[Substrate-specific metabolic responses of model marine bacteria using proteomics] - Normalized protein abundance data and protein annotations for proteomic data from laboratory cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 in 2022 (C-CoMP Model Bacteria Physiological Studies)

Summary:
This dataset includes normalized protein abundance data and protein annotations for proteomic data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002. These model marine bacteria were grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates. The data are sampled so as to capture the metabolic differences the bacteria employ when catabolizing these different substrates and when switching between them. The raw proteomics files are available on the Proteomics IDEntification Database (PRIDE) under accession PXD045824. The proteomic data accompanies the transcriptomic expression data available at BCO-DMO dataset 916134 (https://www.bco-dmo.org/dataset/916134).

cdm_data_type = Other
VARIABLES:
Species (unitless)
Strain (unitless)
gene_callers_id (unitless)
ac_mean_abund (unitless)
glc_mean_abund (unitless)
late_mean_abund (unitless)
early_mean_abund (unitless)
SPO_ID_ACCESSION (unitless)
KOfam_ACCESSION (unitless)
KEGG_Module (unitless)
COG20_FUNCTION (unitless)
Uniprot_accession (unitless)


[Substrate-specific metabolic responses of model marine bacteria] - Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates (C-CoMP Model Bacteria Physiological Studies)

Summary:
This dataset includes metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002. These model marine bacteria were grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates. The data are sampled so as to capture the metabolic differences the bacteria employ when catabolizing these different substrates and when switching between them. The raw RNA sequences (50 bp reads in fastq format) have been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA972985 (https://www.ncbi.nlm.nih.gov/bioproject/972985).

cdm_data_type = Other
VARIABLES:
Sample_Name (unitless)
Accession (unitless)
BioProject (unitless)
Organism (unitless)
Strain (unitless)
Tax_ID (unitless)
Glucose_initial_concentration_uM (micromolar concentration)
Acetate_initial_concentration_uM (micromolar concentration)
Sample_description (unitless)


[Subsurface Nitrospirota and Nitrospinota Origins] - Collection of subsurface bacteria Nitrospirota and Nitrospinota genome data including IMG and NCBI accessions for sequence datasets in June 2021 (Slow Life in Crust project) (Microbial activity in the crustal deep biosphere)

Summary:
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique mitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. We used phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species tree reconciliation methods to investigate the life histories of these two phyla. This dataset includes list of previously-published sequence datasets that were used for the analysis. The data and interpretations are published at DOI 10.1038/s41396-023-01397-x. Additional metadata such as NCBI accessions, assembly release dates, and NCBI taxon ids were added in December 2024.

cdm_data_type = Other
VARIABLES:
ID (unitless)
IMG_genome_id (unitless)
GenBank_assembly (unitless)
Sample (unitless)
Corrected_BioSample (unitless)
BioProject (unitless)
release_date (unitless)
last_updated_date (seconds since 1970-01-01T00:00:00Z)
publication_date (seconds since 1970-01-01T00:00:00Z)
Domain (unitless)
Phylum (unitless)
Class (unitless)
Order (unitless)
Family (unitless)
Genus (unitless)
Species (unitless)
NCBI_organism_taxid (unitless)
Isolation_Source (unitless)
IsolationPlot (unitless)
... (11 more variables)


[Subterranean Estuary In Situ Tracer Experiment Incubation Data, 2019] - In situ tracer injection experiment conducted with 15N-labeled ammonium in a shallow, sandy subterranean estuary in Gloucester Point, USA  in August 2019. (Collaborative Research:  Cryptic nitrogen cycling in the anoxic subterranean estuary)

Summary:
These data are the result of an in situ tracer injection experiment conducted with 15N-labeled ammonium to determine the fate and transport rates of ammonium within a shallow, sandy subterranean estuary in Gloucester Point, VA, USA.

Replicate injections of 15N-labeled ammonium, sulfur hexaflouride, and bromide amended porewater were injected into piezometers at 50cm.  Porewater was then collected overtime from the injection piezometers and tracer piezometers surrounding the injection site ranging in depth from 40-60cm.  At each time point, samples were collected to analyze dissolved inorganic nitrogen (nitrate, nitrite, and ammonium) concentrations, sulfur hexaflouride, bromide, chloride. Nitrate and nitrite samples from porewater were analyzed with an isotope ratio mass spectrometer in order to assess the 15N enrichment of the nitrate in each sample resulting in a delta value (d15N) that allows for the calculation of the mole fraction of 15N-labeled nitrite and nitrate in porewater at each time point. The production or consumption over time constitutes subterranean estuary nitrogen cycling rates (e.g. nitrification, denitrification, etc.).

cdm_data_type = Other
VARIABLES:
Site_Name (unitless)
Latitude (degrees_north)
longitude (degrees_east)
Piezometer (unitless)
Sample_ID (unitless)
Time_Point (unitless)
Date (unitless)
Time (unitless)
Hours_after_Injection (hours (hrs))
Bromide_uM (micromoles per liter (uM))
Chloride_mM (millimoles per liter (mM)
SF6_ppbv (parts per billion per volume (ppbv))
SF6_pM (picoMolar (pM))
Nox_uM (micromoles per liter (uM))
... (4 more variables)


[Subterranean Estuary Sediment Nitrification Incubation Data, 2020] - Sediment Nitrification Incubation data of a subterrarnian estuary core take in July 2020 in Gloucester Point, Virginia (Collaborative Research:  Cryptic nitrogen cycling in the anoxic subterranean estuary)

Summary:
These data are the result of a sediment slurry incubation experiment conducted with 15N-labeled ammonium to quantify nitrification rates in the sediments of a shallow, sandy subterranean estuary in Gloucester Point, VA, USA. Triplicate sediment cores that were 50cm in length were collected and sectioned into 10cm intervals. Homogenized sediment was incubated with porewater from the same depth interval that had been amended with 15N-labeled ammonium. Sediments were incubated in the dark for zero, six and twelve hours. At each time point, samples were collected to analyze dissolved inorganic nitrogen (nitrate, nitrite, and ammonium) concentrations. Samples were analyzed with an isotope ratio mass spectrometer in order to assess the 15N enrichment of the nitrate in each sample resulting in a delta value (d15N) that allows for the calculation of the mole fraction of 15N-labeled nitrate produced by each slurry. This production over time constitutes the sediment nitrification rate for each depth interval.

cdm_data_type = Other
VARIABLES:
Date (unitless)
Site (unitless)
Latitude (degrees_north)
longitude (degrees_east)
Depth_Interval (centimeter (cm))
Replicate (unitless)
Incubation_Time_Point (unitless)
Incubation_Hours (hours (hr))
Sample_ID (unitless)
NOX (micromoles per liter (uM))
NO3 (micromoles per liter (uM))
NO2 (micromoles per liter (uM))
NH4 (micromoles per liter (uM))
d15N (parts per thousand (‰))
Mole_Fraction_15N (unitless)


[Subtidal Ocean Water Temperature at Van Damme State Park, CA] - Subtidal ocean water temperature at Van Damme State Park, California, from May 1992 to August 2023 (Collaborative Research: The effects of marine heatwaves on reproduction, larval transport and recruitment in sea urchin metapopulations)

Summary:
Ocean water temperatures were collected from May 14, 1992 to August 22, 2023 (these logger deployments are ongoing) from 10 meters benthic depth, at Van Damme State Park, Mendocino County, Northern California. Water temperatures were collected with Onset Hobotemp® and TidbiT® temperature loggers in degrees Celsius. Data are presented as daily averages of 10-minute minimum intervals.

Ocean water temperatures were collected to document long-term temperature conditions on the bottom at the level of the reef. Loggers were placed 1 meter off the bottom on stainless steel cages used to monitor juvenile abalone and sea urchin recruitment at this reference location.

Water temperatures are presented as daily averages for the period of record. Some data gaps exist due to equipment failure, loss, or rough conditions precluding placement of data loggers. The data gaps are listed in the “Problems/Issues” section below.

These data are unique in that they are benthic seawater temperature data (1 meter from the bottom where the benthic animals live) which can be used to compare with the more readily available sea surface temperature data.

cdm_data_type = Other
VARIABLES:
Date (unitless)
Mean_Daily_Temperature_C (degrees Celsius)
latitude (Site_latitude, degrees_north)
longitude (Site_longitude, degrees_east)


[Sulfate reduction energetics] - Sulfate reduction energetics at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011 (Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents)

Summary:
Sulfate reduction energetics at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011

cdm_data_type = Other
VARIABLES:
experiment_num (unitless)
latitude (degrees_north)
longitude (degrees_east)
sulfide (molar (M))
sulfate (millimoles (mM))
DOC (micromoles (uM))
citrate (molar (M))
formate (molar (M))
pyruvate (molar (M))
acetate (molar (M))
lactate (molar (M))
bicarbonate (millimoles (mM))
K (molar (M))
Ca (molar (M))
Na (molar (M))
Cl (molar (M))
pH (Sea Water Ph Reported On Total Scale, pH)
temperature (celsius (C))
sulfateRed_formate (Sulfate Red Formate, DeltaGr KJ/mol e-)
sulfateRed_acetate (Sulfate Red Acetate, DeltaGr KJ/mol e-)
sulfateRed_pyruvate (Sulfate Red Pyruvate, DeltaGr KJ/mol e-)
sulfateRed_lactate (Sulfate Red Lactate, DeltaGr KJ/mol e-)
sulfateRed_citrate (Sulfate Red Citrate, DeltaGr KJ/mol e-)
c_limiting_totalEnergy (C Limiting Total Energy, joules (J))
S_limiting_totalEnergy (joules (J))
total_energy (joules (J))


[Sulfate reduction rates] - Sulfate reduction rates at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011 (Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents)

Summary:
Sulfate reduction rates at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011

cdm_data_type = Other
VARIABLES:
inoculum (unitless)
experiment_num (unitless)
latitude (degrees_north)
longitude (degrees_east)
sulfide (molar (M))
DOC (micromoles (uM))
sulfate (millimoles (mM))
pH (Sea Water Ph Reported On Total Scale, pH)
temperature (celsius (C))
SRrate_3day (nmol/gday)
SRrate_3day_replicates (count)
SRrate_7day (nmol/gday)
SRrate_7day_replicates (count)
SRrate_inhibited (nmol/gday)
SRrate_inhibited_replicates (count)


[Sulfide concentrations] - Sulfide concentrations as a function of time from INSPIRE track 1 collected from 2013 to 2017 (INSPIRE Pyrite project) (INSPIRE Track 1: Microbial Sulfur Metabolism and its Potential for Transforming the Growth of Epitaxial Solar Cell Absorbers)

