cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.982204.1
title: Water quality parameters from discrete shoreline and transect sampling in West Maui (Lahaina area), Hawaiʻi, following the Lahaina Wildfires, Aug 2023 to Oct 2024

description: These data include values for various coastal water parameters: carbon chemistry (total alkalinity, dissolved inorganic carbon, and dissolved organic carbon), trace metals, metabolomic composition, nutrient concentrations (NOx, NO2, PO4, SiO2, and NH3), Fluorescence Dissolved Organic Matter, and flow cytometry. Water samples were all collected in West Maui in and around reef systems that were within and adjacent to the burn zone of the Lahaina fires. These samples were collected by boat transect, shoreline grab sampling, and autonomous sampling devices. Some autonomous sampling data from before the fire event are also included. The aim of these data is to understand the effects on coral reef health in response to the urban fires that occurred in August of 2023. Samples were collected by a collaborative effort of scientists Dr. Andrea K Kealoha, Dr. Craig Nelson, Dr. Eileen Nalley, and Dr. Nicholas Hawco.
DOI: 10.26008/1912/bco-dmo.985985.1
title: Discrete Net Community and Gross Primary Production Rates data on the US Northeastern Shelf in the SPIROPA project during spring and summer 2018 and 2019

description: Triple oxygen isotopes and O2/Ar ratios were were measured on discrete bottle samples which were collected from surface Niskins from the CTD. The samples were collected at sea into poisoned, pre-evacuated bottles and then measured on an isotope ratio mass spectrometer. The gas data was then used to calculate mixed layer depth integrated rates of gross primary production (in oxygen units = gross oxygen production) and net community production. The gas data itself is posted on BCO-DMO in the bottle CTD tables associated with this cruise. This data set contains the rates of production calculated from the gas data for those who simply want the rates rather than the gas data.  This data set has rates calculated from samples collected from cruises on the US Northeastern Shelf taking place in Spring 2018 (Ar29), spring 2019 (RB1904) and summer 2019 (TN368). There is no depth associated with each rate since the exact depth the water came from does not matter - the rate represents the production integrated over the mixed layer in all cases and the depth of collection is not the same as the mixed layer depth. CTD data posted on BCO-DMO can be used to determine depths if desired and/or mixed layer depths.
DOI: 10.15468/dl.hxfrfp
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lilium bakerianum delavayi"
 ]
}

 The dataset includes 75 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021508-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26008/1912/bco-dmo.942699.1
title: Continuous rates of net community production and the O2/Ar data on the US Northeastern Shelf in the SPIROPA project during spring and summer 2018 and 2019.

description: An at-sea equilibrator inlet mass spectrometer was used onboard  three cruises in 2018 and 2019 in the Northeastern US Shelf as part of the SPIROPA project in order to measure ratios of O2/Ar in the underway water. The gas ratios were used to calculate rates of net community production at kilometer scale resolution. This dataset thus contains the gas ratios as well as the calculated rates. The data was collected on the R/V Armstrong from 4/16/18 to 4/29/18, on the NOAA ship Ron Brown from 5/12/2019 to 5/25/2019 and on the R/V Thompson from 7/5/2019 to 7/17/2019.  This high spatial resolution data enables us to see submesoscale variability in rates of net community production and to assess whether changes in rates of NCP are co-located with physical processes. This dataset also contains necessary metadata such as location and time as well as useful data from shipboard CTD sensors such as temperature and salinity. Gas transfer rates are required to calculate rates of NCP from gas tracer data. The data includes the gas transfer rates that were used in the calculations, which were determined from NCEP reanalysis winds, a 60 day weighting scheme, and the gas exchange parameterization of Stanley et al., 2009. NCP was calculated based on mass balance with typical assumptions of steady state and negligible vertical and horizontal mixing.  Details on how NCP rates were calculated from the O2/Ar data are available in Stanley et al. (in press at L&O) and Castillo Cieza et al (2024).
DOI: 10.26008/1912/bco-dmo.985574.1
title: GenBank accessions for 18S rRNA gene amplicons from swab specimens collected in the Caribbean and Réunion (France) from May 2022 to Dec 2024

