Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea
Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea
Proteorhodopsins have been suggested as an important strategy among phototrophs to capture solar energy in marine environments. The goals of this study was to investigate the diversity of proteorhodopsin genes and to explore their abundance, distribution, and expression in the coastal surface waters of the northern South China Sea, one of the largest marginal seas of the western North Pacific Ocean. Using 21 metagenomes, we recovered proteorhodopsin genes from a wide range of prokaryotic taxa, and chlorophyll a contributed significantly to the community composition of proteorhodopsin-containing microbes. Most proteorhodopsin sequences were predicted to encode green light-absorbing proton pumps and green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones. The variations in the conserved residues involved in ion pumping and several uncharacterized proteorhodopsins were observed. The gene abundance pattern of proteorhodopsin types were significantly influenced by the levels of total organic carbon and soluble reactive phosphorus. Gene expression analysis confirmed the importance of proteorhodopsin-based phototrophy and revealed different expressional patterns among major phyla. In tandem, we screened 2295 metagenome-assembled genomes to describe the taxonomic distribution of proteorhodopsins. Bacteroidota are the key lineages encoding proteorhodopsins, but proteorhodopsins were predicated from members of Proteobacteria, Marinisomatota, Myxococcota, Verrucomicrobiota and Thermoplasmatota. Our study expanded the diversity of proteorhodopsins and improve our understanding on the significance of proteorhodopsin-mediated phototrophy in the marine ecosystem.
Diversity, Metagenomics, Metatranscriptomes, Phototrophy, Proteorhodopsin genes, South China Sea
Yin, Lingzi
f2838457-0258-4228-9d61-b4373a790ccf
Duan, Li
f4cbd62a-d586-4d35-a9db-77e5b3bfd5e7
Li, Jialing
e7f7fc9c-18e3-46de-ac4c-89589030e1f4
Wang, Pandeng
40a25f5f-248e-44be-ae6b-7d688acc5d01
Gao, Shaoming
a135f3f0-ef73-49f4-b369-7c3ca2580cd6
Xian, Wendong
076d1931-4c98-45b4-aa33-b9dcee11f8d6
Li, Wenjun
715d3e0e-934e-4f27-8682-e2604942646e
7 July 2024
Yin, Lingzi
f2838457-0258-4228-9d61-b4373a790ccf
Duan, Li
f4cbd62a-d586-4d35-a9db-77e5b3bfd5e7
Li, Jialing
e7f7fc9c-18e3-46de-ac4c-89589030e1f4
Wang, Pandeng
40a25f5f-248e-44be-ae6b-7d688acc5d01
Gao, Shaoming
a135f3f0-ef73-49f4-b369-7c3ca2580cd6
Xian, Wendong
076d1931-4c98-45b4-aa33-b9dcee11f8d6
Li, Wenjun
715d3e0e-934e-4f27-8682-e2604942646e
Li, Shanhui, Yin, Lingzi, Duan, Li, Li, Jialing, Wang, Pandeng, Gao, Shaoming, Xian, Wendong and Li, Wenjun
(2024)
Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea.
Environmental Research, 259, [119514].
(doi:10.1016/j.envres.2024.119514).
Abstract
Proteorhodopsins have been suggested as an important strategy among phototrophs to capture solar energy in marine environments. The goals of this study was to investigate the diversity of proteorhodopsin genes and to explore their abundance, distribution, and expression in the coastal surface waters of the northern South China Sea, one of the largest marginal seas of the western North Pacific Ocean. Using 21 metagenomes, we recovered proteorhodopsin genes from a wide range of prokaryotic taxa, and chlorophyll a contributed significantly to the community composition of proteorhodopsin-containing microbes. Most proteorhodopsin sequences were predicted to encode green light-absorbing proton pumps and green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones. The variations in the conserved residues involved in ion pumping and several uncharacterized proteorhodopsins were observed. The gene abundance pattern of proteorhodopsin types were significantly influenced by the levels of total organic carbon and soluble reactive phosphorus. Gene expression analysis confirmed the importance of proteorhodopsin-based phototrophy and revealed different expressional patterns among major phyla. In tandem, we screened 2295 metagenome-assembled genomes to describe the taxonomic distribution of proteorhodopsins. Bacteroidota are the key lineages encoding proteorhodopsins, but proteorhodopsins were predicated from members of Proteobacteria, Marinisomatota, Myxococcota, Verrucomicrobiota and Thermoplasmatota. Our study expanded the diversity of proteorhodopsins and improve our understanding on the significance of proteorhodopsin-mediated phototrophy in the marine ecosystem.
Text
YENRS_119514
- Accepted Manuscript
Restricted to Repository staff only until 7 July 2026.
More information
Accepted/In Press date: 29 June 2024
e-pub ahead of print date: 29 June 2024
Published date: 7 July 2024
Keywords:
Diversity, Metagenomics, Metatranscriptomes, Phototrophy, Proteorhodopsin genes, South China Sea
Identifiers
Local EPrints ID: 494654
URI: http://eprints.soton.ac.uk/id/eprint/494654
ISSN: 0013-9351
PURE UUID: 2c16734b-2afc-4a1e-85b3-0f9c219ac2cc
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Date deposited: 11 Oct 2024 17:00
Last modified: 16 Oct 2024 16:43
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Contributors
Author:
Shanhui Li
Author:
Lingzi Yin
Author:
Li Duan
Author:
Jialing Li
Author:
Pandeng Wang
Author:
Shaoming Gao
Author:
Wendong Xian
Author:
Wenjun Li
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