Summary:
Sulfide concentrations as a function of time from INSPIRE track 1 collected from 2013 to 2017 (INSPIRE Pyrite project)

cdm_data_type = Other
VARIABLES:
experiment_type (unitless)
time2 (Time, hours)
sulfide_culture1 (micromolar (mM))
sulfide_culture2 (micromolar (mM))
sulfide_culture3 (micromolar (mM))
sulfide_culture1_Fe (micromolar (mM))
sulfide_culture2_Fe (micromolar (mM))
sulfide_culture3_Fe (micromolar (mM))
sulfide_culture4_Fe (micromolar (mM))
sulfide_control1_slow (micromolar (mM))
sulfide_control2_slow (micromolar (mM))
culture_medium (unitless)


[Sulfonates in plankton cultures] - Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics (OCE-PRF Track 1 (Broadening Participation): Cryptic Sulfonate Cycling between Marine Phytoplankton and Heterotrophic Bacterioplankton)

Summary:
Intracellular sulfonate metabolites were measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics. These data have been published in Durham et al. (2019). Raw data are available at Metabolomics Workbench under Project ID PR000797.

cdm_data_type = Other
VARIABLES:
Organism (unitless)
replicate (unitless)
cells_filtered (unitless)
DHPS (amol per cell)
cysteic_acid (amol per cell)
sulfolactate (amol per cell)
isethionic_acid (amol per cell)
taurine (amol per cell)


[Sulfur NEXFS Standards] - Sulfur Near Edge X-ray Fluorescence Spectroscopy Data for standard materials (P-NEXFS investigation of the influence of aerosol phosphorus on the Mediterranean Sea)

Summary:
Sulfur Near Edge X-ray Fluorescence Spectroscopy Data for standard materials.

cdm_data_type = Other
VARIABLES:
Energy (electron volts)
Ammonium_Sulfate (Mole Concentration Of Ammonium In Sea Water, x-ray fluorescence counts)
Barite (x-ray fluorescence counts)
Copper_II_Sulfate (x-ray fluorescence counts)
Gypsum (x-ray fluorescence counts)
Iron_Ammonium_Sulfate (Mole Concentration Of Ammonium In Sea Water, x-ray fluorescence counts)
Iron_III_Sulfate (x-ray fluorescence counts)
Jarosite (x-ray fluorescence counts)
Magnesium_Sulfate (x-ray fluorescence counts)
Potassium_Sulfate (x-ray fluorescence counts)
Sodium_Sulfate (x-ray fluorescence counts)


[Summary CTD data] - CTD summary data from phytoplankton monitoring sites in Juneau, AK sampled from 2015-2016 (SEAK-AHAB project) (Enhancing Sustainability of Shellfish Harvest in Alaska: Addressing the Ecology of Alexandrium Blooms and their Sociocultural Impacts)

Summary:
CTD summary data from phytoplankton monitoring sites in Juneau, AK sampled from 2015-2016 (SEAK-AHAB project)

cdm_data_type = Other
VARIABLES:
year (unitless)
investigator (unitless)
instrument (unitless)
station (unitless)
latitude (degrees_north)
longitude (degrees_east)
sampling_event (unitless)
date (unitless)
time_zone (unitless)
time_local (unitless)
depth (Cast Depth, m)
surface_temp (celsius)
s_salinity (Sea Water Practical Salinity, practical salinity units (PSU))
b_salinity (Sea Water Practical Salinity, practical salinity units (PSU))
s_density (kilogram per meter cubed (kg/m3))
b_density (kilogram per meter cubed (kg/m3))
max_fluor (milligram per meter cubed (mg/m3))
data_quality (unitless)
time (ISO Date Time Local, seconds since 1970-01-01T00:00:00Z)


[Summary data from the Heatwaves and Coral-Recovery Database (HeatCRD)] - Summary data from the Heatwaves and Coral-Recovery Database (HeatCRD) covering global coral reef sites from 1977-2020 (Thermal stress and differential recovery of coral reefs)

Summary:
This dataset is a summary table of the Heatwaves and Coral-Recovery Database (HeatCRD) introduced in van Woesik and Kratochwill (2024). The HeatCRD is the most comprehensive reference on coral recovery following marine heatwaves and other disturbances, encompassing 29,205 data records spanning 44 years from 12,266 sites, 83 countries, and 160 data sources. These data provide essential information to coral-reef scientists and managers to best guide coral-reef conservation efforts at both local and regional scales.
The dataset includes metadata for coral reef sampling events, such as site descriptions, geographical coordinates, depth, distance to shore, exposure, turbidity, coral cover percentages, MPA descriptions, temperature measurements, windspeed, and thermal stress indicators over 23 years.

See van Woesik and Kratochwill (2024) https://doi.org/10.1038/s41597-024-03221-3 for more information.

cdm_data_type = Other
VARIABLES:
Site_ID (unitless)
Sample_ID (unitless)
latitude (Latitude_degrees, degrees_north)
longitude (Longitude_degrees, degrees_east)
Ocean_Name (unitless)
Realm_Name (unitless)
Ecoregion_Name (unitless)
Ecoregion_distance (degrees)
Country_Name (unitless)
State_Island_Province_Name (unitless)
Location_Name (unitless)
Site_Name (unitless)
Habitat_Type (unitless)
Habitat_Distance (degrees)
Date_Day (unitless)
Date_Month (unitless)
... (59 more variables)


[Sup_Aug-10-carbon] - Radiocarbon data from R/V Blue Heron cruise BH10-14 on Lake Superior in August 2010 (Lake Superior Radiocarbon project) (How important is quote old unquote Carbon in Lake Superior.  A Radiocarbon Investigation)

Summary:
Radiocarbon data from R/V Blue Heron cruise BH10-14 on Lake Superior in August 2010.

cdm_data_type = Other
VARIABLES:
cruise_id (text)
Receipt_Number (dimensionless)
Date_Reported (unitless)
station_id (text)
latitude (degrees_north)
lon (Longitude, decimal degrees)
Submitter_Identification (text)
Type (text)
Process (text)
Accession_Number (OS-xxxxx)
F_Modern (Unitless)
Fm_Error (Unitless)
Age (Radiocarbon years)
Age_Error (Radiocarbon years)
d13C (D13 C, per mille)
d13C_Source (D13 C Source, text)
D14C (D14 C, per mille)
DIC_Conc (mmol/kg)
DOC_Conc (um/kg)


[Surface Sedimentary Black Carbon Concentrations and Carbon Isotopes Values] - Surface Sedimentary Black Carbon Concentrations, Flux, and Carbon Isotopes Values from the R.V. Endeavor EN651 in the Equatorial Atlantic Ocean from March 2020 (Concentrations and source assessment of black carbon across tropical Atlantic air and sediment)

Summary:
Surface sediments (0-1 cm) were obtained from the equatorial Atlantic Ocean and isolated for black carbon using the chemothermal oxidation at 375°C method (CTO 375). Multicores were taken aboard the R.V. Endeavor (EN651) from March 1st through March 15th, 2020, using a multi corer MC-800. Sediment samples were collected from 12 multicore stations along a west-to-east transect of the equatorial Atlantic centered on about 5˚N. Sediment deposition environments included the Amazon Submarine Fan, a series of sites across the Mid-Atlantic Ridge, and sites on the Sierra Leone Rise and adjacent Sierra Leone Basin. See Figure 1 in the EN651 cruise report (Lohmann 2020) for an illustration of coring site locations.

Background information taken from the EN651 cruise report (Lohmann 2020)

Black carbon (BC) is a highly graphitized incomplete combustion byproduct that could be a sink for fixed carbon, especially when deposited to pelagic sediments (Kuhlbusch 1998). There is a general assumption that rivers deliver most or all BC to the ocean (Coppola et al. 2018; Elmquist et al. 2008; Kuhlbusch 1998; Masiello and Druffel 2001; Mitra et al. 2014, 2002; Suman et al. 1997). Yet the effects and fluxes of BC are not well constrained in general circulation models. For example, few BC flux measurements are available in remote ocean sediments due to the expense and difficulty of obtaining samples. The formation of BC during incomplete combustion results in a fraction of carbon not being available for the biological pump and deep ocean respiration. Once deposited to the ocean, BC is buried in sediments and can account for significant fractions of the organic matter preserved in sediments. Hence, our results would contribute towards accounting for some of the ‘missing' terrestrial OC in sediments, as all BC is landmass derived (Hedges et al. 1997).

cdm_data_type = Other
VARIABLES:
Name (unitless)
Cruise_ID (unitless)
Site_ID (unitless)
Coring_Attempt (unitless)
Core_Letter (unitless)
Collection_Date (unitless)
... (13 more variables)


[Survival - pCO2 x DO effects on Menidia menidia] - Survival data from static and fluctuating pCO2 x dissolved oxygen (DO) experiments on Menidia menidia (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish)

Summary:
Coastal ecosystems experience substantial natural fluctuations in pCO2 and dissolved oxygen (DO) conditions on diel, tidal, seasonal and interannual timescales. Rising carbon dioxide emissions and anthropogenic nutrient input are expected to increase these pCO2 and DO cycles in severity and duration of acidification and hypoxia. How coastal marine organisms respond to natural pCO2 \u00d7 DO variability and future climate change remains largely unknown. Here, we assess the impact of static and cycling pCO2 \u00d7 DO conditions of various magnitudes and frequencies on early life survival and growth of an important coastal forage fish, Menidia menidia. Static low DO conditions severely decreased embryo survival, larval survival, time to 50% hatch, size at hatch and post-larval growth rates. Static elevated pCO2 did not affect most response traits, however, a synergistic negative effect did occur on embryo survival under hypoxic conditions (3.0 mg L-1). Cycling pCO2 \u00d7 DO, however, reduced these negative effects of static conditions on all response traits with the magnitude of fluctuations influencing the extent of this reduction. This indicates that fluctuations in pCO2 and DO may benefit coastal organisms by providing periodic physiological refuge from stressful conditions, which could promote species adaptability to climate change.

cdm_data_type = Other
VARIABLES:
Experiment (unitless)
Tank (unitless)
Bucket (unitless)
Target_Temperature (degrees Celsius)
Cycling_pattern (unitless)
Target_pCO2_uatm (Target P CO2 Uatm, microatmospheres (uatm))
Target_DO_mgL (Target DO Mg L, milligrams per liter (mg L-1))
Embryo_survival (unitless (percent))
Larval_survival_to_15dph (unitless (percent))
Larval_survival_to_6dph (unitless (percent))


[Survival and size] - Survival, length, and growth responses of M. menidia offspring from different females exposed to contrasting CO2 environments. (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish)

Summary:
Wild-caught M.\u00a0menidia\u00a0adults were spawned to test whether offspring
from different mothers differ in their average survival and size responses to
elevated CO2\u00a0conditions.\u00a0The experiment quantified three related
survival and three size traits for each replicate, female, and
CO2\u00a0treatment: embryo survival (fertilization to 1\u00a0dph), larval
survival (1 to 16\u00a0dph), and overall survival (fertilization to
16\u00a0dph); and size (SL) at hatch (1\u00a0dph), SL at 16\u00a0dph, and
larval growth rate\u00a0(GR = (SL16dph\u00a0\u2013 SL1dph)/15).

