Browsing by Author "Thacker, Robert W."

Now showing 1 - 5 of 5
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    Diversity, structure and convergent evolution of the global sponge microbiome
    (Nature Portfolio, 2016) Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Bjoerk, Johannes R.; Easson, Cole; Astudillo-Garcia, Carmen; Olson, Julie B.; Erwin, Patrick M.; Lopez-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Lopez, Jose Victor; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.; University of New South Wales Sydney; University of Adelaide; Centre National de la Recherche Scientifique (CNRS); Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Centro Mediterraneo de Investigaciones Marinas y Ambientales (CMIMA); CSIC - Instituto de Ciencias del Mar (ICM); University of Alabama Tuscaloosa; University of Auckland; University of North Carolina; University of North Carolina Wilmington; Charles Darwin University; Nova Southeastern University; Universidade do Algarve; Carl von Ossietzky Universitat Oldenburg; University of Haifa; University of Munich; University of Chicago; United States Department of Energy (DOE); Argonne National Laboratory; University of California San Diego; State University of New York (SUNY) Stony Brook; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; Australian Institute of Marine Science
    Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.
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    Exploring Individual-to Population-Level Impacts of Disease on Coral Reef Sponges: Using Spatial Analysis to Assess the Fate, Dynamics, and Transmission of Aplysina Red Band Syndrome (ARBS)
    (PLOS, 2013) Easson, Cole G.; Slattery, Marc; Momm, Henrique G.; Olson, Julie B.; Thacker, Robert W.; Gochfeld, Deborah J.; University of Mississippi; Middle Tennessee State University; University of Alabama Tuscaloosa; University of Alabama Birmingham
    Background: Marine diseases are of increasing concern for coral reef ecosystems, but often their causes, dynamics and are unknown. The current study investigated the epidemiology of Aplysina Red Band Syndrome (ARBS), a disease affecting the Caribbean sponge Aplysina cauliformis, at both the individual and population levels. The fates of marked healthy and ARBS-infected sponges were examined over the course of a year. Population-level impacts and transmission mechanisms of ARBS were investigated by monitoring two populations of A. cauliformis over a three year period using digital photography and diver-collected data, and analyzing these data with GIS techniques of spatial analysis. In this study, three commonly used spatial statistics (Ripley's K, Getis-Ord General G, and Moran's Index) were compared to each other and with direct measurements of individual interactions using join-counts, to determine the ideal method for investigating disease dynamics and transmission mechanisms in this system. During the study period, Hurricane Irene directly impacted these populations, providing an opportunity to assess potential storm effects on A. cauliformis and ARBS. Results: Infection with ARBS caused increased loss of healthy sponge tissue over time and a higher likelihood of individual mortality. Hurricane Irene had a dramatic effect on A. cauliformis populations by greatly reducing sponge biomass on the reef, especially among diseased individuals. Spatial analysis showed that direct contact between A. cauliformis individuals was the likely transmission mechanism for ARBS within a population, evidenced by a significantly higher number of contact-joins between diseased sponges compared to random. Of the spatial statistics compared, the Moran's Index best represented true connections between diseased sponges in the survey area. This study showed that spatial analysis can be a powerful tool for investigating disease dynamics and transmission in a coral reef
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    Phylogenetic Diversity, Host-Specificity and Community Profiling of Sponge-Associated Bacteria in the Northern Gulf of Mexico
    (PLOS, 2011) Erwin, Patrick M.; Olson, Julie B.; Thacker, Robert W.; University of Alabama Birmingham; University of Alabama Tuscaloosa
    Background: Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. Methodology/Principal Findings: We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). Conclusions/Significance: The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.
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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