description: Investigating the cause of mass mortality of Diadema antillarum (urn:lsid:marinespecies.org:taxname:124332) identified the etiological agent as the Diadema antillarum Scuticociliatosis Philaster Clade (DaScPc). We sought to investigate the prevalence of this ciliate in sympatric reservoirs in the coral reef environment by targeted PCR using primers designed around this 18S rRNA sequence. We used swab sampling of corals, macroalgae, and other surfaces, followed by phylogenetic analyses, to identify the presence and diversity of this ciliate. We found that DaScPc could be found primarily in association with the coral Siderastrea siderea, and that changes in its prevalence could be explained by disease state of urchins, macroalgal density, and proximity to disease sites. This dataset contains the GenBank accession, sequencing, and collection metadata for the study.
DOI: 10.26008/1912/bco-dmo.985619.1
title: Transcriptome and viral metagenome data from Diadema antillarum collected at St. Thomas (USVI) and Saba (Caribbean Netherlands) in Apr 2022

description: A mass mortality of the tropical echinoderm Diadema antillarum (urn:lsid:marinespecies.org:taxname:124332) occurred beginning in January 2022 and continuing to at least July 2022. We sought to identify flaviviruses associated with this condition by performing viral metagenomics and tissue transcriptomics. We prepared these libraries from grossly normal, abnormal and reference specimens collected from St Thomas, U.S. Virgin Islands (USVI), and Saba, Caribbean Netherlands. This dataset includes the accession information for the sequences performed and archived at the National Center for Biotechnology Information (NCBI) Sequence Read Archive. While we were unsuccessful in recovering flaviviruses from tissues of these organisms, we were able to detect additional pathogenic agents (Philaster apodigitiformis; Ciliophora) from transcriptomes.
DOI: 10.26008/1912/bco-dmo.985655.1
title: Viral metagenomic investigation of the Caribbean echinoderm Holothuria floridana collected in Marathon, Florida on 25 Aug 2023

description: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality. We performed viral surveillance of the coral reef echinoderm Holothuria floridana (urn:lsid:marinespecies.org:taxname:210900), using metagenomics. Grossly normal H. floridana specimens were collected from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2. H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). This dataset includes the accession information for the sequences performed and archived at the National Center for Biotechnology Information (NCBI) Sequence Read Archive.
DOI: 10.26008/1912/bco-dmo.964199.1
title: Benthic sampling survey data from Harrington Sound and Flatts Inlet, Bermuda in October of 2022

description: To acquire a current understanding of the potential benthic prey community to durophagous predators we sampled the abundance and distribution of the benthos of Harrington Sound and Flatts Inlet, Bermuda. This was done using hand-based excavation surveys, which were conducted by divers on SCUBA at historic and new sampling locations in the region. Data were collected by the project team in October 2022.
DOI: 10.26008/1912/bco-dmo.984803.1
title: Dynamics of the Apostichopus californicus-associated flavivirus under suboxic conditions and organic matter amendment in mesocosm experiment

description: Flaviviruses cause some of the most detrimental vertebrate diseases, yet little is known of their impacts on invertebrates. Microbial activities at the animal-water interface are hypothesized to influence viral replication and possibly contribute to pathology of echinoderm wasting diseases due to hypoxic stress. We assessed the impacts of enhanced microbial production and suboxic stress on Apostichopus californicus (urn:lsid:marinespecies.org:taxname:529363) associated flavivirus (PcaFV) load in a mesocosm experiment. Organic matter amendment and suboxic stress resulted in lower PcaFV load, which also correlated negatively with animal mass loss and microbial activity at the animal-water interface. These data suggest that PcaFV replication and persistence was best supported in healthier specimens. Our results do not support the hypothesis that suboxic stress or microbial activity promote PcaFV replication, but rather that PcaFV appears to be a neutral or beneficial symbiont of Apostichopus californicus. This primary dataset contains per-specimen measurements including experimental treatments, microbial productivity (animal surface and mesocosm water), body wall lipid/protein content, animal mass loss, tissue-specific PcaFV viral loads at initial and final timepoints, and collection metadata. The supplemental file provides time-series measurements of dissolved oxygen and temperature in mesocosms, indexed by tank number, treatment, and timestamp.
DOI: 10.26008/1912/bco-dmo.984835.1
title: 16S rRNA V4 sequence metadata from surface swabs from Apostichopus californicus-associated flavivirus experiment under suboxic conditions and organic matter amendment

