Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution

Abstract 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...

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Published in:Microbiome
Main Authors: Liang Shen, Yongqin Liu, Michelle A. Allen, Baiqing Xu, Ninglian Wang, Timothy J. Williams, Feng Wang, Yuguang Zhou, Qing Liu, Ricardo Cavicchioli
Format: Article in Journal/Newspaper
Language:English
Published: BMC 2021
Subjects:
Online Access:https://doi.org/10.1186/s40168-021-01084-z
https://doaj.org/article/9a7930f5b97943e99a8819810c911178
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spelling ftdoajarticles:oai:doaj.org/article:9a7930f5b97943e99a8819810c911178 2023-05-15T17:57:58+02:00 Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Liang Shen Yongqin Liu Michelle A. Allen Baiqing Xu Ninglian Wang Timothy J. Williams Feng Wang Yuguang Zhou Qing Liu Ricardo Cavicchioli 2021-06-01T00:00:00Z https://doi.org/10.1186/s40168-021-01084-z https://doaj.org/article/9a7930f5b97943e99a8819810c911178 EN eng BMC https://doi.org/10.1186/s40168-021-01084-z https://doaj.org/toc/2049-2618 doi:10.1186/s40168-021-01084-z 2049-2618 https://doaj.org/article/9a7930f5b97943e99a8819810c911178 Microbiome, Vol 9, Iss 1, Pp 1-15 (2021) Genomics Metagenomics Psychrophiles Polar environment Alpine environment Microbial adaptation Microbial ecology QR100-130 article 2021 ftdoajarticles https://doi.org/10.1186/s40168-021-01084-z 2022-12-31T05:32:32Z Abstract 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. Video Abstract Article in Journal/Newspaper permafrost Directory of Open Access Journals: DOAJ Articles Microbiome 9 1
institution Open Polar
collection Directory of Open Access Journals: DOAJ Articles
op_collection_id ftdoajarticles
language English
topic Genomics
Metagenomics
Psychrophiles
Polar environment
Alpine environment
Microbial adaptation
Microbial ecology
QR100-130
spellingShingle Genomics
Metagenomics
Psychrophiles
Polar environment
Alpine environment
Microbial adaptation
Microbial ecology
QR100-130
Liang Shen
Yongqin Liu
Michelle A. Allen
Baiqing Xu
Ninglian Wang
Timothy J. Williams
Feng Wang
Yuguang Zhou
Qing Liu
Ricardo Cavicchioli
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution
topic_facet Genomics
Metagenomics
Psychrophiles
Polar environment
Alpine environment
Microbial adaptation
Microbial ecology
QR100-130
description Abstract 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. Video Abstract
format Article in Journal/Newspaper
author Liang Shen
Yongqin Liu
Michelle A. Allen
Baiqing Xu
Ninglian Wang
Timothy J. Williams
Feng Wang
Yuguang Zhou
Qing Liu
Ricardo Cavicchioli
author_facet Liang Shen
Yongqin Liu
Michelle A. Allen
Baiqing Xu
Ninglian Wang
Timothy J. Williams
Feng Wang
Yuguang Zhou
Qing Liu
Ricardo Cavicchioli
author_sort Liang Shen
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 BMC
publishDate 2021
url https://doi.org/10.1186/s40168-021-01084-z
https://doaj.org/article/9a7930f5b97943e99a8819810c911178
genre permafrost
genre_facet permafrost
op_source Microbiome, Vol 9, Iss 1, Pp 1-15 (2021)
op_relation https://doi.org/10.1186/s40168-021-01084-z
https://doaj.org/toc/2049-2618
doi:10.1186/s40168-021-01084-z
2049-2618
https://doaj.org/article/9a7930f5b97943e99a8819810c911178
op_doi https://doi.org/10.1186/s40168-021-01084-z
container_title Microbiome
container_volume 9
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