Advances and Challenges in Studying Cave Microbial Diversity

  • Naowarat Cheeptham
Part of the SpringerBriefs in Microbiology book series (volume 1)


In the last decade, we have seen significant changes in how we study composition and diversity of microbial communities in various environmental samples. Advances in culture-independent molecular phylogenetic techniques have made studies on microbial communities in diverse environments more attractive and feasible (Muyzer et al. 1993; Pace 1997; Torsvik et al. 1998; Hill et al. 2000; Giraffa and Neviani 2001; Kirk et al. 2004; Barton et al. 2004; Leckie 2005; Barton et al. 2006; Malik et al. 2008; Maukonen and Saarela 2009; Hirsch et al. 2010; and Northup et al. 2011). However, using modern molecular techniques alone to study both known and unknown microbial populations in an environment has its own limitations. Several studies suggest that using a combination of both culture-independent and culture-dependent methods gives a more realistic representation of the indigenous microbial diversity (Hill et al. 2000; Gurtner et al. 2000). For example in a 2000 study Gurtner and colleagues reported using of both classical cultivation techniques and molecular approaches to compare bacterial diversity on two medieval biodeteriorated wall paintings from two churches in Austria and Germany. They obtained 70 microbial sequences of 16S rDNA sequence belonging to several genera of bacteria. The molecular approach evaluated the bacterial community by Denaturing gradient gel electrophoresis (DGGE, one of the genetic fingerprinting tools), construction of 16S rDNA clone libraries, and sequence analysis of those libraries. In the same study, isolation of heterotrophic bacteria from one of the samples using Tripticase Soy (TSB) agar and TSB agar supplemented with 10 % sodium chloride (with 3 weeks of incubation at 28 °C) was also done in parallel to the above-mentioned molecular approach (Heyrman et al. 1999). The isolated strains were then characterized using fatty acid methyl ester (FAME) analysis and major FAME clusters found to belong to the genus Bacillus. Results from these two approaches failed to cross-detect similar microbial flora. In the molecular approach, 70 members of Actinobacteria and Proteobacteria including Actinobiospora, Amycolata, Halomonas, Deleya, Rhizobiam, and Salmonella were identified, while it is important to note that there was no Bacillus detected by the molecular approach. Their findings demonstrate that the combined approach of molecular and culturing techniques may provide a better understanding of the community being evaluated. There are other review and original research works that supported using a combined approach to study microbial diversity and function in a community (Dunbar et al 1999; Torsvik and Øvreås 2002; Crecchio et al 2004). Since no individual approach is completely effective to evaluate the microbial biodiversity of a given environment, this integrated approach may provide a closer representation of the microbial community. In its own context each of these approaches should be used and evaluated accordingly.


Microbial Community Microbial Diversity Cave System Lava Tube Cave Environment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Thanks go to Dr. Douglas Stemke of University of Indianapolis for his invaluable and critical suggestions for the manuscript and to Karen Densky and Jerri-Lynne Cameron of Thompson Rivers University for taking time to proofread.


  1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedGoogle Scholar
  2. Banks ED, Taylor NM, Gulley J et al (2010) Bacterial calcium carbonate precipitation in cave environments: a function of calcium homeostasis. Geomicrobiol J 27(5):444–454CrossRefGoogle Scholar
  3. Barton HA (2006) Introduction to cave microbiology: a review for the non-specialist. J Cave Karst Stud 68:43–54Google Scholar
  4. Barton HA, Jurado V (2007) What’s up down there? Microbial diversity in caves. Microbe 2:132–138Google Scholar
