http://lod.bco-dmo.org/id/dataset/883570
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-11-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Prevalence and intensity of oyster parasite species following a reef restoration experiment in Quonochontaug Pond, Rhode Island, USA from 2017-2020
2022-11-10
publication
2022-11-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-23
publication
https://doi.org/10.26008/1912/bco-dmo.883570.1
A. Randall Hughes
Northeastern University
principalInvestigator
Torrance C. Hanley
Northeastern University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: 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). (Version 1) Version Date 2022-11-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883570.1 [access date]
Oyster genetic identity and parasite community structure Dataset Description: Methods and Sampling: <p><strong>Oyster Reef Restoration Experiment</strong><br />
In May 2017, we created nine oyster reefs in Quonochontaug Pond, Rhode Island (RI) (41°20'22.6"N, 71°43'41.2"W), with three separate reefs each located within three distinct regions (West, Northeast, East). Each ~22 square meter (m²) 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>
<p><strong>Reef Monitoring and Oyster Collection</strong><br />
In 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 m² 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>
<p><strong>Parasite Prevalence and Intensity</strong><br />
<em>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: <em>Perkinsus marinus </em>(Dermo disease), <em>Haplosporidium nelsoni</em> (MSX disease), and <em>Haplosporidium costale</em> (SSO disease); macroparasites: <em>Cliona</em> spp. and <em>Polydora</em>spp.).</p>
<p>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 &amp; 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® Tissue DNA Kit.</p>
<p>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 CFX96<sup>TM</sup> Real-Time System with Bio-Rad CFX Manager Software (version 3.1). Each reaction consisted of 1 microliter (μl) template DNA, 3 μl water, 5 μl TaqMan Multiplex Master Mix, and 0.5 μl of each 20X primer/probe master mix, which contained 18 μM of each <em>P. marinus</em> primer and 5 μM of TaqMan<sup>TM</sup> QSY probe (De Faveri<em> et al.</em> 2009) for Dermo, and 18 μM of each <em>H. nelsoni</em> primer and 5 μM of TaqMan<sup>TM</sup> MGB probe (Wilbur et al. 2012) for MSX. qPCR cycling conditions included initial denaturation at 95°C for 30 sec, followed by 40 cycles of 95°C for 10 sec and 60°C for 30 sec. We used gBlocks® (gene fragments containing the target regions from <em>P. marinus</em> and<em> H. nelsoni</em>; Integrated DNA Technologies) to develop standard curves, and extracted DNA from cultures of <em>P. marinus</em> and <em>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 &gt;1 Cq, they were rerun to confirm presence/absence and/or parasite concentration.</p>
<p>We used a modified version of the Stokes &amp; Burreson (2001) SSO protocol to assess <em>H. costale</em> prevalence on a Bio-Rad CT100 thermal cycler. PCR cycling conditions included initial denaturation at 94°C for 2 min, followed by 35 cycles of 94°C for 30 sec, 59°C for 30 sec, and 72°C for 60 sec, and final extension at 72°C 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 &amp; Hanley (2013). For the SSO assay, we used gBlocks® containing the target region from <em>H. costale</em> as positive controls and as standards for estimating parasite concentration based on quantification of band intensity using ImageJ (Abràmoff et al. 2004).</p>
<p>To assess the prevalence and intensity of two common macroparasites, boring sponge (<em>Cliona</em> spp.) and mud blister worm (<em>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 (Abràmoff et al. 2004), following the methods of Hanley et al. (2019).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1652320 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1652320
Funding provided by U.S. Fish & Wildlife Service Wildlife and Sport Fish Restoration Program (USFWS WSFR) Award Number: WSFR F20AF00145
