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

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 14C-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 ß-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.

Isolation of Oxamyl-degrading Bacteria and Identification of cehA as a Novel Oxamyl Hydrolase Gene.

Microbial degradation is the main process controlling the environmental dissipation of the nematicide oxamyl. Despite that, little is known regarding the microorganisms involved in its biotransformation. We report the isolation of four oxamyl-degrading bacterial strains from an agricultural soil exhibiting enhanced biodegradation of oxamyl. Multilocus sequence analysis (MLSA) assigned the isolated bacteria to different subgroups of the genus Pseudomonas. The isolated bacteria hydrolyzed oxamyl to oxamyl oxime, which was not further transformed, and utilized methylamine as a C and N source. This was further supported by the detection of methylamine dehydrogenase in three of the four isolates. All oxamyl-degrading strains carried a gene highly homologous to a carbamate-hydrolase gene cehA previously identified in carbaryl- and carbofuran-degrading strains. Transcription analysis verified its direct involvement in the hydrolysis of oxamyl. Selected isolates exhibited relaxed degrading specificity and transformed all carbamates tested including the oximino carbamates aldicarb and methomyl (structurally related to oxamyl) and the aryl-methyl carbamates carbofuran and carbaryl which share with oxamyl only the carbamate moiety.

Effects of systemic pesticides imidacloprid and metalaxyl on the phyllosphere of pepper plants.

Microbes inhabiting the phyllosphere of crops are exposed to pesticides applied either directly onto plant foliage or indirectly through soil. Although, phyllosphere microbiology has been rapidly evolving, little is still known regarding the impact of pesticides on the epiphytic microbial community and especially on fungi. We determined the impact of two systemic pesticides (metalaxyl and imidacloprid), applied either on foliage or through soil, on the epiphytic fungal and bacterial communities via DGGE and cloning. Both pesticides induced mild effects on the fungal and the bacterial communities. The only exception was the foliage application of imidacloprid which showed a more prominent effect on the fungal community. Cloning showed that the fungal community was dominated by putative plant pathogenic ascomycetes (Erysiphaceae and Cladosporium), while a few basidiomycetes were also present. The former ribotypes were not affected by pesticides application, while selected yeasts (Cryptococcus) were stimulated by the application of imidacloprid suggesting a potential role in its degradation. A less diverse bacterial community was identified in pepper plants. Metalaxyl stimulated an Enterobacteriaceae clone which is an indication of the involvement of members of this family in fungicide degradation. Further studies will focus on the isolation of epiphytic microbes which appear to be stimulated by pesticides application.