[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)

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)

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)

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)

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)

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)

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)

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)


[Sulfate triple oxygen isotope signatures in Messinian evaporite and barite] - Sulfate triple oxygen isotope signatures in Messinian evaporite and barite from cores collected (Collaborative Research: Development of a novel way for understanding ancient Earth atmospheres and marine sulfate using the stable isotope of Oxygen (17O) in marine barite.)

These data include the triple oxygen isotope compositions (Delta'17O and delta18O) of marine sulfate minerals, including Messinian-age evaporite, Messinian-age barite, and modern barite. Samples were collected from outcrop (Messinian evaporite from the Caltanissetta and Sorbas Basins) as well as from Integrated Ocean Drilling Program (IODP) cores (evaporite from the Tyrrhenian Basin, and all barite). Instruments used to measure the oxygen isotope compositions included a High Temperature Conversion Elemental Analyzer (TC/EA) coupled to a Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) and a custom built laser fluorination line coupled to a 253 Plus IRMS, in the Johnston lab at Harvard University. These measurements contributed to our understanding of how closely marine evaporite sulfate records reflect ancient seawater sulfate isotope composition and the degree to which sulfate within an evaporite basin is microbially cycled. Anna Waldeck and Haley Olson, both students in David Johnston's lab, measured the oxygen isotope compositions.

cdm_data_type = Other
VARIABLES:
Identifier_1 (unitless)
Identifier_2 (unitless)
Cycle (unitless)
Estimated_Height (meters (m))
d18O_TCEA (permil)
O2_Yield (percent (%))
d17O_VSMOW_SLAP (permil)
d18O_VSMOW_SLAP (permil)
Delta_prime_17O_VSMOW_SLAP (permil)
n (unitless)
latitude (degrees_north)
longitude (degrees_east)


[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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 WH8102 chemostats] - Semi-quantitative cell proteome of marine Synechococcus WH8102 using DIA-MS, interactive nutrient-temperature responses in stable chemostat bioreactors from laboratory experiments conducted in 2019 (Convergence: RAISE: Linking the adaptive dynamics of plankton with emergent global ocean biogeochemistry)

This proteomic data set was prepared to determine how the distribution of protein-based traits contribute to cellular elemental stoichiometry of a globally-abundant, surface ocean phytoplankton in response to nutrient stress under variable temperature conditions. Cellular proteins are from laboratory chemostat cultures of marine Synechococcus isolate WH8102 (clade III). Proteins were extracted from cells grown under stable, steady-state conditions in a low-phosphorus medium (N:P=80) and a low-nitrate medium (N:P=1.7) across 3 temperatures of 20, 24, and 28˚C (for a total of 6 chemostat cultures) at a white light density of 125 µmol quanta-1 m-2 s-1 on a 12-hour-light:12-hour-dark diel cycle, at a continuous dilution rate of 0.18 d-1, in fall of 2019. Cells and proteins were collected at 5 mid-light-period time points on non-consecutive days to yield a total of 30 samples. Culture work was performed at the University of California, Irvine by Adam Martiny's group. Proteins were analyzed with data-independent acquisition mass spectrometry proteomics methods by Mak Saito's group at the Woods Hole Oceanographic Institution. Data are exclusive peak area intensities of proteins with 2 or more representative peptides, normalized with Scaffold (2.2.1) DIA proteome software. Peptides were analyzed using a Michrom Advance HPLC system coupled to a Q-Exactive mass spectrometer (Thermo Scientific instrument version 2.8) with a Michrom Advance CaptiveSpray source, using the constant injection concentration of 1 µg/µL to allow uniformity across the dataset. Data with more details are published in Garcia et al. (2024) Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change (DOI:10.1093/ismejo/wrae046).

cdm_data_type = Other
VARIABLES:
Protein_ID_long_form (unitless)
Protein_ID_short_form (unitless)
Gene_name1 (unitless)
Gene_name2 (unitless)
Protein_name (unitless)
Molecular_Weight (kilodalton (kDa))
Peptide_Count (unitless)
Sample_Number (unitless)
Temp_chemostat (Degrees Celsius)
... (4 more variables)


[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)

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))

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)


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?)

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?)

