Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes

Soil Biology and Biochemistry

Volumn 41, Issue 4, 2009, Pages 687-694

  Liu, Xin Zhan ^a,b   Zhang, Li Mei ^a   Prosser, James I ^c   He, Ji Zheng ^a  

^a RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Bacteria; Clone libraries; Fertilization; Paddy soil; Quantification; Real time PCR; Sulfate reducing prokaryotes

Indexed keywords

BACTERIA; BACTERIOLOGY; CLONING; COSMIC RAYS; LIBRARIES; NITROGEN FERTILIZERS; PHOSPHORUS; POTASSIUM;

CLONE LIBRARIES; FERTILIZATION; PADDY SOIL; QUANTIFICATION; REAL-TIME PCR; SULFATE REDUCING PROKARYOTES;

SOILS;

ABUNDANCE; AGRICULTURAL SOIL; COMMUNITY RESPONSE; COMMUNITY STRUCTURE; FERTILIZER APPLICATION; PADDY FIELD; POLYMERASE CHAIN REACTION; PROKARYOTE; SEASONAL VARIATION; SOIL MICROORGANISM; SULFATE;

BACTERIA (MICROORGANISMS); CLOSTRIDIA; DELTAPROTEOBACTERIA; DESULFOVIBRIONACEAE; PROKARYOTA;

EID: 62049085009     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2009.01.001     Document Type: Article

References (50)

