Microbial Diversity in Caves

References

• Adetutu EM, Thorpe K, Shahsavari E, Bourne S, Cao X, Mazaheri Nezhad Fard R, Kirby G, Ball AS. 2012. Bacterial community survey of sediments at Naracoorte Caves, Australia. Int J Speleol 41:137–147.
   Web of Science ®Google Scholar
• Angert ER, Northup DE, Reysenbach AL, Peek AS, Goebel BM, Pace NR. 1998. Molecular phylogenetic analysis of a bacterial community in Sulphur River, Parker Cave, Kentucky. Am Mineral 83:1583–1592.
   Web of Science ®Google Scholar
• Baker BJ, Banfield JF. 2003. Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44:139–152.
   PubMed Web of Science ®Google Scholar
• Banerjee S, Joshi SR. 2013. Insights into cave architecture and the role of bacterial biofilm. Proc Natl Acad Sci India Sect B Biol Sci 83:277–290.
   Web of Science ®Google Scholar
• Barns SM, Cain EC, Sommerville L, Kuske CR. 2007. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73:3113–3116.
   PubMed Web of Science ®Google Scholar
• Barton HA, Jurado V. 2007. What's up down there? Microbial diversity in caves. Microbe 2:132–138.
   Google Scholar
• Barton HA, Spear JR, Pace NR. 2001. Microbial life in the underworld: biogenicity of secondary mineral formation. Geomicrobiol J 18:359–368.
   Web of Science ®Google Scholar
• Barton HA, Taylor NM, Kreate MP, Springer AC, Oehrle SA, Bertog JL. 2007. The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. Int J Speleol 36:93–104.
   Web of Science ®Google Scholar
• Bastian F, Alabouvette C, Saiz-Jimenez C. 2009. Bacteria and free-living amoeba in the Lascaux Cave. Res Microbiol 160:38–40.
   PubMed Web of Science ®Google Scholar
• Bastian F, Jurado V, Novakova A, Alabouvette C, Saiz-Jimenez C. 2010. The microbiology of Lascaux Cave. Microbiology 156:644–652.
   PubMed Web of Science ®Google Scholar
• Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. 2011. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 43:1450–1455.
   PubMed Web of Science ®Google Scholar
• Bottomley PJ. 1992. Ecology of Bradyrhizobium, and Gluconoacetobacter diazotrophicusobium. In: Stacey G, Burris RH, Evans HJ, editors. Biological Nitrogen Fixation. London, UK: Chapman and Hall New York, p.293–348.
   Google Scholar
• Brigmon RL, Furlong M, Whitman WB. 2003. Identification of Thiothrix unzii in two distinct ecosystems. Lett Appl Microbiol 36:88–91.
   PubMed Web of Science ®Google Scholar
• Brofft JE, McArthur JV, Shimkets LJ. 2002. Recovery of novel bacterial diversity from a forested wetland impacted by reject coal. Environ Microbiol 4:764–769.
   PubMed Web of Science ®Google Scholar
• Canaveras JC, Sanchez-Moral S, Soler V, Saiz-Jimenez C. 2001. Microorganisms and microbially induced fabrics in cave walls. Geomicrobiol J 18:223–240.
   Web of Science ®Google Scholar
• Carmichael MJ, Carmichael SK, Santelli CM, Strom A, Bräuer SL. 2013. Mn(II)-oxidizing bacteria are abundant and environmentally relevant members of ferromanganese deposits in caves of the upper Tennessee River Basin. Geomicrobiol J 30:779–800.
   Web of Science ®Google Scholar
• Cavicchioli R. 2011. Archaea — timeline of the third domain. Nat Rev Micro 9:51–61.
   PubMed Web of Science ®Google Scholar
• Chelius MK, Moore JC. 2004. Molecular phylogenetic analysis of Archaea and Bacteria in Wind Cave, South Dakota. Geomicrobiol J 21:123–134.
   Web of Science ®Google Scholar
• Chen Y, Wu L, Boden R, Hillebrand A, Kumaresan D, Moussard H, Baciu M, Lu Y, Colin Murrell J. 2009. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. ISME J 3:1093–1104.
   PubMed Web of Science ®Google Scholar
• Chesson P, Pacala SW, Neuhauser C. 2002. Environmental niches and ecosystem functioning. In: Kinzig AP, Pacala SW, Tilman D, editors. The functional consequences of biodiversity: empirical progress and theoretical extensions. New York: Princeton University Press., p. 213–245.
