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What is so Special About Marine Microorganisms? Introduction to the Marine Microbiome—From Diversity to Biotechnological Potential

  • Henk BolhuisEmail author
  • Mariana Silvia Cretoiu
Chapter

Abstract

Marine microscopic life varies from single-celled organisms, simple multicellular, to symbiotic microorganisms encompassing all three domains of life: Bacteria, Archaea and Eukarya as well as biologically active entities such as viruses and viroids. Together they form the Ocean’s “microbiome”. Over billions of years of evolution this microbiome developed a plethora of adaptations and lifestyles and participates in the fluxes of virtually all chemical elements. The importance of the marine microbiome for human society and for the functioning of our living planet is not disputed. In this introductory chapter we bring to your attention some of the most important features of the marine microbiome and try to answer the question what distinguishes it from other microbial systems. Our main goal is to urge the reader to find more information about the taxonomic and functional diversity by exploring the specific chapters.

Keywords

Marine Bacterium Microbial Community Composition High Hydrostatic Pressure Conveyor Belt Euphotic Zone 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 311975. This publication reflects the views only of the authors, and the European Union cannot be held responsible for any use which may be made of the information contained therein.

References

  1. Alldredge AL, Cole JJ, Caron DA (1986) Production of heterotrophic bacteria inhabiting macroscopic organic aggregates (marine snow) from surface waters. Limnol Oceanogr 31:68–78CrossRefGoogle Scholar
  2. Amante C, Eakins BW (2009) ETOPO1 1 arc-minute global relief model: procedures, data sources and analysis. National Oceanic and Atmospheric Administration (NOAA) Technical Memorandum NESDIS NGDC-24, p 19Google Scholar
  3. Arrigo KR (2005) Marine microorganisms and global nutrient cycles. Nature 437:349–355CrossRefPubMedGoogle Scholar
  4. Arrigo KR, Robinson DH, Worthen DL, Robert B. Dunbar RB, DiTullio GR, van Woert M, Lizotte MP (1999) Phytoplankton community structure and the drawdown of nutrients and CO2 in the Southern Ocean. Science 283:365–367Google Scholar
  5. 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 Prog Ser 10:257–263CrossRefGoogle Scholar
  6. Bolhuis H, Cretoiu MS, Stal LJ (2014) Molecular ecology of microbial mats. FEMS Microbiol Ecol 90:335–350PubMedGoogle Scholar
  7. Brown RD, Mote W (2009) The response of northern hemisphere snow cover to a changing climate. J Clim 22:2124–2145CrossRefGoogle Scholar
  8. Cai F, Axen SD, Kerfeld CA (2013) Evidence for the widespread distribution of CRISPR-Cas system in the phylum cyanobacteria. RNA Biol 10(5):687–693CrossRefPubMedPubMedCentralGoogle Scholar
  9. Caron DA (1987) Grazing of attached bacteria by heterotrophic microflagellates. Microb Ecol 13:203–218CrossRefPubMedGoogle Scholar
  10. Cartwright DE (2000) Tides: a scientific history. Cambridge University Press, p 243Google Scholar
  11. Charette MA, Smith WHF (2010) The volume of Earth’s ocean. Oceanography 23(2):104–106CrossRefGoogle Scholar
  12. Comte J, Lindstrom ES, Eiler A, Langenheder S (2014) Can marine bacteria be recruited from freshwater sources and the air? ISME J 8:2423–2430CrossRefPubMedPubMedCentralGoogle Scholar
  13. D’Hondt S, Inagaki F, Zarikian CA, Abrams LJ, Dubois N, Engelhardt T, Evans H, Ferdelman T, Gribsholt B, Harris RN, Hoppie BW et al (2015) Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments. Nat Geosci 8:299–304CrossRefGoogle Scholar
  14. Daffonchio D, Borin S, Brusa T, Brusetti L, van der Wielen PWJJ, Bolhuis H, Yakimov MM, D’Auria G, Giuliano L et al (2006) Stratified prokaryote network in the oxic–anoxic transition of a deep-sea halocline. Nature 440:203–207CrossRefPubMedGoogle Scholar
