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Novel Archaea and Bacteria Dominate Stable Microbial Communities in North America’s Largest Hot Spring

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Abstract

Boiling Springs Lake is an ~12,000 m2, 55 °C, pH 2 thermal feature located in Lassen Volcanic National Park in northern California, USA. We assessed the microbial diversity in the lake by analyzing ~500 sequences from clone libraries constructed using three different primer sets targeted at 16S rRNA genes and one targeted at 18S rRNA genes. We assessed the stability of the microbial community by constructing terminal restriction fragment length polymorphism (T-RFLP) profiles using DNA extracts collected in four separate years over a 7-year period. The four most prevalent phylotypes in the clone libraries shared an average ~85% sequence identity with their closest cultured relatives, and three fourths of the prokaryotic sequences shared less than 91% identity. Phylogenetic analyses revealed novel lineages devoid of cultivated representatives in the Bacterial and Archaeal domains. Many detected phylotypes were related to taxonomically diverse genera previously associated with high-temperature environments, while others were related to diverse Proteobacteria and Firmicutes that would not be expected to grow within BSL conditions. All of the 18S rRNA sequences most closely matched fungi in the phyla Ascomycota and Basidiomycota (91–99% identity). T-RFLP detected fragments corresponding to the most prevalent phylotypes detected in 16S rRNA gene libraries. The T-RFLPs from separate years were similar, and the water-derived T-RFLPs were similar to the sediment-derived (average pairwise Sorenson’s similarity index of 0.74, and 0.78, respectively). Collectively, these results indicate that a stable community of diverse novel microorganisms exists in Boiling Springs Lake.

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References

  1. Abdo Z, Schüette UME, Bent SJ, Williams CJ, Forney LJ, Joyce P (2006) Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction length polymorphisms of 16S rRNA genes. Environ Microbiol 8:929–938

    Article  PubMed  Google Scholar 

  2. Atkinson T, Cairns S, Cowan DA, Danson MJ, Hough DW, Johnson DB, Norris PR, Raven N, Robinson C, Robson R, Sharp RJ (2000) A microbiological survey of Montserrat Island hydrothermal biotopes. Extremophiles 4:305–313

    Article  PubMed  CAS  Google Scholar 

  3. Blackwood CB, Marsh T, Kim SH, Paul EA (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69:926–932

    Article  PubMed  CAS  Google Scholar 

  4. Brock TD (1978) Thermophilic microorganisms and life at high temperatures. Springer-Verlag, New York

    Google Scholar 

  5. Brown P, Wolfe G (2006) Protist genetic diversity in the acidic hydrothermal environments of Lassen Volcanic National Park, USA. J Euk Microbiol 53:420–431

    Article  PubMed  CAS  Google Scholar 

  6. Bryan TS (1995) The geysers of Yellowstone. University Press of Colorado, Boulder, CO

    Google Scholar 

  7. Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM (2007) Candidatus Chloroacidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 317:523–526

    Article  PubMed  CAS  Google Scholar 

  8. Burggraf S, Heyder P, Eis N (1997) A pivotal Archaea group. Nature 385:780

    Article  PubMed  CAS  Google Scholar 

  9. Burton NP, Norris PR (2000) Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analyses. Extremophiles 4:312–320

    Article  Google Scholar 

  10. Cao Y, Hawkins CP, Larsen DP, Van Sickle J (2007) Effects of sample standardization on mean species detectabilities and estimates of relative differences in species richness among assemblages. The Amer Naturalist 170:381–395

    Article  Google Scholar 

  11. Chao A, Chazdon RL, Colwell RK, Shen T-J (2006) Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometric 62:361–371

    Article  Google Scholar 

  12. Doemel WN, Brock TD (1970) The upper temperature limit of Cyanidium caldarium. Archiv fur Mikrobiol 72:326–332

    CAS  Google Scholar 

  13. Donachie SP, Christenson BW, Kunkel DD, Malahoff A, Alam M (2002) Microbial community in acidic hydrothermal waters of volcanically active White Island, New Zealand. Extremophiles 6:419–425

    Article  PubMed  CAS  Google Scholar 

  14. Dorazio RM, Royle JA (2005) Estimating size and composition of biological communities by modeling the occurrence of species. J Am Statistical Assoc 100:389–398

    Article  CAS  Google Scholar 

  15. Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66:2943–2950

    Article  PubMed  CAS  Google Scholar 

  16. Egert M, Friedrich MW (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69:2555–2562

    Article  PubMed  CAS  Google Scholar 

  17. Forney LJ, Xhou X, Brown CJ (2004) Molecular microbial ecology; land of the one-eyed king. Curr Op Microbiol 7:210–220