   Google Scholar
• Coates JD, Ellis DJ, Gaw CV, Lovley DR. 1999. Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49:1615–1622.
   PubMedGoogle Scholar
• DeLong EF. 1998. Everything in moderation: Archaea as ‘non-extremophiles. Curr Opin Genet Dev 8:649–654.
   PubMed Web of Science ®Google Scholar
• Donachie SP, Foster JS, Brown MV. 2007. Culture clash: challenging the dogma of microbial diversity. ISME J 1:97–99.
   PubMed Web of Science ®Google Scholar
• Dorigo U, Volatier L, Humbert JF. 2005. Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res 39:2207–2218.
   PubMed Web of Science ®Google Scholar
• Dworkin M. 2002. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. New York: Springer-Verlag.
   Google Scholar
• Engel AS. 2010. Microbial diversity of cave ecosystems. In: Loy A, Mandl M, Barton LL, editors. Geomicrobiology: molecular and environmental perspective. The Netherlands: Springer Science+Business Media B.V. p219–238.
   Google Scholar
• Engel AS, Lee N, Porter ML, Stern LA, Bennett PC, Wagner M. 2003. Filamentous ‘Epsilonproteobacteria’ dominate microbial mats from sulfidic cave springs. Appl Environ Microbiol 69:5503–5511.
   PubMed Web of Science ®Google Scholar
• Engel AS, Meisinger DB, Porter ML, Payn RA, Schmid M, Stern LA, Schleifer KH, Lee NM. 2010. Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA). ISME J 4:98–110.
   PubMed Web of Science ®Google Scholar
• Engel AS, Porter ML, Kinkle BK, Kane TC. 2001. Ecological assessment and geological significance of microbial communities from Cesspool Cave, Virginia. Geomicrobiol J 8:259–274.
   Google Scholar
• Engel AS, Porter ML, Stern LA, Quinlan S, Bennett PC. 2004. Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic “Epsilonproteobacteria”. FEMS Microbiol Ecol 51:31–53.
   PubMed Web of Science ®Google Scholar
• Frederiksen TM, Finster K. 2004. The transformation of inorganic sulfur compounds and the assimilation of organic and inorganic carbon by the sulfur disproportionating bacterium Desulfocapsa sulfoexigens. Anton Van Leeuwen 85:141–149.
   PubMed Web of Science ®Google Scholar
• Freitas S, Hatosy S, Fuhrman JA, Huse SM, Mark Welch DB, Sogin ML, Martiny AC. 2012. Global distribution and diversity of marine Verrucomicrobia. ISME J 6:1499–1505.
   PubMed Web of Science ®Google Scholar
• Fuchsman CA, Staley JT, Oakley BB, Kirkpatrick JB, Murray JW. 2012. Free-living and aggregate-associated Planctomycetes in the Black Sea. FEMS Microbiol Ecol 80:402–416.
   PubMed Web of Science ®Google Scholar
• Fuerst JA, Sagulenko E. 2011. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Micro 9:403–413.
   PubMed Web of Science ®Google Scholar
• Fukui M, Teske A, Assmus B, Muyzer G, Widdel F. 1999. Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema). Arch Microbiol 172:193–203.
   PubMed Web of Science ®Google Scholar
• Gadd GM. 2010. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156:609–643.
   PubMed Web of Science ®Google Scholar
• Gevertz D, Telang AJ, Voordouw G, Jenneman GE. 2000. Isolation and characterization of strains CVO and FWKO B, two novel nitrate-reducing, sulfide-oxidizing bacteria isolated from oil field brine. Appl Environ Microbiol 66:2491–2501.
   PubMed Web of Science ®Google Scholar
• Golyshina OV, Pivovarova TA, Karavaiko GI, Moore ER, Abracham WR, Lünsdorf H, Timmis KN, Yakimov MM, Golyshin PN. 2000. Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrou-iron-oxidizing, cell-wall-lacking mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiolobiol 50:997–1006.
   PubMed Web of Science ®Google Scholar
• Golyshina OV, Timmis KN. 2005. Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments. Environ Microbiol 7:1277–1288.
   PubMed Web of Science ®Google Scholar
• Gonzales JM, Portillo MC, Saiz-Jimenez C. 2006. Metabolically active Crenarchaeaota in Altamira Cave. Naturwissenschaften 93:42–45.
