Phylogenetic diversity of bacteria in an earth-cave in Guizhou Province, Southwest of China

Journal of Microbiology

Volumn 45, Issue 2, 2007, Pages 105-112

  Zhou, JunPei ^a   Gu, YingQi ^a   Zou, ChangSong ^a   Mo, MingHe ^a  

^a YUNNAN UNIVERSITY   (China)

Author keywords

16S rRNA gene; Bacterial community; Cave; Karst; Microbial ecology

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIUM; CHEMISTRY; CHINA; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

BACTERIA; CHINA; DNA, BACTERIAL; ECOSYSTEM; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VARIATION (GENETICS);

ACIDOBACTERIA; ACTINOBACTERIA; ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); GEMMATIMONADETES; NITROSOMONADALES; NITROSPIRAE; OCEANOSPIRILLALES; PLANCTOMYCETES; PROTEOBACTERIA; RUBROBACTERALES;

EID: 34248196656     PISSN: 12258873     EISSN: 12258873     Source Type: Journal    
DOI: None     Document Type: Article

References (57)

1. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Amann, R.I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification, and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
3. Asami, H., M. Aida, and K. Watanabe. 2005. Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl. Environ. Microbiol. 716, 2925-2933.
4. Bottomley, P.J. 1992. Ecology of Bradyrhizobium, and Gluconoacetobacter diazotrophicusobium, p. 293-348. In G. Stacey, R.H. Burris and H.J. Evans (eds.), Biological Nitrogen Fixation. Chapman, and Hall New York, London, UK.
5. Burrell, P.C., J. Keller, and L.L. Blackall. 1998. Microbiology of a nitrite-oxidizing bioreactor. Appl. Environ. Microbiol. 64, 1878-1883.
6. Caňaveras, J.C., S. Sanchez-Moral, V. Soler, and C. Saiz-Jimenez. 2001. Microorganisms, and microbially induced fabrics in cave walls. Geomicrobiol. J. 18, 223-240.
7. Chen, W.M., S. Laevens, T.M. Lee, T. Coenye, P. De Vos, M. Mergeay, and P. Vandamme. 2001. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species, and sputum of a cystic fibrosis patient. Int. J. Syst. Evol. Microbiol. 51, 1729-1735.
8. Cramm, R., R.A. Siddiqui, and B. Friedrich. 1997. Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16. J. Bacteriol. 179, 6769-6777.
9. Cunningham, K.I., D.E. Northup, R.M. Pollastro, W.G. Wright, and E.J. LaRock. 1995. Bacteria, fungi, and biokarst in Lechuguilla Cave, Carlsbad Caverns National Park, New Mexico. Environ. Geol. 25, 2-8.
10. Engel, A.S., M.I. Porter, B.K. Kinkle, and T.C. Kane. 2001. Ecological assessment, and geological significance of microbial communities from Cesspool Cave, Virginia. Geomicrobiol. J. 18, 259-274.
11. Engel, A.S., M.L. Porter, L.A. Stern, S. Quinlan, and P.C. Bennett. 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.
12. Ghiorse, W.C. and P. Hirsch. 1979. An ultrastructural study of iron, and manganese deposition associated with extracellular polymers of Pedomicrobium-like budding bacteria. Arch. Microbiol. 123, 213-226.
13. Gillieson, D. 1996. Caves, processes, development, and management, p. 324. Blackwell Publishers, Oxford, UK.
14. Glöckner, F.O., M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt. 2003. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. PNAS 14, 8298-8303.
15. Gonzalez, I., L. Laiz, B. Hermosin, B. Guerrero, C. Incerti, and C. Saiz-Jimenez. 1999. Microbial communities of the rock paintings of Atlanterra shelter South Spain. J. Microbiol. Methods 36, 123-127.
16. Groth, I. and C. Saiz-Jimenez. 1999. Actinomycetes in hypogean environments. Geomicrobiol. J. 16, 1-8.
