Rutkowska Natalia, Daroch Maurycy, Marchut-Mikołajczyk Olga
Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland.
School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China.
Front Microbiol. 2025 Jun 30;16:1612860. doi: 10.3389/fmicb.2025.1612860. eCollection 2025.
Endophytes are crucial partners that contribute to the plants' health and overall wellbeing. Apart from the elucidation of the relationship between plants and their microbiota, the metabolic potential of endophytes is also of a special interest. Therefore, it is crucial to isolate and taxonomically identify endophytes, as well as to investigate their genomic potential to determine their significance in plant health and potential as bioactive metabolite producers for industrial application.
In this study, we isolated ten endophytic bacterial strains from different tissues of medicinal plant L. and performed assembly of their genomes using short and long reads. Comparative genomic analysis was conducted to assess the accurate taxonomic identification of the strains. The investigation also focused on the presence of mobile genetic elements and their significance concerning endophytic lifestyles. We performed functional annotation of coding sequences, particularly targeted genes that encode carbohydrate enzymes and secondary metabolites within gene clusters.
Through sequencing using two complementary methods, we obtained 10 bacterial genomes, ranging in size, coding density and number of mobile genetic elements. Our findings provide a first insight into the cultivable bacterial community of the medicinal plant L., their genome biology, and potential for producing valuable bioactive metabolites. Obtained whole genome sequences allowed for complete phylogenetic analysis, which revealed crucial insights into the taxonomic status of bacteria and resulted in the discovery of two putatively novel bacterial species from the and genera, suggesting that plants are hiding a reservoir of novel species with potentially useful properties and unknown mechanisms related to their relationship with plant host.
内生菌是对植物健康和整体福祉至关重要的伙伴。除了阐明植物与其微生物群之间的关系外，内生菌的代谢潜力也备受关注。因此，分离和分类鉴定内生菌，以及研究它们的基因组潜力以确定它们在植物健康中的重要性以及作为工业应用生物活性代谢物生产者的潜力至关重要。
在本研究中，我们从药用植物L.的不同组织中分离出10株内生细菌菌株，并使用短读长和长读长对其基因组进行组装。进行了比较基因组分析以评估菌株的准确分类鉴定。该研究还重点关注了移动遗传元件的存在及其与内生生活方式的相关性。我们对编码序列进行了功能注释，特别是对基因簇内编码碳水化合物酶和次生代谢物的靶向基因进行了注释。
通过使用两种互补方法进行测序，我们获得了10个细菌基因组，其大小、编码密度和移动遗传元件数量各不相同。我们的研究结果首次深入了解了药用植物L.的可培养细菌群落、它们的基因组生物学以及产生有价值生物活性代谢物的潜力。获得的全基因组序列允许进行完整的系统发育分析，这揭示了对细菌分类地位的关键见解，并导致发现了来自和属的两个推测的新细菌物种，这表明植物隐藏着一个具有潜在有用特性和与植物宿主关系相关未知机制的新物种库。