  5. Barton HA, Luiszer F (2005) Microbial metabolic structure in a sulfidic cave hot spring: potential mechanisms of biospeleogenesis. J Cave Karst Stud 67(1):28–38Google Scholar
  6. Barton HA, Northup DE (2007) Geomicrobiology in cave environments: past, current and future prospectives. J Cave Karst Stud 69:163–178Google Scholar
  7. Barton HA, Spear JR, Pace NR (2001) Microbial life in the underworld: biogenicity in secondary mineral formations. Geomicrobiol J 18(3):359–368CrossRefGoogle Scholar
  8. Barton HA, Taylor MR, Pace NR (2004) Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment. Geomicrobiol J 21:11–20CrossRefGoogle Scholar
  9. Barton HA, Taylor NM, Lubbers BR et al (2006) DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database. J Microbiol Methods 66:21–31PubMedCrossRefGoogle Scholar
  10. Barton HA, Taylor NM, Kreate M et al (2007) The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. Int J Speleol 36:93–104Google Scholar
  11. Bent SJ, Forney LJ (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2:689–695PubMedCrossRefGoogle Scholar
  12. Bonacci O, Pipan T, Culver DC (2009) A framework for karst ecohydrology. Environ Geol 56:891–900CrossRefGoogle Scholar
  13. Borda C, Borda D (2006) Airborne microorganisms in show caves from Romania. Biospeleology and physical speleology. Trav Inst Spéol “Émile Racovitza” 43–44:65–74Google Scholar
  14. Borda D, Borda C, Tămaş T (2004) Bats, climate, and air microorganisms in a Romanian cave. Mammalia 68(4):337–343CrossRefGoogle Scholar
  15. Boston PJ, Spilde MN, Northup DE et al (2001) Cave biosignature suites: microbes, minerals and Mars. Astrobiol J 1(1):25–55CrossRefGoogle Scholar
  16. Brown PB, Wolfe GV (2006) Protist genetic diversity in the acidic hydrothermal environments of Lassen Volcanic National Park, USA. J Eukaryot Microbiol 53:420–431PubMedCrossRefGoogle Scholar
  17. Cañaveras JC, Sanchez-Moral S, Soler V, Saiz-Jimenez C (2001) Microorganisms and microbially induced fabrics in cave walls. Geomicrobiol J 18:223–240CrossRefGoogle Scholar
  18. Cardoso P (2012) Diversity and community assembly patterns of epigean vs. troglobiont spiders in the Iberian Peninsula. Int J Speleol 41(1):83–94CrossRefGoogle Scholar
  19. Caumartin V (1963) Review of the microbiology of underground environments. Bull Natl Speleol Soc 25(1):1–14 (ISSN 0146-9517)Google Scholar
  20. Cheeptham N (2011) Drugs from the dark. BC caver: The newsletter of the British Columbia Speleological Federation. Winter 2010–2011, 25(1): 25–27Google Scholar
  21. Chen Y, Wu L, Boden R et al (2009) Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in movile cave. ISME J 3:1093–1104PubMedCrossRefGoogle Scholar
  22. Contos AK, James JM, Heywood B et al (2001) Morphoanalysis of bacterially precipitated subaqueous calcium carbonate from weebubbie cave, Australia. Geomicrobiol J 18(3):331–343CrossRefGoogle Scholar
  23. Crecchio C, Gelsomino A, Ambrosoli R et al (2004) Functional and molecular responses of soil microbial communities under differing soil management practices. Soil Biol Biochem 36(11):1873–1883CrossRefGoogle Scholar
  24. Dahllöf I (2002) Molecular community analysis of microbial diversity. Curr Opin Biotechnol 13(3):213–217PubMedCrossRefGoogle Scholar
  25. de los Ríos A, Bustillo MA, Ascaso C (2011) Bioconstructions in ochreous speleothems from lava tubes on Terceira Island (Azores). Sediment Geol 236(1–2):117–128CrossRefGoogle Scholar
  26. Dickson G (1979) The importance of cave mud sediments in food preferences, growth and mortality of the troglobitic invertebrates. Natl Speleol Soc Bulletin 37:89–93Google Scholar
  27. Dunbar J, Takala S, Barns SM et al (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65(4):1662–1669PubMedGoogle Scholar
  28. Duran M, Haznedaroğlu BZ, Zitomer DH (2006) Microbial source tracking using host specific FAME profiles of fecal coliforms. Water Res 40(1):67–74PubMedCrossRefGoogle Scholar
  29. Engel AS (2010) Microbial diversity of cave ecosystem. In: Barton LL et al (eds) Geomicrobiology: molecular and environmental perspective. Springer Science and Business Media B.V, The Netherlands, pp 219–238CrossRefGoogle Scholar