   PubMed Web of Science ®Google Scholar
• Grotenhuis JT, Smit M, Plugge CM, Xu YS, van Lammeren AA, Stams AJ, Zehnder AJ. 1991. Bacteriological composition and structure of granular sludge adapted to different substrates. Appl Environ Microbiol 57:1942–1949.
   PubMed Web of Science ®Google Scholar
• Groth I, Saiz-Jimenez C. 1999. Actinomycetes in hypogean environments. Geomicrobiol J 16:1–8.
   Web of Science ®Google Scholar
• Groth I, Schumann P, Laiz L, Sanchez-Moral S, Cañaveras JC, Sáiz-Jiménez C. 2001. Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. Geomicrobiol J 18:241–258.
   Web of Science ®Google Scholar
• Groth I, Vettermann R, Schuetze B, Schumann P, Saiz-Jimenez C. 1999. Actinomycetes in karstic caves of northern Spain (Altamira and Tito Bustillo). J Microbiol Methods 36:115–122.
   PubMed Web of Science ®Google Scholar
• Hathaway JJM, Garcia MG, Balasch MM, Spilde MN, Stone FD, Dapkevicius MLNE, Amorim IR, Gabriele R, Borges PAV, Northup DE. 2014. Comparison of bacterial diversity in Azorean and Hawai'ian lava cave microbial mats. Geomicrobiol J 31:205–220.
   PubMed Web of Science ®Google Scholar
• Holmes DE, Nevin KP, Lovley DR. 2004. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54:1591–1599.
   PubMed Web of Science ®Google Scholar
• Howarth R, Unz RF, Seviour EM, Seviour RJ, Blackall LL, Pickup RW, Jones JG, Yaguchi J, Head IM. 1999. Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov. Int J Syst Bacteriol 49:1817–1827.
   PubMedGoogle Scholar
• Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774.
   PubMed Web of Science ®Google Scholar
• Hutchens E, Radajewski S, Dumont MG, McDonald IR, Murrell JC. 2004. Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol 6:111–120.
   PubMed Web of Science ®Google Scholar
• Ikner LA, Toomey RS, Nolan G, Neilson JW, Pryor BM, Maier RM. 2007. Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona. Microb Ecol 53:30–42.
   PubMed Web of Science ®Google Scholar
• Ivanova AO, Dedysh SN. 2012. Abundance, diversity, and depth distribution of planctomycetes in acidic northern wetlands. Front Microbiol 3:1–9.
   PubMed Web of Science ®Google Scholar
• Janssen PH, Schuhmann A, Bak F, Liesack W. 1996. Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen.nov., sp. nov. Arch Microbiol 166:184–192.
   Web of Science ®Google Scholar
• Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396.
   PubMed Web of Science ®Google Scholar
• Jogler C, Niebler M, Lin W, Kube M, Wanner G, Kolinko S, Stief P, Beck AJ, de Beer D, Petersen N et al. 2010. Cultivation-independent characterization of ‘Candidatus Magnetobacterium bavaricum’ via ultrastructural, geochemical, ecological and metagenomic methods. Environ Microbiol 12:2466–2478.
   PubMed Web of Science ®Google Scholar
• Jones B. 2001. Microbial activity in caves - a geological perspective. Geomicrobiol J 18:345–357.
   Web of Science ®Google Scholar
• Jones AA, Bennett PC. 2014. Mineral microniches control the diversity of subsurface microbial populations. Geomicrobiol J 31:246–261.
   Web of Science ®Google Scholar
• Jones DS, Tobler DJ, Schaperdoth I, Mainiero M, Macalady JL. 2010. Community structure of subsurface biofilms in the thermal sulfidic caves of Acquasanta Terme, Italy. Appl Environ Microbiol 76:5902–5910.
   PubMed Web of Science ®Google Scholar
• Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. 2003. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215.
   PubMed Web of Science ®Google Scholar
• Jousset A. 2012. Ecological and evolutive implications of bacterial defences against predators. Environ Microbiol 14:1830–1843.
   PubMed Web of Science ®Google Scholar
• Kalyuzhnaya MG, Bowerman S, Lara JC, Lidstrom ME, Chistoserdova L. 2006. Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae. Int J Syst Evol Microbiol 56:2819–2823.