  15. Debnath M, Paul AK, Bisen PS (2007) Natural bioactive compounds and biotechnological potential of marine bacteria. Curr Pharm Biotechnol 8:253–260CrossRefPubMedGoogle Scholar
  16. Drinkwater KF (2006) The regime shift of the 1920s and 1930s in the North Atlantic. Prog Oceanogr 68:134–151CrossRefGoogle Scholar
  17. Dyurgerov MB, Meier MF (2005) Glaciers and the changing earth system: a 2004 snapshot. Occasional Paper No. 55, INSTAAR, University of ColoradoGoogle Scholar
  18. Elvert M, Greinert J, Suess E, Whiticar MJ (2000) Archaea mediating anaerobic methane oxidation in deep-sea sediments at cold seeps of the eastern aleutian subduction zone. Org Geochem 31:1175–1187CrossRefGoogle Scholar
  19. European Commission Seventh Framework Programme—Marine Biotechnology ERA-NET (2014) Marine study in support of impact assessment work on blue biotechnologyGoogle Scholar
  20. Falkowski PG (2000) Rationalizing elemental ratios in uni-cellular algae. J Phycol 36:3–6CrossRefGoogle Scholar
  21. Fanning KA (1989) Influence of atmospheric pollution on nutrient limitation in the ocean. Nature 339:460–463CrossRefGoogle Scholar
  22. Lauro FM & Bartlett DH (2008) Prokaryotic lifestyles in deep sea habitats. Extremophiles 12:15–25CrossRefPubMedGoogle Scholar
  23. Feistel R, Weinreben S, Wolf H, Seitz S, Spitzer P, Adel B, Nausch G, Schneider B, Wright DG (2010) Density and absolute salinity of the Baltic Sea 2006–2009. Ocean Sci 6:3–24CrossRefGoogle Scholar
  24. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281:237–240CrossRefPubMedGoogle Scholar
  25. Goffredi SK, Orphan VJ (2010) Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ Microbiol 12:344–363CrossRefPubMedGoogle Scholar
  26. Goldman JG, McCarthy JJ, Peavey DG (1979) Growth rate influence on the chemical composition of phytoplankton in oceanic waters. Nature 279:210–215CrossRefGoogle Scholar
  27. Gould SJ (1996) Planet of the bacteria. Wash Post Horiz 119(344):H1Google Scholar
  28. Gruber N, Sarmiento JL (1997) Global patterns of marine nitrogen fixation and denitrification. Global Biogeochem Cycles 11:235–266CrossRefGoogle Scholar
  29. Heinze C, Meyer S, Goris N, Anderson L, Steinfeldt R, Chang N, Le Quéré C, Bakker DCE (2015) The ocean carbon sink – impacts, vulnerabilities and challenges. Earth Syst Dynam 6:327–358Google Scholar
  30. Hoffman PF, Kaufman AJ, Halverson GP, Schrag DP (1998) A Neoproterozoic snowball Earth. Science 281:1342–1346CrossRefPubMedGoogle Scholar
  31. Hou Z, Sket B, Fiser C, Li S (2011) Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification. Proc Natl Acad Sci USA 108:14533–14538CrossRefPubMedPubMedCentralGoogle Scholar
  32. Hsia CCW, Schmitz A, Lambertz M, Perry SF, Maina JN (2013) Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky. Compr Physiol 3:849–915PubMedPubMedCentralGoogle Scholar
  33. Jiao N, Luo T, Zhang R, Yan W, Lin Y, Johnson ZI, Tian J, Yuan D, Yang Q, Zheng Q, Sun J, Hu D, Wang P (2014) Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean. Biogeosciences 11:2391–2400CrossRefGoogle Scholar
  34. Kennedy J, Marchesi J, Dobson A (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7:27CrossRefPubMedPubMedCentralGoogle Scholar
  35. Kim SK (2015) Handbook of marine biotechnology. Springer, Heidelberg, p 1512Google Scholar
  36. Klausmeier CA, Litchman E, Levin SA (2004) Phytoplankton growth and stoichiometry under multiple nutrient limitation. Limnol Oceanogr 49:1463–1470CrossRefGoogle Scholar
  37. Li WKW (1994) Primary production of prochlorophytes, cyanobacteria, and eukaryotic ultraphytoplankton—measurements from flow cytometric sorting. Limnol Oceanogr 39:169–175CrossRefGoogle Scholar
  38. Loladze1 I, Elser JJ (2011) The origins of the Redfield nitrogen-to-phosphorus ratio are in a homoeostatic protein-to-rRNA ratio. Ecol Lett 14:244–250Google Scholar
