Abstract
Marine subsurface sediments that cover more than two-thirds of the Earth harbor remarkable numbers of microbial cells. Subseafloor microbial activities may affect global biogeochemical cycles; however, our knowledge of the deep-subseafloor biosphere remains very limited. Recent molecular ecological studies have shown that subseafloor microbial communities are predominantly composed of yet -uncultivated, -uncharacterized bacteria and archaea with great phylogenetic diversity. Some phylogenetic groups are commonly detected in global marine sediments regardless of location and depth, and environmental factors such as sedimentological, geochemical, and geophysical characteristics probably control their activities, biomass, and community structures. This chapter reviews emerging patterns of microbial diversity in deeply buried marine sediments and discusses the potential ecological roles and distribution of microbial communities.
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References
Auburger G, Winter J (1996) Activation and degradation of benzoate, 3-phenylpropionate and crotonate by Syntrophus buswellii strain GA. Evidence for electron-transport phosphorylation during crotonate respiration. Appl Environ Microbiol 44:807–815
Bale SJ, Goodman K, Rochelle PA, Marchesi JR, 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
Biddle JF, Lipp JS, Lever, MA, Lloyd KG, Sørensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs K-U (2006a) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846–3851
Biddle JF, House CH, Brenchley JE (2006b) Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3:287–295
Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626
Coolen MJL, Cypionka H, Sass AM, Sass H, Overmann J (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296:2407–2410
Cowen JP, Giovannoni SJ, Kenig F, Johnson HP, Butterfield D, Rappe MS, Hutnak M, Lam P (2003) Fluids from aging ocean crust that support microbial life. Science 299:120–123
Davis BD, Luger SM, Tai PC (1986) Role of ribosome degradation in the death of starved Escherichia coli cells. J Bacteriol 166:439–445
D’Hondt S, Rutherford S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067–2070
D’Hondt S, Jørgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, Cypionka H, Dickens GR, Ferdelman T, Hinrichs K-U, Holm NG, Mitterer R, Spivack A, Wang G, Bekins B, Engelen B, Ford K, Gettemy G, Rutherford SD, Sass H, Skilbeck CG, Aiello IW, Guerin G, House C, Inagaki F, Meister P, Naehr T, Niitsuma S, Parkes RJ, Schippers A, Smith DC, Teske A, Wiegel J, Padilla CN, Acosta JLS (2004) Distributions of metabolic activities in deep subseafloor sediments. Science 306:2216–2221
Eek KM, Sessions AL, Lies DP (2007) Carbon-isotopic analysis of microbial cells sorted by flow cytometry. Geobiology 5:85–95
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
Fry JC, Webster G, Cragg BA, Weightman AJ, Parkes RJ (2006) Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol 58:86–98
Garrity GM, Holt, JG (2001) Phylum BVI. Chloroflexi phy. nov. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn. vol 1 (The Archaea and the deeply branching and phototrophic Bacteria). Springer, New York, p 427
Girguis PR, Orphan VJ, Hallam SJ, DeLong EF (2003) Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Appl Environ Microbiol 69:5472–5482
Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, DeLong EF (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103:18296–18301
Huber JA, Johnson HP, Butterfield DA, Baross JA (2006) Microbial life in ridge flank crustal fluids. Environ Microbiol 8:88–99
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376
Hugenholtz P, Stackebrandt E (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 54:2049–2051
Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69:7224–7235
Inagaki F, Tsunogai U, Suzuki M, Kosaka A, Machiyama H, Takai K, Nunoura T, Nealson KH, Horikoshi K (2004) Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70:7445–7455
Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D’Hondt S, Jørgensen BB (2006a) Biogeochemical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean margin. Proc Natl Acad Sci USA 103:2815–2820
Inagaki F, Kuypers MM M, Tsunogai U, Ishibashi J, Nakamura K, Treude T, Ohkubo S, Nakaseama M, Gena K, Chiba H, Hirayama H, Nunoura T, Takai K, Jørgensen BB, Horikoshi K, Boetius A (2006b) Microbial community in a sediment-hosted CO_2 lake of the southern Okinawa Trough hydrothermal system. Proc Natl Acad Sci USA 103:14164–14169
Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB, Boone DR (2006) Methanococcus aeolicus sp. nov., a mesophilic methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 56:1525–1529
Knittel K, Lösekann T, Boetius A, Kort R, Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71:467–479
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
Kormas KA, Smith DC, Edgcomb V, Teske A (2003) Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45:115–125
Kuypers MM, Jørgensen BB (2007) The future of single-cell environmental microbiology. Environ Mirobiol 9:6–7
Kvenvolden KA (1995) A review of the geochemistry of methane in natural gas hydrate. Org Geochem 23:997–1008
Ludwig W, Strunk O, Westram R, 29 other authors (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371
