Metagenomic sequencing reveals microbial gene catalogue of phosphinothricin-utilized soils in South China

In the work, metagenomic sequencing was conducted to investigate the microbial gene catalogue in two samples of phosphinothricin (PPT)-utilized soils from South China. The gene sets contained an overwhelming majority of prevalent microbial genes, and were largely shared between these two samples. Several genus with high abundance were shared, such as norank_d_Bacteria, Nitrososphaera, Candidatus_Nitrosotalea, Candidatus_Nitrosocosmicus, and Rhodanobacter. Bacitracin resistance genes (61.4%) were the most dominant antibiotic resistance genes in two samples, followed by multidrug resistance efflux pump (12.5%). A lot of common virulence factors with high abundance were found in two samples, such as Alginate, Capsule I, ClpC, FbpABC, and HitABC, many of which were used for the iron uptake system. Total 57 putative PPT acetyltransferase were annotated, and two of them were found to be novel putative acetyltransferases for acetylation and detoxification of PPT. In conclusion, the work revealed microbial gene catalogue of PPT-utilized soils and found two novel putative PPT acetyltransferases using metagenomics. The work facilitates the understanding of impact of PPT on complex microbial community structure and physiology resides in PPT-utilized soils. Moreover, two annotated PPT acetyltransferases show important potential for the development of transgenic herbicide -resistant crops.