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Prokaryotic lifestyles in deep sea habitats

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An Erratum to this article was published on 01 December 2007

Abstract

Gradients of physicochemical factors influence the growth and survival of life in deep-sea environments. Insights into the characteristics of deep marine prokaryotes has greatly benefited from recent progress in whole genome and metagenome sequence analyses. Here we review the current state-of-the-art of deep-sea microbial genomics. Ongoing and future genome-enabled studies will allow for a better understanding of deep-sea evolution, physiology, biochemistry, community structure and nutrient cycling.

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References

  • Aertsen A, Michiels CW (2005) Mrr instigates the SOS response after high pressure stress in Escherichia coli. Mol Microbiol 58:1381–1391

    Article  PubMed  CAS  Google Scholar 

  • Aertsen A, Van Houdt R, Vanoirbeek K, Michiels CW (2004) An SOS response induced by high pressure in Escherichia coli. J Bacteriol 186:6133–6141

    PubMed  CAS  Google Scholar 

  • Alazard D, Dukan S, Urios A, Verhe F, Bouabida N, Morel F, Thomas P, Garcia JL, Ollivier B (2003) Desulfovibrio hydrothermalis sp nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents. Int J Syst Evol Microbiol 53:173–178

    PubMed  CAS  Google Scholar 

  • Allen EE, Bartlett DH (2000) FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-sea bacterium Photobacterium profundum strain SS9. J Bacteriol 182:1264–1271

    PubMed  CAS  Google Scholar 

  • Allen EE, Bartlett DH (2002) Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148:1903–1913

    PubMed  CAS  Google Scholar 

  • Allen EE, Facciotti D, Bartlett DH (1999) Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol 65:1710–1720

    PubMed  CAS  Google Scholar 

  • Alpas H, Lee J, Bozoglu F, Kaletunc G (2003) Evaluation of high hydrostatic pressure sensitivity of Staphylococcus aureus and Escherichia coli O157: H7 by differential scanning calorimetry. Int J Food Microbiol 87:229–237

    PubMed  Google Scholar 

  • Aluwihare LI, Repeta DJ, Chen RF (2002) Chemical composition and cycling of dissolved organic matter in the Mid-Atlantic Bight. Deep-Sea Res Part II Top Stud Oceanogr 49:4421–4437

    CAS  Google Scholar 

  • Aluwihare LI, Repeta DJ, Pantoja S, Johnson CG (2005) Two chemically distinct pools of organic nitrogen accumulate in the ocean. Science 308:1007–1010

    PubMed  CAS  Google Scholar 

  • Amundsen SK, Taylor AF, Chaudhury AM, Smith GR (1986) recD: the gene for an essential 3Rd subunit of exonuclease V. Proc Natl Acad Sci USA 83:5558–5562

    PubMed  CAS  Google Scholar 

  • Azam F, Long RA (2001) Oceanography—sea snow microcosms. Nature 414:495–498

    PubMed  CAS  Google Scholar 

  • Azam F, Worden AZ (2004) Microbes, molecules, and marine ecosystems. Science 303:1622–1624

    PubMed  CAS  Google Scholar 

  • Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp nov, a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol 47:515–521

    Article  PubMed  CAS  Google Scholar 

  • Bartlett DH (1992) Microbial life at high-pressures. Sci Prog 76:479–496

    PubMed  CAS  Google Scholar 

  • Bartlett DH (2002) Pressure effects on in vivo microbial processes. Biochim Biophys Acta 1595:367–381

    PubMed  CAS  Google Scholar 

  • Bartlett DH (2006) Extremophilic vibrionaceae. In: Thompson FL, Austin B, Swings J (eds) The biology of vibrios. American Society for Microbiology Press, Washington D.C., pp 156–171

    Google Scholar 

  • Bartlett DH, Welch TJ (1995) ompH gene-expression is regulated by multiple environmental cues in addition to high-pressure in the deep-sea bacterium Photobacterium species strain SS9. J Bacteriol 177:1008–1016

    PubMed  CAS  Google Scholar 

  • Bartlett DH, Lauro FM, Eloe EA (2006) Microbial adaptation to high pressure. In: Gerday C, Glansdorff N (eds) Physiology and biochemistry of extremophiles. American Society for Microbiology Press, Washington D.C. (in press)

