Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem

Soil Biology and Biochemistry

Volumn 65, Issue , 2013, Pages 86-95

  Navarro Noya, Yendi E ^a   Gómez Acata, Selene ^a   Montoya Ciriaco, Nina ^a   Rojas Valdez, Aketzally ^a   Suárez Arriaga, Mayra C ^a   Valenzuela Encinas, César ^a   Jiménez Bueno, Norma ^a   Verhulst, Nele ^b   Govaerts, Bram ^b   Dendooven, Luc ^a  

^a Laboratory of Soil Ecology   (Mexico)

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

Author keywords

Conservational agriculture; Crop rotation; Pyrosequencing; Residue management; Tillage; UniFrac

Indexed keywords

CROP ROTATION; PYROSEQUENCING; RESIDUE MANAGEMENT; TILLAGE; UNIFRAC;

BACTERIA; CROPS; NOBELIUM; RNA; SOCIAL SCIENCES; SOILS;

AGRICULTURAL MACHINERY;

AGRICULTURAL ECOSYSTEM; BACTERIUM; CROP RESIDUE; CROP ROTATION; MAIZE; MICROBIAL COMMUNITY; PHYLOGENETICS; RELATIVE ABUNDANCE; SEMIARID REGION; SOIL MICROORGANISM; TAXONOMY; TILLAGE; WHEAT;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; CYANOBACTERIA; GAMMAPROTEOBACTERIA; GEMMATIMONADETES; TRITICUM AESTIVUM; ZEA MAYS;

EID: 84879274370     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2013.05.009     Document Type: Article

References (55)