  39. Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K (2009) Infrequent marine–freshwater transitions in the microbial world. Trends Microbiol 17:414–422CrossRefPubMedGoogle Scholar
  40. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104:11436–11440CrossRefPubMedPubMedCentralGoogle Scholar
  41. MacLeod RA (1965) The question of the existence of specific marine bacteria. Bacteriol Rev 29:9–23PubMedPubMedCentralGoogle Scholar
  42. MacLeod RA, Matula TI (1962) Nutrition and metabolism of marine bacteria: XI. Some characteristics of the lytic phenomenon. Can J Microbiol 8:883–896CrossRefGoogle Scholar
  43. Martin W, Russell MJ (2003) On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans Roy Soc B 358:59–85CrossRefGoogle Scholar
  44. Martín-Cuadrado AB, Lopez-Garcia P, 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 9:e914CrossRefGoogle Scholar
  45. McCarthy T, Rubisge B (2005) Story of Earth and life. University of the Witwatersrand, School of Geosciences (ed), p 70Google Scholar
  46. Middelburg JJ, Soetaert K, Herman PMJ, Heip CHR (1996) Denitrification in marine sediments: a model study. Global Biogeochem Cycles 10:661–673CrossRefGoogle Scholar
  47. Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, Galbraith ED, Geider RJ, Guieu C, Jaccard SL, Jickells TD, La Roche J, Lenton TM et al (2013) Processes and patterns of oceanic nutrient limitation. Nat Geosci 6:701–710CrossRefGoogle Scholar
  48. 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 75:361–422CrossRefPubMedPubMedCentralGoogle Scholar
  49. Pahlow M, Riebesell U (2000) Temporal trends in deep ocean Redfield ratios. Science 287:831–833CrossRefPubMedGoogle Scholar
  50. Park SJ, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Chung WH, Kwon K et al (2014) Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments. PLoS ONE 9(5):e96449CrossRefPubMedPubMedCentralGoogle Scholar
  51. Pedrós-Alió C, Simó R (2002) Studying marine microorganisms from space. Int Microbiol 5:195–200CrossRefPubMedGoogle Scholar
  52. Pinet PR (1996) Invitation to oceanography. West Publishing Company, St. Paul, pp 126, 134–135Google Scholar
  53. Post WM, Peng T-H, Emanuel WR, King AW, Dale VH, DeAngelis DL (1990) The global carbon cycle. Am Sci 78:310–326Google Scholar
  54. Prieur D, Erauso G, Jeanthon C (1995) Hyperthermophilic life at deep-sea hydrothermal vents. Planet Space Sci 43:115–122CrossRefPubMedGoogle Scholar
  55. Redfield AC (1934) On the proportions of organic derivations in seawater and their relation to the composition of plankton. In Daniel RJ (ed) James Johnstone memorial volume. University Press of Liverpool, Liverpool, pp 176–192Google Scholar
  56. Redfield AC (1958) The biological control of chemical factors in the environment. Am Sci 46:205–221Google Scholar
  57. Redfield AC, Ketchum BH, Richards FA (1963) The influence of organisms on the composition of sea water. In: Hill MN (ed)  The sea. Interscience, New York, pp 26–77Google Scholar
  58. Rhodes ME, Payne WJ (1962) Further observations on effects of cations on enzyme induction in marine bacteria. Antonie van Leeuwenhoek. J Microbiol Serol 28:302–314Google Scholar
  59. Ridgwell A (2011) Evolution of the ocean’s biological pump. In: Proceedings of the national academy of sciences of the United States of America, vol 108, pp 16485–16486Google Scholar
  60. Ross D (1995) Introduction to oceanography. HarperCollins College Publishers, New York, pp 199–226, 339–343Google Scholar
  61. Røy H, Kallmeyer J, Adhikar RR, Pockalny R, Jørgensen BB, D’Hondt S (2012) Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336:922–925CrossRefPubMedGoogle Scholar
  62. Santos-Gandelman JF, Giambiagi-deMarval M, Oelemann WM, Laport MS (2014) Biotechnological potential of sponge-associated bacteria. Curr Pharm Biotechnol 15:143–155CrossRefPubMedGoogle Scholar