These data are\u00a0associated with the corresponding paper:

[Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2017) Potential for maternal
effects on offspring CO2-sensitivities in a coastal marine fish. Journal of
Experimental Marine Biology and Ecology (in
press).](\\https://doi.org/10.1016/j.jembe.2017.11.002\\)

Other datasets related to this paper:

[Fatty acid profiles of M. menidia females and their unfertilized
eggs.](\\https://www.bco-dmo.org/dataset/719379\\)

cdm_data_type = Other
VARIABLES:
Species (unitless)
Collection_site (unitless)
latitude (degrees_north)
longitude (degrees_east)
Collection_date (unitless)
Female (unitless)
Total_length (centimeters)
pH (Sea Water Ph Reported On Total Scale, NIST units)
... (8 more variables)


[Suspended particle total mercury and monomethylmercury in the California Current Ecosystem (CCE)] - Suspended particle total mercury and monomethylmercury in the California Current Ecosystem (CCE) determined from samples collected on R/V Roger Revelle cruise RR2105 (P2107) in July to August 2021 (California Current Ecosystem Long Term Ecological Research site)

Summary:
This dataset includes concentrations of suspended particulate total mercury and monomethylmercury from 8 upwelling stations and 5 offshore stations (13 stations in total, 2-4 depths per station), during the 2021 CCE LTER Process Cruise (P2107), from July 17th to Aug 9th. Suspended particle samples (1 and 51 micrometers (µm)) were collected with a multiple-unit large-volume in situ filtration system. Sampling depths were from the surface (10 meters) to the deep ocean as deep as 1000 meters.

cdm_data_type = Other
VARIABLES:
Cruise_ID (unitless)
Cruise_Name (unitless)
Station_Name (unitless)
ISO_DateTime_PDT (unitless)
time (Iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)
Latitude (degrees_north)
longitude (degrees_east)
Cast_Number (unitless)
depth (Depth_m, m)
tHg_CONC_SSF_fM (femtomolar (fM))
tHg_CONC_SSF_FLAG (unitless)
tHg_CONC_LSF_fM (femtomolar (fM))
tHg_CONC_LSF_FLAG (unitless)
MMHg_CONC_SSF_fM (femtomolar (fM))
MMHg_CONC_SSF_FLAG (unitless)
MMHg_CONC_LSF_fM (femtomolar (fM))
MMHg_CONC_LSF_FLAG (unitless)
Carbon_CONC_SSF_ug_L (microgram per liter (ug/L))
Carbon_CONC_SSF_FLAG (unitless)
Carbon_CONC_LSF (microgram per liter (ug/L))
Carbon_CONC_LSF_FLAG (unitless)


[Suspended particulate organic matter composition] - Suspended particulate organic matter composition of three marsh ponds in PIE-LTER (Rowley, MA) from 2014. (Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary)

Summary:
Suspended particulate organic matter composition of three high marsh ponds within PIE-LTER. Data were collected over 11 weeks in the summer and fall of 2014.

cdm_data_type = Other
VARIABLES:
season (unitless)
Tide (unitless)
week (unitless)
Pond (unitless)
TOC (percent)
mg_C_L (miligrams per liter)
mg_N_L (miligrams per liter)
d13C (D13 C, per mil)
TN (percent)
d15N (D15 N, per mill)


[Swimming Endurance] - Ontogeny of swimming endurance of larval Amphiprion percula, Elacatinus lori, and Elacatinus colini from Belize in 2015. (Collaborative Research: The Role of Larval Orientation Behavior in Determining Population Connectivity)

Summary:
Recorded swimming duration of larval Amphiprion percula, Elacatinus lori, and Elacatinus colini measured throughout development from hatching through settlement.

cdm_data_type = Other
VARIABLES:
date (unitless)
location (unitless)
species (unitless)
batch_id (unitless)
dph (days post hatch)
stand_dph (percent)
speed (centimeters per second)
time_sec (seconds)
dist_cm (centimeters)
TL (milimeters)
SL (milimeters)
BD (milimeters)
PA (milimeters)


[Switch RNAseq] - Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study (Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere)

Summary:
Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study. This dataset contains the processed, QC'ed, normalized sequence data. The full raw data file is deposited in the NCBI BioProject database under accession PRJNA381627.

cdm_data_type = Other
VARIABLES:
Locus_Tag (unitless)
Description (unitless)
Day7_R1 (TPM (transcripts per million))
Day7_R2 (TPM (transcripts per million))
Day9_R1 (TPM (transcripts per million))
Day9_R2 (TPM (transcripts per million))
Day12_R1 (TPM (transcripts per million))
Day12_R2 (TPM (transcripts per million))
Day15_R1 (TPM (transcripts per million))
Day15_R2 (TPM (transcripts per million))
Day18_R1 (TPM (transcripts per million))
Day18_R2 (TPM (transcripts per million))
Day23_R1 (TPM (transcripts per million))
Day23_R2 (TPM (transcripts per million))
Day30_R1 (TPM (transcripts per million))
Day30_R2 (TPM (transcripts per million))
Day37_R1 (TPM (transcripts per million))
Day37_R2 (TPM (transcripts per million))


[Symbiodinium community composition] - Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project) (RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease)

Summary:
Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project)

cdm_data_type = Other
VARIABLES:
genet_clonalPopulation_ID (Genet Clonal Population ID, unitless)
ramet_individualColony_ID (Ramet Individual Colony ID, unitless)
visit (unitless)
bleaching (unitless)
disease (unitless)
mortality (unitless)


[Symbiodinium Fv/Fm over a temperature gradient] - Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures (Coevolution of scleractinian corals and their associated microorganisms)

Summary:
Coral photosynthetic endosymbionts (Symbiodinium) are phylogenetically very diverse, yet the extent of inter- and intraspecific functional variation within clades remains largely underexplored. Understanding this variability will be critical for future research on climate change mediated responses. A properly functioning thylakoid membrane is essential for optimal photosynthetic performance both in free-living and in hospite conditions. Here we analyze the thylakoid membrane melting points of 13  Symbiodinium strains from species in Clades B and A, grown at both control (26 \u00b0C)  and high temperature (31 \u00b0C). We observed a broad range of responses to thermal stress regardless of taxonomic rank. Our results support and augment a growing body of literature demonstrating that functional differences among Symbiodinium spp. are as distinct at lower taxonomic levels (i.e. interspecific) as they are among major clades. These findings highlight the importance of assessing the variability of plastid traits across the Symbiodinium tree.

cdm_data_type = Other
VARIABLES:
Strain (unitless)
Species (unitless)
Treatment (unitless)
Replicate (unitless)
Temperature (degrees Celsius)
Fv_Fm (dimensionless)


[Symbiodinium genotype responses to Nitrogen] - Traits of five Symbiodinium genotypes measured at three different nitrogen levels (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs)

Summary:
Replicates of each Symbiodinium genotype were grown in low (25mg/L), medium (75mg/L), or high (150mg/L) nitrogen environments, after which were measured physiological parameters, including the number of cells, quantum yield, variable fluorescence, and chlorophyll content.

cdm_data_type = Other
VARIABLES:
Genotype (unitless)
Ntreatment (unitless)
Growthrate (cells/day)
QY (unitless ratio)
Vfl (unitless)
Chla (Concentration Of Chlorophyll In Sea Water, Relative Fluorescence Units)
Chlapercell (Relative Fluorescence Units)
lncells (Ln(#cells))


[Symbiodinium genotype responses to temperature] - Traits of three Symbiodinium genotypes measured at ambient and elevated temperatures (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs)

Summary:
Traits of three genotypes measured at ambient and elevated temperatures. Replicates of each Symbiodinium genotype were grown in ambient (26 degrees) and elevated (30 degrees) temperatures, after which were measured physiological parameters, including the number of cells, quantum yield, variable fluorescence, and chlorophyll content.

cdm_data_type = Other
VARIABLES:
Genotype (unitless)
Temp (Temperature, degrees Celsius)
Replicate (unitless)
NumberCells (Number Cells, number cells/milliliter (#/mL))
QY (unitless ratio)
Vfl (unitless)
Chla (Concentration Of Chlorophyll In Sea Water, Relative Fluorescence Units)
Chlapercell (Relative Fluorescence Units)


[Synechococcus accessions] - NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay, July 2017 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)

Summary:
NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay.

cdm_data_type = Other
VARIABLES:
Accession (unitless)
Sample_Name (unitless)
SPUID (unitless)
Organism (unitless)
Tax_ID (unitless)
Isolate (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth (m)


[Synechococcus Batch Culture Sampling Data] - Synechococcus batch culture data (cell quotas and ratios (C,N,P), size, and diameter) from laboratory experiments in 2021 to 2022 with related isolates cultured across a range of temperatures (16-25C) (Collaborative Research: The stoichiometric trait distribution of the marine microbiome)

Summary:
Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16-25°C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We collected data at the time of sampling, after cultures grew for seven doublings or one month.   Experiments were conducted from September of 2021 to early 2022.

This dataset includes cell quotas (fmol) for carbon (QC), nitrogen (QN), and phosphorus (QP). It also includes N:P, C:N, and C:P stoichiometry, cell size, and cell diameter (µm) for each Synechococcus strain and clade under each thermal condition.

cdm_data_type = Other
VARIABLES:
Rep (unitless)
Temp (degrees Celsius (degC))
Strain (unitless)
Clade (unitless)
GR (Growth rate per day (d-1))
QN (femtomoles (fmol))
QP (femtomoles (fmol))
QC (femtomoles (fmol))
FSCH (unitless)
CN (unitless)
NP (unitless)
CP (unitless)
Cell_Diameter_um (micrometers (um))
Grams_N (grams (g))
Grams_P (grams (g))
... (10 more variables)


[Synechococcus DOP Displacement Experiment] - Laboratory-cultured Synechococcus (WH8102 and WH5701) MUF-P hydrolysis inhibition by dissolved organic phosphorus (DOP) from experiments between 2018-2023 (Collaborative Research: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle)

Summary:
The affinity of Synechococcus (WH8102 and WH5701) alkaline phosphatases for different DOP model substrates was examined in laboratory experiments through its ability to inhibit the hydrolysis of the fluorogenic substrate 4-methylumbelliferyl phosphate (MUF-P). These data were collected as part of a study of "Dissolved organic phosphorus bond-class utilization by Synechococcus" (Waggoner et al., 2024).

