Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y.

Zhenzhen Zhao,Hai Yan,Chao Liu,Haiyang Zhang,Qianqian Xu,Shahbaz Ahmad,Yu Pang,Yang Liu,Abudumukeyiti Aikemu

doi:10.1007/s11274-021-03181-5

Zhenzhen Zhao, Hai Yan + Show 7 more

Open Access

https://doi.org/10.1007/s11274-021-03181-5

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Abstract

A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12h at the optimal culture conditions of pH 7.5 and 30℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.

Highlights

Phthalate esters (PAEs), composed of a benzene ring and two side chains at the ortho-position, are the most widely used plasticizers in plastic products, medical supplies, home appliances and toys (Daiem et al 2012)
dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DBP), butyl benzyl phthalate (BBP), diethylhexyl phthalate (DEHP), dinoctyl phthalate (DOP), monoethyl phthalate (MEP), monomethyl phthalate (MMP), monobutyl phthalate (MBP), phthalic acid (PA), protocatechuic acid (PCA) and butanol used for biodegradation experiments was purchased from Aladdin Chemistry Co. (Shanghai, China)
Phylogenetic analyses based on 16S rDNA sequences within genus Microbacterium suggested strain USTB-Y was closest to the species Microbacterium panaciterrae DCY56 (T) (Fig. 1)

Summary

Introduction

Phthalate esters (PAEs), composed of a benzene ring and two side chains at the ortho-position, are the most widely used plasticizers in plastic products, medical supplies, home appliances and toys (Daiem et al 2012). Due to physical bond (such as molecular forces and polymerization forces) to plastic products, PAEs are released into environment (Benjamin et al 2015), such as agricultural soil (Lü et al 2018), water and sediments (Adeogun et al 2015), atmospheric aerosols (Philip et al 2018). In the past 40 years, lots of PAEs-biodegrading bacteria, mainly belonging to genera Pseudomonas, Arthrobacter, Comamonas, Gordonia, Rhodococcus, and Sphingomonas, have been isolated from water, sediment, soil, etc., but microbial resources of high-efficiency and applicable strains were limited (Wang et al 2003; Wu et al 2011; Ren et al 2018; Shen et al 2019). Microbacterium sp. strains were reported to remove DEHP and DBP (Chen et al 2007; Lu et al 2020), few studies on the mechanism and genomic analysis of Microbacterium sp. were found up to now

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