completed
A. Randall Hughes
Northeastern University
781-581-7370
430 Nahant Rd.
Nahant
MA
01908
USA
ann.hughes@northeastern.edu
pointOfContact
Torrance C. Hanley
Northeastern University
4000 Mayflower Hill Diamond 204
Waterville
ME
04901
USA
hanleyt2@sacredheart.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Site
Year
Block
Reef_ID
Seed_Source
Mean_Oyster_Density
Mean_Oyster_Size
Sample_Count
Boring_Sponge_Prevalence
BS_Count_Infected
BS_Count_Uninfected
Mud_Blister_Worm_Prevalence
MBW_Count_Infected
MBW_Count_Uninfected
SSO_Prevalence
SSO_Count_Infected
SSO_Count_Uninfected
Dermo_Prevalence
Dermo_Count_Infected
Dermo_Count_Uninfected
MSX_Prevalence
MSX_Count_Infected
MSX_Count_Uninfected
Dermo_Intensity_SQ_per_mg
SSO_Intensity_pg_per_mg
BS_Intensity
MBW_Intensity
iPhone
Bio-Rad CFX96
Bio-Rad CT100 thermal cycler
theme
None, User defined
site
year
sample description
abundance
height
count
ratio
mean
featureType
BCO-DMO Standard Parameters
Camera
qPCR Thermal Cycler
Thermal Cycler
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
https://osprey.bco-dmo.org/project/709942
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
<p><em>NSF Award Abstract:</em><br />
Disease outbreaks in the ocean are increasing, causing losses of ecologically important marine species, but the factors contributing to these outbreaks are not well understood. This 5-year CAREER project will study disease prevalence and intensity in two marine foundation species - the seagrass Zostera marina and the Eastern oyster Crassostrea virginica. More specifically, host-disease relationships will be explored to understand how genetic diversity and population density of the host species impacts disease transmission and risk. This work will pair large-scale experimental restorations and smaller-scale field experiments to examine disease-host relationships across multiple spatial scales. Comparisons of patterns and mechanisms across the two coastal systems will provide an important first step towards identifying generalities in the diversity-density-disease relationship. To enhance the broader impacts and utility of this work, the experiments will be conducted in collaboration with restoration practitioners and guided by knowledge ascertained from key stakeholder groups. The project will support the development of an early career female researcher and multiple graduate and undergraduate students. Students will be trained in state-of-the-art molecular techniques to quantify oyster and seagrass parasites. Key findings from the surveys and experimental work will be incorporated into undergraduate courses focused on Conservation Biology, Marine Biology, and Disease Ecology. Finally, students in these courses will help develop social-ecological surveys and mutual learning games to stimulate knowledge transfer with stakeholders through a series of workshops.</p>
<p>The relationship between host genetic diversity and disease dynamics is complex. In some cases, known as a dilution effect, diversity reduces disease transmission and risk. However, the opposite relationship, known as the amplification effect, can also occur when diversity increases the risk of infection. Even if diversity directly reduces disease risk, simultaneous positive effects of diversity on host density could lead to amplification by increasing disease transmission between infected and uninfected individuals. Large-scale field restorations of seagrasses (Zostera marina) and oysters (Crassostrea virginica) will be utilized to test the effects of host genetic diversity on host population density and disease prevalence/intensity. Additional field experiments independently manipulating host genetic diversity and density will examine the mechanisms leading to dilution or amplification. Conducting similar manipulations in two marine foundation species - one a clonal plant and the other a non-clonal animal - will help identify commonalities in the diversity-density-disease relationship. Further, collaborations among project scientists, students, and stakeholders will enhance interdisciplinary training and help facilitate the exchange of information to improve management and restoration efforts. As part of these efforts, targeted surveys will be used to document the perceptions and attitudes of managers and restoration practitioners regarding genetic diversity and its role in ecological resilience and restoration.</p>
Seagrass and Oyster Ecosystems
largerWorkCitation
project
eng; USA
oceans
-71.728111
-71.728111
41.33961
41.33961
2017-05-01
2020-10-31
Coastal New England
0
BCO-DMO catalogue of parameters from 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)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/883580.rdf
Name: Site
Units: unitless
Description: <p>location of oyster restoration experiment (Quonochontaug Pond, Charlestown, Rhode Island, US)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883581.rdf