Study Abstract:
Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP's importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5'-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5'-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5'-triphosphate, and then adenosine 5'-monophosphate. The strains' exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus' exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.

cdm_data_type = Other
VARIABLES:
synechococcus_strain (unitless)
MUF_P_conc (micromoles per liter (umol L-1))
... (5 more variables)


[Synechococcus DOP Hydrolysis Experiment - cell counts and IVF] - In vivo fluorescence and flow cytometry cell counts from dissolved organic phosphorus (DOP) hydrolysis experiments with marine cyanobacterium Synechococcus laboratory cultures (WH8102 and WH5701) from 2018-2023 (Collaborative Research: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle)

Summary:
Marine cyanobacterium Synechococcus (WH8102 and WH5701) laboratory culture in vivo fluorescence and flow cytometry cell counts following growth in high and low phosphate media, as part of the DOP hydrolysis experiments in a study of "Dissolved organic phosphorus bond-class utilization by Synechococcus" (Waggoner et al. 2024).

Study Abstract:
Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP's importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5'-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5'-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5'-triphosphate, and then adenosine 5'-monophosphate. The strains' exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus' exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.

cdm_data_type = Other
VARIABLES:
synechococcus_strain (unitless)
time_day (days)
media_and_phosphate_level (unitless)
... (6 more variables)


[Synechococcus DOP Hydrolysis Experiment - hydrolysis rates] - Dissolved organic phosphorus (DOP) hydrolysis rates from marine cyanobacterium Synechococcus (WH8102 and WH5701) laboratory cultures from experiments between 2018-2023 (Collaborative Research: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle)

Summary:
Dissolved organic phosphorus (DOP) hydrolysis rates from marine cyanobacterium Synechococcus (WH8102 and WH5701) laboratory cultures.  These data were collected as part of a study of "Dissolved organic phosphorus bond-class utilization by Synechococcus" (Waggoner et al., submitted).

Study Abstract:
Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP's importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5'-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5'-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5'-triphosphate, and then adenosine 5'-monophosphate. The strains' exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus' exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.

cdm_data_type = Other
VARIABLES:
synechococcus_strain (unitless)
... (7 more variables)


[Synechococcus fluorescence emission spectra] - Fluorescence spectra for 3 strains of Synechococcus while increasing temperatures to detect the photosystem components disassociation temperature (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)

Summary:
Fluorescence spectra from 600-700nm at 530nm excitation for 3 strains of Synechococcus while increasing temperatures to detect the photosystem components disassociation temperature.

cdm_data_type = Other
VARIABLES:
Temperature (degrees Celsius)
Em_nm (nanometers)
LA31_A (percent)
LA31_B (percent)
LA31_C (percent)
LA126_A (percent)
LA126_B (percent)
LA126_C (percent)
LA127_A (percent)
LA127_B (percent)
LA127_C (percent)


[Synechococcus Growth on DOP Experiments - IVF] - Laboratory-cultured Synechococcus (WH8102 and WH5701) growth (vivo fluorescence) on dissolved organic phosphorus (DOP) from experiments between 2018-2023 (Collaborative Research: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle)

Summary:
Laboratory culture Synechococcus (WH8102 and WH5701) growth on dissolved organic phosphorus (DOP). These data were collected as part of a study of "Dissolved organic Phosphorus bond-class utilization by Synechococcus" (Waggoner et al. 2024).

Study Abstract:
Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP's importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5'-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5'-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5'-triphosphate, and then adenosine 5'-monophosphate. The strains' exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus' exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.

cdm_data_type = Other
VARIABLES:
synechococcus_strain (unitless)
experiment_number (unitless)
time_day (days)
DOP_substrate (unitless)
in_vivo_fluorescence_trip1 (relative fluorescence units (RFU))
in_vivo_fluorescence_trip2 (relative fluorescence units (RFU))
in_vivo_fluorescence_trip3 (relative fluorescence units (RFU))


[Synechococcus growth rates] - Growth rates across temperatures for 11 new isolates of marine Synechococcus from Narragansett Bay, July 2017 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)

Summary:
Growth rates across temperatures for 11 new isolates of marine Synechococcus from Narragansett Bay, July 2017.

cdm_data_type = Other
VARIABLES:
Isolate (unitless)
Temp (Temperature, degrees Celsius)
growth_rate_mean (cells/day)
growth_rate_StDev (Growth Rate St Dev, cells/day)


[Synechococcus TPC parameters] - The thermal niche for each of 11 new isolates of marine Synechococcus from Narragansett Bay, July 2017 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)

Summary:
The thermal niche, as calculated from the Thermal Performance Curve (TPC), for each of 11 new isolates of marine Synechococcus from Narragansett Bay, July 2017.

cdm_data_type = Other
VARIABLES:
Isolate (unitless)
topt (degrees Celsius)
tmin (Minimum Temperature, degrees Celsius)
tmax (Maximum Temperature, degrees Celsius)
rsqr (unitless)
width (degrees Celsius)


[Synechococcus_ETSP] - Synechococcus counts determined by epifluorescent microscopy from samples collected on R/V Atlantis cruise AT15-61 in the Eastern Tropical South Pacific in 2010 (Syne_ETSP project) (RAPID: Synechococcus diversity and Fe stress and the relationship to dissolved metals in the Eastern Tropical South Pacific)

Summary:
Synechococcus counts determined by epifluorescent microscopy from samples collected on R/V Atlantis cruise AT15-61 in the Eastern Tropical South Pacific in 2010.

cdm_data_type = Other
VARIABLES:
cruise_id (text)
cruise_synonym (text)
sta (unitless)
date_local (unitless)
month_local (unitless)
day_local (unitless)
year (unitless)
longitude (degrees_east)
lon_360 (Longitude, degrees)
latitude (degrees_north)
depth (m)
cells_per_field (unitless)
vol_filt (mL)
area_filter (um^2)
fields_per_filter (unitless)
abundance (cells/mL)
abund_log (cells/mL)


[Synthesis Product for Ocean Time Series (SPOTS)] - Synthesis Product for Ocean Time Series (SPOTS) (EarthCube RCN for Marine Ecological Time Series (METS))

Summary:
The presented time-series data synthesis pilot product includes data from 12 fixed ship-based time-series programs. The related stations represent unique marine environments within the Atlantic Ocean, Pacific Ocean, Mediterranean Sea, Nordic Seas, and Caribbean Sea. The focus of the pilot has been placed on biogeochemical essential ocean variables: dissolved oxygen, dissolved inorganic nutrients, inorganic carbon (pH, total alkalinity, dissolved inorganic carbon, and partial pressure of CO2), particulate matter, and dissolved organic carbon. The time-series used include a variety of temporal resolutions (monthly, seasonal, or irregular), time ranges (10 to 36 years), and bottom depths (80 to 6000 meters), with the oldest samples dating back to 1983 and the most recent one corresponding to 2021. Besides having been harmonized into the same format (semantics, ancillary data, units), the data were subjected to a qualitative assessment in which the applied methods were evaluated and categorized. Additional data-quality descriptors include precision and accuracy estimates. This data product pilot facilitates a variety of applications that benefit from the collective value of biogeochemical time-series observations and forms the basis for a sustained time-series living data product, complementing relevant products for the global interior ocean carbon data (GLobal Ocean Data Analysis Project), global surface ocean carbon data (Surface Ocean CO2 Atlas; SOCAT), and global interior and surface methane and nitrous oxide data (MarinE MethanE and NiTrous Oxide product).

cdm_data_type = Other
VARIABLES:
TimeSeriesSite (unitless)
CRUISE (unitless)
STNNBR (unitless)
CASTNO (unitless)
BTLNBR (unitless)
DATE (unitless)
TIME_UTC (unitless)
LATITUDE (degrees_north)
longitude (degrees_east)
CTDPRS (decibar (dbar))
SIGMA0 (kilogram per cubic meter (kg/m3))
... (83 more variables)


Summary:
The presented time-series data synthesis pilot product includes data from 12 fixed ship-based time-series programs. The related stations represent unique marine environments within the Atlantic Ocean, Pacific Ocean, Mediterranean Sea, Nordic Seas, and Caribbean Sea. The focus of the pilot has been placed on biogeochemical essential ocean variables: dissolved oxygen, dissolved inorganic nutrients, inorganic carbon (pH, total alkalinity, dissolved inorganic carbon, and partial pressure of CO2), particulate matter, and dissolved organic carbon. The time-series used include a variety of temporal resolutions (monthly, seasonal, or irregular), time ranges (10 to 36 years), and bottom depths (80 to 6000 meters), with the oldest samples dating back to 1983 and the most recent one corresponding to 2021. Besides having been harmonized into the same format (semantics, ancillary data, units), the data were subjected to a qualitative assessment in which the applied methods were evaluated and categorized. Additional data-quality descriptors include precision and accuracy estimates. This data product pilot facilitates a variety of applications that benefit from the collective value of biogeochemical time-series observations and forms the basis for a sustained time-series living data product, complementing relevant products for the global interior ocean carbon data (GLobal Ocean Data Analysis Project), global surface ocean carbon data (Surface Ocean CO2 Atlas; SOCAT), and global interior and surface methane and nitrous oxide data (MarinE MethanE and NiTrous Oxide product).

cdm_data_type = Other
VARIABLES:
TimeSeriesSite (unitless)
CRUISE (unitless)
STNNBR (unitless)
CASTNO (unitless)
BTLNBR (unitless)
DATE (unitless)
TIME (unitless)
LATITUDE (degrees_north)
longitude (degrees_east)
CTDPRS (decibar (dbar))
SIGMA0 (kilogram per cubic meter (kg/m3))
... (98 more variables)


[T Lake 1200-yr Reconstruction] - Record of abundance and δ2H of dinosterol in down core lake sediments from T Lake, Palau collected in September 2013 (Do Parallel Patterns Arise from Parallel Processes?)

Summary:
Record of abundance and \u03b42H of dinosterol in down core lake sediments from T Lake, Palau collected in September 2013 using a 5cm\u2010diameter Colinvaux\u2010Vohnout Livingstone\u2010type rod\u2010operated piston corer.

cdm_data_type = Other
VARIABLES:
depth_cm (Depth, centimeters (cm))
age_ybp (years before present (yr bp))
conc_dino (grams per cubic centimeter (g cm-3))
dbd (micrograms (ug))
flux_dino (micrograms per square centimeter per year (ug cm-2 yr-1))
dino_2H (Dino 2 H, per mil (‰))
dino_2H_1sig (Dino 2 H 1sig, per mil (‰))


[T Lake PC1 Chronology] - 14C dates from core PC1 collected from T Lake, Palau in September 2013 (Do Parallel Patterns Arise from Parallel Processes?)

