title: Bacterial indicator taxa in soils under different long-term agricultural management.
abstract: OBJECTIVE
  In this study, the species indicator test was used to identify key bacterial taxa affected by changes in the soil environment as a result of conservation agriculture or conventional practices.
  
  
  RESULTS
  Soils cultivated with wheat (Triticum spp. L.) and maize (Zea mays L.) under different raised bed planting systems for 20 years, that is, varying crop residue and fertilizer management, were used. Taxonomic- and divergence-based 16S-metagenomics, and IndVal analysis were used to study the bacterial communities and identify indicator taxa (genus and OTU97 ) affected by agricultural practices. Although, some phyla were affected significantly by different treatments, the taxonomic assemblages at phylum level were similar. Bacterial taxa related to different processes of the N-cycle were indicators of different fertilization rates, for example, Azorhizobium, Nostoc and Nitrosomonas. A large number of OTU97 were indicators for conventionally tilled beds and their distribution was defined by soil organic carbon. IndVal analysis identified different taxa in each of the residue management systems. This suggests that although the same organic material remains in the field, crop residue management affects specific taxa. The taxa indicator of the burned residues belonged mainly to the order SBR1031 (Anaerolineae, Chloroflexi), and the genera Bacillus and Alicyclobacillus.
  
  
  CONCLUSIONS
  N-fertilizer application rates affected N-cycling taxa. Tillage affected Actinobacteria members and organic matter decomposers. Although the same crop residue was retained in the field, organic material management was important for specific taxa.
  
  
  CONCLUSIONS
  In this study, we report that agricultural practice affected soil bacterial communities. We also identified distinctive taxa and related their distribution to changes in the soil environment resulting from different agricultural practices.
authors.affiliation: Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico.
authors.forename: N G
authors.initials: NG
authors.lastname: Jiménez-Bueno
authors.affiliation: Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico.
authors.forename: C
authors.initials: C
authors.lastname: Valenzuela-Encinas
authors.affiliation: Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico.
authors.forename: R
authors.initials: R
authors.lastname: Marsch
authors.affiliation: Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico.
authors.forename: D
authors.initials: D
authors.lastname: Ortiz-Gutiérrez
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF, Mexico.
authors.forename: N
authors.initials: N
authors.lastname: Verhulst
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF, Mexico.
authors.forename: B
authors.initials: B
authors.lastname: Govaerts
authors.affiliation: Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico.
authors.forename: L
authors.initials: L
authors.lastname: Dendooven
authors.affiliation: CONACYT Research Fellow - Research Center of Biological Sciences, Tlaxcala Autonomous University, Tlaxcala, Tlaxcala, Mexico.
authors.forename: Y E
authors.initials: YE
authors.lastname: Navarro-Noya
mesh_terms: D000383:Agriculture / Q000379:methods*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D005308:Fertilizers / Q000032:analysis; D056186:Metagenomics; D010802:Phylogeny; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D014908:Triticum / Q000254:growth & development*; D003313:Zea mays / Q000254:growth & development*
chemical_list: D005308:Fertilizers; D012987:Soil
keywords: Cyanobacteria; N fertilizer application; bacterial community structure; conservation agriculture; crop residue management; indicator species; permanent beds; tillage