1. 2 transfer to sulfate and ferric iron-reducing bacteria in acetate consumption in anoxic paddy soil. FEMS Microbiology Ecology 16 (1995) 61-70
2. Barton L.L., and Tomei F.A. Characteristics and activities of sulfate-reducing bacteria. In: Barton L.L. (Ed). Sulfate-reducing bacteria (1995), Peplum Press, New York, NY, USA 1-179
3. Castro H.F., Williams N.H., and Ogram A. Phylogeny of sulfate-reducing bacteria. FEMS Microbiology Ecology 31 (2000) 1-9
4. Castro H., Reddy K.R., and Ogram A. Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades. Applied and Environmental Microbiology 68 (2002) 6129-6137
5. Detmers J., Strauss H., Bergmann U., Knittel K., and Kuever J. FISH shows that Desulfotomaculum spp. are the dominating sulfate-reducing bacteria in a pristine aquifer. Microbial Ecology 47 (2004) 236-242
6. Dhillon A., Teske A., Dillon J., Stahl D.A., and Sogin M.L. Molecular characterization of sulfate-reducing bacteria in the Guaymas basin. Applied and Environmental Microbiology 69 (2003) 2765-2772
7. Elshahed M.S., Senko J.M., Najar F.Z., Kenton S.M., Roe B.A., Dewers T.A., Spear J.R., and Krumholz L.R. Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Applied and Environmental Microbiology 69 (2003) 5609-5621
8. Ge Y., Zhang J.B., Zhang L.M., Yang M., and He J.Z. Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. Journal of Soils and Sediments 8 (2008) 43-50
9. Geets J., Borremans B., Diels L., Springael D., Vangronsveld J., Lelie D.V.D., and Vanbroekhoven K. dsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. Journal of Microbiological Methods 66 (2006) 194-205
10. Gilmour C.C., Riedel G.S., Ederington M.C., Bell J.T., Benoit J.M., Gill G.A., and Stordal M.C. Methylmercury concentrations and production rates across a trophic gradient in the northern Everglades. Biogeochemistry 40 (1998) 327-345
11. Habicht K.S., Salling L., Thamdrup B., and Canfield D. Effect of low sulfate concentrations on lactate oxidation and isotope fraction during sulfate reduction by Archaeoglobus fulgidus strain Z. Applied and Environmental Microbiology 71 (2005) 3770-3777
12. He J.Z., Shen J.P., Zhang L.M., Zhu Y.G., Zheng Y.M., Xu M.G., and Di H.J. Quantification analysis of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environmental Microbiology 9 (2007) 2364-2374
13. He J.Z., Zheng Y., Chen C.R., He Y.Q., and Zhang L.M. Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. Journal of Soils and Sediments 8 (2008) 349-358
14. Hengstmann U., Chin K.J., Janssen P.H., and Liesack W. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Applied and Environmental Microbiology 65 (1999) 5050-5058
15. Jorgensen B.B. Mineralization of organic-matter in the sea bed: the role of sulfate reduction. Nature 296 (1982) 643-645
16. Klappenbach J.L., Saxman P.H., Cole J.R., and Schmidt T.M. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Research 29 (2001) 181-184
17. Klein M., Friedrich M., Roger A.J., Hugenholtz P., Fishbain S., Abicht H., Blackall L.L., Stahl D.A., and Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Applied and Environmental Microbiology 67 (2001) 6028-6035
18. Kondo R., Nedwell D.B., Purdy K.J., and Silva S.Q. Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiology Journal 21 (2004) 145-157
19. Lane D.J. 16S/23S rRNA sequencing. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic acid techniques in bacterial systematics (1991), John Wiley & Sons, New York 115-175
20. Leloup J., Quillet L., Thierry B., and Petit F. Diversity of the dsrAB (dissimilatory sulfite reductase) gene sequences retrieved from two contrasting mudflats of the Seine estuary, France. FEMS Microbiology Ecology 55 (2005) 230-238
21. Leloup J., Loy A., Knab N.J., Borowski C., Wagner M., and Jorgensen B.B. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environmental Microbiology 9 (2007) 131-142
22. Ludemann H., Arth I., and Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Applied and Environmental Microbiology 66 (2000) 754-762
23. Mäder P., Flieβbach A., Dubois D., Gunst L., Fried P., and Niggli U. Soil fertility and biodiversity in organic farming. Science 296 (2002) 1694-1697
24. Magurran A.E. Ecological diversity and its measurement (1988), Princeton University Press, Princeton
25. Ouattara A.S., and Jacq V.A. Characterization of sulfate-reducing bacteria isolated from Senegal rice fields. FEMS Microbiology Ecology 101 (1992) 217-228
26. Oude Elferink S.J.W.H., Mass R.N., Harmsen H.J.M., and Stams A.J.M. Desulforhabdus amnigenus gen.nov.sp.nov., a sulfate reducer isolated from anaerobic granular sludge. Archives of Microbiology 164 (1995) 119-124
27. Ravensschlag K., Sahm K., Knoblauch C., Jorgensen B.B., and Amann R. Community structure, cellular rRNA content and activity of sulfate reducing bacteria in marine arctic sediments. Applied and Environmental Microbiology 66 (2000) 3592-3602
28. Sass H., Cypionka H., and Babenzien H.D. Vertical distribution of sulfate-reducing bacteria at the oxic-anoxic interface in sediments of the oligotrophic Lake Stechlin. FEMS Microbiology Ecology 22 (1997) 245-255
29. Scheid D., and Stubner S. Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots. FEMS Microbiology Ecology 36 (2001) 175-183
30. Schibata A., Toyota K., Miyake K., and Katayama A. Anaerobic biodegradation of 4-alkylphenols in a paddy soil microcosm supplemented with nitrate. Chemosphere 68 (2007) 2096-2103
31. Schippers A., and Neretin L.N. Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environmental Microbiology 8 (2006) 1251-1260
32. Schmalenberger A., Drake H.L., and Kusel K. High unique diversity of sulfate-reducing prokaryotes characterized in a depth gradient in an acidic fen. Environmental Microbiology 9 (2007) 1317-1328
33. Shen J.P., Zhang L.M., Zhu Y.G., Zhang J.B., and He J.Z. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environmental Microbiology 10 (2008) 1601-1611
34. Singleton D.R., Furlong M.A., Rathbu S.L., and Whitman W.B. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Applied and Environmental Microbiology 67 (2001) 4373-4376
35. Smith C.J., Nedwell D.B., Dong L.F., and Osborn A.M. Evaluation of quantitative polymerase chain reaction based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology 8 (2006) 804-815
36. Stackebrandt E., Sproer C., Rainey F.A., Burghardt O.P., and Hippe H. Phylogenetic analysis of the genus Desulfotomaculum: evidence for the misclassification of Desulfotomaculum guttoideum and description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov. International Journal of Systematic and Evolutionary Microbiology 47 (1997) 1134-1139
37. Stubner S. Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen™ detection. Journal of Microbiological Methods 50 (2002) 155-164
38. Stubner S. Quantification of Gram-negative sulphate-reducing bacteria in rice field soil by 16S rRNA gene-targeted real-time PCR. Journal of Microbiological Methods 57 (2004) 219-230
39. Stubner S., and Meuser K. Detection of Desulfotomaculum in an Italian rice paddy soil by 16S ribosomal nucleic acid analysis. FEMS Microbiology Ecology 34 (2000) 73-80
40. Suzuki M.T., Taylor L.T., and Delong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Applied and Environmental Microbiology 66 (2000) 4605-4614
41. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24 (2007) 1596-1599
42. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22 (1994) 4673-4680
43. Wagner M., Roger A.J., Flax J.L., Brusseau G.A., and Stahl D.A. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. Journal of Bacteriology 180 (1998) 2975-2982
44. Wagner M., Loy A., Klein M., Lee N., Ramsing N.B., Stahl D.A., and Friedrich M.W. Functional marker genes for identification of sulfate-reducing prokaryotes. Methods in Enzymology 397 (2005) 469-489
45. Walkley A., and Black I.A. An examination of the Degtjareff method for determining soil organic matter and a proposed modification of chromic acid titration method. Soil Science 37 (1934) 29-38
46. Wind T., and Conrad R. Sulfur compounds, potential turnover of sulfate and thiosulfate, and numbers of sulfate-reducing bacteria in planted and unplanted paddy soil. FEMS Microbiology Ecology 18 (1995) 257-266
47. Wind T., and Conrad R. Localization of sulfate reduction in planted and unplanted rice soil. Biogeochemistry 37 (1997) 253-278
48. Wind T., Stubner S., and Conrad R. Sulfate-reducing bacteria in rice field soil and on rice roots. Systematic and Applied Microbiology 22 (1999) 269-279
49. Yang S.Y., Yoshida N., Bata D., and Katayama A. Anaerobic biodegradation of biphenyl in various paddy soils and river sediment. Chemosphere 71 (2008) 328-336
50. Zheng Y., Zhang L.M., Zheng Y.M., Di H.J., and He J.Z. Abundances and community composition of methanotrophs in a Chinese paddy soil under long-term fertilization practices. Journal of Soils and Sediments 8 (2008) 406-414