Summary:
14C dates from core PC1 collected from T Lake, Palau in September 2013 using a Colinvaux\u2010Vohnout Livingstone\u2010type rod\u2010operated piston corer.

cdm_data_type = Other
VARIABLES:
Labcode (unitless)
depth_top (Depth, centimeters (cm))
mat_dated (unitless)
raw_14C (Raw 14 C, years)
raw_14C_err (Raw 14 C Err, years)
calib_14C_95_lo (Calib 14 C 95 Lo, years)
calib_14C_95_up (Calib 14 C 95 Up, years)


[T. pseudonana starve-recover experiments: Cell information] - Diatom (Thalassiosira pseudonana) cell information from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 (EAGER: Diatom Programmed Cell Death at Single-Cell Resolution)

Summary:
This dataset includes cell information for diatom Thalassiosira pseudonana grown during experiments conducted as part of a study of "Single-Cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms."  See "Related Datasets" section for T. pseudonana physiological data and gene information collected as part of the same study and experiments.

Study description:

Diatoms (Bacillariophyceae) are unicellular photosynthetic algae, accounting for about 40% of total marine primary production (equivalent to terrestrial rainforests) and critical ecological players in the contemporary ocean. Diatoms can form enormous blooms in the ocean that can be seen from space and are the base of food webs in coastal and upwelling systems, support essential fisheries, and are central to the biogeochemical cycling of important nutrients such as carbon and silicon. Over geological time, diatoms have influenced the world's climate by changing the carbon flux into the oceans.

Diatoms have traditionally been studied on a population level. Growth is often measured by the total increase in biomass, and gene expression is analyzed by isolating mRNA from thousands or millions of cells. These methods generate a valuable analysis on the population's average functioning; however, they fail to show how each individual diatom cell contributes to the population phenotype. Bulk transcriptomes confound different stages and variability of cell states in heterogeneous populations. By contrast, single-cell transcriptomics measures gene expression in thousands of individual diatoms providing a quantitative and ultrahigh-resolution picture of transient cell states in population fractions enabling the reconstruction of the various phenotypic trajectories. Thus, the single-cell physiological and molecular parameters analysis allows an unsupervised assessment of cell heterogeneity within a population—a new dimension in diatoms and phytoplankton in general.

In this dataset, we examine the model diatom Thalassiosira pseudonana clonal cells grown in different nitrogen conditions, at the single cell level when grown in a light: dark cycle (12:12 h). Nitrogen is the major limiting nutrient for primary production and growth in the ocean's surface, specifically for diatoms and the food webs they support. We investigate nutrient limitation, starvation and recovery. We used droplet-based, single-cell transcriptomics to analyze ten samples in two stages.  In the first stage ("starvation"), six samples were collected over four days of culture as nutrient levels decreased.  In the second stage ("recovery"), four samples were collected over twelve hours after nutrients were replenished.

cdm_data_type = Other
VARIABLES:
stage (unitless)
... (5 more variables)


[T. pseudonana starve-recover experiments: Gene information] - Diatom (Thalassiosira pseudonana) gene information from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 (EAGER: Diatom Programmed Cell Death at Single-Cell Resolution)

Summary:
This dataset includes gene information for diatom Thalassiosira pseudonana grown during an experiment conducted as part of a study of "Single-Cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms."  See "Related Datasets" section for T. pseudonana physiological data and cell information collected as part of the same study and experiments.

Study description:

Diatoms (Bacillariophyceae) are unicellular photosynthetic algae, accounting for about 40% of total marine primary production (equivalent to terrestrial rainforests) and critical ecological players in the contemporary ocean. Diatoms can form enormous blooms in the ocean that can be seen from space and are the base of food webs in coastal and upwelling systems, support essential fisheries, and are central to the biogeochemical cycling of important nutrients such as carbon and silicon. Over geological time, diatoms have influenced the world's climate by changing the carbon flux into the oceans.

Diatoms have traditionally been studied on a population level. Growth is often measured by the total increase in biomass, and gene expression is analyzed by isolating mRNA from thousands or millions of cells. These methods generate a valuable analysis on the population's average functioning; however, they fail to show how each individual diatom cell contributes to the population phenotype. Bulk transcriptomes confound different stages and variability of cell states in heterogeneous populations. By contrast, single-cell transcriptomics measures gene expression in thousands of individual diatoms providing a quantitative and ultrahigh-resolution picture of transient cell states in population fractions enabling the reconstruction of the various phenotypic trajectories. Thus, the single-cell physiological and molecular parameters analysis allows an unsupervised assessment of cell heterogeneity within a population—a new dimension in diatoms and phytoplankton in general.

In this dataset, we examine the model diatom Thalassiosira pseudonana clonal cells grown in different nitrogen conditions, at the single cell level when grown in a light: dark cycle (12:12 h). Nitrogen is the major limiting nutrient for primary production and growth in the ocean's surface, specifically for diatoms and the food webs they support. We investigate nutrient limitation, starvation and recovery. We used droplet-based, single-cell transcriptomics to analyze ten samples in two stages.  In the first stage ("starvation"), six samples were collected over four days of culture as nutrient levels decreased.  In the second stage ("recovery"), four samples were collected over twelve hours after nutrients were replenished.

cdm_data_type = Other
VARIABLES:
stage (unitless)
... (5 more variables)


[T. pseudonana starve-recover experiments: Physiological data] - Diatom (Thalassiosira pseudonana) physiological data from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 (EAGER: Diatom Programmed Cell Death at Single-Cell Resolution)

Summary:
This dataset includes physiological data for diatom Thalassiosira pseudonana grown during experiments conducted as part of a study of "Single-Cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms."  See "Related Datasets" section for T. pseudonana gene and cell information collected as part of the same study and experiments.

Study description:

Diatoms (Bacillariophyceae) are unicellular photosynthetic algae, accounting for about 40% of total marine primary production (equivalent to terrestrial rainforests) and critical ecological players in the contemporary ocean. Diatoms can form enormous blooms in the ocean that can be seen from space and are the base of food webs in coastal and upwelling systems, support essential fisheries, and are central to the biogeochemical cycling of important nutrients such as carbon and silicon. Over geological time, diatoms have influenced the world's climate by changing the carbon flux into the oceans.

Diatoms have traditionally been studied on a population level. Growth is often measured by the total increase in biomass, and gene expression is analyzed by isolating mRNA from thousands or millions of cells. These methods generate a valuable analysis on the population's average functioning; however, they fail to show how each individual diatom cell contributes to the population phenotype. Bulk transcriptomes confound different stages and variability of cell states in heterogeneous populations. By contrast, single-cell transcriptomics measures gene expression in thousands of individual diatoms providing a quantitative and ultrahigh-resolution picture of transient cell states in population fractions enabling the reconstruction of the various phenotypic trajectories. Thus, the single-cell physiological and molecular parameters analysis allows an unsupervised assessment of cell heterogeneity within a population—a new dimension in diatoms and phytoplankton in general.

In this dataset, we examine the model diatom Thalassiosira pseudonana clonal cells grown in different nitrogen conditions, at the single cell level when grown in a light: dark cycle (12:12 h). Nitrogen is the major limiting nutrient for primary production and growth in the ocean's surface, specifically for diatoms and the food webs they support. We investigate nutrient limitation, starvation and recovery. We used droplet-based, single-cell transcriptomics to analyze ten samples in two stages.  In the first stage ("starvation"), six samples were collected over four days of culture as nutrient levels decreased.  In the second stage ("recovery"), four samples were collected over twelve hours after nutrients were replenished.

cdm_data_type = Other
VARIABLES:
Species (unitless)
... (29 more variables)


[T_pseudonana_growth] - Results from metal limitation experiments (Cu, Zn, Fe, Mn) conducted in the diatom T. pseudonana carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011 (Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery)

Summary:
Results from metal limitation experiments (Cu, Zn, Fe, Mn) conducted in the diatom T. pseudonana carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011

cdm_data_type = Other
VARIABLES:
sample (dimensionless)
metal (dimensionless)
condition (dimensionless)
growth_rate (ln(cell density)/day)
growth_rate_se (dimensionless)
p_fe_prime (dimensionless)
p_cu_prime (dimensionless)
p_mn_prime (dimensionless)
p_zn_prime (dimensionless)


[Table 1 - Physical and chemical parameters during egg experiments] - Table 1: Physical and chemical parameters during Calanus finmarchicus and Meganyctiphanes norvegica egg hatching experiments, 2011-2012 (Ocean Acidification-Category 1- Impact of ocean acidification on survival of early life stages of planktonic copepods in the genus Calanus in the northern)

Summary:
During eggs experiments, the general conditions within the tanks were monitored using electrodes for temperature, pH and its millivolt output, salinity, and dissolved oxygen. Results are published in Preziosi et al (2017), Table 1.

cdm_data_type = Other
VARIABLES:
EXPERIMENT (unitless)
EVENT (unitless)
YEAR (year)
MONTH (unitless)
DAY (unitless)
HR (unitless)
MIN (unitless)
ISO_DateTime_local (ISO Date Time Local)
yrday_local (unitless)
TIME_elapsed (hours)
PURPOSE (unitless)
ROWTYPE (unitless)
TEMP_1 (degrees Celsius)
PH_1 (pH units)
PHMV_1 (millivolts)
SAL_1 (parts per thousand (ppt))
DO_1 (% saturation)
TEMP_2 (degrees Celsius)
PH_2 (pH units)
PHMV_2 (millivolts)
SAL_2 (parts per thousand (ppt))
DO_2 (% saturation)
TEMP_3 (degrees Celsius)
PH_3 (pH units)
PHMV_3 (millivolts)
... (13 more variables)


[Table 1. 210Pb, 210Bi, and 210Po activities in rain and lake water] - Table 1: Pb-210, Bi-210, and Po-210 activity measurements in rain, lake water, and dreissenid (Quagga) mussels collected in the Milwaukee Inner Harbor on Lake Michigan, Nov. 2018 (The measurement and use of bismuth-210 as a tracer of particle flux in aquatic systems)

Summary:
Pb-210, Bi-210, and Po-210 activity measurements in rain, lake water, and dreissenid (Quagga) mussels collected at the School of Freshwater Sciences\u2019 slip in the Milwaukee Inner Harbor on Lake Michigan, Nov. 2018. This is table 1 in Waples (2020), Limnol. Oceanogr. Methods.

cdm_data_type = Other
VARIABLES:
sample (unitless)
type (unitless)
ISO_DateTime_Local (ISO Date Time Local, unitless)
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
Pb_dpm (disintegrations/minute/minute^3 (DPM m-3))
Pb_stdev (disintegrations/minute/minute^3 (DPM m-3))
Pb_calc_method (unitless)
Bi_dpm (disintegrations/minute/minute^3 (DPM m-3))
Bi_stdev (disintegrations/minute/minute^3 (DPM m-3))
Bi_calc_method (unitless)
Po_dpm (disintegrations/minute/minute^3 (DPM m-3))
Po_stdev (disintegrations/minute/minute^3 (DPM m-3))
Po_calc_method (unitless)