  • Berlin DL, Herson DS, Hicks DT, Hoover DG (1999) Response of pathogenic Vibrio species to high hydrostatic pressure. Appl Environ Microbiol 65:2776–2780

    PubMed  CAS  Google Scholar 

  • Bidle KA, Bartlett DH (1999) RecD function is required for high-pressure growth of a deep-sea bacterium. J Bacteriol 181:2330–2337

    PubMed  CAS  Google Scholar 

  • Blackburn N, Fenchel T, Mitchell J (1998) Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282:2254–2256

    PubMed  CAS  Google Scholar 

  • Campanaro S, Vezzi A, Vitulo N, Lauro FM, D’Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G et al (2005) Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics 6:122

    PubMed  Google Scholar 

  • Chi E, Bartlett DH (1993) Use of a reporter gene to follow high-pressure signal-transduction in the deep-sea bacterium Photobacterium sp strain SS9. J Bacteriol 175:7533–7540

    PubMed  CAS  Google Scholar 

  • Chilukuri LN, Fortes PAG, Bartlett DH (1997) High pressure modulation of Escherichia coli DNA gyrase activity. Biochem Biophys Res Commun 239:552–556

    PubMed  CAS  Google Scholar 

  • Dell’Anno A, Danovaro R (2005) Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 309:2179–2179

    PubMed  CAS  Google Scholar 

  • Delong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689

    PubMed  CAS  Google Scholar 

  • Delong EF, Yayanos AA (1985) Adaptation of the membrane-lipids of a deep-sea bacterium to changes in hydrostatic-pressure. Science 228:1101–1102

    PubMed  CAS  Google Scholar 

  • Delong EF, Yayanos AA (1986) Biochemical function and ecological significance of novel bacterial lipids in deep-sea prokaryotes. Appl Environ Microbiol 51:730–737

    PubMed  CAS  Google Scholar 

  • Delong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol Oceanogr 38:924–934

    Article  Google Scholar 

  • DeLong EF, Franks DG, Yayanos AA (1997) Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol 63:2105–2108

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Earl AM, Losick R, Kolter R (2006) Bacillus subtilis genome diversity. J Bacteriol. doi:10.1128/JB.01343-06

  • El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377–2382

    PubMed  CAS  Google Scholar 

  • Elvert M, Suess E, Greinert J, Whiticar MJ (2000) Archaea mediating anaerobic methane oxidation in deep-sea sediments at cold seeps of the eastern Aleutian subduction zone. Org Geochem 31:1175–1187

    CAS  Google Scholar 

  • Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, dos Santos VAPM, Yakimov MM, Timmis KN, Golyshin PN (2005) Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12:895–904

    PubMed  CAS  Google Scholar 

  • 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 USA 102:14683–14688

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, Zhou J (2006) Microarray-based analysis of microbial community RNAs by whole community RNA amplification (WCRA). Appl Environ Microbiol. doi:10.1128/AEM.01771-06

  • Garvey N, Stjohn AC, Witkin EM (1985) Evidence for recA protein association with the cell membrane and for changes in the levels of major outer membrane proteins in SOS-induced Escherichia coli cells. J Bacteriol 163:870–876

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M et al (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242–1245

    PubMed  CAS  Google Scholar 

  • Goldberg SMD, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM et al (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci USA 103:11240–11245

    PubMed  CAS  Google Scholar 

  • Gross M, Jaenicke R (1990) Pressure-induced dissociation of tight couple ribosomes. FEBS Lett 267:239–241

    PubMed  CAS  Google Scholar 

  • Gross M, Jaenicke R (1994) Proteins under pressure. The influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes. Eur J Biochem 221:617–630

    PubMed  CAS  Google Scholar 

  • Gross M, Lehle K, Jaenicke R, Nierhaus KH (1993) Pressure-induced dissociation of ribosomes and elongation cycle intermediates. Stabilizing conditions and identification of the most sensitive functional state. Eur J Biochem 218:463–468

    PubMed  CAS  Google Scholar 

  • Grossart HP, Riemann L, Azam F (2001) Bacterial motility in the sea and its ecological implications. Aquat Microb Ecol 25:247–258

