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Coral Microbiome Project Abstracts

CMP_AA_Bv1v3 -- Apprill, A., K. Hughen, and T.J. Mincer, Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals. Environmental Microbiology, 2013. 15: p. 2063-2072.
Description: V1-V3 region of bacterial SSU rRNA, 454 sequencing platform
Abstract: Cultivation-based studies have demonstrated that yellow-band disease (YBD), a lesion-producing ailment affecting diverse species of coral, is caused by a consortium of Vibrio spp. This study takes the first cultivation-independent approach to examine the whole bacterial community associated with YBD-like lesioned corals. Two species of Fungiidae corals, Ctenactis crassa and Herpolitha limax, displaying YBD-like lesions were examined across diverse reefs throughout the Red Sea. Using a pyrosequencing approach targeting the V1-V3 regions of the SSU rRNA gene, no major differences in bacterial community composition or diversity were identified between healthy and lesioned corals of either species. Indicator species analysis did not find Vibrio significantly associated with the lesioned corals. However, operational taxonomic units belonging to the Ruegeria genus of Alphaproteobacteria and NS9 marine group of Flavobacteria were significantly associated with the lesioned corals. The most striking trend of this dataset was that reef location was found to be the most significant influence on the coral-bacterial community. It is possible that more pronounced lesion-specific bacterial signatures might have been concealed by the strong influence of environmental conditions on coral-bacteria. Overall, this study demonstrates inconsistencies between cultivation-independent and cultivation-based studies regarding the role of specific bacteria in coral diseases.

CMP_Bent_ABv4 -- Unpublished: Shavonna Bent, Carolyn Miller, Colleen Hansel, Koty Sharp, Amy Apprill. Microbiome recovery in symbiotic and aposymbiotic corals following antibiotic disturbance
Description: V4 region of bacterial and archaeal SSU rRNA, Illumina MiSeq sequencing platform
Abstract: Analysis in progress

CMP_JS_Bv1v4 -- Šlapeta J., and M.C. Linares. Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan 'type-N' (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia. PLoS ONE, 2013. 8: e76095. doi:10.1371/journal.pone.0076095
Description: V1-V4 region of bacterial SSU rRNA, 454 sequencing platform
Abstract: BACKGROUND: The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. 'type-N' symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. METHODS & PRINCIPAL FINDINGS: We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. SIGNIFICANCE: This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.

CMP_KM_Bv3v4 -- Morrow, K., A. Moss, N. Chadwick, and M. Liles. Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability. Applied and Environmental Microbiology, 2012. 78: p. 6438-6449.
Description: V3-V4 region of bacterial SSU rRNA, 454 sequencing platform
Abstract: Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.

CMP_LMA_Bv4 -- None
Description: 16S V4 rRNA amplicon of coral reef seawater microbiome
Abstract: 16S rRNA V4 amplicon sequence libraries of reef seawater microbiomes. Samples from 3 reefs in U.S. Virgin Islands and 3 reefs in Florida Reef tract.

CMP_Sharp_ABv4 -- Sharp, K.H., Z.A. Pratte, A.H. Kerwin, R.D. Rotjan, F.J. Stewart. Season, but not symbionts state, drives microbiome structure in the temperate coral Astrangia poculata, 2017. 5:120.
Description: V4 region of bacterial and archaeal SSU rRNA, Illumina MiSeq sequencing platform
Abstract: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition.