  63. Sardans J,  Rivas-Ubach A, Penuelas J (2012) The elemental stoichiometry of aquatic and terrestrial ecosystems and its relationships with organismic lifestyle and ecosystem structure and function: a review and perspectives. Biogeochemistry 111:1–39Google Scholar
  64. Sarmiento JL, Hughes TMC, Stouffer RJ, Manabe S (1998) Simulated response of the ocean carbon cycle to anthropogenic climate warming. Nature 393:245–249CrossRefGoogle Scholar
  65. Silver M (2015) Marine snow: a brief historical sketch. Limnol Oceanogr Bull 24:5–10CrossRefGoogle Scholar
  66. Smetacek V (2001) A watery arms race. Nature 411:745CrossRefPubMedGoogle Scholar
  67. Smith CR, Baco AR (2003) Ecology of whale falls at the deep-sea floor. Oceanogr Mar Biol Annu Rev 41:311–354Google Scholar
  68. Stal LJ, Zehr JP (2008) Cyanobacterial nitrogen fixation in the ocean: diversity, regulation, and ecology. In: Flores E, Herrero A (eds) The cyanobacteria: molecular biology, genomics and evolution. Caister Academic Publishers, Norfolk, pp 423–446Google Scholar
  69. Stanier RY (1941) Studies on marine agar digesting bacteria. J Bacteriol 42:527–559PubMedPubMedCentralGoogle Scholar
  70. Stocker R (2012) Marine microbes see a sea of gradients. Science 338:628–633CrossRefPubMedGoogle Scholar
  71. Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A (2010) Environmental distribution of prokaryotic taxa. BMC Microbiol 10:85CrossRefPubMedPubMedCentralGoogle Scholar
  72. Thiele S, Fuchs BM, Amann R, Iversen MH (2014) Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow. Appl Environ Microbiol 81:1463–1471CrossRefPubMedCentralGoogle Scholar
  73. Thurman H, Burton E (2001) Introductory oceanography, 9th edn. Prentice Hall, Upper Saddle River, New JerseyGoogle Scholar
  74. Trindade M, Van Zyl L, Navarro-Fernández J, Abd Elrazak A (2015) Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front in Microbiol 6:890Google Scholar
  75. Turekian KK (1968) Oceans. Prentice-Hall, Englewood Cliffs, New JerseyGoogle Scholar
  76. Turner JT (2015) Zooplankton fecal pellets, marine snow, phytodetritus and the ocean’s biological pump. Prog Oceanogr 130:205–248CrossRefGoogle Scholar
  77. Tyrrel T (1999) The relative influences of nitrogen and phosphorus on oceanic primary production. Nature 400:525–531CrossRefGoogle Scholar
  78. van der Wielen PWJJ, Bolhuis H, Borin S, Daffonchio D, Corselli C, Giuliano L et al (2005) The enigma of prokaryotic life in deep hypersaline anoxic basins. Science 307:121–123CrossRefPubMedGoogle Scholar
  79. Wächtershäuser G (2006) From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Philos Trans Roy Soc B 361:1787–1808CrossRefGoogle Scholar
  80. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583CrossRefPubMedPubMedCentralGoogle Scholar
  81. Wietz M, Millán-Aguiñaga N, Jensen PR (2014) CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. BMC Genom 25(15):936CrossRefGoogle Scholar
  82. Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ (2015) Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347:1257594Google Scholar
  83. Wu J, Gao W, Johnson RH, Zhang W, Meldrum DR (2013) Integrated metagenomic and metatranscriptomic analyses of microbial communities in the meso- and bathypelagic realm of North Pacific Ocean. Mar Drugs 11:3777–3801CrossRefPubMedPubMedCentralGoogle Scholar
  84. Zhang Y, Zhao Z, Dai M, Jiao N, Herndl GJ (2014) Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Mol Ecol 23:2260–2274CrossRefPubMedPubMedCentralGoogle Scholar
  85. Zobell CE, Rittenberg SC (1938) The occurrence and characteristics of chitinoclastic bacteria in the sea. J Bacteriol 35:275–287Google Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, TexelThe Netherlands

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