   PubMed Web of Science ®Google Scholar
• Kishimoto N, Kosako Y, Tano T. 1991. Acidobacterium capsulatum gen. nov., sp. nov. an acidophilic, chemoorganotrophic bacterium containing menaquinone. Curr Microbiol 22:1–7.
   Web of Science ®Google Scholar
• Kunisawa T. 2010. Evaluation of the phylogenetic position of the sulfate-reducing bacterium Thermodesulfovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes. Int J Syst Evol Microbiol 60:1090–1102.
   PubMed Web of Science ®Google Scholar
• Laiz L, Groth I, Gonzalez I, Saiz-Jimenez C. 1999. Microbiological study of the dripping waters in Altamira Cave (Santillana del Mar, Spain). J Microbiol Methods 36:129–138.
   PubMed Web of Science ®Google Scholar
• Lee NM, Meisinger DB, Aubrecht IR, Kovacik L, Porter ML, Engel AS. 2012. 16 caves and karst environments. Life at extremes: environments, organisms, and strategies for survival 1:320.
   Google Scholar
• Lefèvre CT, Frankel RB, Abreu F, Lins U, Bazylinski DA. 2011. Culture-independent characterization of a novel, uncultivated magnetotactic member of the Nitrospirae phylum. Environ Microbiol 13:538–549.
   PubMed Web of Science ®Google Scholar
• Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki T. 2004. Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the russian space laboratory Mir. Int J Syst Evol Microbiol 54:819–825.
   PubMed Web of Science ®Google Scholar
• Liesack W, Bak F, Kreft JU, Stackebrandt E. 1994. Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162:85–90.
   PubMed Web of Science ®Google Scholar
• Lopez-Garcia P, Duperron S, Philippot P, Foriel J, Susini J, Moreira D. 2003. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ Microbiol 5:961–976.
   PubMed Web of Science ®Google Scholar
• Macalady JL, Dattagupta S, Schaperdoth I, Jones DS, Druschel GK, Eastman D. 2008. Niche differentiation among sulfur-oxidizing bacterial populations in cave waters. ISME J 2(6):590–601.
   PubMed Web of Science ®Google Scholar
• Macalady JL, Jones DS, Lyon EH. 2007. Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Environ Microbiol 9:1402–1414.
   PubMed Web of Science ®Google Scholar
• Macalady JL, Lyon EH, Koffman B, Albertson LK, Meyer K, Galdenzi S, Mariani S. 2006. Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl Environ Microbiol 72:5596–5609.
   PubMed Web of Science ®Google Scholar
• Meisinger DB, Zimmermann J, Ludwig W, Schleifer KH, Wanner G, Schmid M, Bennett PC, Engel AS, Lee NM. 2007. In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA). Environ Microbiol 9:1523–1534.
   PubMed Web of Science ®Google Scholar
• Melim LA, Liescheidt R, Northup DE, Spilde MN, Boston PJ, Queen JM. 2009. A biosignature suite from cave pool precipitates, Cottonwood cave, New Mexico. Astrobiology 9:907–917.
   PubMed Web of Science ®Google Scholar
• Mohn WW, Tiedje JM. 1992. Microbial reductive dehalogenation. Microbiol Rev 56:482–507.
   PubMedGoogle Scholar
• Moter A, Göbel UB. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85–112.
   PubMed Web of Science ®Google Scholar
• Nelson DC, Revsbech NP, Jorgensen BB. 1986. Microoxic-anoxic niche of Beggiatoa spp.: microelectrode survey of marine and freshwater strains. Appl Environ Microbiol 52:161–8.
   PubMed Web of Science ®Google Scholar
• Nemati M, Jenneman GE, Voordouw G. 2001. Mechanistic study of microbial control of hydrogen sulfide production in oil reservoirs. Biotechnol Bioeng 74:424–434.
   PubMed Web of Science ®Google Scholar
• Norris PR, Clark DA, Owen JP, Waterhouse S. 1996. Characteristics of Sulfobacillus acidophilus sp. nov. and other moderately thermophilic mineral-sulphide-oxidizing bacteria. Microbiology 142:775–783.
   PubMed Web of Science ®Google Scholar
• Northup DE, Barns SM, Yu LE, Spilde MN, Schelble RT, Dano KE, Crossey LJ, Connolly CA, Boston PJ, Natvig DO, Dahm CN. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environ Microbiol 5:1071–1086.
