Phylogeny and Metabolic Potential of the Candidate Phylum SAR324
The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the pre...
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ftdoajarticles:oai:doaj.org/article:3a7af3abb99a4aeda92aa8a60095c9e2 2023-08-27T04:10:04+02:00 Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 Lukas Malfertheiner Clara Martínez-Pérez Zihao Zhao Gerhard J. Herndl Federico Baltar 2022-04-01T00:00:00Z https://doi.org/10.3390/biology11040599 https://doaj.org/article/3a7af3abb99a4aeda92aa8a60095c9e2 EN eng MDPI AG https://www.mdpi.com/2079-7737/11/4/599 https://doaj.org/toc/2079-7737 doi:10.3390/biology11040599 2079-7737 https://doaj.org/article/3a7af3abb99a4aeda92aa8a60095c9e2 Biology, Vol 11, Iss 599, p 599 (2022) microbial ecology metagenomics comparative genomics phylogeny metabolism nutrient cycling Biology (General) QH301-705.5 article 2022 ftdoajarticles https://doi.org/10.3390/biology11040599 2023-08-06T00:42:42Z The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin–Benson–Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats. Article in Journal/Newspaper Ice Shelf Ross Ice Shelf Directory of Open Access Journals: DOAJ Articles Calvin ENVELOPE(165.100,165.100,-71.283,-71.283) Ross Ice Shelf Biology 11 4 599 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
microbial ecology metagenomics comparative genomics phylogeny metabolism nutrient cycling Biology (General) QH301-705.5 |
spellingShingle |
microbial ecology metagenomics comparative genomics phylogeny metabolism nutrient cycling Biology (General) QH301-705.5 Lukas Malfertheiner Clara Martínez-Pérez Zihao Zhao Gerhard J. Herndl Federico Baltar Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
topic_facet |
microbial ecology metagenomics comparative genomics phylogeny metabolism nutrient cycling Biology (General) QH301-705.5 |
description |
The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin–Benson–Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats. |
format |
Article in Journal/Newspaper |
author |
Lukas Malfertheiner Clara Martínez-Pérez Zihao Zhao Gerhard J. Herndl Federico Baltar |
author_facet |
Lukas Malfertheiner Clara Martínez-Pérez Zihao Zhao Gerhard J. Herndl Federico Baltar |
author_sort |
Lukas Malfertheiner |
title |
Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
title_short |
Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
title_full |
Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
title_fullStr |
Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
title_full_unstemmed |
Phylogeny and Metabolic Potential of the Candidate Phylum SAR324 |
title_sort |
phylogeny and metabolic potential of the candidate phylum sar324 |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/biology11040599 https://doaj.org/article/3a7af3abb99a4aeda92aa8a60095c9e2 |
long_lat |
ENVELOPE(165.100,165.100,-71.283,-71.283) |
geographic |
Calvin Ross Ice Shelf |
geographic_facet |
Calvin Ross Ice Shelf |
genre |
Ice Shelf Ross Ice Shelf |
genre_facet |
Ice Shelf Ross Ice Shelf |
op_source |
Biology, Vol 11, Iss 599, p 599 (2022) |
op_relation |
https://www.mdpi.com/2079-7737/11/4/599 https://doaj.org/toc/2079-7737 doi:10.3390/biology11040599 2079-7737 https://doaj.org/article/3a7af3abb99a4aeda92aa8a60095c9e2 |
op_doi |
https://doi.org/10.3390/biology11040599 |
container_title |
Biology |
container_volume |
11 |
container_issue |
4 |
container_start_page |
599 |
_version_ |
1775351826312331264 |