Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

Handle URI:
http://hdl.handle.net/10754/622422
Title:
Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans
Authors:
Pernice, Massimo C.; Giner, Caterina R.; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G.; Duarte, Carlos M. ( 0000-0002-1213-1361 ) ; Gasol, Josep M.; Massana, Ramon
Abstract:
<p>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.</p> <span><i>The ISME Journal</i> advance online publication, 9 October 2015; doi:<span>10.1038/ismej.2015.170</span></span>
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC)
Citation:
Pernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, et al. (2015) Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. The ISME Journal 10: 945–958. Available: http://dx.doi.org/10.1038/ismej.2015.170.
Publisher:
Nature Publishing Group
Journal:
The ISME Journal
Issue Date:
9-Oct-2015
DOI:
10.1038/ismej.2015.170
Type:
Article
ISSN:
1751-7362; 1751-7370
Sponsors:
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. Alvarez-Salgado, Teresa S. Catala, Guillem Salazar, Francisco Cornejo-Castillo, Encarna Borrull, Cristina Diez, Elena Lara, Irene Forn, Dolors Vaque, Eugenio Fraile, Veronica Benitez, the crew and the chief scientists of the various cruises for helpful collaboration.
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorPernice, Massimo C.en
dc.contributor.authorGiner, Caterina R.en
dc.contributor.authorLogares, Ramiroen
dc.contributor.authorPerera-Bel, Júliaen
dc.contributor.authorAcinas, Silvia G.en
dc.contributor.authorDuarte, Carlos M.en
dc.contributor.authorGasol, Josep M.en
dc.contributor.authorMassana, Ramonen
dc.date.accessioned2017-01-02T09:28:30Z-
dc.date.available2017-01-02T09:28:30Z-
dc.date.issued2015-10-09en
dc.identifier.citationPernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, et al. (2015) Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. The ISME Journal 10: 945–958. Available: http://dx.doi.org/10.1038/ismej.2015.170.en
dc.identifier.issn1751-7362en
dc.identifier.issn1751-7370en
dc.identifier.doi10.1038/ismej.2015.170en
dc.identifier.urihttp://hdl.handle.net/10754/622422-
dc.description.abstract<p>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.</p> <span><i>The ISME Journal</i> advance online publication, 9 October 2015; doi:<span>10.1038/ismej.2015.170</span></span>en
dc.description.sponsorshipThis 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. Alvarez-Salgado, Teresa S. Catala, Guillem Salazar, Francisco Cornejo-Castillo, Encarna Borrull, Cristina Diez, Elena Lara, Irene Forn, Dolors Vaque, Eugenio Fraile, Veronica Benitez, the crew and the chief scientists of the various cruises for helpful collaboration.en
dc.publisherNature Publishing Groupen
dc.subjectMicrobial ecologyen
dc.subjectWater microbiologyen
dc.titleLarge variability of bathypelagic microbial eukaryotic communities across the world’s oceansen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalThe ISME Journalen
dc.contributor.institutionDepartment of Marine Biology and Oceanography, Institut de Ciències Del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spainen
dc.contributor.institutionIMEDEA (UiB-CSIC), Department of Global Change Research, Institut Mediterraneo de Estudios Avanzados, Esporles, Spainen
kaust.authorDuarte, Carlos M.en
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