[Table 2 - Carbonate data and nutrients during egg experiments] - Table 2: Carbonate data and nutrients measured during Calanus finmarchicus and Meganyctiphanes norvegica egg hatching success experiments, 2011-2012 (Ocean Acidification-Category 1- Impact of ocean acidification on survival of early life stages of planktonic copepods in the genus Calanus in the northern)

Summary:
This dataset presents the carbonate system and nutrients measurements during Calanus finmarchicus and Meganyctiphanes norvegica egg hatching success experiments, 2011-2012. Results are published in Preziosi et al (2017), Table 2.

cdm_data_type = Other
VARIABLES:
EXPERIMENT (unitless)
SAMPLING_DATE (unitless)
EVENT (unitless)
TIME_elapsed (hours)
TANK (unitless)
TEMP (Temperature, degrees Celsius)
SAL (parts per thousand (ppt))
ALKALIN (micromol/kilogram)
TCO2 (micromol/kilogram)
NO3_NO2 (Mole Concentration Of Nitrate In Sea Water, micromol/kilogram)
NH4 (Mole Concentration Of Ammonium In Sea Water, micromol/kilogram)
PO4 (Mass Concentration Of Phosphate In Sea Water, micromol/kilogram)
SI (Mass Concentration Of Silicate In Sea Water, micromol/kilogram)
PHTTL (pH units)
XCO2 (parts per million (ppm) in dry gas)
OMCA (unitless)
OMAR (unitless)


[Table 2. Suspended particulate matter (SPM) concentrations in lake water] - Table 2: Suspended particulate matter (SPM) concentrations in lake water (The measurement and use of bismuth-210 as a tracer of particle flux in aquatic systems)

Summary:
Table 2. Suspended particulate matter (SPM) concentrations in lake water, Lake Michigan, Nov. 2018

cdm_data_type = Other
VARIABLES:
sample (unitless)
ISO_DateTime_Local (ISO Date Time Local, unitless)
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
SPM_b (grams/meter^3 (g m-3))


[Table 3 - Hatching success] - Table 3: Calanus finmarchicus and Meganyctiphanes norvegica egg hatching success, 2011-2012 (Ocean Acidification-Category 1- Impact of ocean acidification on survival of early life stages of planktonic copepods in the genus Calanus in the northern)

Summary:
This dataset reports hatching success for eggs of Calanus finmarchicus and Meganyctiphanes norvegica. Average temperature and pH are reported as well as hatching success for each replicate dish of eggs. Results are published in Preziosi et al (2017), Table 3.

cdm_data_type = Other
VARIABLES:
EXPERIMENT (#)
STARTDATE (unitless)
SPECIES (name)
SOURCE (text)
DURATION (hours)
TANK (#)
AVERAGE_TEMP (degrees C)
AVERAGE_PHTTL (pH units)
HS1 (percent)
HS2 (percent)
HS3 (percent)
HS4 (percent)
HS5 (percent)
HS6 (percent)
HS7 (percent)
HS8 (percent)


[Table 3: 210Pb, 210Bi, and 210Po activities in mussels] - Table 3: 210Pb, 210Bi, and 210Po activities in quagga mussels (Dreissena rostriformis bugensis) from Lake Michigan in 2018, from Waples (2020) Limnol. Oceanogr. Methods. (The measurement and use of bismuth-210 as a tracer of particle flux in aquatic systems)

Summary:
Table 3: 210Pb, 210Bi, and 210Po activities in quagga mussels (Dreissena rostriformis bugensis) from Lake Michigan in 2018, from Waples (2020) Limnol. Oceanogr. Methods.

cdm_data_type = Other
VARIABLES:
sample (unitless)
ISO_DateTime_Local (ISO Date Time Local, unitless)
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
Pb_dpm (disintegrations per minute per gram (DPM g-1))
Pb_stdev (disintegrations per minute per gram (DPM g-1))
Bi_dpm (disintegrations per minute per gram (DPM g-1))
Bi_stdev (disintegrations per minute per gram (DPM g-1))
Po_dpm (disintegrations per minute per gram (DPM g-1))
Po_stdev (disintegrations per minute per gram (DPM g-1))


[Tagged kelp size and depth] - Kelp plant size, holdfast size, and depth from five transects at three sites in Santa Barbara Channel, 2015 to 2017 (Linking nearshore kelp forest dynamics to sandy beach ecosystems)

Summary:
This dataset reports depth and size of kelp found along five transects in Santa Barbara Channel in summer of 2015 and 2016, and fall of 2017.

cdm_data_type = Other
VARIABLES:
Year (unitlesss)
Site (unitlesss)
Transect (unitlesss)
Tag_id (unitlesss)
Month (unitlesss)
Day (unitlesss)
Depth_ft (Depth, feet)
depth_m (Depth, meters)
Distance_m (meters)
Fronds_1_m (meters)
Max_diameter_1_cm (centimeters)
Orthogonal_diameter_cm (centimeters)


[Tank conditions in L. pertusa pH experiments] - Tank conditions for pH experiments on Lophelia pertusa specimens collected in the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico)

Summary:
Tank conditions for pH experiments on Lophelia pertusa specimens collected in the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project)

cdm_data_type = Other
VARIABLES:
location (unitless)
pH_treatment (P H Treatment, unitless)
tank (unitless)
day (dimensionless)
DO (micromoles per kilogram (umol/kg))
ttl_alkalinity (micromoles per kilogram (umol/kg))
salinity (Sea Water Practical Salinity, practical salinity unit (PSU))
temperature (celsius)
pH (Sea Water Ph Reported On Total Scale, unitless)
aragonite_saturation_state (unitless)


[Target site benthic survey reef bioerosion - 2014] - Sea urchin bio-erosion of Clathromorphum nereostratum skeleton at central and western Aleutian Islands, Alaska from visual surveys, July 2014 (Ocean Acidification:  Century Scale Impacts to Ecosystem Structure and Function of Aleutian Kelp Forests)

Summary:
Characterization of the degree to which sea urchins have excavated (bio-eroded) the calcium carbonate skeleton of Clathromorphum nereostratum, a long-lived reef-building coralline alga that forms the structural base of the kelp forest. Estimates were derived from field measurements, photoquadrat surveys, and collections, all performed via SCUBA.

cdm_data_type = Other
VARIABLES:
island (unitless)
site_name (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth_feet (Depth, feet)
habitat_type (unitless)
time (seconds since 1970-01-01T00:00:00Z)
replicate (unitless)
Clathromorphum_cover (percent)
grazed_score (unitless)
quality_rank (unitless)
grazed_cover_median (percent)
max_depth_grazed_mm (millimeters)
pit_volume_cm3 (centimeters^3)


[Target site benthic survey urchin density - 2014] - Sea urchin density at each site studied with respect to Clathromorphum bioerosion, at central and western Aleutian Islands, Alaska from visual surveys, July 2014 (Ocean Acidification:  Century Scale Impacts to Ecosystem Structure and Function of Aleutian Kelp Forests)

Summary:
Sea urchin density with respect to Clathromorphum bioerosion at central and western Aleutian Islands, Alaska from visual surveys, July 2014. Estimates were derived from visual surveys, performed via SCUBA.

cdm_data_type = Other
VARIABLES:
island (unitless)
site_name (unitless)
latitude (degrees_north)
longitude (degrees_east)
time (seconds since 1970-01-01T00:00:00Z)
habitat_type (unitless)
depth_feet (Depth, feet)
replicate (unitless)
urchin_density (count per 0.25 m^2)


[Target site benthic survey urchin size biomass - 2014] - Sea urchin size and biomass with respect to Clathromorphum bioerosion at central and western Aleutian Islands, Alaska from visual surveys, July 2014 (Ocean Acidification:  Century Scale Impacts to Ecosystem Structure and Function of Aleutian Kelp Forests)

Summary:
Sea urchin size and biomass with respect to Clathromorphum bioerosion at central and western Aleutian Islands, Alaska from visual surveys, July 2014. Estimates were derived from visual surveys, performed via SCUBA.

cdm_data_type = Other
VARIABLES:
island (unitless)
site_name (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth_feet (Depth, feet)
habitat_type (unitless)
time (seconds since 1970-01-01T00:00:00Z)
quadrat_count (quadrats)
urchin_diameter_mm (millimeters)
urchin_frequency (urchins)
size_biomass_convert (grams)
sum_biomass_class (grams)
urchin_biomass_grams (grams)


[Target site benthic survey vegetation - 2014] - Kelp forest community structure studied with respect to Clathromorphum bioerosion at central and western Aleutian Islands, Alaska from visual surveys, July 2014 (Ocean Acidification:  Century Scale Impacts to Ecosystem Structure and Function of Aleutian Kelp Forests)

Summary:
Kelp forest community structure studied with respect to Clathromorphum bioerosion at central and western Aleutian Islands, Alaska from visual surveys, July 2014. Estimates were derived from visual surveys, performed via SCUBA.

cdm_data_type = Other
VARIABLES:
island (unitless)
site_name (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth_feet (Depth, feet)
habitat_type (unitless)
time (seconds since 1970-01-01T00:00:00Z)
observer (unitless)
replicate (unitless)
Eualaria_fistulosa_density (count per 0.25 m^2)
Laminaria_spp_density (count per 0.25 m^2)
Laminaria_yezoensis_density (count per 0.25 m^2)
Laminaria_longipes_density (count per 0.25 m^2)
Agarum_clathratum_density (count per 0.25 m^2)
Thalassiophyllum_clathrus_density (count per 0.25 m^2)
Cymathaere_triplicata_density (count per 0.25 m^2)
filamentous_red_algae_cover_score (percent cover per 0.25 m^2)
suspension_feeder_cover_score (percent cover per 0.25 m^2)
Desmarestia_spp_cover_score (percent cover per 0.25 m^2)
Codium_spp_cover_score (percent cover per 0.25 m^2)
crustose_coralline_algae_cover_score (percent cover per 0.25 m^2)
erect_calcified_algae_cover_score (percent cover per 0.25 m^2)
shell_cover_score (percent cover per 0.25 m^2)
sand_cover_score (percent cover per 0.25 m^2)
rock_cover_score (percent cover per 0.25 m^2)


[Temperature Data From Tomales Bay and Bodega Harbor] - Temperature data recorded using HOBO Pendant MX2201 loggers deployed at 14 sites in Tomales Bay and Bodega Harbor during August 2019 (Using genomics to link traits to ecosystem function in the eelgrass Zostera marina)

Summary:
To record water temperature, we deployed HOBO Pendant MX2201 loggers (fastened to PVC pipe) in the area from the 14 sites in Tomales and Bodega Harbors from which we collected genetic samples. The pipe was driven into the sediment until the logger was approximately <15 centimeters (cm) above the sediment surface, positioned to rarely be emersed except during low spring tides. We recorded water temperature at 15-minute intervals during a two-week period at all sites from 16 August to 29 August in 2019.

