Down into the Earth: Microbial diversity of the deepest cave of the world

Biologia

Volumn 70, Issue 8, 2015, Pages 989-1002

  Kieraite Aleksandrova, Ieva ^a   Aleksandrovas, Vilius ^a   Kuisiene, Nomeda ^a  

^a VILNIUS UNIVERSITY   (Lithuania)

Author keywords

16S rRNA gene; deep cave; Krubera Voronja; microbial diversity; pyrosequencing; speleomicrobiology

Indexed keywords

EID: 84942873700     PISSN: 00063088     EISSN: 13369563     Source Type: Journal    
DOI: 10.1515/biolog-2015-0127     Document Type: Article

References (32)

1. Barton H.A., Taylor M.R. & Pace N.R. 2004. Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment. Geomicrobiol. J. 21: 11-20.
2. Bastian F., Alabouvette C. & Saiz-Jimenez C. 2009. Bacteria and free-living amoeba in the Lascaux cave. Res. Microbiol. 160: 38-40.
3. Carmichael M.J., Carmichael S.K., Santelli C.M., Strom A. & Bräuer S.L. 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.
4. Chakravorty S., Helb D., Burday M., Connell N. & Alland D. 2007. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 69: 330-339.
5. Chan K.G. & Chong T.M. 2014. Prevalence of unclassified bacteria in tropical coastal waters of Malaysia revealed by metagenomic approach. Genome Announc. 2: e00419-14.
6. Clarke K.R. 1993. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18: 117-143.
7. Cole J.R., Wang Q., Fish J.A., Chai B., McGarrell D.M., Sun Y., Brown C.T., Porras-Alfaro A., Kuske C.R. & Tiedje J.M. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42: D633-D642.
8. Cuezva S., Fernandez-Cortes A., Porca E., Pašić L., Jurado V., Hernandez-Marine M., Serrano-Ortiz P., Hermosin B., Cañaveras J.C., Sanchez-Moral S. & Saiz-Jimenez C. 2012. The biogeochemical role of Actinobacteria in Altamira Cave, Spain. FEMS Microbiol. Ecol. 81: 281-290.
9. Dillies M.A., Rau A., Aubert J., Hennequet-Antier C., Jeanmougin M., Servant N., Keime C., Marot G., Castel D., Estelle J., Guernec G., Jagla B., Jouneau L., Lalöe D., Le Gall C., Schäeffer B., Le Crom S., Guedj M. & Jaffrézic F. 2013. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinformatics 14: 671-683.
10. Edgar R.C., Haas B.J., Clemente J.C., Quince C. & Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
11. Engel A.S. 2010. Microbial diversity of cave ecosystems, pp. 219- 238. In: Loy A., Mandl M. & Barton L. (eds), Geomicrobiology: Molecular and Environmental Perspective, Springer Science+Business Media B.V., Dordrecht.
12. Engel A.S., Paoletti M.G., Beggio M., Dorigo L., Pamio A., Gomiero T., Furlan C., Brilli M., Dreon A.L., Bertoni R. & Squartini A. 2013. Comparative microbial community composition from secondary carbonate (moonmilk) deposits: implications for the Cansiliella servadeii cave hygropetric food web. Int. J. Speleol. 42: 181-192.
13. Epure L., Meleg I.N., Munteanu C.-M., Roban R.D. & Moldovan O.T. 2014. Bacterial and fungal diversity of quaternary cave sediment deposits. Geomicrobiol. J. 31: 116-127.
14. Gan H.Y., Gan H.M., Tarasco A.M., Busairi N.I., Barton H.A., Hudson A.O. & Savka M.A. 2014. Whole-genome sequences of five oligotrophic bacteria isolated from deep within Lechuguilla Cave, New Mexico. Genome Announc. 2: e01133- 14.
15. Griffin D.W., Gray M.A., Lyles M.B. & Northup D.E. 2014. The transport of nonindigenous microorganisms into caves by human visitation: a case study at Carlsbad Caverns National Park. Geomicrobiol. J. 31: 175-185.
16. Groth I., Schumann P., Laiz L., Sanchez-Moral S., Cańveras J.C. & Saiz-Jimenez C. 2001. Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. Geomicrobiol. J. 18: 241-258.
17. Jones D.S., Schaperdoth I. & Macalady J.L. 2014. Metagenomic evidence for sulfide oxidation in extremely acidic cave biofilms. Geomicrobiol. J. 31: 194-204.
18. Jurado V., Laiz L., Rodriguez-Nava V., Boiron P., Boiron P., Hermosin B., Sanchez-Moral S. & Saiz-Jimenez C. 2010. Pathogenic and opportunistic microorganisms in caves. Int. J. Speleol. 39: 15-24.
19. Klindworth A., Pruesse E., Schweer T., Peplies J., Quast C., Horn M. & Glöckner F.O. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41: e1.
20. Kodama Y., Shumway M. & Leinonen R. 2012. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 40 (Database Issue): D54-D56.
21. Kumaresan D., Wischer D., Stephenson J., Hillebrand-Voiculescu A. & Murrell J.C. 2014. Microbiology of Movile Cave a chemolithoautotrophic ecosystem. Geomicrobiol. J. 31: 186-193.
22. McLellan S.L. & Eren A.M. 2014. Discovering new indicators of fecal pollution. Trends Microbiol. 22: 697-706.
23. Northup D.E. & Lavoie K.H. 2001. Geomicrobiology of caves: a review. Geomicrobiol. J. 18: 199-222.
24. Northup D.E., Melim L.A., Spilde M.N., Hathaway J.J.M., Garcia M.G., Moya M., Stone F.D., Boston P.J., Dapkevicius M.L.N.E. & Riquelme C. 2011. Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology 11: 601-618.
25. Ortiz M., Neilson J.W., Nelson W.M., Legatzki A., Byrne A., Yu Y., Wing R.A., Soderlund C.A., Pryor B.M., Pierson III L.S. & Maier R.M. 2013. Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. Microb. Ecol. 65: 371-383.
26. Porat I., Vishnivetskaya T.A., Mosher J.J., Brandt C.C., Yang Z.K., Brooks S.C., Liang L., Drake M.M., Podar M., Brown S.D., Palumbo A.V. 2010. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb. Ecol. 60: 784-795.
27. Porter M.L., Engel A.S., Kane T.C. & Kinkle B.K. 2009. Productivity-diversity relationships from chemolithoautotrophically based sulfidic karst systems. Int. J. Speleol. 38: 27-40.
28. Portillo M.C., Gonzalez J.M. & 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.
29. Portillo M.C., Saiz-Jimenez C. & Gonzalez J.M. 2009. Molecular characterization of total and metabolically active bacterial communities of "white colonizations" in the Altamira Cave, Spain. Res. Microbiol. 160: 41-47.
30. Schabereiter-Gurtner C., Saiz-Jimenez C., Pińar G., Lubitz W. & Rölleke S. 2002. Altamira cave Paleolithic paintings harbor partly unknown bacterial communities. FEMS Microbiol. Lett. 211: 7-11.
31. Sendra A. & Reboleira A.S.P.S. 2012. The world's deepest subterranean community Krubera-Voronja Cave (Western Caucasus). Int. J. Speleol. 41: 221-230.
32. Studholme D.J., Jackson R.A. & Leak D.J. 1999. Phylogenetic analysis of transformable strains of thermophilic Bacillus species. FEMS Microbiol. Lett. 172: 85-90.