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)

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)

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)

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)

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)


[TA HDPE bottle storage test] - Total alkalinity from an experiment testing the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples using laboratory-manipulated oligotrophic Atlantic surface water (US GEOTRACES GP17-OCE and GP17-ANT: Inorganic Carbon Cycling in the South Pacific and Southern Oceans by Direct Measurement)

Total alkalinity plays an important role in buffering seawater and determining how much anthropogenic carbon dioxide the oceans can absorb and mitigate the rise in atmospheric concentrations. Total alkalinity varies with location, depth, and time making it an important variable needed to quantify and monitor ocean acidification, and potentially for ocean alkalinity enhancement interventions. Currently, best practices are to use expensive high quality borosilicate glass bottles for collecting and storing these samples. However, unlike other carbon system variables, total alkalinity is not affected by gas exchange meaning plastic bottles may be suitable for total alkalinity sample storage. Plastic bottles are lighter, cheaper, and less prone to breakage making them easier to handle and ship. Here, we test the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples through laboratory experiments where HDPE bottles were treated to different cleaning methods and then filled with surface seawater and stored for 15-17 months before analyzing for total alkalinity. It was determined that HDPE is not suitable for long-term storage of total alkalinity samples as there were large changes in total alkalinity over time and precision of duplicate samples was very poor. We hypothesize that HDPE plastic is slightly porous leading to leaching of alkalinity either into or out of the bottle over time impacting the value of the sample. Use of HDPE bottles for total alkalinity samples is not recommended for long term sample storage.

cdm_data_type = Other
VARIABLES:
Bottle_ID (unitless)
Soak_solution (unitless)
Soak_Duration (weeks)
Bottle_Number (unitless)
Analysis_Date_Time_EST (unitless)
Total_Alkalinity (micromoles per kilogram seawater (umol/kg_sw))
Analysis_Flag (unitless)


[TA HDPE glass bottle comparison] - Total alkalinity determined through experiments comparing usage of high-density polyethylene (HDPE) and borosilicate glass bottles for collection and storage of water samples collected on the GEOTRACES GP17-OCE cruise (R/V Roger Revelle RR2214) (US GEOTRACES GP17-OCE and GP17-ANT: Inorganic Carbon Cycling in the South Pacific and Southern Oceans by Direct Measurement)

Total alkalinity plays an important role in buffering seawater and determining how much anthropogenic carbon dioxide the oceans can absorb and mitigate the rise in atmospheric concentrations. Total alkalinity varies with location, depth, and time making it an important variable needed to quantify and monitor ocean acidification, and potentially for ocean alkalinity enhancement interventions. Currently, best practices are to use expensive high quality borosilicate glass bottles for collecting and storing these samples. However, unlike other carbon system variables, total alkalinity is not affected by gas exchange meaning plastic bottles may be suitable for total alkalinity sample storage. Plastic bottles are lighter, cheaper, and less prone to breakage making them easier to handle and ship. Here, we test the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples. Duplicate samples were collected in standard borosilicate glass bottles and HDPE bottles on GEOTRACES GP17-OCE. The samples were analyzed in the laboratory over a year later and the storage methods were compared. It was determined that HDPE is not suitable for long-term storage of total alkalinity samples as there were large changes in total alkalinity over time and precision of duplicate samples was very poor. We hypothesize that HDPE plastic is slightly porous leading to leaching of alkalinity either into or out of the bottle over time impacting the value of the sample. Use of HDPE bottles for total alkalinity samples is not recommended for long term sample storage.

cdm_data_type = Other
VARIABLES:
GEOTRACES_sample (unitless)
Event_number (unitless)
Date (unitless)
time_unitless (Time, unitless)
time (Iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)
Sample_ID (unitless)
Station (unitless)
Cast (unitless)
Niskin (unitless)
latitude (degrees_north)
... (7 more variables)


[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)

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)

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)

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)

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)

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)

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)

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)

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)


[Tapajos River DOM] - Dissolved organic matter, water quality, water isotopes, and discharge measurements of the Tapajós River, Brazil from 2016-2023 (RAPID: El Nino Event Impacts on Organic Matter Export and Composition in the Amazon River)

This data includes near monthly measurements of discharge, water isotopes, water quality, and dissolved organic matter characteristics from the Tapajós River, Brazil between 2016-2023. Dissolved organic matter was characterized via dissolved organic carbon quantification, optical spectroscopy, fluorescence spectroscopy, parallel factor analysis modeling (PARAFAC), and Fourier transform-ion cyclotron resonance mass spectrometry. Pairing geochemical and molecular-level data reveal both seasonal and inter annual patterns of carbon export to the Amazon River system and processing within the river network.

