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Oyster Reef Restoration Experiment<\/strong> Reef Monitoring and Oyster Collection<\/strong> Parasite Prevalence and Intensity<\/strong> To assess microparasite prevalence and intensity, DNA was extracted from up to 32 oysters per reef and then amplified using both a polymerase chain reaction (PCR) assay modified from Stokes & Burreson (2001) SSO protocol, and a multiplex quantitative polymerase chain reaction (qPCR) assay modified from De Faveri et al. (2009) Dermo protocol and Wilbur et al. (2012) MSX protocol. DNA was extracted using 20-40 milligrams (wet weight) of gill and mantle tissue with the Omega Bio-Tek E-Z 96\u00ae Tissue DNA Kit.<\/p>\n We used a modified version of the De Faveri et al. (2009) Dermo protocol and the Wilbur et al. (2012) MSX protocol to analyze the samples on a Bio-Rad CFX96TM Real-Time System with Bio-Rad CFX Manager Software (version 3.1). Each reaction consisted of 1 microliter (\u03bcl) template DNA, 3 \u03bcl water, 5 \u03bcl TaqMan Multiplex Master Mix, and 0.5 \u03bcl of each 20X primer\/probe master mix, which contained 18 \u03bcM of each P. marinus<\/em> primer and 5 \u03bcM of TaqManTM QSY probe (De Faveri et al.<\/em> 2009) for Dermo, and 18 \u03bcM of each H. nelsoni<\/em> primer and 5 \u03bcM of TaqManTM MGB probe (Wilbur et al. 2012) for MSX. qPCR cycling conditions included initial denaturation at 95\u00b0C for 30 sec, followed by 40 cycles of 95\u00b0C for 10 sec and 60\u00b0C for 30 sec. We used gBlocks\u00ae (gene fragments containing the target regions from P. marinus<\/em> and H. nelsoni<\/em>; Integrated DNA Technologies) to develop standard curves, and extracted DNA from cultures of P. marinus<\/em> and H. nelsoni<\/em> with known cell quantities to use as positive controls. All standards, samples, and positive and negative controls were run in duplicate; if samples differed by >1 Cq, they were rerun to confirm presence\/absence and\/or parasite concentration.<\/p>\n We used a modified version of the Stokes & Burreson (2001) SSO protocol to assess H. costale<\/em> prevalence on a Bio-Rad CT100 thermal cycler. PCR cycling conditions included initial denaturation at 94\u00b0C for 2 min, followed by 35 cycles of 94\u00b0C for 30 sec, 59\u00b0C for 30 sec, and 72\u00b0C for 60 sec, and final extension at 72\u00b0C for 5 min. PCR products were visualized on a 1% agarose gel and photographed for analysis of band intensity using ImageJ, following the methods of DeLong & Hanley (2013). For the SSO assay, we used gBlocks\u00ae containing the target region from H. costale<\/em> as positive controls and as standards for estimating parasite concentration based on quantification of band intensity using ImageJ (Abr\u00e0moff et al. 2004).<\/p>\n To assess the prevalence and intensity of two common macroparasites, boring sponge (Cliona<\/em> spp.) and mud blister worm (Polydora<\/em> spp.), we photographed the inside (mud blisters) and\/or outside (sponge holes) of both top and bottom valves for all samples with holes characteristic of boring sponges and blisters characteristic of mud blister worms to quantify the proportion of affected shell area (i.e., [(total infected area\/total shell area)*100]) using ImageJ (Abr\u00e0moff et al. 2004), following the methods of Hanley et al. (2019).<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/ocean-data.org\/schema\/hasBriefDescription":[{"@value":"Oyster genetic identity and parasite community structure","@language":"en-US"}],"http:\/\/www.w3.org\/2000\/01\/rdf-schema#label":[{"@value":"Oyster genetic identity and parasite community structure","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/hasProcessingDescription":[{"@value":" Data Processing<\/strong> BCO-DMO Processing<\/strong>