  30. Engel AS, Porter ML, Kinkle BK (2001) Ecological assessment and geological significance of microbial communities from cesspool cave, Virginia. Geomicrobiol J 18(3):259–274CrossRefGoogle Scholar
  31. Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43(8):1621–1625CrossRefGoogle Scholar
  32. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345(6270):60–63PubMedCrossRefGoogle Scholar
  33. Giraffa G, Neviani E (2001) DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems. Int J Food Micro 67(1–2):19–34CrossRefGoogle Scholar
  34. Gonzalez I, Laiz L, Hermosin B et al (1999) Bacteria isolated from rock art paintings: the case of Atlanterra shelter (south Spain). J Microbiol Methods 36(1–2):123–127CrossRefGoogle Scholar
  35. Gonzalez JM, Portillo MC, Saiz-Jimenez C (2006) Metabolically active crenarchaeota in altamira cave. Naturwissenschaften 93:42–45PubMedCrossRefGoogle Scholar
  36. Groth I, Vettermann R, Schuetze B et al (1999) Actinomycetes in karstic caves of northern Spain (altamira and tito bustillo). J Microbiol Methods 36:115–122PubMedCrossRefGoogle Scholar
  37. Groth I, Schumann P, Laiz L et al (2001) Geomicrobiological study of the grotta dei cervi, Porto Badisco, Italy. Geomicrobiol J 18(3):241–258CrossRefGoogle Scholar
  38. Gurtner C, Heyrman J, Piñar G et al (2000) Comparative analyses of the bacterial diversity on two different biodeteriorated wall paintings by DGGE and 16S rDNA sequence analysis. Int Biodeter Biodegr 46(3):229–239CrossRefGoogle Scholar
  39. Handelsman J (2004) Soils: metagenomics approach. In: Bull TA (ed) Microbial diversity and bioprospecting. ASM, Washington DC, pp 109–119Google Scholar
  40. Henneberger RM, Walter MR, Anitori RP (2006) Extraction of DNA from acidic, hydrothermally modified volcanic soils. Environ Chem 3:100–104CrossRefGoogle Scholar
  41. Herrera A, Cockell CS (2007) Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbiol Methods 70(1):1–12PubMedCrossRefGoogle Scholar
  42. Heyrman J, Mergaert J, Denys R (1999) The use of fatty acid methyl ester analysis (FAME) for the identification of heterotrophic bacteria present on three mural paintings showing severe damage by microorganisms. FEMS Microbiol Lett 181(1):55–62PubMedCrossRefGoogle Scholar
  43. Hill G, Mitkowski NA, Aldrich-Wolfe L et al (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15(1):25–36CrossRefGoogle Scholar
  44. Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry 42(6):878–887CrossRefGoogle Scholar
  45. Höeg OA (1946) Cyanophyceae and bacteria in calcareous sediments in the interior of limestone caves in Nord-Rana. Norway Nytt Mag Naturvidensk 85:99–104Google Scholar
  46. Hose LD, Palmer AN, Palmer MV et al (2000) Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment. Chem Geol 169(3–4):399–423CrossRefGoogle Scholar
  47. Howarth FG (1983) Ecology of cave arthropods. Annu Rev Entomol 28(1):365–389CrossRefGoogle Scholar
  48. Howarth FG (2004) Hawaiian islands, biospeleology. In: Gunn J (ed) Encyclopedia of cave and karst science. Fitzroy Dearborn, New York, pp 417–419Google Scholar
  49. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774PubMedGoogle Scholar
  50. Jones B (2010) Microbes in caves: agents of calcite corrosion and precipitation. Tufas and speleothems: unravelling the microbial and physical controls. University of Alberta, p 9–10.Google Scholar
  51. Jurado V, Groth I, Gonzalez JM et al (2005) Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 55:1897–1901PubMedCrossRefGoogle Scholar
  52. Jurado V, Gonzalez JM, Laiz L et al (2006) Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from altamira cave. Int J Syst Evol Microbiol 56:2583–2585PubMedCrossRefGoogle Scholar
  53. Kirk JL, Beaudette LA, Hart M et al (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58(2):169–188PubMedCrossRefGoogle Scholar
  54. Koch AL (2001) Oligotrophs versus copiotrophs. Bioessays 23:657–661PubMedCrossRefGoogle Scholar
