http://lod.bco-dmo.org/id/dataset/887465 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 2023-01-19 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Gnathiid blood meal identification results 2025-04-11 publication 2025-04-11 revision BCO-DMO Linked Data URI 2025-04-11 creation http://lod.bco-dmo.org/id/dataset/887465 Paul C. Sikkel University of Miami Rosenstiel School of Marine and Atmospheric Science principalInvestigator Maureen Dolan Arkansas State 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: Hendrick, G. C., Nicholson, M., Pagan, J. Andres, Artim, J., Dolan, M., Sikkel, P. C. (2025) Gnathiid blood meal identification results. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/887465 [access date] Methods and Sampling: &lt;p&gt;Fieldwork was conducted between May and August of 2015 and 2016. The coordinates for each site are as follows: 17°57’17.59” N, 67°3’9.96” W (Site 1: Cayo Enrique, La Parguera, PR), 17°56’33.60” N, 67°4’41.02” W (Site 2: San Cristobal, La Parguera, PR, 18°19’3.54” N, 65°19’5.06” W (Site 3: Tamarindo Bay, Culebra, PR), 18°20’25.08” N, 64°58’39.77” W (Site 4: Brewer’s Bay, St. Thomas, USVI), and 18°19’2.17” N, 64°43’21.09” W (Site 5: Great Lameshur Bay, St. John, USVI).&lt;/p&gt; &lt;p&gt;Sites off the coast of La Parguera, PR were accessed using powerboats (approximately 14 – 16 feet) at the Isla Magueyes Marine Laboratories of the University of Puerto Rico at Mayagüez. Our site in Tamarindo Bay, Culebra, PR was accessed from shore and did not require boat use. Sites in St. Thomas and St. John, USVI were accessed from shore and using small powerboats supplied by the University of the Virgin Islands, as necessary.&amp;nbsp;&lt;/p&gt; &lt;p&gt;Gnathiids were collected using lighted plankton traps following the protocol of Artim and Sikkel, 2016. Briefly, light traps were deployed on shallow reefs overnight and sorted to remove visibly fed juvenile gnathiids (pranizae). Specimens were preserved in 100 percent molecular grade ethanol and stored at less than -20 degrees C until being shipped to the Arkansas Biosciences Institute (Arkansas State University, Jonesboro, AR) where they were kept at -80 degrees C.&lt;/p&gt; &lt;p&gt;DNA was extracted from individually fed gnathiids using the PureLink® Genomic DNA extraction kit (Invitrogen, Carlsbad, CA), following the manufacturer’s ‘Mammalian Tissue and Mouse/Rat Tail Lysate’ protocol. Purified DNA was concentrated from 50 microliters (µL) to 15 µL using the ThermoSavant ISS110 SpeedVac® System (Thermo Fisher Scientific, Wilmington, DE).&lt;/p&gt; &lt;p&gt;PCR reactions were carried out following the protocol of Hendrick et al., 2019. Primers of the mitochondrial gene cytochrome c oxidase subunit 1 (cox1, COI, or MT-CO1) (5’-TCAACYAATCAYAAAGATATYGGCAC-3’; 5’-ACTTCYGGGTGRCCRAARAATCA-3’). PCR reactions included 10 µL of concentrated template DNA and 10 µL of master mix solution containing forward and reverse COI primers, 1.25 units GoTaq Hot Start Polymerase, 1x buffer with 1.5 mM MgCl&lt;sub&gt;2&lt;/sub&gt; (Promega, Madison, WI), and 0.2 mM dNTP Mix (Thermo Fisher Scientific, Wilmington, DE). A Veriti 96 Well Thermal Cycler (Applied Biosystem, Foster City, CA) was used to carry out PCR reactions with the following thermocycling conditions: initial denaturation step of 94 degrees C for 2 minutes, 30 cycles of 96 degrees C for 20 seconds, 55 degrees C for 20 seconds, and 72 degrees C for 45 seconds, and a final extension step of 72 degrees C for 7 minutes.&lt;/p&gt; &lt;p&gt;ExoSAP-IT (Applied Biosystem, Foster City, CA) was used for enzymatic digestion of excess PCR reagents prior to Sanger sequencing. All samples were sent to the University of Chicago Comprehensive Cancer Center, DNA Sequencing &amp;amp; Genotyping Facility for sequencing. For samples that did not result in successful host identification after one PCR reaction, a second PCR was performed using 10 µL of PCR product from the initial PCR reaction as template DNA.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Known Issues:&lt;/strong&gt;&lt;br /&gt; The DNA sequences within this dataset originated from partially digested blood meals of gnathiid isopods and should not be used as a reference for the comparison of sequence mutations.