Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3.

Cheng Zhang,Jiahuan Zhang,Hongyu Pan,Zhengyi Zhang,Fengjie Sun,Xianghui Zhang,Qingkai Hao,Hao Zhang

doi:10.3390/ijms20123053

Abstract

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8–10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

Highlights

Chlorimuron-ethyl, known as chlorsulfuron-ethyl, is a type of selective pre- and post-emergence herbicide, which is widely used for the control of broad-leaved weeds in soybean fields [1]
Chlorimuron-methyl is a herbicide with high efficiency and low toxicity, it has a long-lasting effect and is phytotoxic to many types of sensitive crops such as corn, sorghum, rape, melon, potato, and beet, limiting the use of this herbicide [1]
Bacteria in the genus Klebsiella are widespread in nature with several strains shown to be suitable for carrying out bioremediation due to their fast growth, a thick capsule on the surface of the cell wall, and resistance to pollutants [2,3]

Summary

Introduction

Chlorimuron-ethyl, known as chlorsulfuron-ethyl, is a type of selective pre- and post-emergence herbicide, which is widely used for the control of broad-leaved weeds in soybean fields [1]. The degradation of chlorimuron-ethyl in the natural environment is accomplished mainly by chemical hydrolysis and microbial degradation. Microbial degradations of environmental pollutants have been widely studied because of their high efficiency and safety. K. pneumoniae 2N3, a gram-negative bacterium in the family of Enterobacteriaceae, can degrade chlorimuron and other sulfonylurea herbicides such as metsulfuron-methyl, tribenuron-methyl, rimsulfuron, ethametsulfuron, and nicosulfuron [10]. The sulfonylurea bridge in chlorimuron-ethyl is first cleaved, and the intermediate products are converted to saccharin by hydrolysis and amidation. This biodegradation process is similar to those revealed in many other microorganisms that degrade chlorimuron-ethyl [12]

Methods

Results

Conclusion