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Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy
Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10192776/ https://www.ncbi.nlm.nih.gov/pubmed/37213515 http://dx.doi.org/10.3389/fmicb.2023.1161937 |
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author | Sonke, Alexander Trembath-Reichert, Elizabeth |
author_facet | Sonke, Alexander Trembath-Reichert, Elizabeth |
author_sort | Sonke, Alexander |
collection | PubMed |
description | Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of highly productive oxalogens, namely plants. It is hypothesized that oxalotrophic microbes limit oxalate accumulation by degrading oxalate minerals to carbonates via an under-explored biogeochemical cycle known as the oxalate-carbonate pathway (OCP). Neither the diversity nor the ecology of oxalotrophic bacteria is fully understood. This research investigated the phylogenetic relationships of the bacterial genes oxc, frc, oxdC, and oxlT, which encode key enzymes for oxalotrophy, using bioinformatic approaches and publicly available omics datasets. Phylogenetic trees of oxc and oxdC genes demonstrated grouping by both source environment and taxonomy. All four trees included genes from metagenome-assembled genomes (MAGs) that contained novel lineages and environments for oxalotrophs. In particular, sequences of each gene were recovered from marine environments. These results were supported with marine transcriptome sequences and description of key amino acid residue conservation. Additionally, we investigated the theoretical energy yield from oxalotrophy across marine-relevant pressure and temperature conditions and found similar standard state Gibbs free energy to “low energy” marine sediment metabolisms, such as anaerobic oxidation of methane coupled to sulfate reduction. These findings suggest further need to understand the role of bacterial oxalotrophy in the OCP, particularly in marine environments, and its contribution to global carbon cycling. |
format | Online Article Text |
id | pubmed-10192776 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-101927762023-05-19 Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy Sonke, Alexander Trembath-Reichert, Elizabeth Front Microbiol Microbiology Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of highly productive oxalogens, namely plants. It is hypothesized that oxalotrophic microbes limit oxalate accumulation by degrading oxalate minerals to carbonates via an under-explored biogeochemical cycle known as the oxalate-carbonate pathway (OCP). Neither the diversity nor the ecology of oxalotrophic bacteria is fully understood. This research investigated the phylogenetic relationships of the bacterial genes oxc, frc, oxdC, and oxlT, which encode key enzymes for oxalotrophy, using bioinformatic approaches and publicly available omics datasets. Phylogenetic trees of oxc and oxdC genes demonstrated grouping by both source environment and taxonomy. All four trees included genes from metagenome-assembled genomes (MAGs) that contained novel lineages and environments for oxalotrophs. In particular, sequences of each gene were recovered from marine environments. These results were supported with marine transcriptome sequences and description of key amino acid residue conservation. Additionally, we investigated the theoretical energy yield from oxalotrophy across marine-relevant pressure and temperature conditions and found similar standard state Gibbs free energy to “low energy” marine sediment metabolisms, such as anaerobic oxidation of methane coupled to sulfate reduction. These findings suggest further need to understand the role of bacterial oxalotrophy in the OCP, particularly in marine environments, and its contribution to global carbon cycling. Frontiers Media S.A. 2023-05-04 /pmc/articles/PMC10192776/ /pubmed/37213515 http://dx.doi.org/10.3389/fmicb.2023.1161937 Text en Copyright © 2023 Sonke and Trembath-Reichert. 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. |
spellingShingle | Microbiology Sonke, Alexander Trembath-Reichert, Elizabeth Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title | Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title_full | Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title_fullStr | Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title_full_unstemmed | Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title_short | Expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
title_sort | expanding the taxonomic and environmental extent of an underexplored carbon metabolism—oxalotrophy |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10192776/ https://www.ncbi.nlm.nih.gov/pubmed/37213515 http://dx.doi.org/10.3389/fmicb.2023.1161937 |
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