National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural Universitygrid.440622.6, Tai'an, People's Republic of China.
Foshan Haitian Flavouring & Food Co. Ltd. (Haitian), Foshan, Guangdong, People's Republic of China.
Microbiol Spectr. 2022 Apr 27;10(2):e0207221. doi: 10.1128/spectrum.02072-21. Epub 2022 Mar 1.
Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. D. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.
藤仓赤单胞菌菌株长期以来一直被认为具有促进植物生长和生物防治的作用。最近，它已成为人类中的一种新兴机会性病原体。然而，其遗传多样性、致病性和生物技术特性的基因组特征尚未得到全面研究。在这里，我们构建了一个比较泛基因组分析。具有大型灵活基因库的开放泛基因组显示出高度的遗传多样性。纯化选择是驱动泛基因组进化的主要力量。泛基因组不同组成部分之间的进化关系、功能富集和选择压力程度存在显著差异。通过对不同的移动遗传元件（MGEs）、大规模基因组重排和水平基因的确定，表现出高度的遗传可塑性。水平基因转移（HGT）在该细菌的遗传多样性和基因组特征的形成中起着重要作用。我们的结果揭示了与大分子分泌系统相关的多种毒力相关元件、与多种医院感染相关的毒力因子和抗生素耐药性的发生，表明了其致病性。侧鞭毛、T1SS、T2SS、T6SS、Tad 菌毛、IV 型菌毛和部分与毒力相关的基因表现出普遍性，而极性鞭毛、T4SS、部分与毒力相关的基因和耐药基因表现出异质性。泛基因组还包含与次级代谢、碳水化合物活性酶（CAZymes）和磷酸盐转运体相关的丰富遗传特征，表明其具有根际适应性、促进植物生长的潜力，并在农业和生物防治中有很大的应用潜力。这项研究从基因组的角度对这种不常见的物种进行了全面的了解。藤仓赤单胞菌被认为是一种植物促生根际细菌（PGPR）、有机污染物降解菌株和人类中的一种新兴机会性病原体。然而，这些显著特征的遗传多样性、进化动态和遗传基础仍知之甚少。我们为藤仓赤单胞菌构建了一个泛基因组分析，揭示了开放泛基因组、多种移动遗传元件（MGEs）、基因组重排和水平基因所表现出的广泛遗传多样性和遗传可塑性。我们的结果强调，水平基因转移（HGT）和纯化选择是藤仓赤单胞菌遗传进化的重要力量。与大分子分泌系统、毒力因子和抗生素耐药性相关的丰富的毒力相关元件可能有助于该细菌的致病性。因此，临床微生物学家需要意识到藤仓赤单胞菌是一种机会性病原体。次级代谢、碳水化合物活性酶（CAZymes）和磷酸盐转运体的遗传特征可以为藤仓赤单胞菌在农业和生物防治中的潜在应用提供遗传武器库的深入了解。
