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.
- 1Faculty of Biotechnology and Food Sciences, Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, Lodz, 90-537, Poland.
- 2Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, Lodz, 90-530, Poland.
- 3Faculty of Biotechnology and Food Sciences, Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, Lodz, 90-537, Poland. [email protected].
Abstract
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.
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BibTeX
@article{rutkowska2026integrating,
title = {{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.}},
author = {Natalia Rutkowska and Julia Wojtynek and Weronika Śliżewska and Maciej Nielipiński and Marcin Sypka and Zuzanna Kurek and Oliwia Łukanowska and Weronika Prażanowska and Patrycja Modrzejewska and Bartłomiej Lewocha and Wiktoria Horążak and Igor Naporowski and Weronika Bednarek and Dominika Nielipińska and Piotr Drożdżyński and Olga Marchut-Mikołajczyk},
journal = {Microbial cell factories},
year = {2026},
month = aug,
doi = {10.1186/s12934-026-03077-9},
url = {https://europepmc.org/article/MED/42972344},
note = {CC BY},
}
RIS
TY - JOUR
TI - 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.
AU - Natalia Rutkowska
AU - Julia Wojtynek
AU - Weronika Śliżewska
AU - Maciej Nielipiński
AU - Marcin Sypka
AU - Zuzanna Kurek
AU - Oliwia Łukanowska
AU - Weronika Prażanowska
AU - Patrycja Modrzejewska
AU - Bartłomiej Lewocha
AU - Wiktoria Horążak
AU - Igor Naporowski
AU - Weronika Bednarek
AU - Dominika Nielipińska
AU - Piotr Drożdżyński
AU - Olga Marchut-Mikołajczyk
PY - 2026
DA - 2026/08/01
JO - Microbial cell factories
DO - 10.1186/s12934-026-03077-9
UR - https://europepmc.org/article/MED/42972344
AB - 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.
SN - 1475-2859
ER -