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16S metagenomics reveals changes in the soil bacterial community driven by soil organic C, N-fertilizer and tillage-crop residue management

Yosef Chávez-Romero, Yendi E. Navarro-Noya, Silvia C. Reynoso-Martínez, Yohana Sarria-Guzmán, Bram Govaerts, Nele Verhulst, Luc Dendooven, Marco Luna-Guido
Soil & tillage research 2016 v.159 pp. 1-8
Agromyces, Lysobacter, Nitrosovibrio, Promicromonospora, Sinorhizobium, Streptomyces, Triticum, Vertisols, Zea mays, arable soils, bacterial communities, community structure, corn, crop residue management, crop residues, fertilizer application, metagenomics, microbial growth, mineralization, nitrogen, nitrogen fertilizers, pH, soil bacteria, soil organic carbon, sustainable agriculture, tillage, wheat, wheat soils, Mexico
Conservation agriculture is a sustainable alternative to conventional agriculture. However, little is known about their effect on the environment and on the soil microbial community. It was established as a hypothesis that the bacterial community structure would be defined by the different agronomic practices. The objective of this study was, therefore, to investigate how crop residue management, tillage and fertilizer application affected the bacterial community and those groups involved in the degradation of applied plant residues, and increase the knowledge to predict the sustainability of a soil under a specific agronomic practice. Samples from an arable soil from the state of Sonora (México), i.e. Hyposodic Vertisol (Calcaric, Chromic) (IUSS Working Group, 2007), cultivated with wheat (Triticum spp.) and maize (Zea mays L.) in succession on conventionally tilled beds (CTB) with crop residue incorporated, permanent beds (PB) with residue burned or retained, left unfertilized or fertilized (300kgNha−1 for wheat and 103kgNha−1 for maize) was improved with dried young wheat plants to stimulate microbial growth, while the bacterial community structure and C and N mineralization were monitored in an aerobic incubation of 56 days. The soil organic C was significantly higher in the PB-residue retained treatments (average 13.1gkg−1 dry soil) compared with PB-residue burned (average 9.9gkg−1 dry soil) or CTB-residue incorporated (average 10.5gkg−1 dry soil), while pH and EC were significantly higher in the PB-residue burned (averages 8.85 and 1.06dSm−1) compared with the fertilized or unfertilized soil in PB-residue retained (averages 8.65 and 0.78dSm−1) or CTB-residue incorporated (averages 8.75 and 0.95dSm−1). In the unimproved soil, we found a significant effect of soil organic C, application of N fertilizer (highly significant on Nitrosovibrio) and tillage-residue management (principally in fertilized soil) on the bacterial community structure, but not in the improved soil. Treatment had no significant effect on the decomposition of the applied organic material, and on average 48% and 9.4% of the applied C and N, respectively, were mineralized in 56 days. Improvement of soil with wheat plant material increased mainly the relative abundance of Actinobacteria and Firmicutes and decreased a wide range of bacterial groups. On the bacterial level of genus, tillage-residue management was the most important defining factor of the bacterial community inducing differences in the genera involved in the degradation of applied plant material, i.e. Promicromonospora, Bacillus, Agromyces, Streptomyces, Sinorhizobium and Lysobacter, in different treatments. It was found that nitrogen fertilization and tillage-crop residue management defined the soil bacterial community structure in the unimproved soil, but were less determinant in improved soil, and these results supported the hypothesis tested. It was concluded that all the factors tested, i.e. tillage, crop-residue management and fertilizer application, affect the soil bacterial community structure, while the mineralization potential of the soil was preserved. This study contributes to our understanding of how soil use and management practices define the soil bacterial community structure.