http://lod.bco-dmo.org/id/dataset/874478 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 2022-05-17 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) GenBank accession links of the invertebrates collected from Autonomous Reef Monitoring Structures (ARMS) from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea in 2014 2022-05-21 publication 2022-05-21 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-06-08 publication https://doi.org/10.26008/1912/bco-dmo.874478.1 Nancy Knowlton Smithsonian Institution principalInvestigator Laetitia Plaisance Smithsonian Institution 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: Knowlton, N., Plaisance, L. (2022) GenBank accession links of the invertebrates collected from Autonomous Reef Monitoring Structures (ARMS) from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea in 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-05-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.874478.1 [access date] Methods and Sampling: &lt;p&gt;&lt;strong&gt;Sampling Devices&lt;/strong&gt;&lt;br /&gt; This study was conducted in Milne Bay Province, Papua New Guinea at two shallow-water fringing reef localities near Dobu and Upa Upasina (9° 49.45’ S, 150° 49.06’ E) at a depth of 3 meters where almost pure CO2 gas seeps through the seafloor and into the water, changing the water carbonate chemistry and creating sharp gradients in seawater carbonate chemistry parameters within a short distance. Autonomous Reef Monitoring Structures (ARMS) were deployed along the fringing coral reefs at a depth of 4-5 meters at three pH conditions and recovered after approximately 2 years of deployment and all motile organisms greater than 2 millimeters were removed from the structures, photographed, subsampled for genetic analysis, and preserved in 95% ethanol.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Genetic Barcoding&lt;/strong&gt;&lt;br /&gt; DNA was extracted from tissue subsamples using a standard proteinase-k digestion followed by phenol-chloroform extraction on an AutoGenprep 965. The standard Cytochrome Oxidase Subunit I (COI) barcoding fragment (658 bp) was amplified using the jgLCO1490/jgHCO2198 primer pair. Automated sequencing was performed in both directions directly on purified PCR products using Applied Biosystems BigDye terminator V3.1 Sequence reactions were purified using Millipore 96-well plates loaded with Sephadex G-50 and run on an ABI 3130xl genetic analyzer.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558868 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558868 completed Nancy Knowlton Smithsonian Institution 2026330668 PO Box 37012, MRC-163 Washington DC 200137012 US knowlton@si.edu pointOfContact Laetitia Plaisance Smithsonian Institution 202-633-0684 plaisancel@si.edu pointOfContact asNeeded Dataset Version: 1 Unknown Organism Sampling_locality Collection_date Specimen_voucher Accession ABI 3130xl AutoGenprep 965 theme None, User defined taxon site date sample identification accession number featureType BCO-DMO Standard Parameters Automated DNA Sequencer DNA Extractor 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. Investigating Structural Changes In Reef-Associated Biodiversity Along A Natural Gradient In Ocean Acidification https://osprey.bco-dmo.org/project/684407 Investigating Structural Changes In Reef-Associated Biodiversity Along A Natural Gradient In Ocean Acidification <p><em>NSF award abstract:</em></p> <p>Recent research has revealed that ocean acidification, caused by carbon dioxide dissolving into the ocean, has a broad range of negative consequences for marine organisms, especially organisms that build calcium shells or skeletons such as corals. However, most studies have focused on a limited number of species in laboratory settings and have therefore ignored the many indirect effects originating from more complex species interactions that occur in nature. Coral reefs harbor more species than any other marine ecosystem. Moreover, they are economically very important, providing food and other services such as touristic attractions and pharmaceuticals. Because of the sensitivities of coral species to ocean acidification, reef ecosystems are potentially severely threatened, but we still have no idea how entire reef communities will respond. The project will take advantage of a recently discovered, naturally acidified coral reef system in Papua New Guinea that is bathed by waters of variable levels of acidity, including levels comparable to those expected globally by the end of the 21st century. This project investigates the consequences of ocean acidification for the biodiversity of animals that live cryptically within the interstices of coral reefs. These animals represent the bulk of coral reef diversity; they play very important roles in the reef food chain but are poorly understood. Using DNA markers and photo analysis, cryptic species living at three different acidity levels (present day, expected in 50 years, expected in 100 years) will be quantified and identified in order to elucidate the changes occurring in coral reef communities as oceans acidify. Results will broaden understanding of the consequences of ocean acidification and allow for more accurate monitoring and effective management strategies for coral reefs. Scientific results will be shared at international conferences and published in peer-reviewed journals, and data collected will be made publicly available. The project will also foster active collaborations among scientists, professional educators, and science communicators from the Smithsonian Institution and Washington DC high school students underrepresented in Science, Technology, Engineering and Math (STEM) fields. The students will be trained in ocean acidification science and will be involved in developing outreach products for Smithsonian onsite and online audiences, expanding the ability of the Smithsonian to share these results with the general public.