    Google Scholar 

  • Grzymski JJ, Carter BJ, DeLong EF, Feldman RA, Ghadiri A, Murray AE (2006) Comparative genomics of DNA fragments from six antarctic marine planktonic bacteria. Appl Environ Microbiol 72:1532–1541

    PubMed  CAS  Google Scholar 

  • Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457–1462

    PubMed  CAS  Google Scholar 

  • Hormann S, Scheyhing C, Behr J, Pavlovic M, Ehrmann M, Vogel RF (2006) Comparative proteome approach to characterize the high-pressure stress response of Lactobacillus sanfranciscensis DSM 20451. Proteomics 6:1878–1885

    PubMed  Google Scholar 

  • Hou SB, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV et al (2004) Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci USA 101:18036–18041

    PubMed  CAS  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 USA 103:6442–6447

    PubMed  CAS  Google Scholar 

  • Ishii A, Sato T, Wachi M, Nagai K, Kato C (2004) Effects of high hydrostatic pressure on bacterial cytoskeleton FtsZ polymers in vivo and in vitro. Microbiology 150:1965–1972

    PubMed  CAS  Google Scholar 

  • Ishii A, Oshima T, Sato T, Nakasone K, Mori H, Kato C (2005) Analysis of hydrostatic pressure effects on transcription in Escherichia coli by DNA microarray procedure. Extremophiles 9:65–73

    PubMed  CAS  Google Scholar 

  • Janion C, Sikora A, Nowosielska A, Grzesiuk E (2002) Induction of the SOS response in starved Escherichia coli. Environ Mol Mutagen 40:129–133

    PubMed  CAS  Google Scholar 

  • Jannasch HW (1987) Effects of hydrostatic pressure on growth of marine bacteria. In: Jannasch HW, Marquis RE, Zimmerman AM (eds) Current prespectives in high pressure biology. Academic, Toronto, pp 1–15

    Google Scholar 

  • Karl DM, Lukas R (1996) The Hawaii ocean time-series (HOT) program: background, rationale and field implementation. Deep Sea Res Part II Top Stud Oceanogr 43:129–156

    CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Kato C, Bartlett DH (1997) The molecular biology of barophilic bacteria. Extremophiles 1:111–116

    PubMed  CAS  Google Scholar 

  • Kato C, Sato T, Horikoshi K (1995) Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples. Biodivers Conserv 4:1–9

    Google Scholar 

  • Kato C, Li LN, Tamaoka J, Horikoshi K (1997) Molecular analyses of the sediment of the 11000-m deep Mariana Trench. Extremophiles 1:117–123

    PubMed  CAS  Google Scholar 

  • Kato C, Li L, Nogi Y, Nakamura Y, Tamaoka J, Horikoshi K (1998) Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Appl Environ Microbiol 64:1510–1513

    PubMed  CAS  Google Scholar 

  • Kawarai T, Wachi M, Ogino H, Furukawa S, Suzuki K, Ogihara H, Yamasaki M (2004) SulA-independent filamentation of Escherichia coli during growth after release from high hydrostatic pressure treatment. Appl Microbiol Biotechnol 64:255–262

    PubMed  CAS  Google Scholar 

  • Kiorboe T, Jackson GA (2001) Marine snow, organic solute plumes, and optimal chemosensory behavior of bacteria. Limnol Oceanogr 46:1309–1318

    Article  CAS  Google Scholar 

  • Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328–1333

    PubMed  CAS  Google Scholar 

  • Konneke 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

    PubMed  Google Scholar 

  • Kysela DT, Palacios C, Sogin ML (2005) Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environ Microbiol 7:356–364

    PubMed  CAS  Google Scholar 

  • Lauro FM, Bertoloni G, Obraztsova A, Kato C, Tebo BM, Bartlett DH (2004) Pressure effects on Clostridium strains isolated from a cold deep-sea environment. Extremophiles 8:169–173

    PubMed  CAS  Google Scholar 

  • Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH (2006) The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol doi:10.1128/AEM.01726-06

  • Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081

    PubMed  CAS  Google Scholar 

  • Macarthur R (1960) On the relative abundance of species. Am Nat 94:25–36

    Google Scholar 

  • Margesini R, Nogi Y (2004) Psychropiezophilic microorganisms. Cell Mol Biol 50:429–436

    Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  • Meganathan R, Marquis RE (1973) Loss of bacterial motility under pressure. Nature 246:525–527

    PubMed  CAS  Google Scholar 

  • Moreira D, Rodriguez-Valera F, Lopez-Garcia P (2006) Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. Microbiology 152:505–517

    PubMed  CAS  Google Scholar 

  • Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM (2001) DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci USA 98:9853–9858

    PubMed  CAS  Google Scholar 

  • Niven GW, Miles CA, Mackey BM (1999) The effects of hydrostatic pressure on ribosome conformation in Escherichia coli: an in vivo study using differential scanning calorimetry. Microbiology 145:419–425

    Article  PubMed  CAS  Google Scholar 

  • Nogi Y, Kato C (1999) Taxonomic studies of extremely barophilic bacteria isolated from the Mariana Trench and description of Moritella yayanosii sp. nov., a new barophilic bacterial isolate. Extremophiles 3:71–77

    PubMed  CAS  Google Scholar 

  • Nogi Y, Kato C, Horikoshi K (1998a) Moritella japonica sp. nov., a novel barophilic bacterium isolated from a Japan Trench sediment. J Gen Appl Microbiol 44:289–295

    CAS  Google Scholar 

  • Nogi Y, Kato C, Horikoshi K (1998b) Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170:331–338

    CAS  Google Scholar 

  • Nogi Y, Masui N, Kato C (1998c) Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles 2:1–7

    CAS  Google Scholar 

  • Nogi Y, Kato C, Horikoshi K (2002) Psychromonas kaikoae sp nov., a novel piezophilic bacterium from the deepest cold-seep sediments in the Japan Trench. Int J Syst Evol Microbiol 52:1527–1532

    PubMed  CAS  Google Scholar 

  • Nogi Y, Hosoya S, Kato C, Horikoshi K (2004) Colwellia piezophila sp nov., a novel piezophilic species from deep-sea sediments of the Japan Trench. Int J Syst Evol Microbiol 54:1627–1631

    PubMed  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    PubMed  CAS  Google Scholar 

  • Pavlovic M, Hormann S, Vogel RF, Ehrmann MA (2005) Transcriptional response reveals translation machinery as target for high pressure in Lactobacillus sanfranciscensis. Arch Microbiol 184:11–17

    PubMed  CAS  Google Scholar 

  • Prieur D, Erauso G, Jeanthon C (1995) Hyperthermophilic life at deep-sea hydrothermal vents. Planet Space Sci 43:115–122

    PubMed  CAS  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Rice SA, Oliver JD (1992) Starvation response of the marine barophile Cnpt-3. Appl Environ Microbiol 58:2432–2437

    PubMed  CAS  Google Scholar 

  • Schulz E, Ludemann HD, Jaenicke R (1976) High-pressure equilibrium studies on dissociation association of Escherichia coli ribosomes. FEBS Lett 64:40–43

    PubMed  CAS  Google Scholar 

  • Silva JL, Weber G (1993) Pressure stability of proteins. Annu Rev Phys Chem 44:89–113

    PubMed  CAS  Google Scholar 

  • Simonato F, Campanaro S, Lauro FM, Vezzi A, D’Angelo M, Vitulo N, Valle G, Bartlett DH (2006) Piezophilic adaptation: a genomic point of view. J Biotechnol 126:11–25

    PubMed  CAS  Google Scholar 

  • Smith CR, Baco AR (2003) Ecology of whale falls at the deep-sea floor. Oceanography and Marine Biology, vol 41. pp 311–354

  • 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 USA 103:12115–12120

    PubMed  CAS  Google Scholar 

  • Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30:3927–3935

    PubMed  CAS  Google Scholar 

  • Tang GQ, Tanaka N, Kunugi S (1998) In vitro increases in plasmid DNA supercoiling by hydrostatic pressure. Biochim Biophys Acta 1443:364–368

    PubMed  CAS  Google Scholar 

  • Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995

    PubMed  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    PubMed  CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    PubMed  CAS  Google Scholar 

  • Vezzi A, Campanaro S, D’Angelo M, Simonato F, Vitulo N, Lauro FM, Cestaro A, Malacrida G, Simionati B, Cannata N et al (2005) Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307:1459–1461