Name: Year
Units: unitless
Description: <p>year of oyster and parasite sampling (2017-2020); all sampling was conducted in the fall</p>
http://lod.bco-dmo.org/id/dataset-parameter/883582.rdf
Name: Block
Units: unitless
Description: <p>replicate block locations in Quonochontaug Pond (1-3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883583.rdf
Name: Reef_ID
Units: unitless
Description: <p>unique ID for each reef in the oyster restoration experiment; number refers to block and letter refers to treatment (seed source or control)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883584.rdf
Name: Seed_Source
Units: unitless
Description: <p>source of spat deployed on reef as spat on shell; GHP = Green Hill Pond, NAR = Narrow River, HAT = local hatchery</p>
http://lod.bco-dmo.org/id/dataset-parameter/883585.rdf
Name: Mean_Oyster_Density
Units: number per meter-squared (#/m^2)
Description: <p>mean oyster density (number per m^2) based on sampling of six haphazard quadrats per reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/883586.rdf
Name: Mean_Oyster_Size
Units: millimeters (mm)
Description: <p>mean oyster shell height (longest distance from umbo; mm) based on sampling of six haphazard quadrats per reef and measurements of <=50 live and <=30 dead oysters per quadrat</p>
http://lod.bco-dmo.org/id/dataset-parameter/883587.rdf
Name: Sample_Count
Units: number of oysters
Description: <p>number of oysters collected and processed from each reef on each sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/883588.rdf
Name: Boring_Sponge_Prevalence
Units: unitless (proportion)
Description: <p>proportion of oysters with holes characteristic of boring sponge</p>
http://lod.bco-dmo.org/id/dataset-parameter/883589.rdf
Name: BS_Count_Infected
Units: count
Description: <p>count of oysters with holes characteristic of boring sponge</p>
http://lod.bco-dmo.org/id/dataset-parameter/883590.rdf
Name: BS_Count_Uninfected
Units: count
Description: <p>count of oysters without holes characteristic of boring sponge</p>
http://lod.bco-dmo.org/id/dataset-parameter/883591.rdf
Name: Mud_Blister_Worm_Prevalence
Units: unitless (proportion)
Description: <p>proportion of oysters with blisters characteristic of mud blister worm</p>
http://lod.bco-dmo.org/id/dataset-parameter/883592.rdf
Name: MBW_Count_Infected
Units: count
Description: <p>count of oysters with blisters characteristic of mud blister worm</p>
http://lod.bco-dmo.org/id/dataset-parameter/883593.rdf
Name: MBW_Count_Uninfected
Units: count
Description: <p>count of oysters without blisters characteristic of mud blister worm</p>
http://lod.bco-dmo.org/id/dataset-parameter/883594.rdf
Name: SSO_Prevalence
Units: unitless (proportion)
Description: <p>proportion of oysters infected with Haplosporidium costale based on PCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883595.rdf
Name: SSO_Count_Infected
Units: count
Description: <p>count of oysters infected with Haplosporidium costale based on PCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883596.rdf
Name: SSO_Count_Uninfected
Units: count
Description: <p>count of oysters not infected with Haplosporidium costale based on PCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883597.rdf
Name: Dermo_Prevalence
Units: unitless (proportion)
Description: <p>proportion of oysters infected with Perkinsus marinus based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883598.rdf
Name: Dermo_Count_Infected
Units: count
Description: <p>count of oysters infected with Perkinsus marinus based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883599.rdf
Name: Dermo_Count_Uninfected
Units: count
Description: <p>count of oysters not infected with Perkinsus marinus based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883600.rdf
Name: MSX_Prevalence
Units: unitless (proportion)
Description: <p>proportion of oysters infected with Haplosporidium nelsoni based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883601.rdf
Name: MSX_Count_Infected
Units: count
Description: <p>count of oysters infected with Haplosporidium nelsoni based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883602.rdf
Name: MSX_Count_Uninfected
Units: count
Description: <p>count of oysters not infected with Haplosporidium nelsoni based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/883603.rdf
Name: Dermo_Intensity_SQ_per_mg
Units: copy number Perkinsus marinus per milligram (mg) oyster tissue
Description: <p>mean concentration Perkinsus marinus (copy number based on gBlocks standard) per wet weight oyster tissue (in milligrams) (calculated for infected oysters only)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883604.rdf
Name: SSO_Intensity_pg_per_mg
Units: picogram (pg) Haplosporidium costale per milligram (mg) oyster tissue
Description: <p>mean concentration Haplosporidium costale (in picograms) per wet weight oyster tissue (in milligrams) (calculated for infected oysters only)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883605.rdf
