cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.942686.1
title: Environmental sensor data from an underwater imaging system (ISIIS-3) collected during R/V Langseth cruise MGL2207 July 20-28 2022 and R/V Sally Ride cruise SR2317 August 10-20 2023 in the Northern California Current

description: During July 20-28 2022 and August 10-20 2023 an underwater imager (In Situ Ichthyoplankton Imaging System 3, ISIIS-3) was deployed from the R/V Langseth and R/V Sally Ride, respectively. The ISIIS-3 deployments were carried out from these R/Vs in the northern California Current by a team affiliated with Oregon State University, the University of Oregon, and Portland State University.

The ISIIS-3 was equipped with two line scan cameras for collecting plankton imagery in addition to six  environmental sensors.

This dataset contains the processed and quality controlled merged environmental data from the ISIIS imager on this cruise, consisting of temperature, conductivity, pressure, depth, salinity, fluorescence, oxygen, pH, photosynthetically active radiation, and chlorophyll a. Latitude, longitude, date, time, imager horizontal/vertical speeds, and altitude are also included in the dataset. Data were collected on six cross-shelf transects ranging geographically from the border of California and Oregon to  southern Washington. Two transects, one following the Newport Hydrographic Line and the other near Gray’s Harbor, Washington, were 70 nautical miles (~135 km) in length. The four others (near the Columbia River, Cape Meares, Heceta Bank, and the Rogue River) were 40 nautical miles (~73 km). ISIIS was towed continuously in an undulating motion (“tow-yos”) between 0-100m depth, or within 2-5m of the seafloor where the bottom depth was less than 100m. Data were streamed on to the ship in real time using a fiber optic oceanographic cable and written into millisecond time-stamped data files for each sensor. Sensor data files from ISIIS-3, along with latitude and longitude data from ship data streams, were merged using Python scripts into a final dataset based on the millisecond time stamps of the sensors and GPS streams.
DOI: 10.26008/1912/bco-dmo.933832.1
title: Lesion frequencies and sizes after fish feces treatment on coral samples collected on the north shore of Mo’orea, French Polynesia, Oct 2020 to Jun 2021

description: This datafile contains frequencies and sizes (number of polyps killed) developed in coral tissues after the application and removal of fish feces to test whether fish from different guilds affect coral health in distinct ways.There were five treatments: fresh feces from a corallivorous butterflyfish (FC); fresh feces from a grazer/detritivore (FG); sterilized feces from a corallivorous butterflyfish (SC); sterilized feces from a grazer/detritivore (SG); no-feces control (C). For the fresh feces treatments (FC, FG), we applied 100 µl of fresh feces isolated from the hindgut of the butterflyfish Chaetodon ornatissimus (FC) or the grazer/detritivore Ctenochaetus striatus (FG) directly onto each coral fragment. For the sterilized feces treatments (SC, SG), fecal pellets were sterilized in a pressure cooker for 40 minutes at 120°C and then applied in the same manner as fresh feces. The experiment ran for ~22 hours. The experiment was conducted in three iterations in Mo'orea, French Polynesia, over two years (2020, 2021).
DOI: 10.26008/1912/bco-dmo.935908.1
title: Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020

description: Understanding how microbial communities in consumer feces may impact ecosystem health may improve conservation and restoration efforts. To test how microbial communities in fish feces may affect coral reef health, we collected fecal samples from ten fish species, ranging from obligate corallivore to grazer/detritivore. Additionally, samples of corals, algae, sediments, and seawater were collected to test whether bacterial taxa in these samples were also represented in fish feces (N = 5-14 per fish, coral, or algae species/genus). All collections were conducted in October 2020 from the back reef (1-2 m depth) and fore reef (5-10 m depth) in Moorea, between LTER sites 1 and 2 of the Moorea Coral Reef (MCR) Long Term Ecological Research (LTER) site. We conducted bacterial 16S rRNA gene metabarcoding on all samples and found that fecal communities of bacteria differed among fish guilds (obligate corallivores, facultative corallivores, grazer/detritivores). We also used real-time PCR to quantify abundances of Vibrio coralliilyticus, a known coral pathogen,  in all fecal samples. Samples were collected and processed, and data were analyzed, by the authors of Grupstra et al., 2023.
DOI: 10.26008/1912/bco-dmo.2773.2
title: Phytoplankton growth, microzooplankton herbivory from R/V Roger Revelle KIWI6, KIWI7, KIWI8, KIWI9 cruises in the Southern Ocean, 1997-1998 (U.S. JGOFS AESOPS project)