  55. Kuhlman KR, Fusco WG, La Duc MT et al (2006) Diversity of microorganisms within rock varnish in the Whipple Mountains, California. Appl Environ Microbiol 72(2):1708–1715PubMedCrossRefGoogle Scholar
  56. Kuhlman KR, Venkat P, La Duc MT et al (2008) Evidence of a microbial community associated with rock varnish at Yungay, Atacama Desert, Chile. J Geophy Res 113(G04022):14Google Scholar
  57. Laiz L, Groth I, Gonzalez I et al (1999) Microbiological study of the dripping waters in altamira cave (Santillana del mar, Spain). J Microbiol Methods 36:129–138PubMedCrossRefGoogle Scholar
  58. Lavoie KH, Northup DE, Barton HA (2010) Microbe–mineral interactions. In: Sudhir KJ, Khan AA, Rai MA (eds) Cave microbiology. Science Publishers, Enfield, NH, pp 1–45Google Scholar
  59. Leckie SE (2005) Methods of microbial community profiling and their application to forest soils. For Ecol Manage 220(1–3):88–106CrossRefGoogle Scholar
  60. Lerch TZ, Dignac M-F, Nunan N et al (2009) Dynamics of soil microbial populations involved in 2,4-D biodegradation revealed by FAME-based stable isotope probing. Soil Biology and Biochemistry 41(1):77–85CrossRefGoogle Scholar
  61. Léveillé RJ, Datta S (2009) Lava tubes and basaltic caves as astrobiological targets on Earth and Mars: a review. Planet Space Sci. doi: 10.1016/j.pss.2009.06.004
  62. Léveillé RJ, Longstaffe FJ, Fyfe WP (2002) Kerolite in carbon-rich speleothems and microbial deposits from basaltic caves, Kuai, Hawaii. Clays Clay Miner 50(4):514–524CrossRefGoogle Scholar
  63. Lysnes K, Thorseth IH, Steinsbu BO, Øvreås L, Torsvik T, Pedersen RB (2004) Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol 50(3):213–230PubMedCrossRefGoogle Scholar
  64. Macalady J, Banfield JF (2003) Molecular geomicrobiology: genes and geochemical cycling. Earth Planet Sci Lett 212(1–2):1–17CrossRefGoogle Scholar
  65. Malik S, Beer M, Megharaj M et al (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34(2):265–276PubMedCrossRefGoogle Scholar
  66. Maukonen J, Saarela M (2009) Microbial communities in industrial environment. Curr Opin Microbiol 12(3):238–243PubMedCrossRefGoogle Scholar
  67. Maukonen J, Simões C, Saarela M (2012) The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiol Ecol 79(3):697–708PubMedCrossRefGoogle Scholar
  68. Melim LA, Shinglman KM, Boston PJ et al (2001) Evidence for microbial involvement in pool finger precipitation, hidden cave, New Mexico. Geomicrobiol J 18(3):311–329CrossRefGoogle Scholar
  69. Moser DP, Boston PJ, Martin HW (2003) Caves and mines microbiological sampling. Encyclopedia of Environmental Microbiology. Wiley, New YorkGoogle Scholar
  70. Murray AE, Hollibaugh JT, Orrego C (1996) Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 62(7):2676–2680PubMedGoogle Scholar
  71. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73(1):127–141PubMedCrossRefGoogle Scholar
  72. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700PubMedGoogle Scholar
  73. Nakaew N, Pathom-aree W, Lumyong S (2009a) First record of the isolation. Identification and biological activity of a new strain of spirillospora albida from thai cave Soil. Actinomycetologica 23(1):1–7CrossRefGoogle Scholar
  74. Nakaew N, Pathom-aree W, Lumyong S (2009b) Generic diversity of rare actinomycetes from thai cave soils and their possible use as new bioactive compounds. Actinomycetologica 23(2):21–26CrossRefGoogle Scholar
  75. Northup DE, Lavoie KH (2001) Geomicrobiology of caves: a review. Geomicrobiol J 18(3):199–222CrossRefGoogle Scholar
  76. Northup DE, Welbourn WC (1997) Life in the twilight zone: lava tube ecology. New Mexico Bur Mines Miner Resour Bull 156:69–82Google Scholar
  77. Northup DE, Barnes SM, Yu LE et al (2003) Diverse microbial communities inhabiting ferromanganese deposits in lechuguilla and spider caves. Environ Microbiol 5:1071–1086PubMedCrossRefGoogle Scholar
  78. Northup DE, Connolly CA, Trent A et al (2004) The Nature of bacterial communities in four windows cave, El Malpais National Monument, New Mexico, USA. AMCS Bull 19:119–125Google Scholar
