Diversity of glyphosate-degrading bacteria and degradation genes from Xinjiang cotton field’s unique soil environment

To clarify the diversity of glyphosate-degrading bacteria and genes in arid and alkaline soil environments, an efficient bacterial community, named CW, was enriched from the long-term continually cropped saline-alkali cotton soil in Xinjiang. This community could degrade 500 mg/L of glyphosate within 36 h in MSM medium with a pH of 8.0. The CW community was mainly composed of over 20 genera belonging to the phyla Pseudomonadota, Bacillota, and Bacteroidota. Notable genera include Hyphomicrobium, Pseudoxanthomonas, and Aquamicrobium. From this community, twenty-four strains showing glyphosate-degrading ability, representing 9 different genera, were successfully isolated. Notably, 14 strains belonging to six specific genera- Aquamicrobium (6), Shinella (2), Pseudoxanthomonas (2), Nocardioides (1), Chitinophaga (1), and Pseudomonas (2)- displayed complete degradation (100%). In addition, this study marks the first report confirming Aquamicrobium and Shinella as novel genera degrading glyphosate. During the degradation of glyphosate by the bacterial community CW, intermediate metabolites such as AMPA and phosphate were detected. Besides, sarcosine was detected during the degradation by the bacterial strain W6/W7. A detailed analysis of the glyphosate-degrading genes revealed that, besides the thiO, GAT, and phnY gene sequences, the genome of bacterial strain W6/W7 also harbors sequences with high similarity to the previously reported glyphosate-degrading genes soxA, aroA, dadA, phnJ, phnD, and phnA. Notably, the community CW efficiently expressed all the genes. Additionally, genes associated with phosphonate, hypophosphonate, oxalate, and dicarboxylate metabolism were co-expressed during glyphosate degradation. This study reveals that, even in the unique soil environment of Xinjiang, there exists a highly diverse bacterial community which can completely and efficiently degrade glyphosate.