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New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MA...

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Detalles Bibliográficos
Autores principales: Cevallos, Miguel Angel, Degli Esposti, Mauro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879329/
https://www.ncbi.nlm.nih.gov/pubmed/35208909
http://dx.doi.org/10.3390/microorganisms10020455
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author Cevallos, Miguel Angel
Degli Esposti, Mauro
author_facet Cevallos, Miguel Angel
Degli Esposti, Mauro
author_sort Cevallos, Miguel Angel
collection PubMed
description We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new ‘oxycline’ clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.
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spelling pubmed-88793292022-02-26 New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient Cevallos, Miguel Angel Degli Esposti, Mauro Microorganisms Article We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new ‘oxycline’ clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments. MDPI 2022-02-16 /pmc/articles/PMC8879329/ /pubmed/35208909 http://dx.doi.org/10.3390/microorganisms10020455 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cevallos, Miguel Angel
Degli Esposti, Mauro
New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title_full New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title_fullStr New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title_full_unstemmed New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title_short New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
title_sort new alphaproteobacteria thrive in the depths of the ocean with oxygen gradient
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879329/
https://www.ncbi.nlm.nih.gov/pubmed/35208909
http://dx.doi.org/10.3390/microorganisms10020455
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