description: Microbial activities at the animal-water interface are hypothesized to influence viral replication and possibly contribute to pathology of echinoderm wasting diseases due to hypoxic stress. We assessed the impacts of enhanced microbial production and suboxic stress on Apostichopus californicus (urn:lsid:marinespecies.org:taxname:529363) associated flavivirus (PcaFV) load in a mesocosm experiment. This dataset contains 16S rRNA V4 amplicon sequencing metadata for this experiment. Organic matter amendment and suboxic stress resulted in lower PcaFV load, which also correlated negatively with animal mass loss and microbial activity at the animal-water interface. These data suggest that PcaFV replication and persistence was best supported in healthier specimens. Our results do not support the hypothesis that suboxic stress or microbial activity promote PcaFV replication, but rather that PcaFV appears to be a neutral or beneficial symbiont of Apostichopus californicus.
DOI: 10.26008/1912/bco-dmo.944302.1
title: Advanced Laser Fluorescence Analyzer (ALFA) data from the Indonesian Through Flow Region from the R/V Roger Ravelle (RR2201) from January to March 2022

description: The  Automatic Laser Fluorometric Analyzer (ALFA)  is a state-of-the-art instrument, that combines high-resolution spectral measurements of blue (405 nm) and green (532 nm) laser-stimulated fluorescence, with spectral deconvolution techniques to estimate CDOM, phytoplankton variable fluorescence (Fv/Fm), Chl a and three types of phycobiliprotein pigments. This data was collected using the ALFA in Underway fluorescence mode and sampling in the western Eastern Indian Ocean Upwelling region on the R/V Roger Ravelle in January - March 2022 (BLOOFINZ). In underway mode, the ALF is connected to the ship’s uncontaminated seawater flow-through system allowing for continuous measurements in water drawn from approximately 5m below the surface. All fluorescence values are Raman-normalized, with the exception of Chl a, which was calibrated with acetone extracted samples measured in a Turner Designs® Trilogy Fluorometer. The instrument is set up to make these measurements approx. every minute. See RR2201 cruise report in related publications.
DOI: 10.26008/1912/bco-dmo.984849.1
title: Prevalence of PcaFV in Apostichopus californicus specimens collected in Southeast Alaska from Jun to Nov 2021

description: Understanding the prevalence and load of aquatic invertebrate flaviviruses is essential to estimating risk to fisheries. We surveyed the prevalence of the Apostichopus californicus (urn:lsid:marinespecies.org:taxname:529363) associated flavivirus (PcaFV) using two approaches: Loop-mediated isothermal amplification (LAMP) and quantitative reverse transcriptase PCR. We targeted this survey around populations of A. californicus: specimens collected from Sitka Sound, Sitka, Alaska (Baranof Island), Southeast Alaska, and Nanoose, British Columbia, Canada. We found that LAMP detected PcaFV in 21% of tested specimens, and qRT-PCR in 88% of tested specimens. The mean load of PcaFV in copies per ng RNA extracted was significantly higher in specimens that were positive by LAMP compared to those in which LAMP did not detect PcaFV. This dataset contains PcaFV prevalence determined by RT-LAMP and qRT-PCR, as well as associated collection metadata.
DOI: 10.26008/1912/bco-dmo.893615.1
title: Identity and heights of Octocoral species found on transects at 6 sites on the south shore of St John, U.S. Virgin Islands in 2021 and 2022

