Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability.

Xueling Wu,Li Shen,Liangzhi Li,Enhui Wang,Xiangyu Zhou,Xiaoyan Wu,Yichao Gu,Weimin Zeng,Han Zhou

doi:10.3390/microorganisms8050716

Xueling Wu, Li Shen + Show 7 more

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https://doi.org/10.3390/microorganisms8050716

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Journal: Microorganisms	Publication Date: May 12, 2020
Citations: 4	License type: CC BY 4.0

Affiliation: Central South University

Abstract

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

Highlights

Hypersaline industrial wastewaters generated from processes, such as food production, petroleum refining, pharmaceutical manufacturing, printing, and dyeing, often contain large amounts of toxic compounds [1,2,3,4,5], most of which were recalcitrant to conventional biological treatment due to inhibition of salt and generally required expensive physico-chemical treatments to remove the salts as well as the organic matter [6]
The results showed that the top four highly expressed Clusters of Orthologous Groups (COG) classes in L. pakistanensis LZH-9 based on average Codon Adaption Index (CAI) values were COG [J] [F] [O] [C] associated with most essential biological processes including nucleotide metabolism, translation, and energy production, followed by COG [M], [E], [Q], and [G] reflecting high metabolic rate to digest potential carbon or nitrogen sources in potential contaminants, which closely linked with efficient chemical oxygen demand (COD) removal ability of LZH-9, whereas genes that were related to COG [X] were predicted to be most inactively expressed (Figure 7a)
Whole genome sequencing of strain LZH-9 and comparative genomic analysis of eight strains of the Lysinibacillus revealed metabolic versatility of different genomes of Lysinibacillus, and we found a multitude of genes that were involved in xenobiotics biodegradation, resistance to toxic compounds and salinity in all tested genomes of Lysinibacillus, pointing to promising application of Lysinibacillus in bioremediation

Summary

Introduction

Hypersaline industrial wastewaters generated from processes, such as food production, petroleum refining, pharmaceutical manufacturing, printing, and dyeing, often contain large amounts of toxic compounds [1,2,3,4,5], most of which were recalcitrant to conventional biological treatment due to inhibition of salt and generally required expensive physico-chemical treatments to remove the salts as well as the organic matter [6]. RGS applied to decolorize mixture of dyes and actual industrial effluent showed 87% decolorization efficiency with 69% COD reduction at 48 h [23] These studies emphasized the applicability of Lysinibacillus in the treatment of industrial wastewater; little research has been conducted to optimize the contaminant removal efficiency as well as explored the salt tolerance limit of Lysinibacillus spp. Evolutionary drivers, such as horizontal gene transfer (HGT) and natural selection, may contribute to adaptive evolution of Lysinibacillus genomes, whereas their relative contributions were still unexplored

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