Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism

Abstract

Background Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed. Results In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified. Conclusions This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot

“…The key gene in AI-2 QS system, luxS , and the four genes ( spo0A , spo0B , spo0F , and degU ) involved in biofilm formation pathway were found in genome of strain ZF390, and the sequence identity between ZF390 and HS311 (97.64%) exhibited higher values than those between strain ZF390 with SQR-21 (92.42%), HY96-2 (92.42%), or PS04 (91.06%). Key genes related to the plant-resistance inducers in ZF390 were retrieved in light of previous studies, and the identities of these genes among HS311, SQR-21, HY96-2, and PS04 were compared [ 7 , 56 ]. The results demonstrate that the key genes associated with volatile organic compounds belong to systemic resistance inducers, such as 2,3-butanediol, methanethiol, and isoprene synthesis, were all detected in the genomes of the five strains, with sequence identities exceeding 85% ( Supplementary Table S8 ).…”

“…Similar to Bacillus , the Paenibacillus species can be applied in agriculture as phytostimulators, biofertilizers, and bioagents. Paenibacillus strains have exhibited their biocontrol properties, including plant colonization, pathogen inhibition, plant-growth promotion abilities, and the activation of induced systemic resistance [ 6 , 7 ]. Previous studies revealed potential Paenibacillus biocontrol agents to protect plants from pathogens such as Phytophthora tropicalis , P. parasitica , Fusarium oxysporum , and Xanthomonas oryzae [ 8 , 9 , 10 , 11 ].…”

Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms

“…The identities of different functional genes at the amino acid level were compared among the strains by using BLAST, with an E-value cut off of 1e-15 was used for the BLAST search ( Kumar et al, 2019 ). Secondary metabolite gene clusters were predicted by antiSMASH 4.0.2 ( Jiang et al, 2022 ).…”

“…Species in the genus Paenibacillus are either Gram-positive or variable, facultatively anaerobic or strictly aerobic, produce ellipsoidal endospores, and are nonpigmented, rod-shaped and motile ( Ash et al, 1993 ; Siddiqi et al, 2015 ). Currently, the genus Paenibacillus contains 240 species, including the plant-beneficial species of P. polymyxa ( Zhang et al, 2018 ; Timmusk et al, 2019 ), P. ehimensis ( Naing et al, 2015 ), P. alvei ( Emmanouil et al, 2016 ), P. macerans ( Liang et al, 2014 ), P. lentimorbus ( DasGupta et al, 2006 ) and P. peoriae ( Von der Weid et al, 2003 ; Jiang et al, 2022 ). Previously, P. peoriae was reported to act as a plant growth-promoting rhizobacteria (PGPR), which can produce biofilms, stably colonize the rhizosphere of plants and compete with other microbiota ( Von der Weid et al, 2003 ; Vejan et al, 2016 ; Jiang et al, 2022 ).…”

“…Currently, the genus Paenibacillus contains 240 species, including the plant-beneficial species of P. polymyxa ( Zhang et al, 2018 ; Timmusk et al, 2019 ), P. ehimensis ( Naing et al, 2015 ), P. alvei ( Emmanouil et al, 2016 ), P. macerans ( Liang et al, 2014 ), P. lentimorbus ( DasGupta et al, 2006 ) and P. peoriae ( Von der Weid et al, 2003 ; Jiang et al, 2022 ). Previously, P. peoriae was reported to act as a plant growth-promoting rhizobacteria (PGPR), which can produce biofilms, stably colonize the rhizosphere of plants and compete with other microbiota ( Von der Weid et al, 2003 ; Vejan et al, 2016 ; Jiang et al, 2022 ). Meanwhile, P. peoriae has the ability to act as a biological control agent against many plant pathogens, including Fusarium spp., Diplodia macrospora , D. maydis , Verticillium dahlia , Rhizoctonia solani , Colletotrichum gloeosporioides , and C. graminicola ( Von der Weid et al, 2003 ; Yadav D. et al, 2021 ; Jiang et al, 2022 ), and even the antimicrobial peptide purified from P. peoriae could protect against Staphylococcus aureus , Escherichia coli , and Candida albicans ( Ngashangva et al, 2021 ).…”