Kim Minji, Cha In-Tae, Lee Ki-Eun, Li Meng, Park Soo-Je
Department of Biology, Jeju National University , Jeju, South Korea.
Microorganism Resources Division, National Institute of Biological Resources , Incheon, South Korea.
Microbiol Spectr. 2023 Aug 18;11(5):e0100323. doi: 10.1128/spectrum.01003-23.
Members of the genus are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of . Here, we found that species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus diversity exploration and will provide a framework for the way for future ecological characterizations.
该属成员分布广泛，能产生多种多糖降解酶。该属中的许多物种已被分离和鉴定。然而，很少有研究关注海洋分离株或鱼类病原体，并且缺乏深入的基因组分析，特别是对来自不同栖息地类型的分离株的比较分析。在这里，我们从韩国的各种环境中分离出20株该属菌株，并对它们的全长基因组进行了测序。结合已发表的序列数据，我们研究了总共187个已分离物种基因组中的基因组特征、进化、环境适应性和推定的代谢功能，这些物种分为海洋、宿主相关和陆地（包括淡水）类别。泛基因组分析揭示了基因组大小与编码或非编码密度之间的相关性。该属物种具有高度的多样性，通过重组事件产生了新的基因库。在所有基因组中，与防御相关的基因仅占预测基因的约3%。虽然参与代谢途径的基因在分离来源方面没有差异，但基因组特征存在显著差异；特别是，宿主相关组中tRNA和rRNA的丰度高于其他组。宿主相关组中的一个基因组含有一个与肠杆菌噬菌体密切相关的原噬菌体。仅在为本研究分离的四株陆地菌株中鉴定出视紫质蛋白基因。此外，重组事件明显影响了基因组多样性，并可能有助于应对环境压力。这些发现揭示了该属的高遗传变异及其在不同生态系统中的功能作用，这归因于它们的代谢多功能性。重要性该属是一类在各种环境中发现的多样化细菌群体。虽然该属的大多数物种无害，并利用蛋白质和多糖等有机底物，但一些成员可能在其环境中的有机物质循环中发挥重要作用。然而，人们对该属的基因组动态和/或代谢能力知之甚少。在这里，我们发现该属物种可能具有开放的泛基因组，包含各种不同的新基因库。有趣的是，我们发现一个基因组（分类为宿主相关组）含有一个与肠杆菌噬菌体密切相关的原噬菌体。在为本研究分离的一些菌株中，视紫质蛋白可能在光照或氧气压力条件下表达。我们的发现显著有助于理解该属成员的多样性探索，并将为未来生态特征研究提供一个框架。