   PubMed Web of Science ®Google Scholar
• Northup DE, Lavoie KH. 2001. Geomicrobiol of caves: a review. Geomicrobiol J 18:199–222.
   Web of Science ®Google Scholar
• Northup DE, Melim LA, Spilde MN, Hathaway JJ, Garcia MG, Moya M, Stone FD, Boston PJ, Dapkevicius ML, Riquelme C. 2011. Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology 11:601–618.
   PubMed Web of Science ®Google Scholar
• Okibe N, Gericke M, Hallberg KB, Barrie Johnson D. 2003. Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred-tank bioleaching operation. Appl Environ Microbiol 69:1936–1943.
   PubMed Web of Science ®Google Scholar
• Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A, Dunfield PF. 2009. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Reports 1:293–306.
   PubMed Web of Science ®Google Scholar
• Ortiz M, Neilson JW, Nelson WM, Legatzki A, Byrne A, Yu Y, Wing RA, Soderlund CA, Pryor BM, Pierson LS, Maier RM. 2013. Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. Microb Ecol 65:371–383.
   PubMed Web of Science ®Google Scholar
• Pasic L, Kovce B, Sket B, Herzog-Velikonja B. 2010. Diversity of microbial communities colonizing the walls of a karstic cave in Slovenia. FEMS Microbiol Ecol 71:50–60.
   PubMed Web of Science ®Google Scholar
• Pohlman JW, Iliffe TM, Cifuentes LA. 1997. A stable isotope study of organic cycling and the ecology of an anchialine cave ecosystem. Mar Ecol Prog Ser 155:17–27.
   Web of Science ®Google Scholar
• Portillo MC, Gonzalez JM, Saiz-Jimenez C. 2008. Metabolically active microbial communities of yellow and grey colonizations on the walls of Altamira Cave, Spain. J Appl Microbiol 104:681–691.
   PubMed Web of Science ®Google Scholar
• Portillo MC, Saiz-Jimenez C, Gonzalez JM. 2009. Molecular characterization of total and metabolically active bacterial communities of “white colonizations” in the Altamira Cave, Spain. Res Microbiol 160:41–47.
   PubMed Web of Science ®Google Scholar
• Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Environ Microbiol 50:563–575.
   Google Scholar
• Quintana E, Badillo R, Maldonado L. 2013. Characterisation of the first actinobacterial group isolated from a mexican extremophile environment. Anton van Leeuwen 104:63–70.
   PubMed Web of Science ®Google Scholar
• Romero A. 2012. Caves as biological spaces. Polymath: Interdisc Arts Sci J 2:1–15.
   Google Scholar
• Rossmassler K, Engel AS, Twing KI, Hanson TE, Campbell BJ. 2012. Drivers of epsilonproteobacterial community composition in sulfidic caves and springs. FEMS Microbiol Ecol 79:421–432.
   PubMed Web of Science ®Google Scholar
• Rusznyak A, Akob DM, Nietzsche S, Eusterhues K, Totsche KU, Neu TR, Frosch T, Popp J, Keiner R, Geletneky J et al. 2012. Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic Herrenberg Cave. Appl Environ Microbiol 78:1157–1167.
   PubMed Web of Science ®Google Scholar
• Saiz-Jimenez C, Cuezva S, Jurado V, Fernandez-Cortes A, Porca E, Benavente D, Cañaveras JC, Sanchez-Moral S. 2011. Paleolithic art in peril: policy and science collide at Altamira Cave. Science 334:42–43.
   PubMed Web of Science ®Google Scholar
• Sait M, Davis KE, Janssen PH. 2006. Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Environ Microbiol 72:1852–1857.
   PubMed Web of Science ®Google Scholar
• Sait M, Hugenholtz P, Janssen PH. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666.
   PubMed Web of Science ®Google Scholar
• Sánchez Moral S, Cañaveras JC, Laiz Trobajo L, Sáiz-Jiménez C, Bedoya J, Luque Ripoll L. 2003. Biomediated precipitation of CaCO3 metastable phases in hypogean environments: a short review. Geomicrobiol J 20:491–500.
   Web of Science ®Google Scholar
• Sarbu SM. 2000. Movile Cave: a chemoautotrophically based groundwater ecosystem. In: Wilkens H, Culver DC, Humphreys WF, editors. Subterranean Ecosystems. Amsterdam: Elsevier, p.319–343.