    Article  CAS  Google Scholar 

  18. Gross S, Robbins EI (2000) Acidophilic and acid-tolerant fungi and yeasts. Hydrobiologia 433:31–37

    Article  CAS  Google Scholar 

  19. Gross W, Heilmann I, Lenze D, Schnarrenberger K (2001) Biogeography of the Cyanidiaceae (Rhodophyta) based on 18S ribosomal RNA sequence data. Eur J Phycol 36:275–280

    Article  Google Scholar 

  20. Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21

    Article  PubMed  CAS  Google Scholar 

  21. Hewson I, Vargo GA, Fuhrman JA (2003) Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effect of virus infection, containment, and nutrient enrichment. Microb Ecol 46:322–336

    Article  PubMed  CAS  Google Scholar 

  22. Horner-Devine MC, Carney KM, Bohannan BJM (2004) An ecological perspective on bacterial biodiversity. Proc R Soc Lond B 271:113–122

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  24. Hughes-Martiny JB, Bohannan BJM, Brown JH, Colwell R, Fuhrman JA, Green J, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin P, Naeem S, øvreås L, Reysenbach A-L, Smith V, Staley J (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112

    Article  CAS  Google Scholar 

  25. Ingebritsen SE, Sorey ML (1985) A quantitative analysis of the Lassen hydrothermal system, north central California. Water Resour Res 21:853–868

    Article  CAS  Google Scholar 

  26. Inskeep WP, Ackerman GG, Taylor WP, Kozubal M, Korf S, Macur RE (2005) On the energetics of chemolithotrophy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park. Geobiology 3:297–317

    Article  CAS  Google Scholar 

  27. Inskeep WP, Macur RE, Harrison G, Bostick BC, Fendorf S (2004) Biomineralization of As (V)-hydrous ferric oxyhydride mats in an acid-sulfate chloride geothermal spring of Norris Geyser Basin, Yellowstone National Park. Geochim Cosmochim Acta 68:3141–3155

    Article  CAS  Google Scholar 

  28. Inskeep WP, McDermott TR (2005) Geomicrobiology of acid-sulfate-chloride springs in Yellowstone National Park. In: Inskeep WP, McDermott TR (eds) Geothermal biology and geochemistry in YNP. Thermal Biology Institute, Bozeman, Montana, pp 143–162

    Google Scholar 

  29. Jackson CR, Langner HW, Donahoe-Christiansen J, Inskeep WP, McDermott TR (2001) Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring. Environ Microbiol 3:532–542

    Article  PubMed  CAS  Google Scholar 

  30. Johnson DB, Okibe N, Roberto FF (2003) Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics. Arch Microbiol 180:60–68

    Article  PubMed  CAS  Google Scholar 

  31. Johnson DB, Stallwood B, Kimura S, Hallberg KB (2006) Characteristics of Acidicaldus organivorus, gen. nov., sp. nov.; a novel thermo-acidophilic heterotrophic proteobacterium. Arch Microbiol 185:212–221

    Article  PubMed  CAS  Google Scholar 

  32. Kaplan CW, Kitts CL (2003) Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J Microbiol Meth 54:121–125

    Article  CAS  Google Scholar 

  33. Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69:6768–6776

    Article  PubMed  CAS  Google Scholar 

  34. Kvist T, Mengewein A, Manzei S, Ahring BK, Westermann P (2005) Diversity of thermophilic and non-thermophilic crenarchaeota at 80 °C. FEMS Microbiol Lett 244:61–68

    Article  PubMed  CAS  Google Scholar 

  35. Liu W-T, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

    PubMed  CAS  Google Scholar 

  36. Lopez-Archilla AI, Gonzalez AE, Terron MC, Amils R (2004) Ecological study of the fungal populations of the acidic Tinto River in southwestern Spain. Can J Microbiol 50:923–934

    Article  PubMed  CAS  Google Scholar 

  37. Macur RE, Langer HW, Kocar BD, Inskeep WP (2004) Linking geochemical processes with microbial community analysis: successional dynamics in an arsenic-rich, acid-sulphate-chloride geothermal spring. Geobiology 2:163–177

    Article  CAS  Google Scholar 

  38. Maheshwari R, Bharadwaj G, Bhat MK (2000) Thermophilic fungi: their physiology and enzymes. Microbiol Molec Biol Rev 64:461–488

    Article  CAS  Google Scholar 

  39. Männistö MK, Tiirola M, Häggblom MM (2007) Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent. FEMS Microbiol Ecol 59:452–465

    Article  PubMed  CAS  Google Scholar 

  40. Mathur J, Bizzoco RW, Ellis DG, Lipson DA, Poole AW, Levine R, Kelley ST (2007) Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs. Appl Environ Microbiol 73:2612–2623