description: This dataset includes phytoplankton growth and microzooplankton herbivory from R/V Roger Revelle cruises KIWI6, KIWI7, KIWI8, and KIWI9 in the Southern Ocean in 1998.
DOI: 10.26008/1912/bco-dmo.940112.1
title: Winter survey data from Lake Erie from Mar 2023 to May 2024

description: This dataset includes winter survey data from Lake Erie collected on SAR Erie Guardian, USCGC Morro Bay, USCGC Neah Bay, CCGS Griffon, CCGS Samuel Risley, MV Vigilant from March 2023 to May 2024. The survey includes environmental observations, physico-chemical data, chlorophyll, total and dissolved nutrients, plankton taxonomic classification, and cell abundance. The Lake Erie Center for Fresh Waters and Human Health is a five-year, multi-institutional effort aimed at understanding the environmental factors and ongoing changes that influence the growth and toxicity of cyanobacterial harmful algal blooms (cHABs) in Lake Erie.
DOI: 10.26008/1912/bco-dmo.943333.1
title: Specific daily growth of heterotrophic bacteria and grazing mortality on bacteria by microzooplankton from R/V Roger Revelle KIWI6, KIWI7, KIWI8, KIWI9 cruises in the Southern Ocean, 1997-1998 (U.S. JGOFS AESOPS project)

description: This dataset is from dilution experiments conducted on 1997-98 cruises KIWI6, KIWI7, KIWI8, and KIWI9 on R/V Roger Revelle as part of the US JGOFS AESOPS Program in the Southern Ocean. Rate estimates are specific daily growth of heterotrophic bacteria (d-1) and grazing mortality on bacteria by microzooplankton (d-1).
DOI: 10.26008/1912/bco-dmo.893182.4
title: Primary productivity estimates from the incubation of seawater collected at the Bermuda Atlantic Time-series Study (BATS) site from December 1988 through December 2023

description: Data presented are primary production estimates at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from December 1988 (BATS Cruise 3) through December 2023 (BATS cruise 399). The rate of carbon fixation by autotrophs in seawater was determined by tracing the uptake of radioactive 14C from the inorganic form to the particulate organic form. Incubations were performed in situ at depths ranging from the surface to 140 meters from dusk to dawn. Seawater samples were collected prior to sunrise, separated into three light bottles and one dark bottle, and a radioactive 14C tracer added. The bottles were then deployed on an incubation array at their collection depths, and allowed to drift on the array for the full light day. Samples were recovered after sunset and filtered for subsequent analysis on a liquid scintillation counter.
DOI: 10.26008/1912/bco-dmo.893521.6
title: HPLC and fluorometric derived phytoplankton pigment concentrations from seawater collected at the Bermuda Atlantic Time-series Study (BATS) site from October 1988 through December 2023

description: Data presented here contain HPLC derived phytoplankton pigments and fluorometric chlorophyll-a from the BATS site for years 1988 to 2023.  Water samples are typically collected from 12 depths in the upper 250 meters of the water column, and then filtered under low vacuum through a 25mm GF/F filter. The filter is then flash frozen in liquid nitrogen and stored at -80 degrees C. Shoreside, analysis is performed on an HPLC using a method modified by Dr. R. Bidigare from the Wright et al. (1991) procedure.  This method identifies the pigments chlorophyll-c3, chlorophyll-c2, peridinin, 19’-butanoyloxyfucoxanthin, fucoxanthin, 19’-hexanoyloxyfucoxanthin, prasinoxanthin, diadinoxanthin, alloxanthin, diatoxanthin, lutein, zeaxanthin, chlorophyll-b, chlorophyll-a, divinyl chlorophyllide-a, alpha and beta carotene. Additionally, chlorophyll-a and phaeopigments are analyzed using a fluorometric assay.
DOI: 10.26008/1912/bco-dmo.938909.1
title: Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022

