Integrating culture-dependent and culture-independent approaches to explore the diversity of endophytic bacteria associated with Urtica dioica L. in Poland with screening of pigment-producing isolates

Background Plants can thrive in changing environmental conditions with the help of microorganisms that inhabit their tissues, known as endophytes. However, many endophytes do not grow under standard laboratory conditions, but metagenomic analysis provides insights into microbial diversity and community structure. This study aimed to compare communities of endophytic bacteria from stinging nettle ( Urtica dioica L.) isolated throughout different regions of Poland, both culturable and non-culturable, and to identify shared bacterial taxa across all locations, which may represent a putative core microbiome. Results From all regions, 66 bacterial isolates were obtained. 32% of them were identified, mostly as Bacillus and Pseudomonas members, which are common endophytes of many plants. Although a substantial proportion of reads remained unclassified, metagenomic data enabled the tentative identification of several genera present across all samples, including Acinetobacter , Bacillus , Citrobacter , Enterococcus , Escherichia , Klebsiella , Paenibacillus , Salmonella , Vibrio , and Xanthomonas . Among the isolates, Exiguobacterium sp. SP2-R3 exhibited the most intense orange pigmentation. The results indicate that the pigment is putatively quinone-like and demonstrates promising scavenging activity. Conclusions The study deepens our understanding of U. dioica L. endophytic communities and highlights the value of combining cultivation-based methods with metagenomic approaches. Also, among the isolates with visible potential to produce pigments, the best producer was selected and identified. It is recognized that those isolates may possess additional valuable properties that warrant deeper investigation.