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536794 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536794 onGoing Paul C. Sikkel University of Miami Rosenstiel School of Marine and Atmospheric Science 270-293-5489 4600 Rickenbacker Causeway Miami FL 33149-1031 USA pcs75@miami.edu pointOfContact Maureen Dolan Arkansas State University (540) 230-5577 PO Box 599 State University AR 72467 mdolan@astate.edu pointOfContact asNeeded Dataset Version: 1 Unknown Site_Number Site_Location Latitude Longitude Site_Name Sample_ID Family Host_ID Ident_Percent BLAST_sequence None ThermoSavant ISS110 SpeedVac® System Lighted plankton trap Veriti 96 Well Thermal Cycler theme None, User defined site site description latitude longitude sample identification family species scientific name (binomial) No BCO-DMO term sequence featureType BCO-DMO Standard Parameters Automated DNA Sequencer Concentrator Device Plankton Net 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. Beyond Cleaning and Symbiosis: Ecology of &#039;Ticks of the Sea&#039; on Coral Reefs https://osprey.bco-dmo.org/project/562115 Beyond Cleaning and Symbiosis: Ecology of &#039;Ticks of the Sea&#039; on Coral Reefs <p><em>NSF Award Abstract:</em><br /> Most research on the complex biological interactions that inhabit coral reefs has focused on larger organisms that are easily observed by divers. However, marine scientists are increasingly aware of the importance of the tiny organisms that make up the "smaller majority." This includes parasites, organisms that feed on other organisms without killing them, which may make up as many as 80% of the species on coral reefs. Among the most important parasitic organisms on coral reefs are gnathiid isopods, so-called 'ticks of the sea', that share many similarities with blood-feeding ticks and other arthropods on land. Like ticks and mosquitoes, gnathiids transmit malaria-like blood parasites. In high numbers, they can remove enough blood to kill adult fish, but even a single gnathiid can kill a juvenile fish. Thus, gnathiids may have a significant effect on coral reef communities through their effects on coral reef fishes. This project will use an integrative interdisciplinary approach involving field and laboratory observations and experiments, and molecular tools. In addition to contributing to our understanding of life in our oceans, this research will provide continued support for U.S. Doctoral and Masters students and will create valuable research opportunities for undergraduates from multiple institutions. The project will further build on the investigators existing relationships with resource managers, local divers, fishers, and boat operators, as well as K-12 schools and environmental education programs, and will contribute to local economies. A major goal of our outreach efforts will include an exhibit featuring our research at Coral World Ocean Park on St. Thomas, participation in Virgin Islands radio programs, and hosting high school students from South Carolina Governor's School.</p> <p>The overall goal this investigation is to understand the ecology of fish-parasite interactions on coral reef and associated ecosystems. This project focuses on fish-parasitic gnathiid isopods, the most common ectoparasites of coral reef fishes that are best known for their role in cleaning symbiosis, as the major food item of cleaner fishes. However, their abundance, host range, role as micropredator, disease vector, and potential prey item for other species, as well as their strong association with the benthos suggests the potential for much stronger community impacts. The goals for this project are to: 1) characterize the factors influencing local gnathiid isopod density by examining the role of fish-hosts, benthic cover, gnathiid predators including cleaners, and gnathiid conspecific attraction; 2) determine and quantify variation in host exploitation and the effects of gnathiid density on larval fish-host recruitment. To accomplish the first objective, the investigators will trap gnathiids from the substrate at sites in the Caribbean, Australia, and the Philippines. Variables associated with benthic habitat as well as local fish communities will be quantified and compared with local gnathiid abundance. Laboratory experiments will be conducted to determine the effects of different host species on gnathiid growth and reproduction and to determine the role of conspecific attraction in the formation of aggregations. Predators of gnathiids will be identified through examination of gut contents and through laboratory feeding studies. To accomplish the second objective, patterns of host-exploitation will be determined by DNA barcoding of blood meals from wild-caught gnathiids and results compared with the availability of different host species. To determine the effects of gnathiids on early life history stages of coral reef fishes, gnathiid abundance will be manipulated on small artificial patch reefs onto which newly-settled reef fishes will be transplanted.