17. Groth, I., R.B. Vetterman, Schuetzte, P. Schumann, and C. Saiz-Jimenez. 1999. Actinomycetes in karstic caves of northern Spain Altamira, and Tito Bustillo. J. Microbiol. Methods 36, 115-122.
18. Groth, I., P. Schumann, L. Laiz, S. Sanchez-Moral, J.C. Caňaveras, and C. Saiz-Jimenez. 2001. Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. Geomicrobiol. J. 18, 241-258.
19. Head, I.M., J.R. Saunders, and R.W. Pickup. 1998. Microbial evolution, diversity, and ecology, a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35, 1-21.
20. Hiorns, W.D., R.C. Hastings, I.M. Head, G.R. Hall, A.J. McCarthy, J.R. Saunders, and R.W. Pickup. 1995. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of Nitrosospiras in the environment. Microbiology 141, 2793-2800.
21. Holmes, A.J., N.A. Tujula, M. Holley, A. Contos, J.M. James, P. Rogers, and M.R. Gillings. 2001. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor Caves, Australia. Environ. Microbiol. 3, 256-264.
22. Hose L.D., A.N. Palmer, M.V. Palmer, D.E. Northup, P.J. Boston, and H.R. Duchene. 2000. Microbiology, and geochemistry in a hydrogen-sulphide-rich karst environment. Chem. Geol. 169, 399-423.
23. Huang, L.N., H. Zhou, S. Zhu, and L.H. Qu. 2004. Phylogenetic. diversity of bacteria in the leachate of a full-scale recirculating landfill. FEMS Microbiol. Ecol. 50, 175-183.
24. Hugenholtz, P., M.B. Goebel, and N.R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774.
25. Jetten, M., M. Wagner, J. Fuerst, M. van Loosdrecht, G. Kuenen, and M. Strous. 2001. Microbiology, and application of the anaerobic ammonium oxidation "anamox" process. Curr. Opin. Biotechnol. 12, 283-288.
26. Juretschko, S., A. Loy, A. Lehner, and M. Wagner. 2002. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol. 25, 84-99
27. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
28. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3, Integrated software for molecular evolutionary genetics analysis, and sequence alignment. Briefings in Bioinformatics 5, 150-163.
29. Kuske, C.R., S.M. Barns, and J.D. Busch. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63, 3614-3621.
30. Laiz, L., I. Groth, I. Gonzalez, and C. Saiz-Jimenez. 1999. Microbiological study of the dripping water in Altamira Cave Santillana del Mar, Spain. J. Microbiol. Methods 36, 129-138.
31. Laiz, L., I. Groth, P. Schumann, F. Zezza, A. Felske, B. Hermosin, and C. Saiz-Jimenez. 2000. Microbiology of the stalactites from Grotta dei Cervi, Porto Badisco, Italy. Int. Microbiol. 3, 25-30.
32. Lane, D.J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt, and M. Goodfellow (eds.), Nucleic Acid Techniques in Bacterial. Wiley, New York, USA.
33. Liesack, W. and K. Finster. 1994. Phylogenetic analysis of five strains of Gram-negative, obligately anaerobic, sulfur-reducing bacteria, and description of Desulfuromusa gen. nov., including Desulfuromusa kysingii sp. nov., Desulfuromusa bakii sp. nov., and Desulfuromusa succinoxidans sp. nov. Int. J. Syst. Bacteriol. 44, 753-758.
34. Liesack, W., P.H. Janssen, F.A. Rainey, N. Ward-Rainey, and E. Stackebrandt. 1997. Microbial diversity in soil, the need for a combined approach using molecular, and cultivation techniques, p. 375-439. In J.D. van Elsas, J.T. Trevors, and E.M.H. Wellington (eds.), Modern Soil Microbiology. Marcel Dekker, New York, USA.
35. Ludwig, W., S.H. Bauer, M. Bauer, I. Held, I. Kirchhof, R. Schulze, and K.H. Schleifer. 1997. Detection, and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153, 181-190.
36. Maidak, B.L., G.J. Olsen, N. Larsen, R. Overbeek, M.J. McCaughey, and C.R. Woese. 1997. The RDP ribosomal database project. Nucleic Acids Res. 25, 109-110.
