The sponge microbiome project

Moitinho-Silva, Lucas, Nielsen, Shaun, Amir, Amnon, Gonzalez, Antonio, Ackermann, Gail L., Cerrano, Carlo, Astudillo-Garcia, Carmen, Easson, Cole, Sipkema, Detmer, Liu, Fang, Steinert, Georg, Kotoulas, Giorgos, McCormack, Grace P., Feng, Guofang, Bell, James J., Vicente, Jan, Björk, Johannes R, Montoya, Jose M., Olson, Julie B., Reveillaud, Julie, Steindler, Laura, Pineda, Mari-Carmen, Marra, Maria V., Ilan, Micha, Taylor, Michael W., Polymenakou, Paraskevi, Erwin, Patrick M., Schupp, Peter J., Simister, Rachel L., Knight, Rob, Thacker, Robert W., Costa, Rodrigo, Hill, Russell T., Lopez-Legentil, Susanna, Dailianis, Thanos, Ravasi, Timothy, Hentschel, Ute, Li, Zhiyong, Webster, Nicole S. and Thomas, Torsten (2017) The sponge microbiome project GigaScience, 6 (8). DOI 10.1093/gigascience/gix077.

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Abstract

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 269 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) a new high-resolution Deblur protocol resulting in 83,908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host-specificity, convergent evolution, environmental drivers of microbiome structure and the sponge-associated rare biosphere.

Document Type: Article
Keywords: Marine sponges, Archaea, Bacteria, Symbiosis, Microbiome, 16S rRNA gene, Microbial diversity
Research affiliation: OceanRep > GEOMAR > FB3 Marine Ecology > FB3-MI Marine Microbiology
Kiel University
Refereed: Yes
DOI etc.: 10.1093/gigascience/gix077
ISSN: 2047-217X
Date Deposited: 31 Aug 2017 09:05
Last Modified: 31 Aug 2017 09:05
URI: http://eprints.uni-kiel.de/id/eprint/39217

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