</p> Gnathiid isopod ecology largerWorkCitation project eng; USA biota oceans -67.078 -64.723 17.943 18.34 2015-04-01 2016-09-30 Eastern Caribbean, Philippines, Australia 0 BCO-DMO catalogue of parameters from Gnathiid blood meal identification results 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/887711.rdf Name: Site_Number Units: unitless Description: <p>The number given to the site as listed in our results publication currently in review</p> http://lod.bco-dmo.org/id/dataset-parameter/887712.rdf Name: Site_Location Units: unitless Description: <p>Regional location of the site</p> http://lod.bco-dmo.org/id/dataset-parameter/887713.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude of sampling site</p> http://lod.bco-dmo.org/id/dataset-parameter/887714.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude of sampling site (West is negative)</p> http://lod.bco-dmo.org/id/dataset-parameter/887715.rdf Name: Site_Name Units: unitless Description: <p>Name of reef or bay where site is located</p> http://lod.bco-dmo.org/id/dataset-parameter/887716.rdf Name: Sample_ID Units: unitless Description: <p>Unique sample identifier based on site name (L = Site 1, ESG = Site 1 Seagrass, B = Site 2, CSG = Site 2 Seagrass, C = Site 3, TSG = Site 3 Seagrass, T = Site 4, R = Site 4 Seagrass,  J = Site 5) and number of the specimen processed at each site</p> http://lod.bco-dmo.org/id/dataset-parameter/887717.rdf Name: Family Units: unitless Description: <p>Family of the closest matching reference sequence in BLAST results</p> http://lod.bco-dmo.org/id/dataset-parameter/887718.rdf Name: Host_ID Units: unitless Description: <p>Scientific name of the closest matching reference sequence in BLAST results</p> http://lod.bco-dmo.org/id/dataset-parameter/887719.rdf Name: Ident_Percent Units: percent (%) Description: <p>The percent identity according to the results of BLAST queries for each sequence</p> http://lod.bco-dmo.org/id/dataset-parameter/887720.rdf Name: BLAST_sequence Units: unitless Description: <p>The mtDNA sequence entered into BLAST</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 1054797 Host ID sequencing results Sequencing results for individual gnathiid blood meals that could not be identified using BLAST; one sequence where the host family could not be identified with confidence; sequences from individual gnathiid blood meals with homologies to other gnathiid species; BLAST query results matching to bacteria; and results from poor quality sequencing reads (less than 80%) download https://osprey.bco-dmo.org/dataset/887465/data/download download onLine dataset &lt;p&gt;Fieldwork was conducted between May and August of 2015 and 2016. The coordinates for each site are as follows: 17°57’17.59” N, 67°3’9.96” W (Site 1: Cayo Enrique, La Parguera, PR), 17°56’33.60” N, 67°4’41.02” W (Site 2: San Cristobal, La Parguera, PR, 18°19’3.54” N, 65°19’5.06” W (Site 3: Tamarindo Bay, Culebra, PR), 18°20’25.08” N, 64°58’39.77” W (Site 4: Brewer’s Bay, St. Thomas, USVI), and 18°19’2.17” N, 64°43’21.09” W (Site 5: Great Lameshur Bay, St. John, USVI).&lt;/p&gt; &lt;p&gt;Sites off the coast of La Parguera, PR were accessed using powerboats (approximately 14 – 16 feet) at the Isla Magueyes Marine Laboratories of the University of Puerto Rico at Mayagüez. Our site in Tamarindo Bay, Culebra, PR was accessed from shore and did not require boat use. Sites in St. Thomas and St. John, USVI were accessed from shore and using small powerboats supplied by the University of the Virgin Islands, as necessary.&amp;nbsp;&lt;/p&gt; &lt;p&gt;Gnathiids were collected using lighted plankton traps following the protocol of Artim and Sikkel, 2016. Briefly, light traps were deployed on shallow reefs overnight and sorted to remove visibly fed juvenile gnathiids (pranizae). Specimens were preserved in 100 percent molecular grade ethanol and stored at less than -20 degrees C until being shipped to the Arkansas Biosciences Institute (Arkansas State University, Jonesboro, AR) where they were kept at -80 degrees C.&lt;/p&gt; &lt;p&gt;DNA was extracted from individually fed gnathiids using the PureLink® Genomic DNA extraction kit (Invitrogen, Carlsbad, CA), following the manufacturer’s ‘Mammalian Tissue and Mouse/Rat Tail Lysate’ protocol. Purified DNA was concentrated from 50 microliters (µL) to 15 µL using the ThermoSavant ISS110 SpeedVac® System (Thermo Fisher Scientific, Wilmington, DE).