Abiotic selection of microbial genome size in the global ocean

David Ngugi; Silvia G Acinas; Pablo Sanchez; Josep M. Gasol; Susana Agusti; David M. Karl; Carlos M. Duarte

doi:10.1038/s41467-023-36988-x

Abiotic selection of microbial genome size in the global ocean

David Ngugi, Silvia G Acinas, Pablo Sanchez, Josep M. Gasol, Susana Agusti, David M. Karl, Carlos M. Duarte

Marine Science

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Abstract

Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.

Original language	English (US)
Journal	Nature Communications
Volume	14
Issue number	1
DOIs	https://doi.org/10.1038/s41467-023-36988-x
State	Published - Mar 13 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-03-16
Acknowledgements: Open Access funding enabled and organized by Projekt DEAL. DKN was supported through the institutional funding of the Leibniz Institute DSMZ. Additional funding was provided by the DFG (project number NG183/2-1). We also thank the captain and crew of the R/V Hespérides and the scientists involved in the Malaspina Expedition for making this project a reality. The Spanish Ministry of Economy and Competitiveness (MINECO) funded the Malaspina Expedition through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy (Contract No. DE-AC02 05CH11231) to SGA. The Malaspina Vertical Profile microbial metagenomes were sequenced through MALASPINOMICS (CTM2011-15461-E) and MAGGY (CTM2017-87736-R). We thank Edward DeLong for his helpful comments that helped in result interpretation.

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Chemistry
General Physics and Astronomy

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41467-023-36988-x

https://repository.kaust.edu.sa/bitstream/10754/690349/1/s41467-023-36988-x.pdf

Cite this

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title = "Abiotic selection of microbial genome size in the global ocean",

abstract = "Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.",

author = "David Ngugi and Acinas, {Silvia G} and Pablo Sanchez and Gasol, {Josep M.} and Susana Agusti and Karl, {David M.} and Duarte, {Carlos M.}",

note = "KAUST Repository Item: Exported on 2023-03-16 Acknowledgements: Open Access funding enabled and organized by Projekt DEAL. DKN was supported through the institutional funding of the Leibniz Institute DSMZ. Additional funding was provided by the DFG (project number NG183/2-1). We also thank the captain and crew of the R/V Hesp{\'e}rides and the scientists involved in the Malaspina Expedition for making this project a reality. The Spanish Ministry of Economy and Competitiveness (MINECO) funded the Malaspina Expedition through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy (Contract No. DE-AC02 05CH11231) to SGA. The Malaspina Vertical Profile microbial metagenomes were sequenced through MALASPINOMICS (CTM2011-15461-E) and MAGGY (CTM2017-87736-R). We thank Edward DeLong for his helpful comments that helped in result interpretation.",

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AU - Duarte, Carlos M.

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N2 - Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.

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Abiotic selection of microbial genome size in the global ocean

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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