The use of integrated production systems is widespread, mainly in tropical areas. This practice could contribute to soil conservation, increasing biodiversity and environmental services while reducing greenhouse gases emissions. The present work assessed bacterial biodiversity and correlations with nitrous oxide (N2O) and methane (CH4) emissions in soils under integrated production systems. Analyses of bacterial diversity and community structure were carried out using DGGE (denaturing gradient gel electrophoresis). Samples for the evaluation of greenhouse gases were collected in the field and measured using a gas chromatograph. The assessed treatments in a rainy and dry season were: crop (L), pasture (P), planted eucalypt forests (F), pasture followed by crop (IPL), crop followed by pasture (ILP), crop with forest (ILF); pasture with forests (IPF); crop with forest followed by pasture with forests, pasture with forests followed by crop with forest and crop, grassland and forest. In the rainy season, most N2O emissions occurred in the ILP with an average flow of 42.33 µg N m−2 h−1, and the lowest flow was observed in the ILF, with an average flow of 5.53 µg N m−2 h−1. In the dry season, higher emission occurred in the IPL, with an average flow of 4.17 ug N m−2 h−1. In this period, we observed gas consumption in F, the highest N2O consumer with a flow of −4.14 µg N m−2 h−1. In both seasons, CH4 was consumed, with IPF as the most significant consumer with an average flow of −14.19 µg C m−2 h 1(dry); F was the most significant consumer with an average flow −12.32 µg of C m−2 h−1. Bacterial community structure was affected by the agricultural production system and the seasons. Methane emissions and pH showed a correlation with bacterial diversity in different treatments. In contrast, nitrous oxide was negatively correlated with bacterial diversity. Based on our results, we suggest that integrated production systems and plant coverage modulate soil bacterial community structure and biodiversity which, in turn, affect soil processes related to higher or lower methane and nitrous oxide emissions.
