Molecular characterization of soil bacterial communities in contrasting zero tillage systems

Plant and Soil

Volumn 329, Issue 1, 2010, Pages 127-137

  Ceja Navarro, Javier A ^a   Rivera, Flor N ^a   Patiño Zúñiga, Leonardo ^a   Govaerts, Bram ^b   Marsch, Rodolfo ^a   Vila Sanjurjo, Antón ^c   Dendooven, Luc ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

16S rDNA; Phylogenetic analysis; Residues management; Zero tillage

Indexed keywords

DNA; MAIZE; MONOCULTURE; PHYLOGENETICS; SOIL MICROORGANISM; ZERO TILLAGE;

ACIDOBACTERIA; BACILLALES; BACTERIA (MICROORGANISMS); BURKHOLDERIALES; CHROMATIALES; LEGIONELLALES; NITROSOMONADALES; OSCILLATORIALES; PROTEOBACTERIA; PSEUDOMONADALES; PSEUDOMONAS; PSEUDOMONAS SP.; TRITICUM AESTIVUM; ZEA MAYS;

EID: 77950338708     PISSN: 0032079X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11104-009-0140-9     Document Type: Article

References (43)

1. Alfano JR, Collmer A (1996) Bacterial pathogens in plants: Life up against the wall. Plant Cell 8: 1683-1698.
2. Altschul SF, Gish W, Miller W, Myers E, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Alvear M, Rosas A, Rouanet JL, Borie F (2005) Effects of three soil tillage systems on some biological activities in an Ultisol from Southerm Chile. Soil Till Res 82: 195-202.
4. 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 9: 752-764.
5. Braid MD, Daniels LM, Kitts CL (2003) Removal of PCR inhibitors from soil DNA by chemical flocculation. J Microbiol Meth 52: 389-393.
6. Brons JK, van Elsas JD (2008) Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers. Appl Environ Microbiol 74: 2717-2727.
7. Brussaard L, de Ruiter PC, Brown GG (2007) Soil biodiversity for agricultural sustainability. Agr Ecosyst Environ 121: 233-244.
8. Camargo JA (1992) Can dominance influence stability in competitive interactions? Oikos 64: 605-609.
9. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16 S ribosomal RNA. Nucl Acids Res 17: 7843-7853.
10. El Banna N, Winkelmann G (1998) Pyrrolnitrin from Burkholderia cepacia: antibiotic activity against fungi and novel activities against streptomycetes. J Appl Microbiol 85: 69-78.
11. Erb RW, Wagner-Dobler I (1993) Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 59: 4065-4073.
12. FAO (1978) Report on the agro-ecological zones project (Vol. 1, Methodology and results for Africa). FAO World Resource Report 48. Food and Agricultural Organization of the United Nations, Rome, Italy, pp. 158.
13. Felske A, de Vos WM, Akkermans ADL (2000) Spatial distribution of 16 S rRNA levels from uncultured acidobacteria in soil. Lett Appl Microbiol 31: 118-122.
14. Fischer RA, Santiveri F, Vidal IR (2002) Crop rotation, tillage and crop residue management for wheat and maize in the sub-humid tropical highlands II. Maize and system performance. Field Crops Res 79: 123-137.
15. Govaerts B, Sayre KD, Deckers J (2005) Stable high yields with zero tillage and permanent bed planting? Field Crops Res 94: 33-42.
16. Govaerts B, Sayre KD, Deckers J (2006a) A minimum data set for soil quality assessment of wheat and maize cropping in the highlands of Mexico. Soil Tillage Res 87: 163-174.
17. Govaerts B, Mezzalama M, Sayre KD, Crosa J, Nicol JM, Deckers J (2006b) Long-term consequences of tillage, residue management, and crop residue on maize/wheat root rot and nematode populations. Appl Soil Ecol 32: 305-315.
18. Govaerts B, Mezzalama M, Sayre KD, Crossa J, Lichter K, Troch V et al (2008) Long-term consequences of tillage, residue management, and crop rotation on selected soil micro-flora groups in the subtropical highlands. Appl Soil Ecol 38: 197-210.
19. Hall GEM, Vaive JE, MacLaurin AI (1996) Analytical aspects of the application of sodium pyrophosphate reagent in the specific extraction of the labile organic component of humus and soils. J Geochem Explor 56: 23-36.
20. Hobbs PR, Sayre K, Gupta R (2008) The role of conservation agriculture in sustainable agriculture. Phil Trans R Soc B 363: 543-555.
21. Hugenholtz P, Goebel BM, Pace RN (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774.
22. Huss-Danell K (1997) Tansley review no. 93. Actinorhizal symbioses and their N-2 fixation. New Phytol 136: 375-405.
23. IUSS Working Group WRB, World Reference Base For Soil Resources (2006) FAO. Rome, Italy, pp 128.
24. Karlen DL, Wollenhaupt NC, Erbach DC, Berry EC, Swan JB, Eash NS et al (1994) Crop residue effects on soil quality following 10-years of no-till corn. Soil Till Res 31: 149-167.
25. Lupwayi NZ, Rice WA, Clayton GW (1998) Soil microbial diversity and community structure under wheat as influenced by tillage and crop rotation. Soil Biol Biochem 30: 1733-1741.
26. O'Sullivan DJ, O'Gara F (1992) Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiol Rev 56: 662-676.
27. 4 in the central highlands of Mexico: a laboratory study. Plant Soil 314: 231-241.
28. Posada D (2008) jModelTest: Phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
29. Raaijmakers JM, Weller DM (1998) Natural plant protection by 2, 4-diacetylphloroglucinol-producing Pseudomonas spp., in take-all decline soils. Mol Plant Microbe In 11: 144-152.
30. Ranjard L, Lejon DPH, Mougel C, Schehrer L, Merdinogu D, Chaussod R (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNa fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5: 1111-1120.
31. Roselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39-67.
32. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
33. Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16 S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-4376.
34. Six J, Ogle SM, Breidt FJ, Conant RT, Mosier A, Paustian K (2004) The potential to mitigate global warming with no-tillage management is only realized when practiced in the long term. Global Change Biol 10: 155-160.
35. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 103: 12115-12120.
36. Soil Survey Staff (1998) Keys to Soil Taxonomy. United States Department of Agriculture, Natural Resources Conservation Service, Washington, DC, USA, pp 328.
37. Swofford DL (1998) PAUP*: Phylogenetic Analysis Using Parsimony, ver. 4. 0b10. Sinauer Associates, Sunderland, Massachusetts.
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
39. Trân van V, Berge O, Ke SN, Balandreau J, Heulin T (2000) Repeated beneficial effects of rice inoculation with a strain of Burkholderia vietnamiensis on early and late yield components in low fertility sulphate acid soils of Vietnam. Plant Soil 218: 273-284.
40. Tsai YL, Olson BH (1991) Rapid method for extraction of DNA from soil and sediments. Appl Environ Microb 57: 1070-1074.
41. Wardle DA (1992) A comparative assessment of factors which influence microbial biomass carbon and nitrogen levels in soil. Biol Rev 67: 321-358.
42. Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70: 4800-4806.
43. Zhou J, Brunis MA, Tiedje JM (1995) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.