Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism

Yuanchan Luo; Lei Chen; Zhibo Lu; Weijian Zhang; Wentong Liu; Yuwei Chen; Xinran Wang; Wei Du; Jinyan Luo; Hui Wu

doi:10.1186/s40643-022-00563-x

Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism

Bioresour Bioprocess. 2022 Jul 18;9(1):74. doi: 10.1186/s40643-022-00563-x.

Authors

Yuanchan Luo¹, Lei Chen², Zhibo Lu¹, Weijian Zhang¹, Wentong Liu¹, Yuwei Chen¹, Xinran Wang¹, Wei Du³, Jinyan Luo⁴, Hui Wu^{5

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Affiliations

¹ Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
² Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China.
³ Agricultural Technology Extension Station of Ningxia, 2, West Shanghai Road, Yinchuan, 750001, China.
⁴ Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China. toyanzi@126.com.
⁵ Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China. hwu@ecust.edu.cn.
⁶ State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China. hwu@ecust.edu.cn.
⁷ Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China. hwu@ecust.edu.cn.
⁸ Key Laboratory of Bio-Based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai, 200237, China. hwu@ecust.edu.cn.

Abstract

Plant growth-promoting rhizobacteria (PGPR) or Biocontrol strains inevitably encounter heavy metal excess stress during the product's processing and application. Bacillus amyloliquefaciens Bam1 was a potential biocontrol strain with strong heavy metal resistant ability. To understand its heavy metal resistance mechanism, the complete genome of Bam1 had been sequenced, and the comparative genomic analysis of Bam1 and FZB42, an industrialized PGPR and biocontrol strain with relatively lower heavy metal tolerance, was conducted. The comparative genomic analysis of Bam1 and the other nine B. amyloliquefaciens strains as well as one Bacillus velezensis (genetically and physiologically very close to B. amyloliquefaciens) was also performed. Our results showed that the complete genome size of Bam1 was 3.95 Mb, 4219 coding sequences were predicted, and it possessed the highest number of unique genes among the eleven analyzed strains. Nine genes related to heavy metal resistance were detected within the twelve DNA islands of Bam1, while only two of them were detected within the seventeen DNA islands of FZB42. When compared with B. amyloliquefaciens type strain DSM7, Bam1 lacked contig L, whereas FZB42 lacked contig D and I, as well as just possessed contig B with a very small size. Our results could also deduce that Bam1 promoted its essential heavy metal resistance mainly by decreasing the import and increasing the export of heavy metals with the corresponding homeostasis systems, which are regulated by different metalloregulators. While Bam1 promoted its non-essential heavy metal resistance mainly by the activation of some specific or non-specific exporters responding to different heavy metals. The variation of the genes related to heavy metal resistance and the other differences of the genomes, including the different number and arrangement of contigs, as well as the number of the heavy metal resistant genes in Prophages and Genomic islands, led to the significant different resistance of Bam1 and FZB42 to heavy metals.

Keywords: Bacillus amyloliquefaciens; Comparative genomic analysis; Heavy metal resistance mechanism; Resistance to essential heavy metals; Resistance to non-essential heavy metals.

Abstract

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