Assessment of the effects of oxamyl on the bacterial community of an agricultural soil exhibiting enhanced biodegradation

Abstract Modern agricultural practices largely rely on pesticides to protect crops against various pests and to ensure high yields. Following their application to crops a large amount of pesticides ends up in soil where they may affect non-target organisms, among which microorganisms. We assessed the effects of the carbamate nematicide oxamyl on the whole bacterial diversity of an agricultural soil exhibiting enhanced biodegradation of oxamyl through 16S rRNA amplicon next generation sequencing (NGS) and on the oxamyl-degrading bacterial community through cehA q-PCR analysis and 14 C-oxamyl mineralization assays. Oxamyl was rapidly mineralized by the indigenous microorganisms reaching >70% within a month. Concomitantly, a significant increase in the number of oxamyl-degrading microorganisms was observed. NGS analysis of the total (DNA) and active (RNA) bacterial community showed no changes in α-diversity indices in response to oxamyl exposure. Analysis of the β-diversity revealed significant changes in the composition of the soil bacterial community after 13 and 30 days of oxamyl exposure only when the active fraction of the bacterial community was considered. These changes were associated with seven OTUs related to Proteobacteria (5), Acidobacteria (1) and Actinobacteria (1). The relative abundance of the dominant bacterial phyla were not affected by oxamyl, except of Bacteroidetes and Gemmatimonadetes which decreased after 13 and 30 days of oxamyl exposure respectively. To conclude, oxamyl induced changes in the abundance of oxamyl-degrading microorganisms and on the diversity of the soil bacterial community. The latter became evident only upon RNA-based NGS analysis emphasizing the utility of such approaches when the effects of pesticides on the soil microbial community are explored.