1. Aguilar-Chávez A., Diaz-Rojas M., Cárdenas-Aquino M.R., Dendooven L., Luna-Guido M. Greenhouse gas emissions from a wastewater sludge amended soil cultivated with wheat (Triticum spp. L.) as affected by different application rates of charcoal. Soil Biology and Biochemistry 2012, 52:90-95.
2. Alvear M., Rosas A., Rouanet J.L., Borie F. Effects of three soil tillage systems on some biological activities in an Ultisol from Southern Chile. Soil and Tillage Research 2005, 82:195-202.
3. Alvey S., Yang C.H., Buerkert A., Crowley D.E. Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biology and Fertility of Soils 2003, 37:73-82.
4. Balsanelli E., Serrato R.V., de Baura V.A., Sassaki G., Yates M.G., Rigo L.U., Pedrosa F.O., de Souza E.M., Monteiro R.A. Herbaspirillum seropedicae rfbB and rfbC genes are required for maize colonization. Environmental Microbiology 2010, 12:2233-2244.
5. Bernard L., Chapuis-Lardy L., Razafimbelo T., Razafindrakoto M., Pablo A.L., Legname E., Poulain J., Brüls T., O'Donohue M., Brauman A., Chotte J.L., Blanchart E. Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil. The ISME Journal 2012, 6:213-222.
6. Bragina A., Berg C., Cardinale M., Shcherbakov A., Chebotar V., Berg G. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle. The ISME Journal 2012, 6:802-813.
7. Caesar-TonThat T.C., Lenssen A.W., Caesar A.J., Sainju U.M., Gaskin J.F. Effects of tillage on microbial populations associated to soil aggregation in dryland spring wheat system. European Journal of Soil Biology 2010, 46:119-127.
8. Caporaso J.G., Bittinger K., Bushman F.D., DeSantis T.Z., Andersen G.L., Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26:266-267.
9. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 2010, 7:335-336.
10. Ceja-Navarro J.A., Rivera-Orduña F.N., Patiño-Zúñiga L., Vila-Sanjurjo A., Crossa J., Govaerts B., Dendooven L. Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Applied and Environmental Microbiology 2010, 76:3685-3691.
11. Cookson W.R., Murphy D.V., Roper M.M. Characterizing the relationships between soil organic matter components and microbial function and composition along a tillage disturbance gradient. Soil Biology and Biochemistry 2008, 40:763-777.
12. Doran J.W., Elliott E.T., Paustian K. Soil microbial activity, nitrogen cycling, and long-term changes in organic carbon pools as related to fallow tillage management. Soil and Tillage Research 1998, 49:3-18.
13. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
14. Enwall K., Nyberg K., Bertilsson S., Cederlund H., Stenstrom J., Hallin S. Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biology and Biochemistry 2007, 39:106-115.
15. Esperschuetz J., Gattinger A., Mader P., Schloter M., Fliessbach A. Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations. FEMS Microbiology Ecology 2007, 61:26-37.
16. Faith D.P. Conservation evaluation and phylogenetic diversity. Biological Conservation 1992, 61:1-10.
17. Falkowski P.G., Fenchel T., Delong E.F. The microbial engines that drive Earth's biogeochemical cycles. Science 2008, 320:1034-1039.
18. Faoro H., Alves A.C., Souza E.M., Rigo L.U., Cruz L.M., Al-Janabi S.M., Monteiro R.A., Baura V.A., Pedrosa F.O. Influence of soil characteristics on the diversity of bacteria in the Southern Brazilian Atlantic forest. Applied and Environmental Microbiology 2010, 76:4744-4749.
19. Fierer N., Bradford M.A., Jackson R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
20. Govaerts B., Mezzalama M., Sayre K.D., Crossa J., Lichter K., Troch V., Vanherck K., de Corte P., Deckers J. Long-term consequences of tillage, residue management, and crop rotation on selected soil micro-flora groups in the subtropical highlands. Applied Soil Ecology 2008, 38:197-210.
21. Govaerts B., Mezzalama M., Unno Y., Sayre K.D., Luna-Guido M., Vanherck K., Dendooven L., Deckers J. Influence of tillage, residue management, and crop rotation on soil microbial biomass, and catabolic diversity. Applied Soil Ecology 2007, 37:18-30.
22. Govaerts B., Sayre K.D., Deckers J. Stable high yields with zero tillage and permanent bed planting?. Field Crops Research 2005, 94:33-42.
23. Govaerts B., Sayre K.D., Deckers J. Aminimum data set for soil quality assessment of wheat and maize cropping in the highlands of Mexico. Soil and Tillage Research 2006, 87:163-174.
24. Gyaneshwar P., Hirsch A.M., Moulin L., Chen W.M., Elliott G.N., Bontemps C., Estrada-de Los Santos P., Gross E., Dos Reis F.B., Sprent J.I., Young J.P., James E.K. Legume-nodulating Betaproteobacteria: diversity, host range, and future prospects. Molecular Plant Microbe Interactions 2011, 24:1276-1288.
25. Haas B.J., Gevers D., Earl A.M., Feldgarden M., Ward D.V., Giannoukos G., Ciulla D., Tabbaa D., Highlander S.K., Sodergren E., Methé B., DeSantis T.Z., Petrosino J.F., Knight R., Birren B.W. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 2011, 21:494-504. Human Microbiome Consortium.
26. Hamady M., Lozupone C., Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME Journal 2010, 4:17-27.
27. Hartmann M., Widmer F. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Applied and Environmental Microbiology 2006, 72:7804-7812.