\nIn May 2017, we created nine oyster reefs in Quonochontaug Pond, Rhode Island (RI) (41\u00b020'22.6\"N, 71\u00b043'41.2\"W), with three separate reefs each located within three distinct regions (West, Northeast, East). Each ~22 square meter (m\u00b2) reef (0.5-0.8 m height) was constructed from a base layer of steam-shucked clam shell topped with clean, recycled oyster shell, and then seeded with remote-set spat on shell (see Davenport et al. 2022 for a detailed description of reef construction). A goal of this study was to compare the performance of different oyster sources and the consequent structure of associated parasite communities, so one replicate reef per oyster source was constructed in each of the three regions of Quonochontaug Pond (hereafter, blocks). The oyster seed sources included one line from a regional commercial hatchery, as well as two wild progenitor lines spawned from broodstock collected from nearby existing wild populations in Green Hill Pond, RI and Narrow River, RI. All oyster lines were spawned at local hatcheries, transferred to Roger Williams University Shellfish Hatchery and set on oyster shell in June 2016, and then stored in cages on an oyster lease in Quonochontaug Pond until reef construction in May 2017.<\/p>\n
\nIn the fall of each year for four years post-restoration (2017-2020), we monitored oyster density and size distribution by non-destructively sampling six haphazard 0.25 m\u00b2 quadrats per reef and recording the number of live and dead oysters, as well as shell height of a subsample of up to 50 live and 30 dead oysters (following methods of Griffin et al. 2012 (see Supplemental Files) and guidance of Baggett et al. 2015). Coincident with each fall monitoring event, we harvested ~35 haphazardly-selected live oysters from each reef for analysis of parasite communities; samples were transported to the Northeastern University Marine Science Center on ice and then stored at -80 degrees Celsius prior to processing.<\/p>\n
Crassostrea virginica<\/em> is commonly infected by a variety of micro- and macro-parasites simultaneously. We assessed the prevalence (proportion of sampled oysters infected per oyster reef) and intensity (parasite concentration per infected host) of five common parasite species (microparasites: Perkinsus marinus <\/em>(Dermo disease), Haplosporidium nelsoni<\/em> (MSX disease), and Haplosporidium costale<\/em> (SSO disease); macroparasites: Cliona<\/em> spp. and Polydora<\/em>spp.).<\/p>\n
\nFor oyster density, we calculated the mean number of live oysters per reef as the average density across the six replicate quadrats sampled. For oyster size, we calculated the mean shell height of up to 50 live oysters per quadrat and then took the average across the six replicates per reef. For each parasite, we calculated reef-level prevalence as [number of infected oysters] \/ [number of oysters sampled], and reef-level intensity as the mean parasite concentration per infected host (i.e., uninfected hosts were not included).<\/p>\n
\n- replaced \"NA\" with \"nd\" (no data value);
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To address this knowledge gap, we tested how host genetic identity affects parasite communities on restored reefs seeded with juvenile oysters from different sources \u2013 a regional commercial hatchery or one of two wild progenitor lines. We assessed the prevalence and intensity of three micro- and two macro-parasite species for four years following restoration. Despite the spatial proximity of restored reefs, oyster source identity strongly predicted parasite community prevalence across all years, with sources varying in their relative susceptibility to different parasites. Oyster seed source also predicted reef-level parasite intensities across space and through time. Our results highlight that host intraspecific variation can shape parasite community structure in natural systems, and reinforce the importance of considering source identity and diversity in restoration design.","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/rights":[{"@id":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"http:\/\/ocean-data.org\/schema\/deprecated":[{"@value":"false","@type":"xsd:boolean"}],"http:\/\/ocean-data.org\/schema\/temporalExtent":[{"@value":"_:temporalExtent883570"}],"http:\/\/ocean-data.org\/schema\/spatialCoverage":[{"@value":"_:spatialCoverage883570"}],"http:\/\/purl.org\/dc\/terms\/bibliographicCitation":[{"@value":"Hughes, A. R., Hanley, T. C. (2022) Prevalence and intensity of oyster parasite species following a reef restoration experiment in Quonochontaug Pond, Rhode Island, USA from 2017-2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). 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