Agricultural practice negatively affects soil bacterial diversity and nitrogen functional genes comparing to adjacent native forest soils

Soil bacterial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from forest, transition, to crop soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on the bacterial 16S rRNA gene was performed for bacterial diversity and community analyses. Nitrifying and denitrifying functional genes (amoA and nirK respectively) of bacteria were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences was significantly different between crop and forest soils (p < 0.01) as well as between crop and transition soils (p = 0.01), however, there was no significant difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial relative abundance, richness, and Shannon diversity. Soil pH and nitrate contents together contributed highest to the observed different bacterial communities (Correlations = 0.381). Two operational taxonomic units (OTUs) belonging to Acidobacteriales species (OTU5, OTU8) decreased in crop soils, however, agricultural practices significantly increased an OTU of Nitrobacteraceae (OTU4). The relative abundance of ammonia-oxidizing bacteria (AOB) amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed, and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Soil pH and organic contents together contributed highest to the observed different nirK communities (Correlations = 0.443). Anthropogenic effects through agricultural practices decreased bacterial richness and Shannon diversity, increased abundance of nitrifying bacteria, and decreased diversity of denitrifying bacteria, potentially affecting the N cycling processes for healthy soils, plant productivity, and water and air quality.