Abstract
Many bacteria belonging to Paenibacillus polymyxa are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as biological control agents (BCAs). However, the growth promotion and biocontrol mechanisms of P. polymyxa have not been thoroughly elucidated thus far. In this investigation, the genome sequences of two P. polymyxa strains, ZF129 and ZF197, with broad anti-pathogen activities and potential for growth promotion were comparatively studied. Comparative and functional analyses of the two sequenced P. polymyxa genomes showed that the ZF129 genome consists of one 5,703,931 bp circular chromosome and two 79,020 bp and 37,602 bp plasmids, designated pAP1 and pAP2, respectively. The complete genome sequence of ZF197 consists of one 5,507,169 bp circular chromosome and one 32,065 bp plasmid, designated pAP197. Phylogenetic analysis revealed that ZF129 is highly similar to two P. polymyxa strains, HY96-2 and SQR-21, while ZF197 is highly similar to P. polymyxa strain J. The genes responsible for secondary metabolite synthesis, plant growth-promoting traits, and systemic resistance inducer production were compared between strains ZF129 and ZF197 as well as other P. polymyxa strains. The results indicated that the variation of the corresponding genes or gene clusters between strains ZF129 and ZF197 may lead to different antagonistic activities of their volatiles or cell-free supernatants against Fusarium oxysporum. This work indicates that plant growth promotion by P. polymyxa is largely mediated by phytohormone production, increased nutrient availability and biocontrol mechanisms. This study provides an in-depth understanding of the genome architecture of P. polymyxa, revealing great potential for the application of this bacterium in the fields of agriculture and horticulture as a PGPR.
Highlights
Plant growth-promoting rhizobacteria (PGPR) have been identified as environmentally friendly alternatives to traditional agrochemicals for improving crop yield and quality (Kloepper et al, 1980)
Antagonistic spectrum assays showed that strains ZF129 and ZF197 presented broad, strong antipathogenic activities against various plant-pathogenic fungi and bacteria, including Verticillium dahlia, Corynespora cassiicola, Botrytis cinereal, Fusarium oxysporum, Colletotrichum spp., Rhizoctonia solani, Xanthomonas campestris pv. campestris, Clavibacter michiganensis subsp. sepedonicum, Ralstonia solanacearum, Pseudomonas syringae pv. tomato, and P. syringae pv. lachrymans (Supplementary Table S4 and Supplementary Figure S2)
The mycelia treated with ZF129 or ZF197 volatile compounds (VOCs) and the cell-free supernatant of ZF197 exhibited morphological aberrations such as enlargement, distortion and shriveling, whereas no similar changes were noted in the control mycelia
Summary
Plant growth-promoting rhizobacteria (PGPR) have been identified as environmentally friendly alternatives to traditional agrochemicals for improving crop yield and quality (Kloepper et al, 1980). P. polymyxa has been reported to produce various potent antimicrobial and volatile compounds that reduce plant disease severity (Eastman et al, 2014), such as antifungal and antibacterial metabolites (Zhao et al, 2011; Mageshwaran et al, 2012; Raza et al, 2015; Liu et al, 2018), thereby promoting growth (Anand et al, 2013; Padda et al, 2016) and inducing plant defenses (Mei et al, 2014; Shi et al, 2017; Luo et al, 2018). P. polymyxa can produce several kinds of antibiotic compounds, that can suppress the growth of pathogens under both laboratory and field conditions, including polymyxins and antifungal compounds such as fusaricidin (Choi et al, 2009; Padda et al, 2017; Liu et al, 2018). It has been reported that P. polymyxa secretes other types of antibiotics, such as 1-octen-3-ol, benzothiazole, citronellol (Zhao et al, 2011), paenibacillin (Huang and Yousef, 2015), di-n-butyl phthalate (Deng et al, 2011), lipopeptide (Mageshwaran et al, 2012), and phenazine-1-carboxylic acid (Tupinamba et al, 2008), and systemic resistance inducers, including 2,3-butanediol, methanethiol and isoprene (Gao et al, 2010; Lee et al, 2012)
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