Romanenko Maria N, Shikov Anton E, Savina Iuliia A, Nizhnikov Anton A, Antonets Kirill S
All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia.
Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
Microorganisms. 2024 Nov 24;12(12):2410. doi: 10.3390/microorganisms12122410.
Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2's genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1.
无农药农业是环境友好型农业的一个基本支柱。为此，人们积极寻找能够合成次生代谢产物和毒素的新细菌菌株，以保护作物免受病原体和害虫侵害。在本研究中，我们从俄罗斯达吉斯坦共和国采集的土壤样本中分离出了一种新型菌株d21.2。利用基于Illumina的全基因组组装的多种生物信息学方法，我们发现该菌株含有某些杀虫基因座（编码Bmp和Vpa的假定同源物），还包含多个生物合成基因簇（BGCs），包括牡丹菌素、koranimine、裂褶菌素和丰原素。总共预测有21个BGCs可合成具有杀菌和/或杀真菌作用的代谢产物。重要的是，通过应用重新搭建支架流程，我们成功地可靠预测了与BGCs相关的移动遗传元件（MGEs），这意味着其具有高遗传可塑性。此外，d21.2的基因组中没有编码肠道毒素的基因，这意味着其使用安全。与该菌株的现有基因组进行比较发现，这里描述的菌株比该物种的其他成员含有更多功能重要的基因座。因此，由于可能表现出杀菌、杀真菌、促进生长和其他有用特性，菌株d21.2在农业中具有应用潜力。组装好的基因组可在NCBI基因库中以ASM4106054v1的名称获取。