  79. Northup DE, Melim LA, Spilde MN et al (2011) Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology 11(7):601–618PubMedCrossRefGoogle Scholar
  80. Onac BP, Forti P (2011) Minerogenetic mechanisms occurring in the cave environment: an overview. Int J Speleol 40(2):79–98CrossRefGoogle Scholar
  81. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740PubMedCrossRefGoogle Scholar
  82. Palmer AN (2007) Cave geology and speleogenesis over the past 65 years: Roles of the national speleological society in advancing the science. J Cave Karst Stud 69(1):3–12Google Scholar
  83. Pankratov TA, Serkebaeva YM, Kulichevskaya IS et al (2008) Substrate-induced growth and isolation of Acidobacteria from acidic sphagnum peat. ISME J 2:551–560PubMedCrossRefGoogle Scholar
  84. Pedersen K (2000) Exploration of deep intraterrestrial microbial life: current perspectives. FEMS Microbiol Lett 185(1):9–16PubMedCrossRefGoogle Scholar
  85. Priscu JC, Adams EE, Lyons WB et al (1999) Geomicrobiology of subglacial ice above Lake Vostok, Antarctica. Science 286(5447):2141–2144PubMedCrossRefGoogle Scholar
  86. Purdy KJ, Embley TM, Takii S et al (1996) Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl Environ Microbiol 62:3905–3907Google Scholar
  87. Rastogi G, Sani RK (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In: Ahmad I et al (eds) Microbes and microbial technology; agricultural and environmental applications. Springer Science  +  Business Media, LLC., New York, pp 29–57, DOI  10.1007/978-1-4419-7391-5_2 CrossRefGoogle Scholar
  88. Rheims H, Rainey FA, Stackebrandt E (1996) A molecular approach to search for diversity among bacteria in the environment. J Ind Microbiol 17:159–169CrossRefGoogle Scholar
  89. Robe P, Nalin R, Capellano C, Vogel T, Simonet P (2003) Extraction of DNA from soil. Euro J Soil Biol 39(4):183–190CrossRefGoogle Scholar
  90. Rohwerder T, Sand W, Lascu C (2003) Preliminary evidence for a sulphur cycle in movile cave, Romania. Acta Biotechnol 23(1):101–107CrossRefGoogle Scholar
  91. Rondon MR, Goodman RM, Handelsman J (1999) The Earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17(10):403–409PubMedCrossRefGoogle Scholar
  92. Rule D, Sadoway T, Moote P et al (2011) Cures from caves: cave microbiomes and their potential for drug discovery. Oral presentation presented at the 111th American Society for microbiology general meeting, New Orleans, LA, 21–24 May 2011Google Scholar
  93. Rusu A, Hillebrand A, Persoiu A (2011) Biodiversity of microorganisms in perennial ice deposits from Scarisoara ice cave (Romania). First international planetary caves workshop: implications for astrobiology, climate, detection, and exploration, Carlsbad, New Mexico, 25–28 Oct 2011. LPI contribution no. 1640, p 37Google Scholar
  94. Sadoway T, Cheeptham N (2011) Susceptibility of three drug–resistant, gram–negative pathogens to antimicrobial compounds produced by cave actinomycetes. Poster presented at the 111th American Society for microbiology general meeting, New Orleans, LA, 21–24 May 2011Google Scholar
  95. Sărbu SM (1991) The unusual fauna of a cave with thermomineral waters containing hydrogen sulfide from southern Dobrogea Romania. Mémoir Biospéol 17:191–196Google Scholar
  96. Sărbu SM, Popa R (1992) A unique chemoautotrophically based cave ecosystem. In: Camacho AI (ed) The natural history of biospeleology, Museo Nacional de Ciencias Naturales. Consejo Superior de Investigaciones Científicas, Madrid, pp 637–666Google Scholar
  97. Sărbu SM, Kane TC, Kinkle BK (1996) A chemoautotrophically based cave ecosystem. Science 272(5270):1953–1955PubMedCrossRefGoogle Scholar
  98. Schabereiter-Gurtner C, Lubitz W, Rölleke S (2003) Application of broad-range 16S rRNA PCR amplification and DGGE fingerprinting for detection of tick-infecting bacteria. J Microbiol Methods 52(2):251–260PubMedCrossRefGoogle Scholar
  99. Simon KS, Benfield EF, Macko SA (2003) Food web structure and the role of epilithic biofilms in cave streams. Ecology 84:2395–2406CrossRefGoogle Scholar
