Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of nov...
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ftpubmed:oai:pubmedcentral.nih.gov:9207381 2023-05-15T17:58:08+02:00 Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics Cooper, Zachary S. Rapp, Josephine Z. Shoemaker, Anna M. D. Anderson, Rika E. Zhong, Zhi-Ping Deming, Jody W. 2022-06-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207381/ http://www.ncbi.nlm.nih.gov/pubmed/35733954 https://doi.org/10.3389/fmicb.2022.879116 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207381/ http://www.ncbi.nlm.nih.gov/pubmed/35733954 http://dx.doi.org/10.3389/fmicb.2022.879116 Copyright © 2022 Cooper, Rapp, Shoemaker, Anderson, Zhong and Deming. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Front Microbiol Microbiology Text 2022 ftpubmed https://doi.org/10.3389/fmicb.2022.879116 2022-06-26T00:35:07Z Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has ... Text permafrost Alaska PubMed Central (PMC) Frontiers in Microbiology 13 |
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English |
topic |
Microbiology |
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Microbiology Cooper, Zachary S. Rapp, Josephine Z. Shoemaker, Anna M. D. Anderson, Rika E. Zhong, Zhi-Ping Deming, Jody W. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
topic_facet |
Microbiology |
description |
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has ... |
format |
Text |
author |
Cooper, Zachary S. Rapp, Josephine Z. Shoemaker, Anna M. D. Anderson, Rika E. Zhong, Zhi-Ping Deming, Jody W. |
author_facet |
Cooper, Zachary S. Rapp, Josephine Z. Shoemaker, Anna M. D. Anderson, Rika E. Zhong, Zhi-Ping Deming, Jody W. |
author_sort |
Cooper, Zachary S. |
title |
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
title_short |
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
title_full |
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
title_fullStr |
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
title_full_unstemmed |
Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
title_sort |
evolutionary divergence of marinobacter strains in cryopeg brines as revealed by pangenomics |
publisher |
Frontiers Media S.A. |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207381/ http://www.ncbi.nlm.nih.gov/pubmed/35733954 https://doi.org/10.3389/fmicb.2022.879116 |
genre |
permafrost Alaska |
genre_facet |
permafrost Alaska |
op_source |
Front Microbiol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207381/ http://www.ncbi.nlm.nih.gov/pubmed/35733954 http://dx.doi.org/10.3389/fmicb.2022.879116 |
op_rights |
Copyright © 2022 Cooper, Rapp, Shoemaker, Anderson, Zhong and Deming. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2022.879116 |
container_title |
Frontiers in Microbiology |
container_volume |
13 |
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1766166678622699520 |