Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine

Abstract

Change of bacterial community occurring along a hot water stream in the Hishikari gold mine, Japan, was investigated by applying a combination of various culture-independent techniques. The stream, which is derived from a subsurface anaerobic aquifer containing plentiful CO2, CH4, H2, and NH +4 , emerges in a mine tunnel 320 m below the surface providing nutrients for a lush microbial community that extends to a distance of approximately 7 m in the absence of sunlight-irradiation. Over this distance, the temperature decreases from 69°C to 55°C, and the oxidation-reduction potential increases from −130 mV to +59 mV. In the hot upper reaches of the stream, the dominant phylotypes were: 1) a deeply branching lineage of thermophilic methane-oxidizing γ-Proteobacteria, and 2) a thermophilic hydrogen- and sulfur-oxidizing Sulfurihydrogenibium sp. In contrast, the prevailing phylotypes in the middle and lower parts of the stream were closely related to ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira spp.. Changes in the microbial metabolic potential estimated by competitive PCR analysis of genes encoding the enzymes, particulate methane monooxygenase (pmoA), ammonia monooxygenase (amoA), and putative nitrite oxidoreductase (norB), also substantiated the community shift indicated by 16S rRNA gene analysis. The diversity of putative norB lineages was assessed for the first time in the hot water environment. Estimation of dominant phylotypes by whole-cell fluorescent in situ hybridization and changes in inorganic nitrogen compounds such as decreasing ammonium and increasing nitrite and nitrate in the mat-interstitial water along the stream were consistent with the observed transition of the bacterial community structure in the stream.

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

Fig. 1
Fig. 2A
Fig. 3
Fig. 4

References

  1. Alfreider A, Pernthaler J, Amann R, Sattler B, Glockner F, Wille A, Psenner R (1996) Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl Environ Microbiol 62:2138–2144

    Google Scholar 

  2. Allen SE, Grimshaw HM, Parkinson JA, Quarmby C (1974) Inorganic constituents: nitrogen. In: Allen SE (ed) Chemical analysis of ecological materials. Blackwell Scientific Publications, London, pp 184–206

    Google Scholar 

  3. Bedard C, Knowles R (1989) Physiology, biochemistry, and specific inhibitors of CH4, NH +4 , and CO oxidation by methanotrophs and nitrifiers. Microbiol Rev 53:68–84

    Google Scholar 

  4. Bodrossy L, Kovács KL, McDonald IR, Murrell JC (1999) A novel thermophilic methane-oxidising γ-Proteobacterium. FEMS Microbiol Lett 170:335–341

    Google Scholar 

  5. Bruins ME, Janssen AE, Boom RM (2001) Thermozymes and their applications: a review of recent literature and patents. Appl Biochem Biotechnol 90:155–186

    Google Scholar 

  6. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  CAS  PubMed  Google Scholar 

  7. Costello AM, Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066–5074

    CAS  PubMed  Google Scholar 

  8. Dionisi HM, Layton AC, Harms G, Gregory IR, Robinson KG, Sayler GS (2002) Quantification of Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and Nitrospira spp from full-scale wastewater treatment plants by competitive PCR. Appl Environ Microbiol 68:245–253

    Google Scholar 

  9. Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E (1995) A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp nov and its phylogenetic relationship. Arch Microbiol 164:16–23

    Article  CAS  PubMed  Google Scholar 

  10. Ferris MJ, Ward DM (1997) Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 63:1375–1381

    Google Scholar 

  11. Hayashi NR, Ishida T, Yokota A, Kodama T, Igarashi Y (1999) Hydrogenophilus thermoluteolus gen nov, sp nov, a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol 2:783–786

    Google Scholar 

  12. Hiraishi A, Umezawa T, Yamamoto H, Kato K, Maki Y (1999) Changes in quinone profiles of hot spring microbial mats with a thermal gradient. Appl Environ Microbiol 65:198–205

    CAS  PubMed  Google Scholar 

  13. Hirota R, Yamagata A, Kato J, Kuroda A, Ikeda T, Takiguchi N, Ohtake H (2000) Physical map location of the multicopy genes coding for ammonia monooxygenase and hydroxylamine oxidoreductase in the ammonia-oxidizing bacterium Nitrosomonas sp strain ENI-11. J Bacteriol 182:825–828

    Google Scholar 

  14. Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132:203–208

    Google Scholar 

  15. Hommes NG, Sayavedra-Soto LA, Arp DJ (1998) Mutagenesis and expression of amo, which codes for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol 180:3353–3359

    Google Scholar 

  16. Hooper AB, Terry KR (1974) Photoinactivation of ammonia oxidation in Nitrosomonas. J Bacteriol 119:899–906

    CAS  PubMed  Google Scholar 

  17. Huber H, Stetter KO (1998) Hyperthermophiles and their possible potential in biotechnology. J Biotechnol 64:39–52

    Article  CAS  Google Scholar 

  18. Huber R, Huber H, Stetter KO (2000) Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties. FEMS Microbiol Rev 24:615–623

    Google Scholar 

  19. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376

    CAS  PubMed  Google Scholar 

  20. Inagaki F, Takai K, Hirayama H, Yamato Y, Nealson KH, Horikoshi K (2003) Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine. Extremophiles 7:307–317

    Google Scholar 

  21. Izawa E, Urashima Y, Ibaraki K, Suzuki R, Yokoyama T, Kawasaki K, Koga A, Taguchi S (1990) The Hishikari gold deposit: high-grade epithermal veins in Quaternary volcanics of southern Kyushu, Japan. J Geochem Explor 36:1–56

