Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.
College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.
BMC Genomics. 2019 Apr 11;20(1):283. doi: 10.1186/s12864-019-5646-9.
Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis.
A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis.
This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.
芽孢杆菌属的成员是重要的植物促生根际细菌，可用作生物防治剂。Bacillus paralicheniformis MDJK30 是从牡丹根际分离得到的一种 PGPR，可抑制植物病原菌和真菌。为了进一步揭示 MDJK30 及其密切相关菌株的促生特性的遗传机制，我们利用比较基因组学深入了解芽孢杆菌属 paralicheniformis 与 B. licheniformis 之间的遗传多样性和进化关系。
基于芽孢杆菌属 paralicheniformis MDJK30 和 55 株先前报道的芽孢杆菌菌株进行了比较基因组学分析。通过研究核心基因组的系统发育、种群结构分析和 ANI 结果，评估了 MDJK30 的进化位置以及芽孢杆菌属 paralicheniformis 与 B. licheniformis 之间的进化关系。比较基因组分析揭示了芽孢杆菌属 paralicheniformis 的各种特征，这些特征有助于其在根际中形成共生生活方式，包括开放的泛基因组、多样化的运输以及碳水化合物和氨基酸的代谢。与 B. licheniformis 相比，芽孢杆菌属 paralicheniformis 的插入序列、噬菌体、基因组岛和次级代谢合成酶操纵子的数量和位置存在显著差异。特别是，我们发现丰原素、杆菌肽和 Lantipeptide 的大多数基因簇仅存在于芽孢杆菌属 paralicheniformis 中，并且是通过水平基因转移（HGT）获得的，这些簇可能被用作区分芽孢杆菌属 paralicheniformis 和 B. licheniformis 的遗传标记。
本研究表明，MDJK30 和 paralicheniformis 谱系的其他菌株在遗传水平上具有促生特性，可以作为 PGPR 在农业中开发和商业化应用。核心基因组系统发育和种群结构分析已被证明是区分芽孢杆菌属 paralicheniformis 和 B. licheniformis 的有力工具。比较基因组分析说明了 paralicheniformis-licheniformis 组在根际适应方面的遗传差异。