   Google Scholar
• Schabereiter-Gurtner C, Saiz-Jimenez C, Pinar G, Lubitz W, Rolleke S. 2002a. Altamira Cave paleolithic paintings harbor partly unknown bacterial communities. FEMS Microbiol Lett 211:7–11.
   PubMed Web of Science ®Google Scholar
• Schabereiter-Gurtner C, Saiz-Jimenez C, Pinar G, Lubitz W, Rolleke S. 2002b. Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in Tito Bustillo Cave, Spain, and on its palaeolithic paintings. Environ Microbiol 4:392–400.
   PubMed Web of Science ®Google Scholar
• Schabereiter-Gurtner C, Saiz-Jimenez C, Pinar G, Lubitz W, Rolleke S. 2004. Phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two Spanish caves (Llonin and La Garma). FEMS Microbiol Ecol 47:235–247.
   PubMed Web of Science ®Google Scholar
• Schleper C, Jurgens G, Jonuscheit M. 2005. Genomic studies of uncultivated Archaea. Nat Rev Microbiol 3:479–488.
   PubMed Web of Science ®Google Scholar
• Schrenk MO, Edwards KJ, Goodman RM, Hamers RJ, Banfield JF. 1998. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: implications for generation of acid mine drainage. Science 279:1519–1522.
   PubMed Web of Science ®Google Scholar
• Shabarova T, Pernthaler J. 2010. Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types. Environ Microbiol 12:1061–1074.
   PubMed Web of Science ®Google Scholar
• Spilde MN, Northup DE, Boston PJ, Schelble RT, Dano KE, Crossey LJ, Dahm CN. 2005. Geomicrobiology of cave ferromanganese deposits: a field and laboratory investigation. Geomicrobiol J 22:99–116.
   Web of Science ®Google Scholar
• Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755.
   PubMed Web of Science ®Google Scholar
• Tetu SG, Breakwell K, Elbourne LDH, Holmes AJ, Gillings MR, Paulsen IT. 2013. Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism. ISME J 7:1227–1236.
   PubMed Web of Science ®Google Scholar
• Tomova I, Lazarkevich I, Tomova A, Kambourova M, Vasileva-Tonkova E. 2012. Diversity and biosynthetic potential of culturable aerobic heterotrophic bacteria isolated from Magura Cave, Bulgaria. Int J Speleol 42:65–76.
   Web of Science ®Google Scholar
• Torsvik V, Ovreas L. 2002. Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245.
   PubMed Web of Science ®Google Scholar
• Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43.
   PubMed Web of Science ®Google Scholar
• Urzì C, De Leo F, Bruno L, Albertano P. 2010. Microbial diversity in paleolithic caves: a study case on the phototrophic biofilms of the Cave of Bats (Zuheros, Spain). Microb Ecol 60:116–129.
   PubMed Web of Science ®Google Scholar
• Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms. Proposal for the domains Archaea, Bacteria and Eukcarya. Proc Natl Acad Sci USA 87:4576–4579.
   PubMed Web of Science ®Google Scholar
• Wooley JC, Godzik A, Friedberg I. 2010. A primer on metagenomics. PLoS Comput Biol 6(2):e1000667.
   PubMed Web of Science ®Google Scholar
• Yamada T, Sekiguchi Y. 2009. Cultivation of uncultured chloroflexi subphyla: significance and ecophysiology of formerly uncultured chloroflexi ‘subphylum i’ with natural and biotechnological relevance. Microbes Environ 24:205–216.
   PubMed Web of Science ®Google Scholar
• Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphateaccumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53:1155–1163.
   PubMed Web of Science ®Google Scholar
• Zhou J, Gu Y, Zou C, Mo M. 2007. Phylogenetic diversity of bacteria in an earth-cave in Guizhou province, southwest of China. J Microbiol 45:105–112.
   PubMed Web of Science ®Google Scholar
• Zimmermann J, Gonzalez JM, Saiz-Jimenez C. 2005a. Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in Altamira Cave using 23S rRNA sequence analyses. Geomicrobiol J 22:379–388.
   Web of Science ®Google Scholar
• Zimmermann J, Gonzalez JM, Saiz-Jimenez C. 2005b. Epilithic biofilms in Saint Callixtus Catacombs (Rome) harbour a broad spectrum of Acidobacteria. Anton van Leeuwen 89:203–208.
   Web of Science ®Google Scholar