cdm_data_type = Other
VARIABLES:
site (unitless)
Latitude (degrees_north)
longitude (degrees_east)
ISO_DateTime_PDT (unitless)
time (Iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)
temp (degrees Celsius)


[Temperature Data] - Temperature data collected in the bottoms of intertidal rock tide pools at Bodega Marine Reserve intertidal zone, between October 2017 and August 2019 (Collaborative Research: Context-dependency of top-down vs. bottom-up effects of herbivores on marine primary producers)

Summary:
Temperature data collected in the bottoms of intertidal rock tide pools at Bodega Marine Reserve intertidal zone, between October 2017 and August 2019.

cdm_data_type = Other
VARIABLES:
time (Datetimeutc, seconds since 1970-01-01T00:00:00Z)
Site (unitless)
Pool (unitless)
Latitude (degrees_north)
longitude (degrees_east)
TempC (degrees Celsius (°C))
TidBitID (unitless)
Block (unitless)
TrtGroup (unitless)
HerbivoreTreat (unitless)
TempTreat (unitless)
NutrientTreat (unitless)


[Temperature from thermistor chain] - Temperature from a thermistor chain deployed along a 30m depth contour at Mission Beach, CA in June of 2016 (Quantifying plankton dynamics in the internal tide using swarms of buoyancy-controlled robots)

Summary:
Temperature from a thermistor chain deployed along a 30m depth contour at Mission Beach, CA in June of 2016.

cdm_data_type = Other
VARIABLES:
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)
Surface_height (Sea Surface Height, meters (m))
T_surface (degrees Celsius)
T_27_25 (degrees Celsius)
T_26_25 (degrees Celsius)
T_25_25 (degrees Celsius)
T_24_25 (degrees Celsius)
T_23_25 (degrees Celsius)
T_22_25 (degrees Celsius)
T_21_25 (degrees Celsius)
T_20_25 (degrees Celsius)
T_19_25 (degrees Celsius)
T_18_25 (degrees Celsius)
T_17_25 (degrees Celsius)
T_16_25 (degrees Celsius)
T_15_25 (degrees Celsius)
T_14_25 (degrees Celsius)
T_13_25 (degrees Celsius)
T_12_25 (degrees Celsius)
T_11_25 (degrees Celsius)
T_10_25 (degrees Celsius)
T_9_25 (degrees Celsius)
T_8_25 (degrees Celsius)
T_7_25 (degrees Celsius)
T_6_25 (degrees Celsius)
T_5_25 (degrees Celsius)
... (4 more variables)


[Temperature Time Series] - In situ temperature measurements collected at the height of El Niño at Jarvis Island in 2015 and 2016 (Skeletal Records of Coral Reef Bleaching in the Central Equatorial Pacific)

Summary:
This dataset contains in situ temperature measurements collected at the height of El Ni\u00f1o on 12-15 November 2015 and after severe El Ni\u00f1o conditions had subsided on 16-24 May 2016 for the west and east sides of Jarvis Island at 7-10 m depth.

cdm_data_type = Other
VARIABLES:
datetime_UTC (unitless)
latitude (degrees_north)
longitude (degrees_east)
location_label (unitless)
temperature (degrees Celcius (°C))
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)


[Temperature-dependence of juvenile Black sea bass growth and lipid accumulation - Experiment 2] - Temperature-dependence of juvenile Black sea bass growth and lipid accumulation determined through lab experiments conducted from September 2021 to February 2022 at UConn Avery Point (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish)

Summary:
The northern stock of Black sea bass (BSB, Centropristis striata) has greatly expanded over the past decade, potentially due to warming Northwest Atlantic shelf waters affecting overwintering especially in juveniles. To gather better empirical data we quantified winter growth and lipid accumulation in BSB juveniles from Long Island Sound using two complementing experiments. The data from Experiment 2 are presented here.

The data from Experiment 1 are presented in a related dataset (https://www.bco-dmo.org/dataset/897895). Experiment 2 measured the same traits as Experiment 1 but exposed juveniles to a simulated thermal overwinter profile (October - March) with seasonally varying food rations. Monthly individual length growth (GR) and weight-specific growth (SGR) responded in the direction of seasonal food level changes, showing reduced growth in December-February in a 'Winter dip' treatment, but compensatory growth in a 'Winter pulse' treatment. A 6-month consumption average of 1.7% feeding-1 ('Winter pulse') elicited a mean GR of 0.15 millimeters per day (mm d-1) and SGR of 0.55% d-1, whereas juveniles consuming on average 3.8% per feeding ('Winter dip') had significantly faster GR (0.20 mm d-1) and SGR (0.71% d-1). Growth efficiencies ranged between 15-30% and were inversely related to food consumption.

In both experiments, juveniles disproportionally accumulated lipid over lean mass, with lipid proportions tripling in Exp2 from 4% at 65 mm to 12% at 120 mm.

cdm_data_type = Other
VARIABLES:
Site (unitless)
longitude (degrees_east)
latitude (degrees_north)
Date_col (unitless)
Species (unitless)
Tank (unitless)
BSB_ID (unitless)
Group (unitless)
Treat (unitless)
... (34 more variables)


[Temporal Comparison of Mussel (Mytilus californianus) Shell Thickness] - Temporal comparison of mussel (Mytilus californianus) shell thickness determined from shells collected from six study sites along the west coast of North America from 2000 to 2019 (Coastal mosaics of local adaptation and the eco-evolutionary dynamics of a marine predator-prey interaction)

Summary:
Climate change, specifically ocean acidification, is impacting calcification of marine organisms. A reduction in pH has been shown to affect mussel growth and shell thickness along the Pacific coast of North America. Mussels, Mytilus californianus, are a foundation species in rocky shore ecosystems and are prey for a number of taxa, including the Channeled Dogwhelk, Nucella canaliculata, which feeds by drilling a hole through the shell of their prey. Previous research has documented geographic variation in N. canaliculata predator drilling phenotype on Mytilus californianus. However, few studies have assessed how variation in mussel shell traits shape the evolution of this co-evolving predator. Thus, we analyzed M. californianus shell thickness over two decades (2000-2001, 2008-2009, and 2019) and across ~1,000 kilometers of coastline to quantify the prey-driven selection landscape. We analyzed mussel shell thickness at 1/3 the length of the mussel shell as this is the most commonly drilled region. Mussel shells from the central Oregon coast were thicker than those from California. This pattern is associated with geographic variation in predator drilling phenotypes. However, the selective landscape appears to be changing, with recent mussel shells being thinner than a decade prior, particularly on the central Oregon coast. This research highlights the importance of studying species interactions across broad spatial and temporal scales.

cdm_data_type = Other
VARIABLES:
Site (unitless)
Site_Code (unitless)
State (unitless)
Latitude (degrees_north)
longitude (degrees_east)
Date_Collected (unitless)
Year_Collected (unitless)
Time_Period (unitless)
Quadrat_num (unitless)
Mussel_num (unitless)
Shell_Length (millimeters (mm))
Height (millimeters (mm))
... (11 more variables)


[Temporal genetic patterns in plankton] - Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices. (Basin-scale genetics of marine zooplankton)

Summary:
This dataset\u00a0consists of mitochondrial sequence data and specimen
information for two species of copepods, Haloptilus longicornis and
Pleuromamma xiphias, collected at an open ocean time series site in the North
Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the
routine Hawai'i Ocean Time-series (HOT) research cruises from September of
2012 to October of 2013 (HOT-246 to HOT-256).\u00a0Data for Haloptilus
longicornis include\u00a0a 546 base-pair fragment of mitochondrial cytochrome
c oxidase subunit II for each of 483 individuals (mean of 44 animals per
cruise). Data for Pleuromamma xiphias include\u00a0a 551 base-pair fragment of
mitochondrial cytochrome c oxidase subunit I for each of 510 individuals (mean
of 46 animals per cruise). Information is also provided on the HOT cruise
number, date, and specific tow from which each individual was collected. Life
stage and sex of each animal are also noted when identifiable

These data are associated with the forthcoming publication:
 Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It\u2019s about
time: Insights into temporal genetic patterns in oceanic zooplankton from
biodiversity indices.\u00a0 Limnology and Oceanography \u00a0

The unique haplotypes in these data are also available under NCBI accession
numbers KY560470 - KY560514 [Haloptilus longicornis], KY560515 -
KY560565\u00a0[Pleuromamma xiphias].

The following files have been included in this dataset (note that the sequence
IDs in these files differ from the NCBI sequence IDs):
 HOT-HALO.fasta: A fasta-formatted text file containing sequences for a
portion of the mitochondrial cytochrome c oxidase subunit II gene (COII; 546
bp) for 483 Haloptilus longicornis individuals collected at Station ALOHA.

HOT-PLXI.fasta: A fasta-formatted text file containing sequences for a portion
of the mitochondrial cytochrome c oxidase subunit I gene (COI; 551 bp) for 510
Pleuromamma xiphias individuals collected at Station ALOHA.

HALO.csv and PLXI.csv: Converted to csv from an Excel file consisting of one
worksheet for Haloptilus longicornis and one worksheet for Pleuromamma
xiphias. In each worksheet, column headings designate:
 sample_id: the sample ID number associated with the original organism
collected, DNA extraction, and PCR amplification.
 sequence_id: the sample ID number associated with sequences analysed for the
project.
 genus: Genus of the collected organism.
 species: Species of the collected organism.
 cruise: The cruise number for the Hawai'i Ocean Time Series (HOT) cruise on
which the specimen was collected.
 tow: The net tow number on which the specimen was collected.
 collection_date: The date on which the specimen was collected, formatted as
yyyy-mm-dd.
 stage_sex: The life stage (Copepodite or Adult) of the individual, and the
sex (Copepodite, Female, Male).
 stage: The life stage (Copepodite or Adult) of the individual. Column added
by BCO-DMO\u00a0from the original stage_sex column for ease of use.
 sex: The sex (Copepodite, Female, or Male) of the individual.\u00a0Column
added by BCO-DMO\u00a0from the original stage_sex column for ease of use.
 mtCO*_sequence: The mtDNA sequence (COII for Haloptilus longicornis; COI for
Pleuromamma xiphias) associated with that individual. This sequence matches
the sequence associated with the Sequence ID number in the respective fasta
file.

cdm_data_type = Other
VARIABLES:
file_link (unitless)
description (unitless)


[Th-234 activity] - Water column Th-234 activity determined using a 4-L technique from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) (Costa Rica Dome FLUx and Zinc Experiments)

Summary:
Water column Thorium-234 and Uranium-238 measured on the MV1008 cruise in the Costa Rica Dome (CRD) region of the Eastern Tropical Pacific Ocean.