37. Moore, G.W. 1981. Manganese deposition in limestone caves, p. 642-645. In B.F. Beck (eds.), Proceedings 8th International Congress of Speleology, II. Kentucky, USA.
38. Nealson, K.H. and D. Saffarini. 1994. Iron, and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Ann. Rev. Microbiol. 48, 311-343.
39. Neef, A., R. Amann, H. Schlesner, and K.H. Schleifer. 1998. Monitoring a widespread bacterial group, in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144, 3257-3266.
40. Northup, D.E., C.N. Dahm, L.A. Melim, M.N. Spilde, L.J. Crossey, and K.H. Lavoie. 2000. Evidence for geomicrobiological interactions in Guadalupe Caves. J. Caves Kars.t Stud. 62, 80-90.
41. Northup, D.E. and K.H. Lavoie. 2001. Geomicrobiology of caves, a review. Geomicrobiol. J. 18, 199-222.
42. Northup, D.E., S.M. Barns, L.E. Yu, M.N. Spilde, R.T. Schelble, and K.E. Dano. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environ. Microbiol. 5, 1071-1086.
43. Ozeki, S., I. Baba, N. Takaya, and H. Shoun. 2001. A novel C1-using denitrifier Alcaligenes sp. STC1, and its genes for copper-containing nitrite reductase, and azurin. Biosci. Biotechnol. Biochem. 65, 1206-1210.
44. Peck, S.B. 1986. Bacterial deposition of iron, and manganese oxides in North American caves. NSS. Bull 48, 26-30.
45. Quaiser, A., T. Ochsenreiter, C. Lanz, S. C. Schuster, A. H. Treusch, J. Eck, and C. Schleper. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50, 563-575.
46. Saitou, N., M. Nei, and L.S. Lerman. 1987. The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
47. Sarbu S.M., T.C. Kane, and B.K. Kinkle. 1996. A chemoautotrophically based cave ecosystem. Science 272, 1953-1954.
48. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Piñar, W. Lubitz, and S. Rölleke. 2002a. Altamira Cave Paleolithic paintings harbour partly unknown bacterial communities. FEMS Microbiol. Lett. 211, 7-11.
49. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Piñar, W. Lubitz, and S. Rölleke. 2002b. Phylogenetic 16S rRNA analysis reveals the presence of complex, and partly unknown bacterial communities in Tito Bustillo Cave, Spain, and on its Paleolithic paintings. Environ. Microbiol. 4, 392-400.
50. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Piñar, W. Lubitz, and S. Rölleke. 2003. Phylogenetic diversity of bacteria associated with Paleolithic paintings, and surrounding rock walls in two Spanish caves Llonín, and La Garma. FEMS Microbiol. Ecol. 1606, 1-13.
51. Schirmer, A., R. Gadkari, C.D. Reeves, F. Ibrahim, E.F. DeLong, and C.R. Hutchinson. 2005. Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl. Environ. Microbiol. 71, 4840-4849.
52. Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, and M. Jetten. 2000. Molecular evidence for a genus-level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. System. Appl. Microbiol. 23, 93-106.
53. Smart, P.L, A.C. Waltham, M.D. Yang, and Y.J. Zhang. 1986. Karst geomorphology of western Guizhou, China. Cave Science 13, 89-104.
54. Suzuki, I., U. Dular, and S.C. Kwok. 1974. Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas cells, and extracts. J. Bacteriol. 120, 556-558.
55. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgens. 1997. The Clustal X windows interface, flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
56. Vlasceanu, L., S.M. Sarbu, A.S. Engel, and B.K. Kinkle. 2000. Acidic cave-wall biofilms located in the Frasassi Gorge, Italy. Geomicrobiol. J. 17, 125-140.
57. Zhang Y.J., M.D. Yang, and C.H. He. 1992. Karst geomorphology, and environmental implication in Guizhou. Cave Science 19, 13-20.