Name: BS_Intensity
Units: percent
Description: <p>mean percent of oyster shell (top and bottom valves) with holes characteristic of boring sponge ([(total infected area/total shell area)*100]), calculated for infected oysters only</p>
http://lod.bco-dmo.org/id/dataset-parameter/883606.rdf
Name: MBW_Intensity
Units: percent
Description: <p>mean percent of oyster shell (top and bottom valves) with blisters characteristic of mud blister worm ([(total infected area/total shell area)*100]), calculated for infected oysters only</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
5244
https://darchive.mblwhoilibrary.org/bitstream/1912/29528/1/dataset-883570_oyster-genetic-identity-and-parasite-community-structure__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883570.1
download
onLine
dataset
<p><strong>Oyster Reef Restoration Experiment</strong><br />
In May 2017, we created nine oyster reefs in Quonochontaug Pond, Rhode Island (RI) (41°20'22.6"N, 71°43'41.2"W), with three separate reefs each located within three distinct regions (West, Northeast, East). Each ~22 square meter (m²) 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>
<p><strong>Reef Monitoring and Oyster Collection</strong><br />
In 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 m² 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>
<p><strong>Parasite Prevalence and Intensity</strong><br />
<em>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: <em>Perkinsus marinus </em>(Dermo disease), <em>Haplosporidium nelsoni</em> (MSX disease), and <em>Haplosporidium costale</em> (SSO disease); macroparasites: <em>Cliona</em> spp. and <em>Polydora</em>spp.).</p>
<p>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 &amp; 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® Tissue DNA Kit.</p>
<p>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 CFX96<sup>TM</sup> Real-Time System with Bio-Rad CFX Manager Software (version 3.1). Each reaction consisted of 1 microliter (μl) template DNA, 3 μl water, 5 μl TaqMan Multiplex Master Mix, and 0.5 μl of each 20X primer/probe master mix, which contained 18 μM of each <em>P. marinus</em> primer and 5 μM of TaqMan<sup>TM</sup> QSY probe (De Faveri<em> et al.</em> 2009) for Dermo, and 18 μM of each <em>H. nelsoni</em> primer and 5 μM of TaqMan<sup>TM</sup> MGB probe (Wilbur et al. 2012) for MSX. qPCR cycling conditions included initial denaturation at 95°C for 30 sec, followed by 40 cycles of 95°C for 10 sec and 60°C for 30 sec. We used gBlocks® (gene fragments containing the target regions from <em>P. marinus</em> and<em> H. nelsoni</em>; Integrated DNA Technologies) to develop standard curves, and extracted DNA from cultures of <em>P. marinus</em> and <em>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 &gt;1 Cq, they were rerun to confirm presence/absence and/or parasite concentration.</p>
<p>We used a modified version of the Stokes &amp; Burreson (2001) SSO protocol to assess <em>H. costale</em> prevalence on a Bio-Rad CT100 thermal cycler. PCR cycling conditions included initial denaturation at 94°C for 2 min, followed by 35 cycles of 94°C for 30 sec, 59°C for 30 sec, and 72°C for 60 sec, and final extension at 72°C 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 &amp; Hanley (2013). For the SSO assay, we used gBlocks® containing the target region from <em>H. costale</em> as positive controls and as standards for estimating parasite concentration based on quantification of band intensity using ImageJ (Abràmoff et al. 2004).</p>
<p>To assess the prevalence and intensity of two common macroparasites, boring sponge (<em>Cliona</em> spp.) and mud blister worm (<em>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 (Abràmoff et al. 2004), following the methods of Hanley et al. (2019).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing</strong><br />
For 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>
<p><strong>BCO-DMO Processing</strong><br />
- replaced "NA" with "nd" (no data value);<br />
- renamed fields to comply with BCO-DMO naming conventions.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
iPhone
iPhone
PI Supplied Instrument Name: iPhone PI Supplied Instrument Description:An iPhone (various models) on a tripod was used to photograph oysters for image analysis. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Bio-Rad CFX96
Bio-Rad CFX96
PI Supplied Instrument Name: Bio-Rad CFX96 PI Supplied Instrument Description:Bio-Rad CFX96TM Real-Time System – used for qPCR analysis of oyster microparasites Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
Bio-Rad CT100 thermal cycler
Bio-Rad CT100 thermal cycler
PI Supplied Instrument Name: Bio-Rad CT100 thermal cycler PI Supplied Instrument Description:Bio-Rad CT100 thermal cycler – used for PCR analysis of oyster microparasites Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)