cdm_data_type = Other
VARIABLES:
event (integer)
cast (integer)
cycle (integer)
depth (m)
niskin (integer)
sample (unitless)
latitude (degrees_north)
longitude (degrees_east)
sal (practical salinity units (PSU))
density (kilograms per cubic meter (kg m-3))
U238_activity (decays per minute per liter (dpm L-1))
Th234_activity (decays per minute per liter (dpm L-1))
uncertainty (decays per minute per liter (dpm L-1))
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)


[Thalassiosira pseudonana CCMP1335 endometabolite uptake by Ruegeria pomeroyi DSS-3] - Thalassiosira pseudonana CCMP1335 endometabolite uptake by Ruegeria pomeroyi DSS-3 (Effects of Climate Change Variables on Microbial Autotroph-Heterotroph Carbon Flux)

Summary:
The ocean's temperature increase has fundamental implications for physiological rates and processes of marine microbes. In this study, a marine diatom Thalassiosira pseudonana CCMP1335 was acclimated for three months at temperatures below (14°C), equal to (20°C), and above (28°C). Heterotrophic bacterium Ruegeria pomeroyi DSS-3 was inoculated into cultures, and transporter expression was compared between temperatures.  R. pomeroyi transporter expression leveraged as  a biosensor of available diatom exometabolites indicated temperature-related substitution of diatom osmolytes dimethylsulfoniopropionate (DMSP), dihydroxypropanesulfonate (DHPS), and homarine (dominating carbon transfer at lower temperatures) with glycine betaine and choline (dominating at higher temperatures). T. pseudonana endometabolome pools and biosynthetic pathway expression indicated increased availability of amino acids and glycerol-3-phosphate at higher temperatures. Overall trends across datasets supported a greater importance of organic sulfur compounds in diatom-bacterial metabolite transfer at lower temperatures and greater importance of organic nitrogen compounds at higher temperatures.

cdm_data_type = Other
VARIABLES:
Experiment (unitless)
Sample_ID (unitless)
Metabolomics_Workbench_Project_ID (unitless)
Metabolomics_Workbench_Study_ID (unitless)
Metabolomics_Workbench_Sample_ID (unitless)
Number (unitless)
Temperature (degrees Celsius (°C))
Replicate (unitless)
Culture (unitless)
JGI_Sample_ID (unitless)
Time_Point_h (hours (h))
Bacteria_presence (unitless)
Glycine_Betaine (NMR peak intensity per biovolume)
Proline (NMR peak intensity per biovolume)
DHPS (NMR peak intensity per biovolume)
... (13 more variables)


[Thalassiosira wessiflogii growth rate and TEP] - Results from growth rate experiment with the diatom Thalassiosira wessiflogii in semi-continuous culture; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project) (Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms)

Summary:
Data from laboratory experiment on growth rate and transparent exopolymer particles (TEP) in the diatom Thalassiosira wessiflogii (CCMP 1051) in a semi-continuous culture (four replicate cultures).

cdm_data_type = Other
VARIABLES:
day (dimensionless)
dilution_rate (per day (day-1))
culture (dimensionless)
cell_abundance (cells per milliliter)
cell_vol_mean (cubic micrometers (um^3))
cell_vol_sd (cubic micrometers (um^3))
cell_vol_n (dimensionless)
chla (Concentration Of Chlorophyll In Sea Water, micrograms per liter (ug L-1))
chla_per_cell (Concentration Of Chlorophyll In Sea Water, picograms per cell (pg cell-1))
chla_per_cell_vol (Concentration Of Chlorophyll In Sea Water, femtograms per cubic micrometer (fg um-3))
tot_carb (micrograms per milliliter (ug mL-1))
tot_carb_per_cell (picograms per cell (pg cell-1))
tot_carb_per_cell_vol (femtograms per cubic micrometer (fg um-3))
TEP (TEP per milliliter (TEP mL-1))
TEP_mean_size (square micrometers (um^2))
TEP_sd (square micrometers (um^2))
TEP_n (dimensionless)
tot_TEP_area (square millimeters per milliliter (mm^2 mL-1))
TEP_prod_rate (square millimeters per milliliter per day  (mm^2 mL-1 day-1))
vol_conc (microliters per liter (uL L-1))
vol_conc_sd (microliters per liter (uL L-1))
vol_conc_n (dimensionless)
agg_vol_conc (microliters per liter (uL L-1))
agg_vol_conc_sd (microliters per liter (uL L-1))
agg_vol_conc_n (dimensionless)
... (5 more variables)


[Thaumarchaea transcriptomes] - Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. (Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea)

Summary:
Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.

cdm_data_type = Other
VARIABLES:
Accession (unitless)
Sample_Name (unitless)
Organism (unitless)
Tax_ID (unitless)
Strain (unitless)


[Thermal limits of Acartia tonsa and the effect of isopod parasitism] - Thermal limits of Acartia tonsa and the effect of isopod parasitism from Critical Thermal Maxima (CTmax) experiments conducted with copepods collected from Key Largo, Florida in February 2023 (Linking eco-evolutionary dynamics of thermal adaptation and grazing in copepods from highly seasonal environments)

Summary:
Acartia tonsa were collected from Key Largo, Florida in February 2023. A portion of the adult female copepods in this collection were parasitized by juvenile bopyrid isopods. We measured thermal limits (as Critical Thermal Maximum) for individuals with and without these parasites. Data were collected by Dr. Matthew Sasaki.

cdm_data_type = Other
VARIABLES:
experiment (unitless)
experiment_date (unitless)
experiment_day (unitless)
experiment_month (unitless)
experiment_year (unitless)
tube (unitless)
bopyrid (unitless)
ctmax (degrees Celsius)


[Thread mechanics] - Lab study on the effect of temperature and pCO2 on mussel byssal attachment (thread mechanics) with mussels collected in May 2012 from Argyle Creek, San Juan Island, WA (48.52˚ N, 123.01˚ W) (Effects of Ocean Acidification on Coastal Organisms: An Ecomaterials Perspective)

Summary:
These data were used in a structural analysis study to evaluate how pCO2 and an additional stressor, elevated temperature, influences byssal thread quality and production. Mussels (M. trossulus) were collected in May 2012 from Argyle Creek, San Juan Island, WA (48.52\u02da N, 123.01\u02da W) and held in a mesh box submerged under the dock at Friday Harbor Laboratories (FHL), San Juan Island, WA for up to 14 d. Mussels were placed in controlled temperature and pCO2 treatments in the Ocean Acidification Experimental Laboratory (OAEL), then newly produced threads were counted and pulled to failure to determine byssus strength.

cdm_data_type = Other
VARIABLES:
Mussel_ID (unitless)
Temp (Temperature, degrees Celcius (°C))
pH (Sea Water Ph Reported On Total Scale, unitless)
pCO2_Target (P CO2 Target, microatmosphere (uatm))
Treatment_ID (unitless)
Trial (unitless)
GI (unitless)
CI (gram per cubic millimeter (g/mm^3))
Distal_Diam (millimeter (mm))
Prox_Major (millimeter (mm))
Prox_Minor (millimeter (mm))
Yield (Newton (N))
Location (unitless)
Breaking_Ext (millimeter (mm))
Breaking_Force (Newton (N))
Plaque_Force (Newton (N))
Proximal_Force (Newton (N))
Distal_Force (Newton (N))
Breaking_Stress (Newton per square millimeter (N/mm^2))
Youngs_Mod (Newton per square millimeter (N/mm^2))
Thread_Stiffness (Newton per square millimeter (N/mm^2))
Thread_Ext (unitless)


[Thread number] - Lab study on the effect of temperature and pCO2 on mussel byssal attachment (thread number) with mussels collected in May 2012 from Argyle Creek, San Juan Island, WA (48.52˚ N, 123.01˚ W) (Effects of Ocean Acidification on Coastal Organisms: An Ecomaterials Perspective)

Summary:
These data were used in a structural analysis study to evaluate how pCO2 and an additional stressor, elevated temperature, influences byssal thread quality and production. Mussels (M. trossulus) were collected in May 2012 from Argyle Creek, San Juan Island, WA (48.52\u02da N, 123.01\u02da W) and held in a mesh box submerged under the dock at Friday Harbor Laboratories (FHL), San Juan Island, WA for up to 14 d. Mussels were placed in controlled temperature and pCO2 treatments in the Ocean Acidification Experimental Laboratory (OAEL), then newly produced threads were counted and pulled to failure to determine byssus strength.

cdm_data_type = Other
VARIABLES:
Mussel_ID (unitless)
Temp (Temperature, degrees Celcius (°C))
pH (Sea Water Ph Reported On Total Scale, unitless)
pCO2_Target (P CO2 Target, micro atmosphere (uatm))
pCO2_Measured (P CO2 Measured, micro atmosphere (uatm))
Treatment_ID (unitless)
Thread_Count (unitless)
Trial (unitless)


[Three-Prime Tag-Sequencing (3' Tag-Seq) Data for Pisaster ochraceus] - Bioproject accession information on tag-sequence data for Pisaster ochraceus samples collected from Bodega Bay, CA, in July 2019 (Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath)

Summary:
Outbreaks of sea star wasting (SSW) have killed millions of sea stars across over 20 taxa in the last decade alone, threatening the health and stability of coastal communities around the world. While the causative agent remains unknown, it has recently been postulated that hypoxia exposure may play a dominant role in the onset of SSW. We leveraged a study that subjected ochre sea stars to organic matter amendment in a controlled laboratory setting to induce hypoxia and used a repeated sampling design to collect non-invasive tissue samples from both healthy and wasting individuals. Following tag-based RNAseq (TagSeq), we analyzed differential gene expression (DGE) patterns among and within these individuals sampled strategically throughout the 15-day experiment. Transcriptional profiles reveal a progressive change in gene expression accompanying the advancement of SSW, reflecting a transition from asymptomatic stars to the onset of characteristic SSW lesions that progressively worsen until, in some cases, the star dies of their symptoms. Included in this dataset is the accession information for 89 individual TagSeq samples across 20 individual Pisaster ochraceus sea stars at multiple time points during the study to make them available for subsequent re-evaluation. The sequence data have been deposited into the NCBI archive under BioProject PRJNA1116313 and will be publicly available on 2025-08-01.

cdm_data_type = Other
VARIABLES:
sample_name (unitless)
bioproject_accession (unitless)
bioproject_ncbi (unitless)
assay_type (unitless)
organism (unitless)
isolate_id (unitless)
isolation_source (unitless)
collection_date (unitless)
geo_loc_name (unitless)
latitude (degrees_north)
longitude (degrees_east)
tissue (unitless)
biomaterial_provider (unitless)
collected_by (unitless)
host_tissue_sampled (unitless)