Phylogenetic analysis on the soil bacteria distributed in karst Forest

Brazilian Journal of Microbiology

Volumn 40, Issue 4, 2009, Pages 827-837

  Zhou, Junpei ^a   Huang, Ying ^a   Mo, Minghe ^a  

^a YUNNAN UNIVERSITY   (China)

Author keywords

16S rRNA gene; Bacteria; Karst forest

Indexed keywords

ACIDOBACTERIA; ACTINOBACTERIA; ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); FIRMICUTES; NITROSPIRAE; PLANCTOMYCETES; PROTEOBACTERIA; VERRUCOMICROBIA;

EID: 70350147031     PISSN: 15178382     EISSN: 16784405     Source Type: Journal    
DOI: 10.1590/S1517-83822009000400013     Document Type: Article

References (45)

1. Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Amann, R.I.; Ludwig, W.; Schleifer, K.H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 59, 143-169.
3. Asami, H.; Aida, M.; Watanabe, K. (2005). Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl. Environ. Microbiol., 71, 2925-2933.
4. Axelrood, P.E.; Chow, M.L.; Radomski, C.C.; McDermott, J.M.; Davies J. (2002). Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can. J. Microbiol., 48, 655-674.
5. Berg, B.; Hofsten, B.V.; Pettersson, G. (1972). Electronmicroscopic obsetvations on the degradation of cellulose fibres by Cellvibrio fulvus and Sporoctphaga myxococcoides. J. Appl. Bact., 35, 215-219.
6. Borneman, J.; Triplett, E.W. (1997). Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol., 63, 2647-2653.
7. Bottomley, P.J. (1992). Ecology of Bradyrhizobium and Gluconoacetobacter diazotrophicusobium. In Biological Nitrogen Fixation. Edited by Stacey, G.; Burris, R.H.; H.J. Evans. Chapman and Hall New York, London, pp. 293-348.
8. Burrell, P.C.; Keller, J.; Blackall, L.L. (1998). Microbiology of a nitrite-oxidizing bioreactor. Appl. Environ. Microbiol., 64, 1878-1883.
9. Busse, M.D.; Beattie, S.E.; Powers, R.F.; Sanchez, F.G.; Tiarks, A.E. (2006). Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control. Can. J. For. Res., 36, 577-588.
10. Chan, O.C.; Yang, X.; Fu, Y.; Feng, Z.; Sha, L.; Casper, P.; Zou, X. (2006). 16S rRNA gene analyses of bacterial community structures in the soils of evergreen broad-leaved forests in south-west China. FEMS Microb. Ecol., 58, 247-259.
11. Chen, W.M.; Laevens, S.; Lee; T.M.; Coenye, T.; De Vos, P.; Mergeay, M.; Vandamme, P. (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.
12. Chow, M.L.; Radomski, C.C.; McDermott, J.M.; Davies, J.; Axelrood, P.E. (2002). Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol. Ecol., 42, 347-357.
13. DE Vrind-DE Jong, E.W.; Corstjens, P.L.A.M.; Kempers, E.S.; Westbroek, P.; DE Vrind, J.P.M. (1990). Oxidation of manganese and iron by Leptothrix discophora: use of N,N,N',N'-tetramethyl-p- phenylenediamine as an indicator of metal oxidation. Appl. Environ. Microbiol., 56, 3458-3462.
14. Engel, A.S.; Porter, M.L.; Stern, L.A.; Quinlan, S.; Bennett, P.C. (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.
15. Fierer, N.; Jackson, R.B. (2006). The diversity and biogeography of soil bacterial communities. PNAS., 103, 626-631.
16. Ghiorse, W.C.; Hirsch, P. (1978). Iron and manganese deposition by budding bacteria. In Environmental Biogeochemistry and Geotnicrohiology Vol. 3 ed. Krumbein, W.E. pp. 897-910. Ann Arbor, Michigan: Ann Arbor Science Publishers.
17. Hackl, E.; Zechmeister-Boltenstern, S.; Bodrossy, L.; Sessitsch, A. 2004. Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl. Environ. Microbiol., 70, 5057-5065.
18. Holmes, A.J.; Tujula, N.A.; Holley, M.; Contos, A.; James, J.M.; Rogers, P.; Gillings, M.R. (2001). Phylogenetic structure of unusual aquatic microbial formations in Nullarbor Caves, Australia. Environ. Microbiol., 3, 256-264.
19. Huang, L.N.; Zhou, H.; Zhu, S.; Qu, L.H. (2004). Phylogenetic diversity of bacteria in the leachate of a full-scale recirculating landfill. FEMS Microbiol. Ecol., 50, 175-183.
