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Background <p>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 (<i>Urtica dioica</i> 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.</p> Results <p>From all regions, 66 bacterial isolates were obtained. 32% of them were identified, mostly as <i>Bacillus</i> and <i>Pseudomonas</i> 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 <i>Acinetobacter</i>, <i>Bacillus</i>, <i>Citrobacter</i>, <i>Enterococcus</i>, <i>Escherichia</i>, <i>Klebsiella</i>, <i>Paenibacillus</i>, <i>Salmonella</i>, <i>Vibrio</i>, and <i>Xanthomonas</i>. Among the isolates, <i>Exiguobacterium</i> sp. SP2-R3 exhibited the most intense orange pigmentation. The results indicate that the pigment is putatively quinone-like and demonstrates promising scavenging activity.</p> Conclusions <p>The study deepens our understanding of <i>U. dioica</i> 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.</p>

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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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月4日

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  • Natalia Rutkowska,
  • Julia Wojtynek,
  • Weronika Śliżewska,
  • Maciej Nielipiński,
  • Marcin Sypka,
  • Zuzanna Kurek,
  • Oliwia Łukanowska,
  • Weronika Prażanowska,
  • Patrycja Modrzejewska,
  • Bartłomiej Lewocha,
  • Wiktoria Horążak,
  • Igor Naporowski,
  • Weronika Bednarek,
  • Dominika Nielipińska,
  • Piotr Drożdżyński,
  • Olga Marchut-Mikołajczyk

摘要

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.