Comparative analysis of yellow microbial communities growing on the walls of geographically distinct caves indicates a common core of microorganisms involved in their formation

FEMS Microbiology Ecology

Volumn 81, Issue 1, 2012, Pages 255-266

  Porca, Estefania ^a   Jurado, Valme ^a   Žgur Bertok, Darja ^b   Saiz Jimenez, Cesareo ^a   Pašić, Lejla ^b  

^a INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SEVILLA   (Spain)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

Author keywords

16S rRNA gene; Bacteria; Cave; Diversity; Hypogean environments; Yellow microbial communities

Indexed keywords

RNA 16S;

BACTERIUM; CAVE; CLONE; COMMUNITY STRUCTURE; COMPARATIVE STUDY; GEOGRAPHICAL VARIATION; LIMESTONE; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MORPHOLOGY;

ARTICLE; BACTERIUM; CAVE; CLASSIFICATION; COMPARATIVE STUDY; CZECH REPUBLIC; GAMMAPROTEOBACTERIA; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; RNA GENE; SLOVENIA; SPAIN;

BACTERIA; CAVES; CZECH REPUBLIC; GAMMAPROTEOBACTERIA; GENES, RRNA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SLOVENIA; SPAIN;

CZECH REPUBLIC; SLOVENIA; SPAIN;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CHROMATIALES; OTUS; XANTHOMONADALES;

EID: 84862318622     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01383.x     Document Type: Article

References (45)