    PubMed  CAS  Google Scholar 

  • Welch TJ, Farewell A, Neidhardt FC, Bartlett DH (1993) Stress response of Escherichia coli to elevated hydrostatic pressure. J Bacteriol 175:7170–7177

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68:2535–2541

    PubMed  CAS  Google Scholar 

  • Wirsen CO, Molyneaux SJ (1999) A study of deep-sea natural microbial populations and barophilic pure cultures using a high-pressure chemostat. Appl Environ Microbiol 65:5314–5321

    PubMed  CAS  Google Scholar 

  • Witte U, Wenzhofer F, Sommer S, Boetius A, Heinz P, Aberle N, Sand M, Cremer A, Abraham WR, Jorgensen BB et al (2003) In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor. Nature 424:763–766

    PubMed  CAS  Google Scholar 

  • Worden AZ, Cuvelier ML, Bartlett DH (2006) In-depth analyses of marine microbial community genomics. Trends Microbiol 14:331–336

    PubMed  CAS  Google Scholar 

  • Wu LY, Liu X, Schadt CW, Zhou JZ (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72:4931–4941

    PubMed  CAS  Google Scholar 

  • Wu LY, Thompson DK, Li GS, Hurt RA, Tiedje JM, Zhou JZ (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67:5780–5790

    PubMed  CAS  Google Scholar 

  • Xu Y, Nogi Y, Kato C, Liang ZY, Ruger HJ, De Kegel D, Glansdorff N (2003a) Moritella profunda sp nov and Moritella abyssi sp nov., two psychropiezophilic organisms isolated from deep Atlantic sediments. Int J Syst Evol Microbiol 53:533–538

    CAS  Google Scholar 

  • Xu Y, Nogi Y, Kato C, Liang ZY, Ruger HJ, De Kegel D, Glansdorff N (2003b) Psychromonas profunda sp nov., a psychropiezophilic bacterium from deep Atlantic sediments. Int J Syst Evol Microbiol 53:527–532

    CAS  Google Scholar 

  • Yasui A, McCready SJ (1998) Alternative repair pathways for UV-induced DNA damage. Bioessays 20:291–297

    PubMed  CAS  Google Scholar 

  • Yayanos AA (1995) Microbiology to 10,500 meters in the deep-sea. Annu Rev Microbiol 49:777–805

    PubMed  CAS  Google Scholar 

  • Yayanos AA, Pollard EC (1969) A study of effects of hydrostatic pressure on macromolecular synthesis in Escherichia coli. Biophys J 9:1464–1482

    Article  PubMed  CAS  Google Scholar 

  • Yayanos AA, DeLong EF (1987) Deep-sea bacterial fitness to environmental temperatures and pressure. In: Jannasch HW, Marquis RE, Zimmerman AM (eds) Current perspectives in high pressure biology. Academic, Toronto, pp 17–32

    Google Scholar 

  • Yayanos AA, Dietz AS, Vanboxtel R (1979) Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 205:808–810

    PubMed  CAS  Google Scholar 

  • Zaballos M, Lopez-Lopez A, Ovreas L, Bartual SG, D’Auria G, Alba JC, Legault B, Pushker R, Daae FL, Rodriguez-Valera F (2006) Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbiol Ecol 56:389–405

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Zengler K, Walcher M, Clark G, Haller I, Toledo G, Holland T, Mathur EJ, Woodnutt G, Short JM, Keller M (2005) High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol 397:124–130

    PubMed  CAS  Google Scholar 

  • Zhou JH (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294

    PubMed  CAS  Google Scholar 

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Acknowledgments

We are grateful to the National Science Foundation for their support (MCB02-37059, MCB04-009 and MCB05-44524) and to Xavier Mayali for insightful discussion.

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Correspondence to Douglas H. Bartlett.

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Communicated by D. A. Cowan.

An erratum to this article can be found at http://dx.doi.org/10.1007/s00792-007-0110-1

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Lauro, F.M., Bartlett, D.H. Prokaryotic lifestyles in deep sea habitats. Extremophiles 12, 15–25 (2008). https://doi.org/10.1007/s00792-006-0059-5

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