Skip to main content

Advertisement

SpringerLink
Log in

Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

“A meta-enzyme approach” is proposed as an ecological enzymatic method to explore the potential functions of microbial communities in extreme environments such as the deep marine subsurface. We evaluated a variety of extra-cellular enzyme activities of sediment slurries and isolates from a deep subseafloor sediment core. Using the new deep-sea drilling vessel “Chikyu”, we obtained 365 m of core sediments that contained ∼2% organic matter and considerable amounts of methane from offshore the Shimokita Peninsula in Japan at a water depth of 1,180 m. In the extra-sediment fraction of the slurry samples, phosphatase, esterase, and catalase activities were detected consistently throughout the core sediments down to the deepest slurry sample from 342.5 m below seafloor (mbsf). Detectable enzyme activities predicted the existence of a sizable population of viable aerobic microorganisms even in deep subseafloor habitats. The subsequent quantitative cultivation using solid media represented remarkably high numbers of aerobic, heterotrophic microbial populations (e.g., maximally 4.4 × 107 cells cm−3 at 342.5 mbsf). Analysis of 16S rRNA gene sequences revealed that the predominant cultivated microbial components were affiliated with the genera Bacillus, Shewanella, Pseudoalteromonas, Halomonas, Pseudomonas, Paracoccus, Rhodococcus, Microbacterium, and Flexibacteracea. Many of the predominant and scarce isolates produced a variety of extra-cellular enzymes such as proteases, amylases, lipases, chitinases, phosphatases, and deoxyribonucleases. Our results indicate that microbes in the deep subseafloor environment off Shimokita are metabolically active and that the cultivable populations may have a great potential in biotechnology.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • 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 

  • Batzke A, Engelen B, Sass H, Cypionka H (2007) Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from equatorial Pacific Ocean and Peru margin sediments. Geomicrobiol J 24:261–273

    Article  CAS  Google Scholar 

  • Biddle JF, House CH, Brenchley JE (2005) Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3:287–295

    Article  CAS  Google Scholar 

  • Boschker HTS, Cappenberg TE (1998) Patterns of extracellular enzyme activities in littoral sediments of Lake Gooimeer, The Netherland. FEMS Microbiol Ecol 25:79–86

    Article  CAS  Google Scholar 

  • D’Hondt S, Rutherfold S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067–2070

    Article  PubMed  CAS  Google Scholar 

  • 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, Ailleo IW, Guerin G, House CH, Inagaki F, Meister P, Naehr T, Niitsuma S, Parkes RJ, Schippers A, Smith DC, Teske A, Wiegel J, Padilla CN, Acosta JLS (2004) Distribution of microbial activities in deep subseafloor sediments. Science 306:2216–2221

    Article  PubMed  CAS  Google Scholar 

  • Hoppe H-G (2003) Phosphatase activity in the sea. Hydrobiologia 493:187–200

    Article  CAS  Google Scholar 

  • Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson K, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69:7224–7235

    Article  PubMed  CAS  Google Scholar 

  • Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever A, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D’Hondt S, Jørgensen BB (2006) Biogeographical 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ (1991) 16S/23S sequencing. In: Stackbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, pp 115–176

    Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Yadhukumar HM, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  PubMed  CAS  Google Scholar 

  • Mikuchi 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Parkes RJ, Cragg BA, Bale SJ, Getliff JM, Goodman K, Rochelle PA, Fry JC, Weightman AJ, Harvey SM (1994) Deep bacterial biosphere in Pacific Ocean sediments. Nature 371:410–413

    Article  Google Scholar 

  • Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and progresses in subseafloor sediments: a review. Hydrogeol J 8:11–28

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Poremba K, Hoppe H-G (1995) Spatial variation of benthic microbial production and hydrolytic enzymatic activity down the continental slope of the Celtic Sea. Mar Ecol Prog Ser 118:237–245

    Article  Google Scholar 

  • Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68:3759–3770

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Sørensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596–4603

    Article  PubMed  CAS  Google Scholar 

  • Süß 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

    Article  PubMed  CAS  Google Scholar 

  • Taira A (2005) Shimokita area site survey: Northern Japan Trench seismic survey, northern Honshu, Japan. CDEX Tech Rep Vol. 2, pp 155. Available from: http://sio7.jamstec.go.jp/publication/pdf/TechRep/CDEXTRV02.pdf

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Wellsbury P, Goodman K, Cragg BA, Parkes RJ (2000) The geomicrobiology of deep marine sediments from Black Ridge containing methane hydrate (sites 994, 995, and 997) In: Paul CK, Matsumoto R, Wallace PJ, Dillon WP (eds) Proc ODP Sci Results 164, vol 164. Ocean Drilling Program, College Station, TX, pp 379–391

    Chapter  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M, Jacobs E, Röske I (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic states. FEMS Microb Ecol 46:331–347

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Extremobiosphere Research Center of Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, 237-0061, Japan

    Tohru Kobayashi, Osamu Koide, Kozue Mori, Shigeru Shimamura, Takeshi Miura, Yoshihiro Takaki, Yuki Morono, Takuro Nunoura, Hiroyuki Imachi, Fumio Inagaki, Ken Takai & Koki Horikoshi

  2. Department of Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama, 350-8585, Japan

    Takae Matsuura

  3. Kochi Institute for Core Sample Research, JAMSTEC, B200 Monobe, Nankoku, Kochi, 783-8502, Japan

    Yuki Morono & Fumio Inagaki

Authors
  1. Tohru Kobayashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Osamu Koide
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kozue Mori
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shigeru Shimamura
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Takae Matsuura
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Takeshi Miura
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yoshihiro Takaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yuki Morono
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Takuro Nunoura
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hiroyuki Imachi
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Fumio Inagaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Ken Takai
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Koki Horikoshi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tohru Kobayashi.

Additional information

Communicated by G. Antranikian.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(PPT 775 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kobayashi, T., Koide, O., Mori, K. et al. Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12, 519–527 (2008). https://doi.org/10.1007/s00792-008-0157-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-008-0157-7

Keywords

Search

Navigation