1. Ahmad M, Roberts JN, Hardiman EM, Singh R, Eltis LD & Bugg TDH (2011) Identification of DypB from Rhodococcus jostii RHA 1 as a lignin peroxidase. Biochemistry 50: 5096-5107.
2. Barton HA & Jurado V (2007) What's up down there? Microbial diversity in caves. Microbe Wash DC, 2: 132-138.
3. 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.
4. Burnham KP & Overton WS (1978) Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika 65: 625-633.
5. Burnham KP & Overton WS (1979) Robust estimation of population size when capture probabilities vary among animals. Ecology 60: 927-936.
6. Chao A (1984) Non-parametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
7. Chao A, Ma MC & Yang MCK (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80: 193-201.
8. Cuezva S, Sanchez-Moral S, Saiz-Jimenez C & Cañaveras JC (2009) Microbial communities and associated mineral fabrics in Altamira Cave, Spain. Int J Speleol 38: 83-92.
9. Culver DC & Pipan T (2009) The Biology of Caves and Other Subterranean Habitats. Oxford University Press, Oxford.
10. Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR & Vogel TM (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77: 1315-1324.
11. DeLong EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 89: 5685-5689.
12. Diez B, Pedros-Alio C & Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67: 2932-2941.
13. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
14. Fahrbach M, Kuever J, Remesch M, Huber BE, Kämpfer P, Dott W & Hollender J (2008) Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol 58: 2215-2223.
15. Galán C (2011) Nuevos datos sobre Mycetozoa cavernícolas (Amoebozoa) en cuevas de la Sierra de Aralar y Macizo de Otsabio.
16. Galán C & Nieto M (2010) Mycetozoa: curiosas formas de vida en cuevas de Gipuzkoa. Nuevos hallazgos en caliza Urgoniana en los karsts de Aizkorri (Igitegi), Izarraitz (Aixa), y Udalaitz (Montxon koba)
17. Gardes M & Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118.
18. 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.
19. Horath T & Bachofen R (2009) Molecular characterization of an endolithic microbial community in dolomite rocks in the central Alps (Switzerland). Microb Ecol 58: 290-306.
20. Jones DS, Albrecht HL, Dawson KS, Schaperdoth I, Freeman KH, Pi Y, Pearson A & Macalady JL (2012) Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J 6: 158-170.
21. Jurado V, Boiron P, Kroppenstedt RM et al. (2008) Nocardia altamirensis sp. nov., isolated from Altamira cave, Cantabria, Spain. Int J Syst Evol Microbiol 58: 2210-2214.
22. Jurado V, Fernandez-Cortes A, Cuezva S, Laiz L, Cañaveras JC, Sanchez-Moral S & Saiz-Jimenez C (2009) The fungal colonization of rock art caves. Naturwissenschaften 96: 1027-1034.
23. Lado C & Moreno G (1981) Contribución al estudio de los Myxomycetes en la Península Ibérica. IV. Pais Vasco. Munibe 33: 63-78.
24. Lado C & Ronikier A (2009) Nivicolous myxomycetes from the Pyrenees: notes on the taxonomy and species diversity. Part 2. Stemonitales. Nova Hedwigia 89: 131-145.
25. Lee NM, Meisinger DB, Aubrecht R, Kovacik L, Saiz-Jimenez C, Baskar S, Baskar R, Liebl W, Porter M & Engel AS (2012) Caves and karst environments. Life at Extremes: Environments, Organisms and Strategies for Survival ( Bell EM, ed), pp. 320-344. CAB International, Wallingford.
26. Maskey RP, Kock I, Helmke E & Laatsch H (2003) Isolation and structure determination of phenazostatin D, a new phanazine from a marine actinomycete isolate Pseudonocardia sp. B6273. Z Naturforsch 58: 692-694.
27. McCarthy AJ (1987) Lignocellulose-degrading actinomycetes. FEMS Microbiol Lett 46: 145-163.
28. Northup DE, Melim LA, Spilde MN, Hathaway JJM, Garcia MG, Moya M, Stone FD, Boston PJ, Dapkevicius MLNE & Riquelme C (2011) Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology 11: 601-618.
29. Pašić L, Kovče 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.
30. 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.
31. Portillo MC, Saiz-Jimenez C & Gonzalez JM (2009) Molecular characterization of total and metabolically active bacterial communities of 'white colonization' in the Altamira Cave, Spain. Res Microbiol 160: 41-47.
32. Qin S, Su YY, Zhang YQ, Jiang CL, Xu LH & LI WJ (2008) Pseudonocardia ailaonensis sp. nov., isolated from soil in China. Int J Syst Evol Microbiol 58: 2086-2089.
33. Saiz-Jimenez C & Hermosin B (1999) The nature of the organic matter present in dripping waters from Altamira cave. J Anal Appl Pyrol 49: 337-347.
34. 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.
35. Schabereiter-Gurtner C, Saiz-Jimenez C, Piñar G, Lubitz W & Rölleke S (2002) Altamira cave Paleolithic paintings harbor partly unknown bacterial communities. FEMS Microbiol Lett 211: 7-11.
36. Schabereiter-Gurtner C, Saiz-Jimenez C, Piñar G, Lubitz W & Rölleke S (2004) Phylogenetic diversity of bacteria associated with palaeolithic paintings and surrounding rock walls in two Spanish caves (Llonin and La Garma). FEMS Microbiol Ecol 47: 235-247.
37. Schloss PD (2008) Evaluating different approaches that test whether microbial communities have the same structure. ISME J 2: 265-275.
38. Schloss PD, Larget BR & Handelsman J (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-5492.
39. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
40. Shannon CE & Weaver W (1949) The Mathematical Theory of Communication. University of Illinois Press, Champaign, IL.
41. Simpson EH (1949) Measurement of diversity. Nature 163: 688.
42. Stomeo F, Portillo MC, Gonzalez JM, Laiz L & Saiz-Jimenez C (2008) Pseudonocardia in white colonizations in two caves with Paleolithic paintings. Int Biodeter Biodegr 62: 483-486.
43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
44. White TJ, Bruns T, Lee S & Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications ( Innis MA, Gelfand DH, Sninsky JJ & White TJ, eds), pp. 315-322. Academic Press, New York.
45. Zhao GZ, Li J, Zhu WY, Li XP, Tian SZ, Zhao LX, Xu LH & Li WJ (2011) Pseudonocardia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisia annua L. Antonie Van Leeuwenhoek 100: 35-42.