CMP_TB_Bv1v2 -- Bayer T., A. Chatchanit, C. Ferrier-Pages, D. Zoccola, M. Aranda, and C. Voolstra. Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini. Marine Ecology Progress Series, 2013. 479: p. 75-84.
Description: V1-V2 region of bacterial SSU rRNA, 454 sequencing platform
Abstract: Forming dense beds that provide the structural basis of a distinct ecosystem, the gorgonian Eunicella cavolini (Octocorallia) is an important species in the Mediterranean Sea. Despite the importance and prevalence of this temperate gorgonian, little is known about its microbial assemblage, although bacteria are well known to be important to hard and soft coral functioning. Here, we used massively parallel pyrosequencing of 16S rRNA genes to determine the composition and relative abundances of bacteria associated with E. cavolini collected from different depths at a site on the French Mediterranean coast. We found that whereas the bacterial assemblages of E. cavolini were distinct and less diverse than those of the surrounding water column, the water depth did not affect the bacterial assemblages of this gorgonian. Our data show that E. cavolini?s microbiome contains only a few shared species and that it is highly dominated by bacteria from the genus Endozoicomonas, a Gammaproteobacteria that is frequently found to associate with marine invertebrates.

CMP_TB_Bv5v6 -- Bayer, T., M. Neave, A. Alsheikh-Hussain, M. Aranda, L. Yum, T. J. Mincer, K. Hughen, A. Apprill, and C. Voolstra. The Microbiome of the Red Sea Coral Stylophora pistillata Is Dominated by Tissue-Associated Endozoicomonas Bacteria. Applied and Environmental Microbiology, 2013. 79: p. 4759-4762.
Description: V5-V6 region of SSU rRNA, 454 sequencing platform
Abstract: Endozoicomonas bacteria were found highly associated with the coral Stylophora pistillata, and these bacteria are also ubiquitously associated with diverse corals worldwide. Novel Endozoicomonas-specific probes revealed that Endozoicomonas bacteria were abundant in the endodermal tissues of S. pistillata and appear to have an intimate relationship with the coral.

ICM_CCB_Av6, ICM_CCB_Bv6 -- Sunagawa S, C.M. Woodley, and M. Medina. Threatened Corals Provide Underexplored Microbial Habitats, 2010. PLoS ONE, 5: e9554. doi:10.1371/journal.pone.0009554
Description: V6 region of bacterial and archael SSU rRNA, 454 sequencing platform
Abstract: Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

LTR_MCR_Av6, LTR_MCR_Bv6, LTR_MCR_Ev9 -- McCliment, E., C. Nelson, C. Carlson, A. Alldredge, J. Witting, and L. Amaral-Zettler. An all-taxon microbial inventory of the Moorea coral reef ecosystem. The ISME Journal, 2012. 6: p. 309-319.
Description: V6 region of bacterial & archael SSU rRNA, eukaryotic V9 hypervariable region of SSU rRNA, 454 sequencing platform
Abstract: The Moorea Coral Reef Long Term Ecological Research (LTER) Site (17.50°S, 149.83°W) comprises the fringe of coral reefs and lagoons surrounding the volcanic island of Moorea in the Society Islands of French Polynesia. As part of our Microbial Inventory Research Across Diverse Aquatic LTERS biodiversity inventory project, we characterized microbial community composition across all three domains of life using amplicon pyrosequencing of the V6 (bacterial and archaeal) and V9 (eukaryotic) hypervariable regions of small-subunit ribosomal RNA genes. Our survey spanned eight locations along a 130-km transect from the reef lagoon to the open ocean to examine changes in communities along inshore to offshore gradients. Our results illustrate consistent community differentiation between inshore and offshore ecosystems across all three domains, with greater richness in all domains in the reef-associated habitats. Bacterial communities were more homogenous among open ocean sites spanning &gt;100 km than among inshore sites separated by &lt;1 km, whereas eukaryotic communities varied more offshore than inshore, and archaea showed more equal levels of dissimilarity among subhabitats. We identified signature communities representative of specific geographic and geochemical milieu, and characterized co-occurrence patterns of specific microbial taxa within the inshore ecosystem including several bacterial groups that persist in geographical niches across time. Bacterial and archaeal communities were dominated by few abundant taxa but spatial patterning was consistent through time and space in both rare and abundant communities. This is the first in-depth inventory analysis of biogeographic variation of all three microbial domains within a coral reef ecosystem.