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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ftdoajarticles:oai:doaj.org/article:e35f17158e0549aa8bf771dcbad38a6a 2023-05-15T17:58:09+02:00 Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics Zachary S. Cooper Josephine Z. Rapp Anna M. D. Shoemaker Rika E. Anderson Zhi-Ping Zhong Jody W. Deming 2022-06-01T00:00:00Z https://doi.org/10.3389/fmicb.2022.879116 https://doaj.org/article/e35f17158e0549aa8bf771dcbad38a6a EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fmicb.2022.879116/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2022.879116 https://doaj.org/article/e35f17158e0549aa8bf771dcbad38a6a Frontiers in Microbiology, Vol 13 (2022) cryopeg extremophile bacteria evolution ecology pangenomics oceanography Microbiology QR1-502 article 2022 ftdoajarticles https://doi.org/10.3389/fmicb.2022.879116 2022-12-31T02:48:17Z 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 ... Article in Journal/Newspaper permafrost Alaska Directory of Open Access Journals: DOAJ Articles Frontiers in Microbiology 13 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
cryopeg extremophile bacteria evolution ecology pangenomics oceanography Microbiology QR1-502 |
spellingShingle |
cryopeg extremophile bacteria evolution ecology pangenomics oceanography Microbiology QR1-502 Zachary S. Cooper Josephine Z. Rapp Anna M. D. Shoemaker Rika E. Anderson Zhi-Ping Zhong Jody W. Deming Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics |
topic_facet |
cryopeg extremophile bacteria evolution ecology pangenomics oceanography Microbiology QR1-502 |
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 |
Article in Journal/Newspaper |
author |
Zachary S. Cooper Josephine Z. Rapp Anna M. D. Shoemaker Rika E. Anderson Zhi-Ping Zhong Jody W. Deming |
author_facet |
Zachary S. Cooper Josephine Z. Rapp Anna M. D. Shoemaker Rika E. Anderson Zhi-Ping Zhong Jody W. Deming |
author_sort |
Zachary S. Cooper |
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 |
https://doi.org/10.3389/fmicb.2022.879116 https://doaj.org/article/e35f17158e0549aa8bf771dcbad38a6a |
genre |
permafrost Alaska |
genre_facet |
permafrost Alaska |
op_source |
Frontiers in Microbiology, Vol 13 (2022) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fmicb.2022.879116/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2022.879116 https://doaj.org/article/e35f17158e0549aa8bf771dcbad38a6a |
op_doi |
https://doi.org/10.3389/fmicb.2022.879116 |
container_title |
Frontiers in Microbiology |
container_volume |
13 |
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1766166700607143936 |