Research and Publications - Department of Biological Sciences

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Browsing Research and Publications - Department of Biological Sciences by Author "Ackermann, Gail L."

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    The sponge microbiome project
    (Oxford University Press, 2017) 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; Bjork, 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.; Thomas, Torsten; University of New South Wales Sydney; University of California San Diego; Marche Polytechnic University; University of Auckland; Nova Southeastern University; Wageningen University & Research; Shanghai Jiao Tong University; Hellenic Centre for Marine Research; Ollscoil na Gaillimhe-University of Galway; Victoria University Wellington; University of Notre Dame; Centre National de la Recherche Scientifique (CNRS); Universite de Toulouse; Universite Toulouse III - Paul Sabatier; University of Alabama Tuscaloosa; INRAE; CIRAD; University of Haifa; Australian Institute of Marine Science; Tel Aviv University; University of North Carolina; University of North Carolina Wilmington; Carl von Ossietzky Universitat Oldenburg; University of British Columbia; State University of New York (SUNY) Stony Brook; Universidade de Lisboa; Instituto Superior Tecnico; University of Maryland Baltimore; University of Maryland Center for Environmental Science; Institute of Marine & Environmental Technology; King Abdullah University of Science & Technology; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; University of Kiel; University of Queensland
    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 268 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 (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) 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.
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    The sponge microbiome project (vol 6, pg 1, 2017)
    (Oxford University Press, 2018) 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; Bjork, 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.; Thomas, Torsten; University of New South Wales Sydney; University of California San Diego; Marche Polytechnic University; University of Auckland; Nova Southeastern University; Wageningen University & Research; Shanghai Jiao Tong University; Hellenic Centre for Marine Research; Ollscoil na Gaillimhe-University of Galway; Victoria University Wellington; University of Notre Dame; Centre National de la Recherche Scientifique (CNRS); Universite de Toulouse; Universite Toulouse III - Paul Sabatier; University of Alabama Tuscaloosa; INRAE; CIRAD; University of Haifa; Australian Institute of Marine Science; Tel Aviv University; University of North Carolina; University of North Carolina Wilmington; Carl von Ossietzky Universitat Oldenburg; University of British Columbia; State University of New York (SUNY) Stony Brook; Universidade de Lisboa; Instituto Superior Tecnico; University of Maryland Baltimore; University of Maryland Center for Environmental Science; Institute of Marine & Environmental Technology; King Abdullah University of Science & Technology; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; University of Kiel; University of Queensland