description: Transect surveys were conducted at 6 sites on the south shore of St John, within the U.S. Virgin Islands National Park during the summers of 2021 and 2022.  Depending on the site, 3 to 6 transects were established.  Identity and heights of all arborescent octocorals greater than or equal to 5 centimeters were recorded from 1 square meter quadrats on the transects.  The position of colonies relative to the site, meter on the transect, and side of the quadrat are included.   Surveys were conducted by Drs. Howard Lasker and Christopher Wells of the University at Buffalo.
DOI: 10.26008/1912/bco-dmo.893866.1
title: Octocoral Recruitment surveys on transects at 6 sites on the south shore of St. John, U.S. Virgin Islands in 2021 and 2022

description: This dataset represents octocoral recruitment censuses conducted on survey transects at 6 sites Booby Rock (18° 18.176' N; 064° 42.626' W), Grootpan Bay (previously noted as E Cabritte or East Cabritte 18° 18.551 ' N: 0.64° 43.129' W), Europa (18° 19.003' N; 064° 43.796' W), Tektite (18° 18.775' N; 064° 43.796' W), Deep Tektite (18° 18.582’ N, 064° 43.371 W), Yawzi (18° 18.912’ N, 064° 43.500’ W) on the south shore of St. John, U.S. Virgin Islands between 2021 and 2022.
DOI: 10.26008/1912/bco-dmo.984527.1
title: Measurements of C–P lyase phosphate thresholds in Stutzerimonas frequens cultures (North Pacific Methane Project)

description: This dataset contains results from an experiment investigating the phosphate concentration threshold for C-P lyase activity in cultures of Stutzerimonas frequens. The dataset includes measurements of total dissolved phosphorus (TDP), soluble reactive phosphorus (SRP), and dissolved organic phosphorus (DOP) in the culture medium at the end of incubation. Additional parameters include cell concentrations from cultures, methane produced by the cultures during the experiment, and rates of C-P lyase activity (CLA).

TDP, SRP, and DOP were measured using standard colorimetric methods. Cell concentrations were determined by flow cytometry. Methane concentrations and δ¹³C values were measured with a Picarro gas analyzer, and CLA was quantified using a fluorescently labeled phosphonate probe.

These data demonstrate that C-P lyase activity is regulated by dissolved phosphate concentrations and that S. frequens upregulates C-P lyase genes when phosphate concentrations drop below 90 nM. The cultures were grown by Dr. Oscar Sosa, and the samples were analyzed by Dr. Benjamin Granzow.
DOI: 10.15468/dl.sbr4dx
title: Occurrence Download

description: A dataset containing 1168141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Collembola)",
 "OccurrenceStatus is one of (Present)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "Year is greater than or equal to 1970"
 ]
}

 The dataset includes 1168141 records from 868 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021468-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26008/1912/bco-dmo.984885.1
title: Phytoplankton abundance in seawater samples collected from Project &quot;DaVINCi&quot; incubations in the Gulf of Naples, Italy from April to May 2022

description: Phytoplankton abundance was measured on Lugol's-fixed seawater samples collected from nutrient amendment experiments conducted on surface water collected at the Long-Term Ecological Monitoring Station, MareChiara, in the Gulf of Naples, Italy, between April 20 and May 19, 2022. Phytoplankton were counted on an inverted microscope following Utermhöl settling. These incubations were part of a field study on &quot;Diatom Virus Infection of Natural Communities&quot; (DaVINCi) and were aimed at understanding the role of silicon limitation in driving diatom viral infection.
DOI: 10.26008/1912/bco-dmo.985357.1
title: Dissolved inorganic nutrient concentrations in seawater samples collected from Project &quot;DaVINCi&quot; incubations in the Gulf of Naples, Italy from April to May 2022

description: Dissolved inorganic nutrient concentrations were measured in seawater samples collected from nutrient amendment experiments conducted on surface water collected at the Long-Term Ecological Monitoring Station, MareChiara, in the Gulf of Naples, Italy, between April 20 and May 19, 2022.  These incubations were part of a field study on &quot;Diatom Virus Infection of Natural Communities&quot; (DaVINCi) and were aimed at understanding the role of silicon limitation in driving diatom viral infection.
DOI: 10.26008/1912/bco-dmo.985410.1
title: Algal Percent Cover Data collected in the nearshore shallow subtidal during eight field experiments conducted at Cerro Mundo Bay in the Galapagos Islands between Sep 2021 and Apr 2023

