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

Jiali Lou; Min Liu; Jiali Gu; Qinghai Liu; Li Zhao; Yushu Ma; Dongzhi Wei

doi:10.1016/j.gene.2019.143942

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

Gene. 2019 Aug 30:711:143942. doi: 10.1016/j.gene.2019.143942. Epub 2019 Jun 22.

Authors

Jiali Lou¹, Min Liu², Jiali Gu³, Qinghai Liu⁴, Li Zhao⁵, Yushu Ma⁶, Dongzhi Wei⁷

Affiliations

¹ State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
² State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China. Electronic address: lmin@ecust.edu.cn.
³ Huzhou University, College of Life Science, Huzhou, China. Electronic address: gujiali@zjhu.edu.cn.
⁴ State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China. Electronic address: liuqinghai@ecust.edu.cn.
⁵ State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China. Electronic address: zhaoli@ecust.edu.cn.
⁶ State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China. Electronic address: myushu@ecust.edu.cn.
⁷ State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China. Electronic address: dzhwei@ecust.edu.cn.

PMID: 31238090
DOI: 10.1016/j.gene.2019.143942

Abstract

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.

Keywords: Antibiotic resistance genes; Metagenomics; Microbial community; N-acetyltransferase; Phosphinothricin; Virulence factors.

MeSH terms

Aminobutyrates / metabolism*
Bacteria / classification*
Bacteria / genetics
Bacteria / metabolism
Bacterial Proteins / genetics*
Drug Resistance, Microbial
Metagenomics / methods*
Phylogeny
Sequence Analysis, DNA / methods
Soil Microbiology

Substances

Aminobutyrates
Bacterial Proteins
phosphinothricin