Abstract
Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
Highlights
Paenibacillus polymyxa is a multifunctional Gram-positive (G+) bacterium that has been reported to have applications in agriculture (Hao and Chen, 2017), medicine (Galea et al, 2017; Yu et al, 2017), and industry (Lal and Tabacchioni, 2009)
In 2004, P. polymyxa strain HY96-2 from the tomato rhizosphere was developed as the first microbial biopesticide based on P. polymyxa and registered in China, for the control of soil-borne diseases caused by R. solanacearum on tomatoes and F. oxysporum on watermelons, as well as leaf diseases caused by B. cinerea and Pseudomonas syringae on cucumbers2
As an important biocontrol agent, P. polymyxa is a relatively novel species and the number of registered products based on this species is growing rapidly8
Summary
Paenibacillus polymyxa is a multifunctional Gram-positive (G+) bacterium that has been reported to have applications in agriculture (Hao and Chen, 2017), medicine (Galea et al, 2017; Yu et al, 2017), and industry (Lal and Tabacchioni, 2009). P. polymyxa has been in the list of substances reported under the Toxic Substance Control Act (TSCA) by the United States Environmental Protection Agency (EPA). P. polymyxa has been in the list of substances reported under the Toxic Substance Control Act (TSCA) by the United States Environmental Protection Agency (EPA)1 It means P. polymyxa is a safe and commercially available microbe. P. polymyxa is an important biocontrol agent that has been reported to suppress a large variety of fungal and bacterial plant diseases, such as those caused by the fungi Fusarium oxysporum and Botrytis cinerea and the bacteria Xanthomonas campestris and Ralstonia solanacearum (Xu et al, 2006; Kim et al, 2010; Fan et al, 2012; Weselowski et al, 2016). Microbial biopesticides derived from P. polymyxa HY96-2 have been manufactured and sold in 24 provinces across China, further research into its precise biocontrol mechanism, especially at the molecular level, is still needed
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