    Google Scholar 

  22. Kieft TL, Fredrickson JK, Onstott TC, Gorby YA, Kostandarithes HM, Bailey TJ, Kennedy DW, Li SW, Plymale AE, Spadoni CM, Gray MS (1999) Dissimilatory reduction of Fe (III) and other electron acceptors by a Thermus isolate. Appl Environ Microbiol 65:1214–1221

    Google Scholar 

  23. Kirstein K, Bock E (1993) Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases. Arch Microbiol 160:447–453

    Google Scholar 

  24. Kurosawa N, Itoh YH, Iwai T, Sugai A, Uda I, Kimura N, Horiuchi T, Itoh T (1998) Sulfurisphaera ohwakuensis gen nov, sp nov, a novel extremely thermophilic acidophile of the order Sulfolobales. Int J Syst Bacteriol 2:451–456

    Google Scholar 

  25. Lane DJ (1991) 16S/23S sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, pp 115–175

    Google Scholar 

  26. Manz W, Szewzyk U, Ericsson P, Amann R, Schleifer KH, Stenstrom TA (1993) In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl Environ Microbiol 59:2293–2298

    Google Scholar 

  27. Marteinsson VT, Hauksdóttir S, Hobel CFV, Kristmannsdóttir H, Hreggvidsson GO, Kristjánsson JK (2001) Phylogenetic diversity analysis of subterranean hot springs in Iceland. Appl Environ Microbiol 67:4242–4248

    Google Scholar 

  28. McTavish H, Fuchs JA, Hooper AB (1993) Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol 175:2436–2444

    CAS  PubMed  Google Scholar 

  29. Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177:139–149

    Article  CAS  PubMed  Google Scholar 

  30. Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops H-P, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA Sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66:5368–5382

    Article  CAS  PubMed  Google Scholar 

  31. Reysenbach AL, Wickham GS, Pace NR (1994) Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol 60:2113–2119

    Google Scholar 

  32. Reysenbach AL, Ehringer M, Hershberger K (2000) Microbial diversity at 83°C in calcite springs, Yellowstone National Park: another environment where the Aquificales and “Korarchaeota” coexist. Extremophiles 4:61–67

    Google Scholar 

  33. Ruff-Roberts AL, Kuenen JG, Ward DM (1994) Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats. Appl Environ Microbiol 60:697–704

    Google Scholar 

  34. Schramm A, de Beer D, Wagner M, Amann R (1998) Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl Environ Microbiol 64:3480–3485

    Google Scholar 

  35. Semrau JD, Chistoserdov A, Lebron J, Costello A, Davagnino J, Kenna E, Holmes AJ, Finch R, Murrell JC, Lidstrom ME (1995) Particulate methane monooxygenase genes in methanotrophs. J Bacteriol 177:3071–3079

    CAS  PubMed  Google Scholar 

  36. Shears JH, Wood PM (1985) Spectroscopic evidence for a photosensitive oxygenated state of ammonia mono-oxygenase. Biochem J 226:499–507

    Google Scholar 

  37. Skirnisdottir S, Hreggvidsson GO, Hjörleifsdottir S, Marteinsson VT, Petursdottir SK, Holst O, Kristjansson JK (2000) Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66:2835–2841

    Google Scholar 

  38. Stetter KO (1999) Extremophiles and their adaptation to hot environments. FEBS Lett 452:22–25

    Google Scholar 

  39. Stolyar S, Costello AM, Peeples TL, Lidstrom ME (1999) Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145:1235–1244

    CAS  PubMed  Google Scholar 

  40. Takacs CD, Ehringer M, Favre R, Cermola M, Eggertsson G, Palsdottir A, Reysenbach AL (2001) Phylogenetic characterization of the blue filamentous bacterial community from an Icelandic geothermal spring. FEMS Microbiol Ecol 35:123–128

    Google Scholar 

  41. Takai K, Komatsu T, Horikoshi K (2001) Hydrogenobacter subterraneus sp nov, an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water. Int J Syst Evol Microbiol 51:1425–1435

    CAS  PubMed  Google Scholar 

  42. Takai K, Hirayama H, Sakihama Y, Inagaki F, Yamato Y, Horikoshi K (2002) Isolation and metabolic characteristics of previously uncultured members of the order Aquificales in a subsurface gold mine. Appl Environ Microbiol 68:3046–3054

    Google Scholar 

  43. Takai K, Kobayashi H, Nealson KH, Horikoshi K (2003) Sulfurihydrogenibium subterraneum gen nov, sp nov, from a subsurface hot aquifer. Int J Syst Evol Microbiol 53:823–827

    Google Scholar 

  44. Ward DM, Ferris MJ, Nold SC, Bateson MM (1998) A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev 62:1353–1370

    CAS  PubMed  Google Scholar 

  45. Weller R, Bateson MM, Heimbuch BK, Kopczynski ED, Ward DM (1992) Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat. Appl Environ Microbiol 58:3964–3969

    Google Scholar 

  46. Yamamoto H, Hiraishi A, Kato K, Chiura HX, Maki Y, and Shimizu A (1998) Phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in Japan. Appl Environ Microbiol 64:1680–1687

    Google Scholar 

Download references

Acknowledgments

We are grateful to the management of the Sumitomo Metal Mining Co. Ltd. for its cooperation in and understanding of our research.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Hisako Hirayama.

Additional information

Communicated by W.D. Grant

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hirayama, H., Takai, K., Inagaki, F. et al. Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine. Extremophiles 9, 169–184 (2005). https://doi.org/10.1007/s00792-005-0433-8

Download citation

Keywords

  • Methane-oxidizer
  • Ammonia-oxidizer
  • Nitrite-oxidizer
  • Aquificales
  • Subsurface