Maintenance of N cycling gene communities with crop-livestock integration management in tropical agriculture systems

Five different agricultural management systems and a forest fragment at two farms were investigated for effects on soil bacterial indicators. This study was conducted in southern Mato Grosso do Sul, Brazil, in January 2014, at two farms that incorporated integrated crop-livestock systems in Hapludox soil. Impacts of management were assessed through evaluation of functional bacterial communities using quantitative PCR (qPCR) of nitrogen cycling genes (amoA, nirK, and nosZ), PCR-DGGE of the nirK community composition, and by investigating relationships of the nirK community with soil properties. The nirK gene community showed that reference forest soil maintained relatively large nirK, nosZ, but small amoA gene abundances and large range weighted nirK richness (Rr). The introduction of pasture into crop-livestock integration management (inclusion of the second and third year of grazing within a crop-livestock integration system, CL-2 and CL-3, respectively) or the field in its first year of crop rotation after grazing pasture (CL-b) increased nosZ and amoA abundance. Three years of grazing pasture in crop-livestock integration (CL-a) increased nirK abundance, while multiple years of crop rotation in crop-livestock integration management systems increased soil OM and promoted a richer nirK community composition. The nirK community Rr that was not significantly different from the forest was observed in the second or third year of crop rotation after grazing (CL-c or CL-d, respectively) and (CL-3). In contrast, fields in pasture (CL-a, continuous pasture (CP)) and the first year of crop rotation after pasture (CL-b) had reduced Rr and functional organization curves, indicating communities less resilient to future stress. Management systems under integrated crop-livestock farming in tropical soil maintained a relatively diverse N cycling bacterial community, possibly promoting soil quality and N cycling processes.