal LJ, Cretoiu MS (eds) (2016) The marine microbiome. An untapped source of biodiversity and biotechnological potential. Springer, Switzerland, p 498

    Google Scholar 

  • Stal LJ, Walsby AE (2000) Photosynthesis and nitrogen fixation in a cyanobacterial bloom in the Baltic Sea. Eur J Phycol 35:97–108

    Article  Google Scholar 

  • Stal LJ, Staal M, Villbrandt M (1999) Nutrient control of cyanobacterial blooms in the Baltic Sea. Aq Microb Ecol 18:165–173

    Article  Google Scholar 

  • Staley JT, Konopka A (1985) Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346

    Article  CAS  Google Scholar 

  • Stanier RY (1941) Studies on marine agar-digesting bacteria. J Bact 42:527–559

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stanier RY, van Niel CB (1962) The concept of a bacterium. Arch Mikrobiol 42:17–35

    Article  CAS  PubMed  Google Scholar 

  • Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d’Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P (2015) Structure and function of the global ocean microbiome. Science 348(6237):1261359

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Suttle CA (2005) Viruses in the sea. Nature 437:356–361

    Article  CAS  PubMed  Google Scholar 

  • Thamdrup B, Dalsgaard T (2002) Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl Env Microbiol 68:1312–1318

    Article  CAS  Google Scholar 

  • They NH, Amado AM, Cotner JB (2017) Redfield ratios in inland waters: higher biological control of C:N:P ratios in tropical semi-arid high water residence time lakes. Front Microbiol 8:1505

    Article  PubMed  PubMed Central  Google Scholar 

  • Thingstad TF, Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aq Microb Ecol 13:19–27

    Article  Google Scholar 

  • Thompson AW, Foster RA, Krupke A, Carter BJ, Musat N, Vaulot D, Kuypers MMM, Zehr JP (2012) Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science 337:1546–1550

    Article  CAS  PubMed  Google Scholar 

  • Tyrrell T (1999) The relative influences of nitrogen and phosphorus on oceanic primary production. Nature 400:525–531

    Article  CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson W, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  CAS  PubMed  Google Scholar 

  • Wallmann K, Suess E, Westbrook GH, Winckler G, Cita MB (1997) Salt brines on the Mediterranean Sea floor. Nature 387:31–32

    Article  CAS  Google Scholar 

  • Watanabe K, Kasai A, Antonio ES, Suzuki K, Ueno M, Yamashita Y (2014) Influence of salt-wedge intrusion on ecological processes at lower trophic levels in the Yura estuary, Japan. Est Coast Shelf Sci 139:67–77

    Article  CAS  Google Scholar 

  • Waterbury JB, Watson SW, Guillard RRL, Brand LE (1979) Widespread occurrence of a unicellular marine planktonic cyanobacterium. Nature 277:293–293

    Article  Google Scholar 

  • Waterbury JB, Willey JM, Franks DG, Valois FW, Watson SW (1985) A cyanobacterium capable of swimming motility. Science 230:74–76

    Article  CAS  PubMed  Google Scholar 

  • Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF (2016) The physiology and habitat of the last universal common ancestor. Nat Microbiol 1:116

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilkins JS (2006) The concept and causes of microbial species. Hist Philos Life Sci 28:329–348

    Google Scholar 

  • Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Sinninghe Damsté JS (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci U S A 33:12317–12322

    Article  CAS  Google Scholar 

  • Wurl O, Bird K, Cunliffe M, Landing WM, Miller U, Mustaffa NIH, Ribas-Ribas M, Witte C, Zappa CJ (2018) Warming and inhibition of salinization at the ocean’s surface by cyanobacteria. Geophys Res Lett 45:4230–4237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia J-M, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC (2007) The sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLOS Biol 5(3):e16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zehr JP, Capone DG (2021) Marine nitrogen fixation. Springer, Cham, Switzerland, p 186

    Book  Google Scholar 

  • Zehr JP, Waterbury JB, Turner PJ, Montoya JP, Omoregie E, Steward GF, Hansen A, Karl DM (2001) Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature 412:635–638

    Article  CAS  PubMed  Google Scholar 

  • Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, Affourtit JP (2008) Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322:1110–1112

    Article  CAS  PubMed  Google Scholar 

  • Zehr JP, Shilova IN, Farnelid HM, del Carmen M-MM, Turk-Kubo K (2016) Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A. Nature Microbiol 2:16214

    Article  CAS  Google Scholar 

  • Zehr JP, Weitz JS, Joint I (2017) How microbes survive in the open ocean. Science 357:646–647

    Article  CAS  PubMed  Google Scholar 

  • Zengler K, Toledo G, Rappé M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci U S A 99:15681–15686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Ning K (2015) The Tara oceans project: new opportunities and greater challenges ahead. Genom Proteom Bioinform 13:275–277

    Article  Google Scholar 

  • Zhang Y, Kieft B, Hobson BW, Ryan JP, Barone B, Preston CM, Roman B, Raanan B-Y, Marin R III, O’Reilly TC, Rueda CA, Pargett D, Yamahara KM, Poulos S, Romano AE, Foreman G, Ramm H, Wilson ST, DeLong EF, Karl DM, Birch JM, Bellingham JG, Scholin CA (2020) Autonomous tracking and sampling of the deep chlorophyll maximum layer in an open-ocean eddy by a long-range autonomous underwater vehicle. IEEE J Ocean Eng 45:1308–1321

    Article  Google Scholar 

  • ZoBell CE (1946) Marine microbiology, a monograph on hydrobacteriology. Mass, Waltham, p 240

    Google Scholar 

  • ZoBell CE, Rittenberg SC (1938) The occurrence and characteristics of chitinoclastic bacteria in the sea. J Bact 35:275–287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Stal, L.J. (2022). A Sea of Microbes: What’s So Special about Marine Microbiology. 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_1

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