description: Increased standing macroalgal biomass in upwelling zones is generally assumed to result from higher nutrient flux associated with upwelled waters. However, other factors can also strongly impact macroalgal communities. For example, herbivory and temperature—through their effects on primary producers and the metabolic demands of consumers—can influence macroalgal biomass and productivity, respectively. Although there are numerous studies examining the interactive effects of herbivores and nutrients in both temperate regions, few have addressed these dynamics in tropical or subtropical upwelling systems. The purpose of this study was to assess the effects of herbivores, temperature, and nutrient availability on standing macroalgal biomass and total algal cover. Macroalgal biomass is presented in the related dataset. We manipulated nutrient availability and herbivory in eight field experiments conducted under contrasting productivity and thermal regimes (cool upwelling vs. warm, non-upwelling seasons) on a subtidal nearshore rocky reef.

Here, we present the algal percent cover data collected from the shallow subtidal zone during September 2021 to April 2023 field experiments.
DOI: 10.26008/1912/bco-dmo.962576.1
title: Saanich Inlet field and laboratory methods related to experimental rate data acquired aboard the R/V John Strickland during two cruises in August, 2021 and June, 2022

description: These data include oceanographic, chemical, and biogeochemical rate measurements relating to oxygen, nitrogen, and sulfur species from Saanich Inlet, British Columbia, Canada, spanning lower oxycline and anoxic depths in the basin. Data and samples were collected aboard the R/V John Strickland during two cruises in August, 2021 and June, 2022. Data from 2021 capture the dynamics of an oxygen renewal event of the deep anoxic basin, which occurred between the second and third sampling days. Data from 2022 were collected during stable, stratified conditions with complete anoxia in the deep basin throughout the sampling period. 

Rate measurements are from 15N-labeled tracer experiments tracking the production and consumption of nitrous oxide (N2O), a potent greenhouse gas that is produced under hypoxic and anoxic conditions. These data evaluate the extent to which consumption of N2O in the deep basin balances out is production in overlying waters and were collected by Dr. Sheryl Murdock (Arizona State University) and Dr. Laura Bristow (University of Gothenburg).
DOI: 10.26008/1912/bco-dmo.962616.1
title: Saanich Inlet field and laboratory methods related to environmental data acquired aboard the R/V John Strickland during two cruises in August, 2021 and June, 2022

description: These data include oceanographic, chemical, and biogeochemical rate measurements relating to oxygen, nitrogen, and sulfur species from Saanich Inlet, British Columbia, Canada, spanning lower oxycline and anoxic depths in the basin. Data and samples were collected aboard the R/V John Strickland during two cruises in August, 2021 and June, 2022. Data from 2021 capture the dynamics of an oxygen renewal event of the deep anoxic basin, which occurred between the second and third sampling days. Data from 2022 were collected during stable, stratified conditions with complete anoxia in the deep basin throughout the sampling period.
DOI: 10.26008/1912/bco-dmo.964636.1
title: Macrofaunal morphospecies from hard-substrate methane seep samples collected on R/V Atlantis cruise AT50-12, Southern California Borderland from July 2023 (Methanosphere project)

description: This dataset documents macrofaunal communities associated with hard substrates (carbonate, phosphorite, and wood) collected from methane seeps in the Southern California Borderland. Samples were obtained with the HOV Alvin during R/V Atlantis cruise AT50-12 (July 16–28, 2023). The dataset provides morphospecies-level counts of macrofauna together with collection and sample metadata.
DOI: 10.26008/1912/bco-dmo.984494.1
title: Chlorophyll a concentrations collected from Project &quot;DaVINCi&quot; incubations in the Gulf of Naples, Italy from April to May 2022

description: Chlorophyll a was measured on seawater samples collected from nutrient amendment incubation experiments conducted on surface water collected at the Long-Term Ecological Monitoring Station, MareChiara, in the Gulf of Naples, Italy, between April 20 and May 19, 2022.