20. Hugenholtz, P.; Goebel, M.B.; Pace, N.R. (1998). Impact of culture- independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol., 180, 4765-4774.
21. Jetten, M.; Wagner, M.; Fuerst, J.; van Loosdrecht, M.; Kuenen, G.; Strous, M. (2001). Microbiology and application of the anaerobic ammonium oxidation anamox process. Curr. Opin. Biotechnol., 12, 283-288.
22. Kim, J.S.; Sparovek, G.; Regina M.L., MELO, W.J.; Crowley, D. (2007). Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol. Biochem. 39, 684-690.
23. 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.
24. Krave, A.S.; Lin, B.; Braster, M.; Laverman, A.M.; van Straalen, N.M.; Roling, W.F.M.; van Verseveld, H.W. (2002). Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia. Environ. Microbiol., 4, 361-373.
25. Kumar, S.; Tamura, K.; Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform., 5, 150-163.
26. Lane, D.J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Edited by Stackebrandt, E.; Goodfellow, M. Wiley, New York, pp. 115-175.
27. Lednicka, D.; Mergaert, J.; Cnockaert, M.C.; Swings, J. (2002). Isolation and identification of cellulolytic bacteria involved in the degradation of natural cellulosic fibres. Syst. Appl. Microbiol., 23, 292-299.
28. Long, J.; Li, J.; Jiang, X.R.; Huang, C.Y. (2004). Soil microbial activities in Maolan karst forest, Giuzhou province. Acta Pedologica Sinica, 41, 597-602.
29. Ludwig, W.; Bauer, S.H.; Bauer, M.; Held, I.; Kirchhof, I.; Schulze, R.; Schleifer, K.H. (1997). Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett., 153, 181-190.
30. Maidak, B.L.; Olsen, G.J.; Larsen, N.; Overbeek, R.; McCaughey, M.J.; Woese, C.R. (1997). The RDP ribosomal database project. Nucleic Acids Res., 25, 109-110.
31. Neufeld J.D.; Mohn W.W. (2005). Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl. Environ. Microbiol., 71, 5710-5718.
32. Northup, D.E.; Lavoie, K.H. (2001). Geomicrobiology of caves: a review. Geomicrobiol. J., 18, 199-222.
33. Nüsslein, K.; Tiedje, J.M. (1999). Soil Bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl. Envir. Microbiol., 65, 3622-3626.
34. Pace, N.R. (1997). A molecular view of microbial diversity and the biosphere. Science, 276, 734-740.
35. Quaiser, A.; Ochsenreiter, T.; Lanz, C.; Schuster, S.C.; Treusch, A.H.; Eck, J.; Schleper, C. (2003). Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol., 50, 563-575.
36. Saitou, N.; Nei, M.; Lerman, L.S. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
37. Schirmer, A.; Gadkari, R.; Reeves, C.D.; Ibrahim, F.; DeLong, E.F.; Hutchinson, C.R. (2005). Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl. Environ. Microbiol., 71, 4840-4849.
38. Shannon, C.E; Weaver, W. (1963). The mathematical theory of communication. University of Illinois Press, Urbana, pp. 81-96.
39. Suzuki, I.; Dular, U.; Kwok, S.C. (1974). Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas cells and extracts. J. Bacteriol.; 120, 556-558.
40. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgens, D.G. (1997). The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 24, 4876-4882.
41. Tu, Y.L. (1989). Karst forests in Guizhou. Carsologica Sinica, 8, 282-290.
42. Yang, H. (1994). Discussion on variation of karst environmental quality. In Human Activity and Karst Environment. Edited by Xie, Y.; Yang, M. Beijing Science and Technology Press, Beijing, pp. 1-7.
43. Yu, L.F. (2000). The assessment on the natural restoration of degraded Karst forests. Forest. Sci., 36, 12-19.
44. Zhang, Y.J.; Yang, M.D.; He, C.H. (1992). Karst geomorphology and environmental implication in Guizhou. Cave Science, 19, 13-20.
45. Zhu, S.Q. (1997). Ecological research on Karst Forests (α). Guizou Sci-Tech Press, Guiyang, pp. 57-63.