28. Helgason B.L., Walley F.L., Germida J.J. Fungal and bacterial abundance in long-term no-till and intensive-till soils of the northern great plains. Soil Science Society of America Journal 2009, 73:120-127.
29. Horn R., Taubner H., Wuttke M., Baumgartl T. Soil physical properties related to soil structure. Soil and Tillage Research 1994, 30:184-216.
30. Jangid K., Williams M.A., Franzluebbers A.J., Schmidt T.M., Coleman D.C., Whitman W.B. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties. Soil Biology and Biochemistry 2011, 43:2184-2193.
31. Jiang X., Wright A.L., Wang X., Liang F. Tillage-induced changes in fungal and bacterial biomass associated with soil aggregates: a long-term field study in a subtropical rice soil in China. Applied Soil Ecology 2011, 48:168-173.
32. Kihara J., Martius C., Bationo A., Thuita M., Lesueur D., Herrmann L., Amelung W., Vlek P.L.G. Soil aggregation and total diversity of bacteria and fungi in various tillage systems of sub-humid and semi-arid Kenya. Applied Soil Ecology 2012, 58:12-20.
33. Kirby R. Chromosome diversity and similarity within the Actinomycetales. FEMS Microbiology Letters 2011, 319:1-10.
34. Kuramae E.E., Yergeau E., Wong L.C., Pijl A.S., van Veen J.A., Kowalchuk G.A. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiology Ecology 2012, 79:12-24.
35. Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry 2008, 40:2407-2415.
36. Lupwayi N.Z., Clayton G.W., O'Donovan J.T., Harker K.N., Turkington T.K., Rice W.A. Soil microbiological properties during decomposition of crop residues under conventional and zero tillage. Canadian Journal of Soil Science 2004, 84:411-419.
37. Lupwayi N.Z., Lafond G.P., Ziadi N., Grant C.A. Soil microbial response to nitrogen fertilizer and tillage in barley and corn. Soil and Tillage Research 2012, 118:139-146.
38. Madari B., Machado P.L.O.A., Torres E., de Andrade A.G., Valencia L.I.O. No tillage and crop rotations effects on soil aggregation and organic carbon in a Rhodic Ferrasol from southern Brazil. Soil and Tillage Research 2005, 80:185-200.
39. Meriles J.M., Vargas S., Conforto G.C., Figoni G., Lovera E., March G.J., Guzmán C.A. Soil microbial communities under different soybean cropping systems: characterization of microbial population dynamics, soil microbial activity, microbial biomass, and fatty acid profiles. Soil and Tillage Research 2009, 103:271-281.
40. Monteiro R.A., Balsanelli E., Wassem R., Marin A.M., Brusamarello-Santos L.C.C., Schmidt M.A., Tadra-Sfeir M.Z., Pankievicz V.C.S., Cruz L.M., Chubatsu L.S., Pedrosa F.O., Souza E.M. Herbaspirillum-plant interactions: microscopical, histological and molecular aspects. Plant and Soil 2012, 356:175-196.
41. Nemergut D.R., Costello E.K., Hamady M., Lozupone C., Jiang L., Schmidt S.K., Fierer N., Townsend A.R., Cleveland C.C., Stanish L., Knight R. Global patterns in the biogeography of bacterial taxa. Environmental Microbiology 2011, 13:135-144.
42. Price M.N., Dehal P.S., Arkin A.P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 2009, 26:1641-1650.
43. SAS Institute Statistic Guide for Personal Computers 1989, Version 6.0. (ed), SAS Institute, Cary.
44. Schneider S., Hartmann M., Enkerli J., Widmer F. Fungal community structure in soils of conventional and organic farming systems. Fungal Ecology 2010, 3:215-224.
45. Sena M.M., Frighetto R.T.S., Valarini P.J., Tokeshi H., Poppi R.J. Discrimination of management effects on soil parameters by using principal component analysis: a multivariate analysis case study. Soil and Tillage Research 2002, 67:171-181.
46. Six J., Elliot E.T., Paustian K. Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under notillage agriculture. Soil Biology and Biochemistry 2000, 32:2099-2103.
47. Spedding T.A., Hamel C., Mehuys G.R., Madramootoo C.A. Soil microbial dynamics in maize-growing soil under different tillage and residue management systems. Soil Biology and Biochemistry 2004, 36:499-512.
48. Ussiri D.A.N., Lal R., Jarecki M.K. Nitrous oxide and methane emissions from long-term tillage under continuous corn cropping system in Ohio. Soil and Tillage Research 2009, 104:247-255.
49. Van Groenigen K.J., Bloem J., Bååth E., Boeckx P., Rousk J., Bodé S., Forristal D., Jones M.B. Abundance, production and stabilization of microbial biomass under conventional and reduced tillage. Soil Biology and Biochemistry 2010, 42:48-55.
50. Wang J.J., Li X.Y., Zhu A.N., Zhang X.K., Zhang H.W., Liang W.J. Effects of tillage and residue management on soil microbial communities in North China. Plant, Soil and Environment 2012, 58:28-33.
51. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
52. Wessén E., Hallin S., Philippot L. Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management. Soil Biology and Biochemistry 2010, 42:1759-1765.
53. Xuan D.T., Guong V.T., Rosling A., Alström S., Chai B., Högberg N. Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa. Biology and Fertility of Soils 2012, 48:217-225.
54. Yin C., Jones K.L., Peterson D.E., Garret K.A., Hulbert S.H., Paulitz T.C. Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biology and Biochemistry 2010, 42:2111-2118.
55. Zotarelli L., Alves B.J.R., Urquiaga S., Boddey R.M., Six J. Impact of tillage and crop rotation on light fraction and intra-aggregate soil organic matter in two oxisols. Soil and Tillage Research 2007, 95:196-206.