description: These are the raw data files from 5 cohorts of pacific herring embryos collected from Feb through April of 2022.  Embryos were homogenized, and digested for proteomic analysis on a Lumos Orbitrap.  Pooled samples were used with narrow window scans for library generation. The purpose of this data set is exploratory analysis for seasonal differences between early life stage proteome of pacific herring.  All embryos are believed to be from the Semiahmoo Bay population since the Cherry Point population had no spawn detected in 2022.
DOI: 10.26008/1912/bco-dmo.737596.1
title: Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016

description: Relative protein abundance data of the upper 1000m water column from the ProteOMZ R/V Falkor expedition. There are 109952 unique peptides, each with spectral counts associated with each of the 103 samples, for 10 million data points.
DOI: 10.26008/1912/bco-dmo.737620.3
title: Total spectral count of proteins from R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific in 2016

description: Relative protein abundance data of the upper 1000m water column from the ProteOMZ R/V Falkor expedition. There are 56,577 protein identifications over 102 samples, for ~6 million data points.
DOI: 10.26008/1912/bco-dmo.2773.1
title: Phytoplankton growth, microzooplankton herbivory from R/V Roger Revelle KIWI6, KIWI7, KIWI8, KIWI9 cruises in the Southern Ocean, 1998 (U.S. JGOFS AESOPS project)

description: This dataset includes phytoplankton growth and microzooplankton herbivory from R/V Roger Revelle cruises KIWI6, KIWI7, KIWI8, and KIWI9 in the Southern Ocean in 1998.
DOI: 10.26008/1912/bco-dmo.708495.3
title: R/V Falkor 160115 McLane pump log from the ProteOMZ expedition in the Central Pacific during 2016 (ProteOMZ project)

description: false
DOI: 10.26008/1912/bco-dmo.737611.3
title: FASTA file of identified protein sequences from the R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific during 2016

description: FASTA file of protein identifications from FK160115 in 2016. Individual sequences of all proteins identified in the ProteOMZ Protein dataset (737630, see &quot;Related Datasets&quot; section). Each entry begins with a “&gt; “ and is followed by the ProteinIdentifier.
DOI: 10.26008/1912/bco-dmo.3782.6
title: Discrete bottle samples collected at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from October 1988 through December 2023

description: Data presented here are discrete bottle samples from the Bermuda Atlantic Time-series Study (BATS) site located 80 km SE of Bermuda (31°40N, 64°10W) in the Sargasso Sea for October 1988 (cruise 10001) through December 2023 (cruise 10411). Measurements were collected from the core monthly BATS cruises and the near-biweekly (depending on ship availability) BATS Bloom cruises during February through April. The sample parameter list has been mostly consistent for the full time-series record and includes: salinity, dissolved oxygen, dissolved inorganic carbon, alkalinity, nutrients (nitrate + nitrite, nitrite, phosphate, silicate), particulate organics (carbon, nitrogen, phosphorous), particulate silicate, total organic carbon and nitrogen, total dissolved phosphorus, bacterial enumeration, and flow cytometry counts of picoplankton. The HPLC derived phytoplankton pigment data which are collected synoptically with many of the above parameters are reported in a separate dataset.
DOI: 10.26008/1912/bco-dmo.939210.7
title: Two decibar averaged CTD profiles collected during BATS Validation (BVAL) cruises from April 1991 through July 2023

description: Data presented here are 2 dbar CTD for BATS Validation (BVAL) cruises from Jun 1991 (BVAL cruise #50016) through July 2023 (BVAL cruise #50060). Profiles of primary CTD measurements (Pressure, Depth, Temperature, and Salinity) are reported along with auxiliary data for dissolved oxygen, beam attenuation coefficient, relative fluorescence, and photosynthetic Active Radiation (PAR). Profiles were collected using a standard Sea-Bird SBE-09 plus CTD. Data are processed following the methods of Knap et al., 1997 with the final product being reported as two decibar averages and all profiles. It should be noted that the two decibar profiles are reported for the downcast only and bottle marker data collected on the upcast are presented with the bottle data.
DOI: 10.26008/1912/bco-dmo.3918.8
title: Two decibar averaged CTD profiles collected at the Bermuda Atlantic Time-series Study (BATS) site from October 1988 through December 2023

