Recovery of novel bacterial diversity from mangrove sediment

Marine Biology

Volumn 150, Issue 5, 2007, Pages 739-747

  Liang, Jun Bin ^a   Chen, Yue Qin ^a   Lan, Chong Yu ^a   Tam, Nora F Y ^b   Zan, Qi Jie ^c   Huang, Li Nan ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^c Guangdong Neilingding Futian National Nature Reserve   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; MANGROVE; PHYLOGENETICS; RNA; SEDIMENT; SPECIES DIVERSITY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); CHLAMYDIAE/VERRUCOMICROBIA GROUP; CHLOROFLEXI; CHLOROFLEXI (CLASS); CYTOPHAGA; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FIBROBACTERES/ACIDOBACTERIA GROUP; FIRMICUTES; FLEXIBACTER; FUSOBACTERIA; GAMMAPROTEOBACTERIA; PLANCTOMYCETES; PROTEOBACTERIA;

EID: 33846512283     PISSN: 00253162     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00227-006-0377-2     Document Type: Article

References (41)

1. Alongi DM (1996) The dynamics of benthic nutrient pools and Xuxes in tropical mangrove forests. J Mar Res 54:123-148
2. Alongi DM, Sasekumar A, Tirendi F, Dixon P (1998) The influence of stand age on benthic decomposition and recycling of organic matter in managed mangrove forests of Malaysia. J Exp Mar Biol Ecol 225:197-218
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
4. 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
5. Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463-2483
6. Bowman JP, McCammon SA, Gibson JA, Robertson L, Nichols PD (2003) Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediment. Appl Environ Microbiol 69:2448-2462
7. Cho JC, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70:432-440
8. Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert RA, Rodríguez-Valera F (2000) Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 66:1715-1719
9. Curtis TP, Sloan WT, Scannel JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10491-10499
10. DeLong EF, Pace NR (2001) Environmental diversity of bacteria and Archaea. Syst Biol 50:470-478
11. Dilling W, Liesack W, Pfennig N (1995) Rhabdochromatium marinum gen. nom. rev., sp. nov., a purple sulfur bacterium from a salt marsh microbial mat. Arch Microbiol 164:125-131
12. Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869-3877
13. Etchebehere C, Errazquin MI, Dabert P, Muxi L (2002) Community analysis of a denitrifying reactor treating landfill leachate. FEMS Microbiol Ecol 40:97-106
14. Gray JP, Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62:4049-4059
15. Griepenburg U, Ward-Rainey N, Mohamed S, Schlesner H, Marxsen H, Rainey FA, Stackebrandt E, Auling G (1999) Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales. Int J Syst Bacteriol 49:689-696
16. Hagstrom A, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68:3628-3633
17. Hirayama H, Takai K, Inagaki F, Yamato Y, Suzuki M, Nealson KH, Horikoshi K (2005) Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine. Extremophiles 9:169-184
18. Holguin G, Vazquez P, Bashan Y (2001) The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol Fert Soils 33:265-278
19. Hutson RA, Thompson DE, Collins MD (1993) Genetic interrelationships of saccharolytic Clostridium botulinum types B, E, and F and related clostridia as revealed by small-subunit rRNA gene sequences. FEMS Microbiol Lett 108:103-110
20. Jackson CR, Harper JP, Willoughby D, Roden E, Churchill PF (1997) A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl Environ Microbiol 63:4993-4995
21. Jennerjahn TC, Ittekkot V (2002) Relevance of mangroves for the production and deposition of organic matter along tropical continental margins. Naturwissenschaften 89:23-30
22. Kato S, Haruta S, Cui ZJ, Ishii M, Yokota A, Igarashi Y (2004) Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community. Int J Syst Evol Microbiol 54:2043-2047
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. Kristensen E, King GM, Banta GT, Holmer M, Jensen MH, Hansen K, Bussarawit N (1994) Sulfate reduction, acetate turnover and carbon metabolism in sediments of the Ao-Nam-Bor mangrove, Phuket, Thailand. Mar Ecol Prog Ser 109:245-255
25. Kristensen E, Andersen FØ, Holmboe N, Holmer M, Thongtham N (2000) Carbon and nitrogen mineralization in sediments of the Bangrong mangrove area, Phuket, Thailand. Aquat Microb Ecol 22:199-213
26. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, NY, pp 115-175
27. Li L, Kato C, Horikoshi K (1999) Bacterial diversity in deep-sea sediments from different depths. Biodivers Conserv 8:659-677
28. Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109-110
29. Mussmann M, Ishii K, Rabus R, Amann R (2005) Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol 7:405-418
30. Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982-3989
31. Ravenschlag K, Sahm K, Amann R (2001) Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Appl Environ Microbiol 67:387-395
32. Roest K, Heilig HG, Smidt H, de Vos WM, Stams AJ, Akkermans AD (2005) Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater. Syst Appl Microbiol 28:175-185
33. Saitou N, Nei M (1987) The neighbor-joining method: a method for constructing phylogenetic trees. Mol Biol Evol 4:406-425
34. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. 2nd edn. Cold Spring Harbor Laboratory Press, New York
35. Shao P, Chen YQ, Zhou H, Qu LH, Ma Y, Li HY, Jiao NZ (2004) Phylogenetic diversity of Archaea in prawn farm sediment. Mar Biol 146:133-142
36. Sjoling S, Mohammed MS, Lyimo JT, Kyaruzi JJ (2005) Benthic bacterial diversity and nutrient processes in mangroves: impact of deforestation. Estuar Coast Shelf Sci 63:397-406
37. Swofford DL (1999) PAUP: phylogenetic analysis using parsimony, version 4.0. Illinois Natural History Survey, Champaign, IL
38. Tam NFY, Li SH, Lan CY, Chen GZ, Li MS, Wong YS (1995) Nutrients and heavy metal contamination of plants and sediments in Futian mangrove forest. Hydrobiologia 295:149-158
39. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070-1074
40. Urakawa H, Kita-Tsukamoto K, Ohwada K (1999) Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145:3305-3315
41. Wieder RK, Lang GE (1982) A critique of the analytical methods used in examining decomposition data obtained from litter bags. Ecology 63:1636-1642