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Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia

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Abstract

To investigate the biomass and phylogenetic diversity of the microbial community inhabiting the deep aquifer of the Great Artesian Basin (GAB), geothermal groundwater gushing out from the aquifer was sampled and analyzed. Microbial cells in the groundwater were stained with acridine orange and directly counted by epifluorescence microscopy. Microbial cells were present at a density of 108–109 cells per liter of groundwater. Archaeal and bacterial small-subunit rRNA genes (rDNAs) were amplified by PCR with Archaea- and Bacteria-specific primer sets, and clone libraries were constructed separately. A total of 59 clones were analyzed in archaeal and bacterial 16S rDNA libraries, respectively. The archaeal 16S rDNA clones were divided into nine operated taxonomic units (OTUs) by restriction fragment length polymorphism. These OTUs were closely related to the methanogenic genera Methanospirillum and Methanosaeta, the heterotrophic genus Thermoplasma, or miscellaneous crenarchaeota group. More than one-half of the archaeal clones (59% of total 59 clones) were placed beside phylogenetic clusters of methanogens. The majority of the methanogen-related clones (83%) was closely related to a group of hydrogenotrophic methanogens (genus Methanospirillum). The bacterial OTUs branched into seven phylogenetic clusters related to hydrogen-oxidizing thermophiles in the genera Hydrogenobacter and Hydrogenophilus, a sulfate-reducing thermophile in the genus Thermodesulfovibrio, chemoheterotropic bacteria in the genera Thermus and Aquaspirillum, or the candidate division OP10. Clones closely related to the thermophilic hydrogen-oxidizers in the genera Hydrogenobacter and Hydrogenophilus were dominant in the bacterial clone library (37% of a total of 59 clones). The dominancy of hydrogen-users strongly suggested that H2 plays an important role as a primary substrate in the microbial ecosystem of this deep geothermal aquifer.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Apps JA, van de Kamp PC (1993) Energy gases of abiogenic origin in the Earth’s crust. In: Reston VA (ed) The future of energy gases. US Geological Survey, pp 81–132

  • Button DK, Robertson BR (2001) Determination of DNA content of aquatic bacteria by flow cytometry. Appl Environ Microbiol 67:1636–1645

    Article  CAS  PubMed  Google Scholar 

  • Byers HK, Stackebrandt E, Hayward C, Blackall LL (1998) Molecular investigation of a microbial mat associated with the Great Artesian Basin. FEMS Microbial Ecol 25:391–403

    Article  CAS  Google Scholar 

  • Chandler DP, Brockman FJ, Bailey TJ, Fredrickson JK (1998) Phylogenetic diversity of archaea and bacteria in a deep subsurface paleosol. Microbial Ecol 36:37–50

    Article  CAS  Google Scholar 

  • Chung AP, Rainey FA, Valente M, Nobre MF, da Costa MS (2000) Thermus igniterrae sp nov and Thermus antranikianii sp nov, two new species from Iceland. Int J Syst Evol Microbiol 50:209–217

    Google Scholar 

  • Collon P, Kutschera W, Loosli HH, Lehmann BE, Purtschert R, Love A, Sampson L, Anthony D, Cole D, Davids B, Morrissey DJ, Sherrill BM, Steiner M, Pardo RC, Paul M (2000) 81 Kr in the Great Artesian Basin, Australia: a new method for dating very old groundwater. Earth Planet Sci Lett 182:103–113

    Article  CAS  Google Scholar 

  • Darland G, Brock TD, Samsonoff W, Conti SF (1970) A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170:1416–1418

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Elmore D, Fulton BR, Clover MR, Marsden JR, Gove HE, Naylor H, Purser KH, Kilius LR, Beukens RP, Litherland AE (1979) Analysis of 36 Cl in environmental water samples using an electrostatic accelerator. Nature 277:22–25

    CAS  Google Scholar 

  • Ferry JG, Smith PH, Wolfe RS (1974) Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungateii sp nov. Int J Syst Bacteriol 24:465–469

    Google Scholar 

  • Großkopf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64:960–969

    PubMed  Google Scholar 

  • Habermehl MA (1980) The Great Artesian Basin, Australia. BMR J Aust Geol Geophys 5:9–38

    Google Scholar 

  • 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 49:783–786

    Google Scholar 

  • Henry EA, Devereux R, Maki JS, Gilmour CC, Woese CR, Mandelco L, Schauder R, Remsen CC, Mitchell R (1994) Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen nov and sp nov: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol 161:62–69

    CAS  PubMed  Google Scholar 

  • Hobbie JE, Daley RJ, Jasper S (1977) Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33:1225–1228

    CAS  PubMed  Google Scholar 

  • Hudson JA, Morgan HW, Daniel RM (1987) Thermus filiformis sp, nov, a filamentous caldoactive bacterium. Int J Syst Bacteriol 37:431–436

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Kamagata Y, Kawasaki H, Oyaizu H, Nakamura K, Mikami E, Endo G, Koga Y, Yamasato K (1992) Characterization of three thermophilic strains of Methanothrix (“Methanosaeta”) thermophila sp nov and rejection of Methanothrix (“Methanosaeta”) thermoacetophila. Int J Syst Bacteriol 42:463–468

    Google Scholar 

  • Kawasumi T, Igarashi Y, Kodama T, Minoda Y (1984) Hydrogenobacter thermophilus gen nov, sp nov, an extremely thermophilic, aerobic, hydrogen-oxidizing bacteria. Int J System Bacteriol 34:5–10

    Google Scholar 

  • Kimura H, Fukuba T, Naganuma T (1999) Biomass of thraustochytrid protoctists in coastal water. Mar Ecol Prog Ser 189:27–33