Marchesi JR, Weightman AJ, Cragg BA, Parkes RJ, Fry JC (2001) Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol 34:221–228
Massana R, Murray AE, Preston CM, DeLong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl Environ Microbiol 63:50–56
Mauclaire L, Zepp K, Meister P, Mckenzie J (2004) Direct in situ detection of cells in deep-sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229). Geobiology 2: 217–223
Maymo-Gatell X, Chien Y-T, Gossett JM, Zinder SH (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568–1571
Mikucki JA, Liu Y, Delwiche M, Colwell FS, Boone DR (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarines sp. nov. Appl Environ Microbiol 69:3311–3316
Milkov AV (2004) Global estimates of hydrate-bound gas in marine sediments: how much is really out there? Earth-Sci Rev 66:183–197
Mills HJ, Martinez RJ, Story S, Sobecky PA (2005) Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries. Appl Environ Microbiol 71:3235–3247
Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation. Microbiol Rev 56:482–507
Morris RM, Rappe MS, Urbach E, Connon SA, Giovannoni SJ (2004) Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl Environ Microbiol 70:2836–2842
Nakagawa S, Inagaki F, Suzuki Y, Steinsbu BO, Lever MA, Takai K, Engelen B, Sako Y, Wheat CG, Horikoshi K (2006) Microbial community in black rust exposed to hot ridge flank crustal fluids. Appl Environ Microbiol 72:6789–6799
Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ, Fry JC (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol 6:274–287
Nunoura T, Hirayama H, Takami H, Oida H, Nishi S, Shimamura S, Suzuki Y, Inagaki F, Takai K, Nealson KH, Horikoshi K (2005) Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ Microbiol 7:1967–1984
Orphan VJ, Hinrichs K-U, Ussler W III, Paull CK, Taylor LT, Sylva SP, Hayes JM, DeLong EF (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67:1922–1934
Parkes RJ, Cragg BA, Bale SJ, Getllff JM, Goodman K, Rochele PA, Fry JC, Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific ocean sediments. Nature 371: 410–413
Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8:11–28
Parkes RJ, Webster G., Cragg BA, Weightman AJ, Newberry CJ, Ferdelman TG, Kallmeyer J, Jørgensen BB, Aiello IW, Fry JC (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390–394
Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M (2007) Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73:3205–3214
Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediment in a forearc basin. Appl Environ Microbiol 68:3759–3770
Rochelle PA, Cragg BA, Fry JC, Parkes RJ, Weightman AJ (1994) Effect of sample handling on estimation of bacteria diversity in marine sediments by 16S rRNA gene sequence diversity. FEMS Microbiol Ecol 15:215–226
Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, Parkes RJ, Jørgensen BB (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861–864
Schnell S, Bak F, Pfenning N (1989) Anaerobic degradation of aniline and dihydroxybenzenes by newly isolated sulfate-reducing bacteria and description of Desulfobacterium anilini. Arch Microbiol 152:556–563
Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov., and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851
Sørensen KB, Lauer A, Teske A (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2:151–161
Sørensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603
Suss J, Engelen B, Cypionka H, Sass H (2004) Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods. FEMS Microbiol Ecol 51:109–121
Suss J, Schubert K, Sass H, Cypionka H, Overmann J, Engelen B (2006) Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments. Environ Microbiol 8:1753–1763
Swofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (and other methods), version 4. Sinauer Associates, Sunderland, MA
Takai K, Horikoshi K (1999) Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–1297
Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67:5750–5760
Teske A, Hinrichs K-U, Edgcomb V, Gomez A de V, Kysela D, Sylva SP, Sogin ML, Jannasch HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68:1994–2007
Teske A, Sørensen KB (2008). Uncultured Archaea in deep marine subsurface sediments: have we caught them all? The ISME Journal 2:3–18
Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 65:4375–4384
Webster G, Parkes RJ, Fry JC, Weightman AJ (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70:5708–5713
Webster G, Parkes RJ, Cragg BA, Newberry CJ, Weightman AJ, Fry JC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol 58:65–85
Wilms R, Kopke B, Sass H, Chang TS, Cypionka H, Engelen B (2006) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8:709–719
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56:1331–1340
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Inagaki, F., Nakagawa, S. (2008). Spatial Distribution of the Subseafloor Life: Diversity and Biogeography. In: Dilek, Y., Furnes, H., Muehlenbachs, K. (eds) Links Between Geological Processes, Microbial Activities&Evolution of Life. Modern Approaches in Solid Earth Sciences, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8306-8_4
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DOI: https://doi.org/10.1007/978-1-4020-8306-8_4
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