</p> <p>Ocean acidification (OA) is now affecting the fragile coral reef ecosystems already impacted by decades of local pressures (e.g., pollution, overfishing). Numerous laboratory experiments have shown deleterious effects of low pH on calcification, growth, and reproduction of reef organisms. Studies have also highlighted differences in species' responses depending on whether they are tested alone or in multi-species assemblages, suggesting the importance of indirect effects in sensitivity to OA that cannot be assessed from laboratory experiments. For this reason, shallow tropical submarine carbon dioxide seeps provide invaluable opportunities to assess the ecological consequences of long-term exposure to low pH for coral reefs in situ by providing a natural gradient in pH across reef seascapes. Among these are the reefs at Milne Bay Province, Papua New Guinea, which exhibit a strong gradient from normal to low pH waters but otherwise resemble normal reef conditions in terms of other chemical properties and temperature. Most work to date on acidified reefs, including at Milne Bay, has focused on corals and other conspicuous organisms. However, the vast majority of reef diversity is comprised of the understudied cryptic communities living within the reef structure. These trophically crucial groups are likely to be at risk from OA due to reduction in three-dimensional complexity typical of acidified reefs, but there are scant data. This research will measure structural changes in these communities across the well-characterized pH gradients of the Milne Bay reefs. The investigators will study diversity patterns in volumetrically standardized sampling structures deployed at three pH regimes (regular ~8.0, medium ~7.8-7.9 and low ~7.6-7.8) spanning the pH range predicted over the next one hundred years. Using photo analysis, and DNA barcoding of the bigger motile and sessile taxa and metabarcoding of the bulk sessile and small motile fractions , the investigators will evaluate spatial coverage, diversity and abundance of the species present across the pH gradient. The study will test the hypothesis that invertebrate diversity will decrease with decreasing pH and that taxonomic composition will shift to a community more resistant to acidified waters (e.g. non-calcifiers). Thus, the project's overall goal is to assess the likely impacts of future ocean acidification on the highly diverse cryptic fauna associated with coral reef ecosystems. This research has implications for both our understanding of the ecology of coral reefs and management strategies in the light of global changes.</p> OA_Gradient_Biodiversity largerWorkCitation project eng; USA biota oceans 150.817667 150.817667 -9.824167 -9.824167 2014-04-01 2014-11-30 Papua New Guinea, Esa’ Ala province 0 BCO-DMO catalogue of parameters from GenBank accession links of the invertebrates collected from Autonomous Reef Monitoring Structures (ARMS) from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea in 2014 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/874525.rdf Name: Organism Units: unitless Description: <p>Taxonomic identification to the lowest rank available</p> http://lod.bco-dmo.org/id/dataset-parameter/874526.rdf Name: Sampling_locality Units: unitless Description: <p>Specific locality where the organism was sampled</p> http://lod.bco-dmo.org/id/dataset-parameter/874529.rdf Name: Collection_date Units: date Description: <p>Sampling date in format YYYY-MM</p> http://lod.bco-dmo.org/id/dataset-parameter/874530.rdf Name: Specimen_voucher Units: unitless Description: <p>Voucher number in the collections of the National Museum of Natural History</p> http://lod.bco-dmo.org/id/dataset-parameter/874531.rdf Name: Accession Units: unitless Description: <p>COI NCBI GenBank accession number</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 134315 https://darchive.mblwhoilibrary.org/bitstream/1912/28976/1/dataset-874478_invertebrate-barcodes-papua-new-guinea__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.874478.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Sampling Devices&lt;/strong&gt;&lt;br /&gt; This study was conducted in Milne Bay Province, Papua New Guinea at two shallow-water fringing reef localities near Dobu and Upa Upasina (9° 49.45’ S, 150° 49.06’ E) at a depth of 3 meters where almost pure CO2 gas seeps through the seafloor and into the water, changing the water carbonate chemistry and creating sharp gradients in seawater carbonate chemistry parameters within a short distance. Autonomous Reef Monitoring Structures (ARMS) were deployed along the fringing coral reefs at a depth of 4-5 meters at three pH conditions and recovered after approximately 2 years of deployment and all motile organisms greater than 2 millimeters were removed from the structures, photographed, subsampled for genetic analysis, and preserved in 95% ethanol.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Genetic Barcoding&lt;/strong&gt;&lt;br /&gt; DNA was extracted from tissue subsamples using a standard proteinase-k digestion followed by phenol-chloroform extraction on an AutoGenprep 965. The standard Cytochrome Oxidase Subunit I (COI) barcoding fragment (658 bp) was amplified using the jgLCO1490/jgHCO2198 primer pair. Automated sequencing was performed in both directions directly on purified PCR products using Applied Biosystems BigDye terminator V3.1 Sequence reactions were purified using Millipore 96-well plates loaded with Sephadex G-50 and run on an ABI 3130xl genetic analyzer.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;BCO-DMO processing description:&lt;/strong&gt;&lt;br /&gt; - Adjusted field/parameter names to comply with BCO-DMO naming conventions&lt;br /&gt; - Added a conventional header with dataset name, PI names, version date&lt;br /&gt; - Converted dates to YYYY-MM&lt;/p&gt; 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 ABI 3130xl ABI 3130xl PI Supplied Instrument Name: ABI 3130xl PI Supplied Instrument Description:ABI 3130xl: Laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. 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. AutoGenprep 965 AutoGenprep 965 PI Supplied Instrument Name: AutoGenprep 965 PI Supplied Instrument Description:The AutoGenprep 965 is a high-throughput, automated platform that performs DNA extraction. Instrument Name: DNA Extractor Instrument Short Name: Instrument Description: A device that is used to isolate and collect DNA for subsequent molecular analysis.