Abstract
In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8–20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.
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Acknowledgements
This project was supported by the Spanish Ministry of Economy and Competitiveness through project Consolider-Ingenio Malaspina-2010 (CSD2008–00077) to CMD and FLAME (CGL2010-16304) to RM. RL was supported by a Juan de la Cierva Fellowship (JCI-2010-06594, Spanish Ministry of Economy and Competitiveness, Spain). Sequencing at the JGI was supported by US Department of Energy (DOE) JGI 2011 Microbes Program grant CSP 602 grant to SGA. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Additional funding was provided by the Spanish Ministry of Economy and Competitivity grant MALASPINOMICS (CTM2011-15461-E). The authors were also supported by the Generalitat de Catalunya Research Group grants 2014SGR/1179. We thank our colleagues Xose A. Álvarez-Salgado, Teresa S. Catalá, Guillem Salazar, Francisco Cornejo-Castillo, Encarna Borrull, Cristina Díez, Elena Lara, Irene Forn, Dolors Vaqué, Eugenio Fraile, Verónica Benitez, the crew and the chief scientists of the various cruises for helpful collaboration.
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Pernice, M., Giner, C., Logares, R. et al. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. ISME J 10, 945–958 (2016). https://doi.org/10.1038/ismej.2015.170
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DOI: https://doi.org/10.1038/ismej.2015.170
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