Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake
The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been...
Published in: | Frontiers in Microbiology |
---|---|
Main Authors: | , , , |
Format: | Text |
Language: | English |
Published: |
Frontiers Media S.A.
2021
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542988/ https://doi.org/10.3389/fmicb.2021.741077 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:8542988 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:8542988 2023-05-15T13:52:28+02:00 Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake Williams, Timothy J. Allen, Michelle A. Berengut, Jonathan F. Cavicchioli, Ricardo 2021-10-11 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542988/ https://doi.org/10.3389/fmicb.2021.741077 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542988/ http://dx.doi.org/10.3389/fmicb.2021.741077 Copyright © 2021 Williams, Allen, Berengut and Cavicchioli. 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 2021 ftpubmed https://doi.org/10.3389/fmicb.2021.741077 2021-10-31T00:52:33Z The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake. Text Antarc* Antarctic PubMed Central (PMC) Ace Lake ENVELOPE(78.188,78.188,-68.472,-68.472) Antarctic Vestfold Vestfold Hills Frontiers in Microbiology 12 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Microbiology |
spellingShingle |
Microbiology Williams, Timothy J. Allen, Michelle A. Berengut, Jonathan F. Cavicchioli, Ricardo Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
topic_facet |
Microbiology |
description |
The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake. |
format |
Text |
author |
Williams, Timothy J. Allen, Michelle A. Berengut, Jonathan F. Cavicchioli, Ricardo |
author_facet |
Williams, Timothy J. Allen, Michelle A. Berengut, Jonathan F. Cavicchioli, Ricardo |
author_sort |
Williams, Timothy J. |
title |
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
title_short |
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
title_full |
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
title_fullStr |
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
title_full_unstemmed |
Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake |
title_sort |
shedding light on microbial “dark matter”: insights into novel cloacimonadota and omnitrophota from an antarctic lake |
publisher |
Frontiers Media S.A. |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542988/ https://doi.org/10.3389/fmicb.2021.741077 |
long_lat |
ENVELOPE(78.188,78.188,-68.472,-68.472) |
geographic |
Ace Lake Antarctic Vestfold Vestfold Hills |
geographic_facet |
Ace Lake Antarctic Vestfold Vestfold Hills |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Front Microbiol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542988/ http://dx.doi.org/10.3389/fmicb.2021.741077 |
op_rights |
Copyright © 2021 Williams, Allen, Berengut and Cavicchioli. 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.2021.741077 |
container_title |
Frontiers in Microbiology |
container_volume |
12 |
_version_ |
1766256761782665216 |