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Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils

Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded function...

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Autores principales: Gorecki, Adrian, Holm, Stine, Dziurzynski, Mikolaj, Winkel, Matthias, Yang, Sizhong, Liebner, Susanne, Wagner, Dirk, Dziewit, Lukasz, Horn, Fabian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8528913/
https://www.ncbi.nlm.nih.gov/pubmed/34012103
http://dx.doi.org/10.1038/s41396-021-01003-y
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author Gorecki, Adrian
Holm, Stine
Dziurzynski, Mikolaj
Winkel, Matthias
Yang, Sizhong
Liebner, Susanne
Wagner, Dirk
Dziewit, Lukasz
Horn, Fabian
author_facet Gorecki, Adrian
Holm, Stine
Dziurzynski, Mikolaj
Winkel, Matthias
Yang, Sizhong
Liebner, Susanne
Wagner, Dirk
Dziewit, Lukasz
Horn, Fabian
author_sort Gorecki, Adrian
collection PubMed
description Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.
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spelling pubmed-85289132021-10-22 Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils Gorecki, Adrian Holm, Stine Dziurzynski, Mikolaj Winkel, Matthias Yang, Sizhong Liebner, Susanne Wagner, Dirk Dziewit, Lukasz Horn, Fabian ISME J Article Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold. Nature Publishing Group UK 2021-05-19 2021-11 /pmc/articles/PMC8528913/ /pubmed/34012103 http://dx.doi.org/10.1038/s41396-021-01003-y Text en © The Author(s) 2021 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Gorecki, Adrian
Holm, Stine
Dziurzynski, Mikolaj
Winkel, Matthias
Yang, Sizhong
Liebner, Susanne
Wagner, Dirk
Dziewit, Lukasz
Horn, Fabian
Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title_full Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title_fullStr Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title_full_unstemmed Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title_short Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils
title_sort metaplasmidome-encoded functions of siberian low-centered polygonal tundra soils
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8528913/
https://www.ncbi.nlm.nih.gov/pubmed/34012103
http://dx.doi.org/10.1038/s41396-021-01003-y
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