description: Data presented here are profiles of primary CTD parameters (pressure, depth, temperature, and salinity) plus auxiliary measurements of dissolved oxygen, beam attenuation, relative fluorescence, and photosynthetic active radiation (PAR) at the BATS site (31° 40' N 64° 10'W) for years 1988-2023. Profiles were collected using a standard Sea-Bird SBE-09 plus CTD during the monthly core BATS cruises and near biweekly BATS bloom cruises during the months of February through April depending on ship availability. Data are processed following the methods of Knap et al., 1997 with the final product being reported as two decibar averages and all profiles for each cruise reported in a single cruise file. It should be noted that the two decibar profiles are reported for the downcast only and bottle marker data collected on the upcast are presented with the BATS bottle dataset.
DOI: 10.26008/1912/bco-dmo.916411.2
title: CTD profiles from R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

description: Oceanographic samples were collected onboard the R/V Atlantic Explorer between June 16th - 28th 2019, along a transect beginning at the Bermuda Atlantic Time-series Station (BATS) in the Sargasso Sea and terminating in northeast US continental shelf waters. The R/V Atlantic Explorer CTD provided physicochemical contextualization (temperature, oxygen, fluorescence, turbidity) and was deployed at all stations except the last one, St. 9, due to time restrictions.
DOI: 10.26008/1912/bco-dmo.926526.1
title: Amended Rolling Deck to Repository (R2R) event log (ELOG) taken on the R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

description: The Electronic Logger (ELOG) tracked all deployments on the AE1913 cruise, including CTD, McLane pump, trace metal rosette, and AUV Clio deployment/recoveries, flow-through seawater sampling, sediment trap and plankton nets. Corresponding CTD files from each deployment are recorded in the &quot;comments&quot; column.

R/V Atlantic Explorer cruise AE1913 was conducted between June 16th - 28th, 2019 in the Sargasso Sea, beginning at Bermuda Atlantic Time-series Station (BATS) and ending in the northeast shelf of Woods Hole Oceanographic Institution (WHOI).
DOI: 10.26008/1912/bco-dmo.916411.1
title: CTD profiles from R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

description: Oceanographic samples were collected onboard the R/V Atlantic Explorer between June 16th - 28th 2019, along a transect beginning at the Bermuda Atlantic Time-series Station (BATS) in the Sargasso Sea and terminating in northeast US continental shelf waters. The R/V Atlantic Explorer CTD provided physicochemical contextualization (temperature, oxygen, fluorescence, turbidity) and was deployed at all stations except the last one, St. 9, due to time restrictions.
DOI: 10.26008/1912/bco-dmo.926546.1
title: Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

description: Pigment concentration data from R/V Atlantic Explorer cruise AE1913 (June 2019) in which seawater was collected across a 1,050 km section in the western North Atlantic.
DOI: 10.26008/1912/bco-dmo.916429.1
title: Macronutrients and dissolved and particulate trace metals collected from the R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

description: This data includes macronutrients and dissolved and particulate trace metals collected from the AE1913 expedition on the R/V Atlantic Explorer in June 2019. Seawater was collected with a trace metal rosette and filtered through a 0.2 um filter. Filtrate was used for nutrients and dissolved trace metals, and the filter was saved for the particulate metal analysis at select sites. Instruments used were a Alpkem Rapid Flow Analyzer, Technicon AutoAnalyzer II, and iCAP Q inductively coupled plasma mass spectrometer (ICP-MS). The goal of this analysis was to explore the relationship between trace metal/macronutrient availability and microbial metabolism across a section of the North Atlantic Ocean. This data was collected by Mak Saito and Natalie Cohen.
DOI: 10.26008/1912/bco-dmo.934718.1
title: Peptides associated with scaffold-derived metaproteomic proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019

description: These are individual peptides associated with scaffold-derived metaproteomic proteins (includes total spectral counts for each peptide).  Samples were taken during R/V Atlantic Explorer cruise AE1913 in Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea and ending in coastal Northeast US shelf waters in June of 2019.
DOI: 10.26008/1912/bco-dmo.934706.1
title: Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019

description: These are the Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins.  Samples were taken during R/V Atlantic Explorer cruise AE1913 in Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea  and ending in coastal Northeast US shelf waters in June of 2019.
DOI: 10.26008/1912/bco-dmo.934727.1
title: Protein identification FASTA file (scaffold-derived metaproteomic proteins) from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019