    CAS  Google Scholar 

  • Kimura H, Asada R, Masta A, Naganuma T (2003) Distribution of microorganisms in the subsurface of the Manus Basin hydrothermal vent field in Papua New Guinea. Appl Environ Microbiol 69:644–648

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Lipman DJ, Person WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435–1441

    CAS  PubMed  Google Scholar 

  • Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Moreira C, Rainey FA, Nobre MF, da Silva MT, da Costa MS (2000) Tepidimonas ignava gen nov, sp nov, a new chemolithoheterotrophic and slightly thermophilic member of the beta-Proteobacteria. Int J Syst Evol Microbiol 50:735–742

    Google Scholar 

  • Morita RY (2000) Is H2 the universal energy source for long-term survival?. Microb Ecol 38:307–320

    Article  Google Scholar 

  • Page RD (1996) Tree view: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    CAS  PubMed  Google Scholar 

  • Patel GB (1992) A contrary view of the proposal to assign a neotype strain for Methanothrix soehngenii. Int J Syst Bacteriol 42:324–326

    Google Scholar 

  • Polak EJ, Horsfall CL (1979) Geothermal gradients in the Great Artesian Basin, Australia. Bull Aust Soc Explor Geophys 10:144–148

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Segerer A, Langworthy TA, Stetter KO (1988) Thermoplasma acidophilum and Thermoplasma volcanium sp nov from solfatara fieds. Syst Appl Microbiol 10:161–171

    Google Scholar 

  • Seidel G (1980) Application of the GABHYD groundwater model of the Great Artesian Basin, Australia. BMR J Aust Geol Geophys 5:39–45

    Google Scholar 

  • Sekiguchi Y, Kamagata Y, Syutsubo K, Ohashi A, Harada H, Nakamura K (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144:2655–2665

    CAS  PubMed  Google Scholar 

  • Senior BR, Mond A, Harrison PL (1978) Geology of the Eromanga Basin Bulletin 167. Bureau of Mineral Resources, Australia

    Google Scholar 

  • Shima S, Suzuki KI (1993) Hydrogenobacter acidophilus sp nov, a thermoacidophilic, aerobic, hydrogen-oxidizing bacterium requiring elemental sulfur for growth. Int J Syst Bacteriol 43:703–708

    Google Scholar 

  • Somerville CC, Knight IT, Straube WL, Colwell RR (1989) Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55:548–554

    CAS  PubMed  Google Scholar 

  • Spanevello MD, Yamamoto H, Patel BKC (2002) Thermaerobacter subterraneus sp nov, a novel aerobic bacterium from the Great Artesian Basin of Australia, and emendation of the genus Thermaerobacter. Int J Syst Evol Microbiol 52:795–800

    Google Scholar 

  • Stackebrandt E, Charfreitag O (1990) Partial 16S rRNA primary structure of five Actimomyces species: phylogenetic implications and development of an Actinomyces israelii-specific oligonucleotide probe. J Gen Microbiol 136:37–43

    CAS  PubMed  Google Scholar 

  • Stahl DA, Amann R (1991) Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley and Sons, New York, pp 205–248

    Google Scholar 

  • Summit M, Baross JA (2001) A novel microbial habitat in the mid-ocean ridge subseafloor. Proc Natl Acad Sci USA 98:2158–2163

    Article  CAS  PubMed  Google Scholar 

  • Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66:5066–5072

    Article  CAS  PubMed  Google Scholar 

  • Takai K, Gamo T, Tsunogai U, Nakayama N, Hirayama H, Nelson KH, Horikoshi K (2004) Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles 8:269–282

    Article  CAS  PubMed  Google Scholar 

  • Teske A, Hinrichs K-U, Edgcomb V, Gomez AV, 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

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    CAS  PubMed  Google Scholar 

  • Welhan JA, Lupton JE (1987) Light hydrocarbon gases in Guaymas Basin hydrothermal fluids: thermogenic vs abiogenic origin. Bull Assoc Petrol Geol 71:215–223

    CAS  Google Scholar 

  • Wen A, Fegan M, Hayward C, Chakraborty S, Sly LI (1999) Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen nov, comb nov. Int J Syst Bacteriol 49:567–576

    Google Scholar 

  • Williams RA, Smith KE, Welch SG, Micallef J (1996) Thermus oshimai sp nov, isolated from hot springs in Portugal, Iceland, and the Azores, and comment on the concept of a limited geographical distribution of Thermus species. Int J Syst Bacteriol 46:403–408

    Google Scholar 

Download references

Acknowledgments

This study was partly supported by the Japanese Ministry of Education, Culture, Sports, Science and Technology by a Grant-in aid for Creative Basic Research (14405016), “Research for thermophilic and chemoautotrophic microorganisms inhibiting geothermal area in Oceania” (a representative, Dr. Hiroyuki Yamamoto).

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Authors and Affiliations

  1. Department of Biology and Geosciences, Faculty of Science, Shizuoka University, 836 Oya, Suruga, Shizuoka, 422-8529, Japan

    Hiroyuki Kimura & Kenji Kato

  2. Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1, Higashi, Tsukuba,, Ibaraki 305-8566, Japan

    Maki Sugihara & Satoshi Hanada

  3. Marine Ecosystems Research Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka,, Kanagawa 237-0061, Japan

    Hiroyuki Yamamoto

  4. School of Biomolecular and Biomedical Sciences, Faculty of Science, Griffith University, Brisbane, Queensland, 4111, Australia

    Bharat K. C. Patel

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  1. Hiroyuki Kimura
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Correspondence to Satoshi Hanada.

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Communicated by K. Horikoshi

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Kimura, H., Sugihara, M., Yamamoto, H. et al. Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia. Extremophiles 9, 407–414 (2005). https://doi.org/10.1007/s00792-005-0454-3

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