    Article  PubMed  CAS  Google Scholar 

  41. Meyer-Dombard DR, Shock EL, Amend JP (2005) Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology 3:211–227

    Article  Google Scholar 

  42. Morales SE, Mouser PJ, Ward N, Hudman SP, Gotelli NJ, Ross DS, Lewis TA (2006) Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 52:34–44

    Article  PubMed  CAS  Google Scholar 

  43. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740

    Article  PubMed  CAS  Google Scholar 

  44. Pandey J, Ganesan K, Jain RK (2007) Variation in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J Microbiol Meth 68:633–638

    Article  CAS  Google Scholar 

  45. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730

    PubMed  CAS  Google Scholar 

  46. Ramette A, Tiedje JM (2007) Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology and evolution. Microb Ecol 53:197–207

    Article  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  48. Reysenbach A-L, Liu YT, Banta AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, Von Damm K, Voytek MA (2006) Isolation of a ubiquitous obligate thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442:444–447

    Article  PubMed  CAS  Google Scholar 

  49. Reysenbach A-L, Pace NR (1995) Reliable amplification of hyperthermophilic Archaeal 16S rRNA genes by the polymerase chain reaction, in Archaea-a laboratory manual (thermophiles). In: Robb FT, Place AR (eds) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 101–106

  50. Schwarz CJ, Seber GAF (1999) Estimating animal abundance: review III. Stat Sci 14:427–456

    Article  Google Scholar 

  51. Siering PL, Clarke JM, Wilson MS (2006) Geochemical and biological diversity of acidic, hot springs in Lassen Volcanic National Park. Geomicrobiol J 23:129–141

    Article  CAS  Google Scholar 

  52. Simmons S, Norris R (2002) Acidophiles of saline water at thermal vents of Vulcano, Italy. Extremophiles 6:201–207

    Article  PubMed  CAS  Google Scholar 

  53. Sittenfeld A, Mora M, Ortega JM, Albertazzi F, Cordero A, Roncel M, Sanchez E, Vargas M, Fernandez M, Weckesser J, Serrano A (2002) Characterization of a photosynthetic Euglena strain isolated from an acidic hot mud pool of a volcanic area of Costa Rica. FEMS Microbiol Ecol 42:151–161

    CAS  PubMed  Google Scholar 

  54. Smith CJ, Danilowicz BS, Clear AK, Costello FJ, Wilson B, Meijer WG (2005) T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol Ecol 54:375–380

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  56. Tansey MR, Brock TD (1972) The upper temperature limit for eukaryotic organisms. Proc Natl Acad Sci 69:2426–2428

    Article  PubMed  CAS  Google Scholar 

  57. Thompson JM (1985) Chemistry of thermal and nonthermal springs in the vicinity of Lassen Volcanic National Park. J Volcanol and Geotherm Energy 25:81–104

    Article  CAS  Google Scholar 

  58. USGS (2005) Steam explosions, earthquakes, and volcanic eruptions—what’s in Yellowstone’s Future? U.S. Geological Survey Fact Sheet 2005–3024. doi:http://pubs.usgs.gov/fs/2005/3024/

  59. von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  60. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science 301:976–978

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

Funding was provided by the California State University Program for Research and Education in Biotechnology (CSUPERB), Humboldt State University (HSU) Foundation, HSU Office of Research and Graduate Studies, and a departmental Howard Hughes Medical Institute undergraduate science education grant (Jacob Varkey, PI, grant no. 52002680). Anthony Baker (HSU) helped with logistical aspects, and Gordon Wolfe (CSU Chico) and Ken Stedman (Portland State University) assisted with sampling and thoughtful discussions. We would like to thank the anonymous reviewers for their comments, which led to significant improvements in the manuscript. We also thank LVNP Park staff, in particular Louise Johnson and Michael Magnuson, for their generous efforts assisting with site access and use of LVNP Science Center facilities for sample processing.

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  1. Department of Biology, Humboldt State University, 1 Harpst St., Arcata, CA, 95521, USA

    Mark S. Wilson, Patricia L. Siering, Christopher L. White, Michelle E. Hauser & Andrea N. Bartles

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  1. Mark S. Wilson
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  2. Patricia L. Siering
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  4. Michelle E. Hauser
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Correspondence to Mark S. Wilson.

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Wilson, M.S., Siering, P.L., White, C.L. et al. Novel Archaea and Bacteria Dominate Stable Microbial Communities in North America’s Largest Hot Spring. Microb Ecol 56, 292–305 (2008). https://doi.org/10.1007/s00248-007-9347-6

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