Table_2_Comparative and Functional Analyses of Two Sequenced Paenibacillus polymyxa Genomes Provides Insights Into Their Potential Genes Related to Plant Growth-Promoting Features and Biocontrol Mechanisms.DOCX

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.

隶属于多粘类芽孢杆菌（Paenibacillus polymyxa）类群的诸多菌株均为植物促生根际菌（plant growth-promoting rhizobacteria，PGPR），兼具促进植物生长、抑制植物病原菌的潜力，且已被开发为生物防治剂（biological control agents，BCAs）。然而，迄今学界尚未完全阐明多粘类芽孢杆菌的促生与生防机制。本研究针对两株兼具广谱抗病原菌活性与促生潜力的多粘类芽孢杆菌菌株ZF129与ZF197的基因组序列开展了比较分析。对上述两株已测序的多粘类芽孢杆菌基因组进行比较与功能分析后发现，菌株ZF129的基因组包含一条长5703931 bp的环状染色体，以及两条分别为79020 bp与37602 bp的质粒，分别命名为pAP1与pAP2。菌株ZF197的完整基因组则包含一条长5507169 bp的环状染色体，以及一条长32065 bp的质粒，命名为pAP197。系统发育分析结果显示，菌株ZF129与多粘类芽孢杆菌HY96-2、SQR-21两株菌株具有高度同源性，而ZF197则与多粘类芽孢杆菌菌株J亲缘关系极近。研究团队比较了菌株ZF129、ZF197与其他多粘类芽孢杆菌菌株中，负责次级代谢产物合成、植物促生特性及系统抗性诱导物生成的相关基因。研究结果表明，ZF129与ZF197菌株间对应基因或基因簇的差异，可能导致二者的挥发性代谢产物或无细胞上清液对尖孢镰刀菌（Fusarium oxysporum）的拮抗活性存在差异。本研究证实，多粘类芽孢杆菌的促生作用主要通过植物激素合成、提升养分可利用性与生防机制三大途径实现。本研究深化了对多粘类芽孢杆菌基因组结构的认知，为该菌株作为PGPR在农业与园艺领域的应用提供了重要理论依据。