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Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria

Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%),...

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Autores principales: Weeraphan, Trinset, Somphong, Achiraya, Poengsungnoen, Vasun, Buaruang, Kawinnat, Harunari, Enjuro, Igarashi, Yasuhiro, Tanasupawat, Somboon, Phongsopitanun, Wongsakorn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10073151/
https://www.ncbi.nlm.nih.gov/pubmed/37016075
http://dx.doi.org/10.1038/s41598-023-32759-2
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author Weeraphan, Trinset
Somphong, Achiraya
Poengsungnoen, Vasun
Buaruang, Kawinnat
Harunari, Enjuro
Igarashi, Yasuhiro
Tanasupawat, Somboon
Phongsopitanun, Wongsakorn
author_facet Weeraphan, Trinset
Somphong, Achiraya
Poengsungnoen, Vasun
Buaruang, Kawinnat
Harunari, Enjuro
Igarashi, Yasuhiro
Tanasupawat, Somboon
Phongsopitanun, Wongsakorn
author_sort Weeraphan, Trinset
collection PubMed
description Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.
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spelling pubmed-100731512023-04-06 Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria Weeraphan, Trinset Somphong, Achiraya Poengsungnoen, Vasun Buaruang, Kawinnat Harunari, Enjuro Igarashi, Yasuhiro Tanasupawat, Somboon Phongsopitanun, Wongsakorn Sci Rep Article Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria. Nature Publishing Group UK 2023-04-04 /pmc/articles/PMC10073151/ /pubmed/37016075 http://dx.doi.org/10.1038/s41598-023-32759-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Weeraphan, Trinset
Somphong, Achiraya
Poengsungnoen, Vasun
Buaruang, Kawinnat
Harunari, Enjuro
Igarashi, Yasuhiro
Tanasupawat, Somboon
Phongsopitanun, Wongsakorn
Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title_full Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title_fullStr Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title_full_unstemmed Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title_short Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
title_sort bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10073151/
https://www.ncbi.nlm.nih.gov/pubmed/37016075
http://dx.doi.org/10.1038/s41598-023-32759-2
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