Qi Dengfeng, Zou Liangping, Zhou Dengbo, Zhang Miaoyi, Wei Yongzan, Zhang Lu, Xie Jianghui, Wang Wei
Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
College of Life Science, Hainan Normal University, Haikou, China.
Front Microbiol. 2021 Nov 4;12:722661. doi: 10.3389/fmicb.2021.722661. eCollection 2021.
Banana is an important fruit crop. wilt caused by f. sp. tropical race 4 (Foc TR4) seriously threatens the global banana industry. It is difficult to control the disease spread using chemical measures. In addition, commercial resistant cultivars are also lacking. Biological control is considered as a promising strategy using antagonistic microbes. Actinomycetes, especially , are potential sources of producing novel bioactive secondary metabolites. Here, strain SCA2-4 with strong antifungal activity against Foc TR4 was isolated from the rhizospheric soil of in a dry hot valley. The morphological, physiological and chemotaxonomic characteristics of the strain were consistent with the genus . Based on the homology alignment and phylogenetic trees of 16S gene, the taxonomic status of strain SCA2-4 exhibited a paradoxical result and low bootstrap value using different algorithms in the MEGA software. It prompted us to further discriminate this strain from the closely related species by the multilocus sequence analysis (MLSA) using five house-keeping gene alleles (, , , , and ). The MLSA trees calculated by three algorithms demonstrated that strain SCA2-4 formed a distinct clade with NBRC 13819 . The MLSA distance was above 0.007 of the species cut-off. Average nucleotide identity (ANI) values between strain SCA2-4 genome and two standard strain genomes were below 95-96% of the novel species threshold. Strain SCA2-4 was assigned to a novel species of the genus and named as sp. nov. The sequenced complete genome of SCA2-4 encoded 51 putative biosynthetic gene clusters of secondary metabolites. Genome alignment revealed that ten gene clusters were involved in the biosynthesis of antimicrobial metabolites. It was supported that strain SCA2-4 showed strong antifungal activities against the pathogens of banana fungal diseases. Extracts abstracted from the culture filtrate of strain SCA2-4 seriously destroyed cell structure of Foc TR4 and inhibited mycelial growth and spore germination. These results implied that strain SCA2-4 could be a promising candidate for biological control of banana wilt.
香蕉是一种重要的水果作物。由尖孢镰刀菌古巴专化型热带4号生理小种（Foc TR4）引起的枯萎病严重威胁着全球香蕉产业。使用化学措施难以控制该病的传播。此外，也缺乏商业抗性品种。生物防治被认为是一种利用拮抗微生物的有前景的策略。放线菌，尤其是链霉菌，是产生新型生物活性次生代谢产物的潜在来源。在此，从干热河谷中香蕉的根际土壤中分离出了对Foc TR4具有强抗真菌活性的菌株SCA2-4。该菌株的形态、生理和化学分类特征与链霉菌属一致。基于16S rRNA基因的同源性比对和系统发育树，在MEGA软件中使用不同算法时，菌株SCA2-4的分类地位呈现出矛盾的结果和较低的自展值。这促使我们通过使用五个管家基因等位基因（atpD、gyrB、recA、rpoB和trpB）的多位点序列分析（MLSA），将该菌株与近缘物种进一步区分开来。由三种算法计算得到的MLSA树表明，菌株SCA2-4与链霉菌NBRC 13819形成了一个独特的分支。该物种截断值的MLSA距离高于0.007。菌株SCA2-4基因组与两个标准菌株基因组之间的平均核苷酸同一性（ANI）值低于新物种阈值的95 - 96%。菌株SCA2-4被归入链霉菌属的一个新物种，并命名为链霉菌新种。SCA2-4的测序完整基因组编码了51个推定的次生代谢物生物合成基因簇。基因组比对显示，有十个基因簇参与了抗菌代谢物的生物合成。这支持了菌株SCA2-4对香蕉真菌病害病原体具有强抗真菌活性。从菌株SCA2-4的培养滤液中提取的提取物严重破坏了Foc TR4的细胞结构，并抑制了菌丝生长和孢子萌发。这些结果表明，菌株SCA2-4可能是香蕉枯萎病生物防治的一个有前景的候选菌株。
