Background: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts. Results: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. Conclusions: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities.
Bibliographical noteKAUST Repository Item: Exported on 2023-06-02
Acknowledged KAUST grant number(s): OSR no. 3362
Acknowledgements: Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio programme (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the US Department of Energy Joint Genome Institute, supported by the Office of Science of the US Department of Energy under contract no. DE-AC02 05CH11231 to S. G. A. (CSP 612 “Microbial metagenomics and transcriptomics from a global deep-ocean expedition”). Additional funding was provided by the project MAGGY (CTM2017-87736-R) to S. G. A. from the Spanish Ministry of Economy and Competitiveness, Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya, and King Abdullah University of Science and Technology (KAUST) under contract OSR no. 3362). The ICM researchers have had the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S). FHC was supported by a Juan de la Cierva — Incorporación fellowship (Grant IJC2019-039859-I). CBS was supported by the NASA Exobiology Program (80NSSC23K0676 to CBS). We thank the R/V Hespérides captain and crew, the chief scientists in Malaspina expedition legs, and all project participants for their help in making this project possible. High-performance computing analyses were run at the Marine Bioinformatics Service (MARBITS, https://marbits.icm.csic.es) of the Institut de Ciències del Mar (ICM-CSIC).
ASJC Scopus subject areas
- Microbiology (medical)