&lt;/p&gt; &lt;p&gt;PCR reactions were carried out following the protocol of Hendrick et al., 2019. Primers of the mitochondrial gene cytochrome c oxidase subunit 1 (cox1, COI, or MT-CO1) (5’-TCAACYAATCAYAAAGATATYGGCAC-3’; 5’-ACTTCYGGGTGRCCRAARAATCA-3’). PCR reactions included 10 µL of concentrated template DNA and 10 µL of master mix solution containing forward and reverse COI primers, 1.25 units GoTaq Hot Start Polymerase, 1x buffer with 1.5 mM MgCl&lt;sub&gt;2&lt;/sub&gt; (Promega, Madison, WI), and 0.2 mM dNTP Mix (Thermo Fisher Scientific, Wilmington, DE). A Veriti 96 Well Thermal Cycler (Applied Biosystem, Foster City, CA) was used to carry out PCR reactions with the following thermocycling conditions: initial denaturation step of 94 degrees C for 2 minutes, 30 cycles of 96 degrees C for 20 seconds, 55 degrees C for 20 seconds, and 72 degrees C for 45 seconds, and a final extension step of 72 degrees C for 7 minutes.&lt;/p&gt; &lt;p&gt;ExoSAP-IT (Applied Biosystem, Foster City, CA) was used for enzymatic digestion of excess PCR reagents prior to Sanger sequencing. All samples were sent to the University of Chicago Comprehensive Cancer Center, DNA Sequencing &amp;amp; Genotyping Facility for sequencing. For samples that did not result in successful host identification after one PCR reaction, a second PCR was performed using 10 µL of PCR product from the initial PCR reaction as template DNA.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Known Issues:&lt;/strong&gt;&lt;br /&gt; The DNA sequences within this dataset originated from partially digested blood meals of gnathiid isopods and should not be used as a reference for the comparison of sequence mutations.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;The DNA sequences within this dataset had the primer sequences removed and ends trimmed using Geneious R10 (Biomatters Limited, Auckland, New Zealand). DNA sequences were identified using the Basic Local Alignment Search Tool (BLAST) on the National Center for Biotechnology Information (NCBI) website. Sequence similarity of greater than or equal to 98 percent was considered species-level identification. For sequence similarity of less than 98 percent, host families were identified using neighbor-joining trees of the BLAST results as outlined by Jones et al., 2007.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) - Import &quot; - Adjusted field/parameter names to comply with BCO-DMO naming conventions - Added a conventional header with dataset name, PI names, version date - Added columns for “Latitude” and “Longitude” - Rounded columns: “Latitude” and “Longitude” to 3 decimal places (or to the thousandth place) Specified by BCO-DMO Data Managers 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 None None PI Supplied Instrument Name: None PI Supplied Instrument Description:All samples were sent to the University of Chicago Comprehensive Cancer Center, DNA Sequencing & Genotyping Facility for sequencing. For samples that did not result in successful host identification after one PCR reaction, a second PCR was performed using 10 µL of PCR product from the initial PCR reaction as template DNA. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. ThermoSavant ISS110 SpeedVac® System ThermoSavant ISS110 SpeedVac® System PI Supplied Instrument Name: ThermoSavant ISS110 SpeedVac® System Instrument Name: Concentrator Device Instrument Short Name: Instrument Description: A concentrator is a device designed to increase the weight per unit volume of a substance. This category includes vacuum centrifuge concentrator, which include a vacuum chamber within which a centrifuge rotor is mounted for spinning a plurality of vials containing a solution at high speed while subjecting the solution to a vacuum condition for concentration and evaporation. Alternative names: sample concentrator; speed vacuum; speed vac. Lighted plankton trap Lighted plankton trap PI Supplied Instrument Name: Lighted plankton trap Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/ Veriti 96 Well Thermal Cycler Veriti 96 Well Thermal Cycler PI Supplied Instrument Name: Veriti 96 Well Thermal Cycler PI Supplied Instrument Description:A Veriti 96 Well Thermal Cycler (Applied Biosystem, Foster City, CA) was used to carry out PCR reactions with the following thermocycling conditions: initial denaturation step of 94 °C for 2 min, 30 cycles of 96 °C for 20 s, 55 °C for 20 s, and 72 °C for 45 s, and a final extension step of 72 °C for 7 min. 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)