Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution
BACKGROUND: Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining importan...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196931/ http://www.ncbi.nlm.nih.gov/pubmed/34118971 https://doi.org/10.1186/s40168-021-01084-z |
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ftpubmed:oai:pubmedcentral.nih.gov:8196931 2023-05-15T17:57:58+02:00 Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang Liu, Yongqin Allen, Michelle A. Xu, Baiqing Wang, Ninglian Williams, Timothy J. Wang, Feng Zhou, Yuguang Liu, Qing Cavicchioli, Ricardo 2021-06-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196931/ http://www.ncbi.nlm.nih.gov/pubmed/34118971 https://doi.org/10.1186/s40168-021-01084-z en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196931/ http://www.ncbi.nlm.nih.gov/pubmed/34118971 http://dx.doi.org/10.1186/s40168-021-01084-z © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY Microbiome Research Text 2021 ftpubmed https://doi.org/10.1186/s40168-021-01084-z 2021-06-20T00:40:32Z BACKGROUND: Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult. RESULTS: Here we examined the bacterial genus Arthrobacter and, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at −1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A Arthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature. CONCLUSION: The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-021-01084-z. Text permafrost PubMed Central (PMC) Microbiome 9 1 |
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Research Shen, Liang Liu, Yongqin Allen, Michelle A. Xu, Baiqing Wang, Ninglian Williams, Timothy J. Wang, Feng Zhou, Yuguang Liu, Qing Cavicchioli, Ricardo Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
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Research |
description |
BACKGROUND: Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult. RESULTS: Here we examined the bacterial genus Arthrobacter and, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at −1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A Arthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature. CONCLUSION: The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-021-01084-z. |
format |
Text |
author |
Shen, Liang Liu, Yongqin Allen, Michelle A. Xu, Baiqing Wang, Ninglian Williams, Timothy J. Wang, Feng Zhou, Yuguang Liu, Qing Cavicchioli, Ricardo |
author_facet |
Shen, Liang Liu, Yongqin Allen, Michelle A. Xu, Baiqing Wang, Ninglian Williams, Timothy J. Wang, Feng Zhou, Yuguang Liu, Qing Cavicchioli, Ricardo |
author_sort |
Shen, Liang |
title |
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
title_short |
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
title_full |
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
title_fullStr |
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
title_full_unstemmed |
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution |
title_sort |
linking genomic and physiological characteristics of psychrophilic arthrobacter to metagenomic data to explain global environmental distribution |
publisher |
BioMed Central |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196931/ http://www.ncbi.nlm.nih.gov/pubmed/34118971 https://doi.org/10.1186/s40168-021-01084-z |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
Microbiome |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196931/ http://www.ncbi.nlm.nih.gov/pubmed/34118971 http://dx.doi.org/10.1186/s40168-021-01084-z |
op_rights |
© The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s40168-021-01084-z |
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Microbiome |
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