  100. Slabbinck B, De Baets B, Dawyndt P et al (2009) Towards large-scale FAME-based bacterial species identification using machine learning techniques. Syst Appl Microbiol 32(3):163–176PubMedCrossRefGoogle Scholar
  101. Smalla K (2004) Microorganisms culture-independent microbiology. In: Bull TA (ed) Microbial diversity and bioprospecting. ASM, Washington DC, pp 88–99Google Scholar
  102. Snider JR, Goin C, Miller R et al (2009) Ultraviolet radiation sensibility in cave bacteria: evidence of adaptation to the subsurface? Int J Speleol 38(1):13–22Google Scholar
  103. Spear JR, Barton HA, Robertson CE et al (2007) Microbial community biofabrics in a geothermal mine adit. Appl Environ Microbiol 73(19):6172–6180PubMedCrossRefGoogle Scholar
  104. Storrie-Lombardi MC, Sattler B (2009) Laser-induced fluorescence emission (L.I.F.E.): in situ nondestructive detection of microbial life in the ice covers of Antarctica Lakes. Astrobiology 9(7):659–671PubMedCrossRefGoogle Scholar
  105. Storrie-Lombardi MC, Muller JP, Fisk MR et al (2009) Laser-induced fluorescence emission (L.I.F.E.): searching for mars organics with a UV-enhanced PanCam. Astrobiology 9(7):953–964PubMedCrossRefGoogle Scholar
  106. Sugita T, Kikuchi K, Makimura K et al (2005) Trichosporon species isolated from guano samples obtained from bat-inhabited caves in Japan. Appl Environ Microbiol 71(11):7626–7629PubMedCrossRefGoogle Scholar
  107. Takada Hoshino Y, Matsumoto N (2005) Skim milk drastically improves the efficacy of DNA extraction from andisol, a vulcanic ash soil. Jpn Agri Res Quat 39:247–252Google Scholar
  108. Thorseth IH, Torsvik T, Torsvik V, Daae FL, Pedersen RB, Party K-S (2001) Diversity of life in ocean floor basalt. Earth Planet Sci Lett 194:31–37CrossRefGoogle Scholar
  109. Tiedje JM, Asuming-Brempong S, Nüsslein K (1999) Opening the black box of soil microbial diversity. Applied Soil Ecology 13(2):109–122CrossRefGoogle Scholar
  110. Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5(3):240–245PubMedCrossRefGoogle Scholar
  111. Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56(3):782–787PubMedGoogle Scholar
  112. Torsvik V, Daae FL, Sandaa RA et al (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64(1):53–62PubMedCrossRefGoogle Scholar
  113. Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309(1):1–7PubMedGoogle Scholar
  114. Volossiouk T, Robb EJ, Nazar RN (1995) Direct DNA extraction for PCR–mediated assays of soil organisms. Appl Environ Microbiol 61:3972–3976PubMedGoogle Scholar
  115. Wade BD, Garcia-Pichel F (2003) Evaluation of DNA extraction methods for molecular analyses of microbial communities in Modern calcareous microbialites. Geomicrobiol J 20:549–561CrossRefGoogle Scholar
  116. Walker JJ, Pace NR (2007) Phylogenetic composition of rocky mountain endolithic microbial ecosystems. Appl Environ Microbiol 73(11):3497–3504PubMedCrossRefGoogle Scholar
  117. Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434:1011–1014CrossRefGoogle Scholar
  118. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345(6270):63–65PubMedCrossRefGoogle Scholar
  119. Weidler GW, Dornmayr-Pfaffenhuemer M, Gerbl FW et al (2007) Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing crenarchaeota. Appl Environ Microbiol 73(1):259–270PubMedCrossRefGoogle Scholar
  120. Willerslev E, Hansen AJ, Poinar HN (2004) Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol 19:141–147PubMedCrossRefGoogle Scholar
  121. Yakimov MM, Giuliano L, Crisafi E et al (2002) Microbial community of a saline mud volcano at San Biagio–Belpasso, Mt. Etna (Italy). Environ Microbiol 4:256CrossRefGoogle Scholar
  122. Yücel S, Yamaç M (2010) Selection of streptomyces isolates from Turkish karstic caves against antibiotic resistant microorganisms. Pak J Pharm Sci 23(1):1–6PubMedGoogle Scholar
  123. Zhou J, Gu Y, Zou C et al (2007) Phylogenetic diversity of bacteria in an earth-cave in Guizhou province, southwest of China. J Microbiol 45(2):105–112PubMedGoogle Scholar

Copyright information

© Naowarat Cheeptham 2013

Authors and Affiliations

  1. 1.Thompson Rivers UniversityKamloopsCanada

Personalised recommendations