description: This is a FASTA file of protein identifications (scaffold-derived metaproteomic proteins). Samples were taken during R/V Atlantic Explorer cruise AE1913 in Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea and ending in coastal Northeast US shelf waters in June of 2019.
DOI: 10.26008/1912/bco-dmo.940088.1
title: Particulate metals from a scandium incubation experiment during the PUPCYCLE I R/V Oceanus cruise 1905B in the California Current System in 2019

description: We performed an incubation experiment with added dissolved scandium and/or iron in waters sampled in the California Current System during the PUPCYCLE I cruise in 2019 with Chief Scientist Adrian Marchetti. PUPCYCLE I (Phytoplankton response to the UPwelling CYCLE) took place in summer 2019 onboard the R/V Oceanus (OC 1905b). Water for the incubation was collected from 15 m just off the Big Sur coast 2 June 2019. This was in a region with an extremely narrow shelf. There were five total treatments run in triplicate: control (no addition), +5 nmol/kg dissolved Fe, +5 nmol/kg dissolved Sc, +5 nmol/kg dissolved Fe and +5 nmol/kg dissolved Sc, and filtered seawater with +5 nmol/kg dissolved Fe and +5 nmol/kg dissolved Sc. After 24 hours incubating, the incubation was harvested and analyzed for chlorophyll, nutrients, and dissolved and particulate Fe and Sc concentrations. The effort was to investigate similarities and differences in the oceanic chemical cycling of Fe and Sc.
DOI: 10.26008/1912/bco-dmo.940093.1
title: Dissolved Fe and Sc concentrations, chlorophyll, nutrients from a scandium incubation experiment during the PUPCYCLE I R/V Oceanus cruise 1905B in the California Current System in 2019

description: We performed an incubation experiment with added dissolved scandium and/or iron in waters sampled in the California Current System during the PUPCYCLE I cruise in 2019 with Chief Scientist Adrian Marchetti. PUPCYCLE I (Phytoplankton response to the UPwelling CYCLE) took place in summer 2019 onboard the R/V Oceanus (OC 1905b). Water for the incubation was collected from 15 m just off the Big Sur coast 2 June 2019. This was in a region with an extremely narrow shelf. There were five total treatments run in triplicate: control (no addition), +5 nmol/kg dissolved Fe, +5 nmol/kg dissolved Sc, +5 nmol/kg dissolved Fe and +5 nmol/kg dissolved Sc, and filtered seawater with +5 nmol/kg dissolved Fe and +5 nmol/kg dissolved Sc. After 24 hours incubating, the incubation was harvested and analyzed for chlorophyll, nutrients, and dissolved and particulate Fe and Sc concentrations. The effort was to investigate similarities and differences in the oceanic chemical cycling of Fe and Sc.
DOI: 10.26008/1912/bco-dmo.940678.1
title: Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020

description: These files support the publication &quot;Multiple lineages of transmissible neoplasia in the basket cockle (C. nuttallii) with repeated horizontal transfer of mitochondrial DNA,&quot; which has been submitted to bioRxiv (doi:10.1101/2023.10.11.561945). Details of locations and dates of cockle collection, specific primer sequences, methods for design of the primers, and analysis of results can be found there.  

These files are fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State. For each cockle DNA was extrcted from a solid tissue sample (T) and a hemolymph sample (H). These were used to identify bivalve transmissible neoplasia in several cockle samples in these populaitons (together with other genetic data from other nuclear and mitochondrial markers). Microsatellites were amplified from DNA extracted from both hemocyte and tissue using Taq polymerase (Genesee Scientific) for a select number of individuals: all possible neoplastic animals based on positive qPCR screen (n=26) and one randomly selected, non-neoplastic animal from each collection (n=12). Microsatellites were amplified using primers for 8 polymorphic loci: Cnu48, Cnu55, Cnu58, Cnu63, Cnu68, Cnu72, Cnu78, and Cnu81. Allele sizes were identified by fragment analysis using fluorescent primers (6-FAM, PET, NED, and VIC) and a 3730xl Genetic Analyzer with the LIZ-500 size standard (Applied Biosystems, operated by Genewiz). For each sample, two reactions were run: &quot;1&quot; with (Cnu48, blue; Cnu55, yellow; Cnu58, red; Cnu63, green) and &quot;2&quot; with (Cnu68, blue; Cnu72, yellow; Cnu79, red; Cnu81, green).