cdm_data_type = Other
VARIABLES:
Sample_Name (unitless)
Date (unitless)
Date_ISO (unitless)
latitude (Lat_dd, degrees_north)
longitude (Lon_dd, degrees_east)
Discharge_on_sampling_day (cubic meters per second (m3 s-1))
Mean_monthly_discharge (cubic meters per second (m3 s-1))
Mean_daily_air_temp (degrees Celsius (degC))
Daily_precipitation (millimeters (mm))
Mean_monthly_air_temp (degrees Celsius (degC))
Monthly_precipitation (millimeters (mm))
DOC (milligrams per liter (mg L-1))
FI (unitless)
a350 (per meter (m-1))
S275_to_295 (per nanometer (nm-1))
S350_to_400 (per nanometer (nm-1))
SUVA254 (liters per milligram carbon per meter (L mg C-1 m-1))
perc_CHO (percent (%))
perc_CHON (percent (%))
perc_CHOS (percent (%))
perc_CHONS (percent (%))
... (32 more variables)


[Tapajos River FT-ICR MS peaks] - Fourier Transform-Ion Cyclotron Resonance Mass spectrometry (FT-ICR MS) peaks lists from the Tapajós River, Brazil from 2016-2023 (RAPID: El Nino Event Impacts on Organic Matter Export and Composition in the Amazon River)

This dataset includes assigned mass spectral peak lists from river water sampled near-monthly from the Tapajós River, Brazil between 2016-2023. Data were collected on a 21 T Fourier Transform-Ion Cyclotron Mass Spectrometer in electrospray negative ionization from solid phase DOM extracts. Trends in peak presence/absence and relative abundance reveal changes to DOM sourcing based on hydroclimate and multiyear climate anomalies.

cdm_data_type = Other
VARIABLES:
Sample (unitless)
Date_ISO (unitless)
latitude (Lat_dd, degrees_north)
longitude (Lon_dd, degrees_east)
Exp_mass (Daltons (Da))
Theor_mz (Daltons (Da))
Error (parts per million (ppm))
Filez_RA (unitless)
DBE (unitless)
HC (unitless)
OC (unitless)
Molecular_Formula (unitless)
C (count)
Hion (count)
N (count)
O (count)
S (count)
C13 (count)
H (count)
P (count)
AImod (unitless)
NC (unitless)
SC (unitless)
NOSC (unitless)
Formula (unitless)
Class (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)

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)

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)

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)

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)


[Targeted metabolomics data from coral and sea anemone larvae exposed to normoxic or hypoxic conditions] - Targeted metabolomics data from coral and sea anemone larvae exposed to normoxic or hypoxic conditions in lab and field experiments performed in USA and Bermuda during 2023-2024 (CAREER: Helping or hindering? Determining the influence of repetitive marine heatwaves on acclimatization of reef-building corals across biological scales)

These data arose from larvae of the sea anemone Nematostella vectensis and corals Galaxea fascicularis and Porites astreoides exposed to normoxic (i.e., control) or hypoxic conditions. Larvae were sampled in groups of 20-30 and these samples were processed for targeted metabolomics at the University of Pennsylvania Metabolomics Core. The dataset contains the species from which metabolomics data originate, experimental treatment (normoxia or hypoxia), experiment metadata, and abundance of each metabolite in each sample.

cdm_data_type = Other
VARIABLES:
Species (units)
Treatment (units)
Cohort (units)
Group (units)
Life_stage (units)
Hours_post_treatment (hours)
ADP (nmol mg protein-1)
AMP (nmol mg protein-1)
ATP (nmol mg protein-1)
cAMP (nmol mg protein-1)
CMP (nmol mg protein-1)
CTP (nmol mg protein-1)
GDP (nmol mg protein-1)
GMP (nmol mg protein-1)
GTP (nmol mg protein-1)
ITP (nmol mg protein-1)
NAD (nmol mg protein-1)
NADP (nmol mg protein-1)
NAM (nmol mg protein-1)
NMN (nmol mg protein-1)
TTP (nmol mg protein-1)
UMP (nmol mg protein-1)
... (67 more variables)


[Temp & DO effects on sponges: mesocosm experimental data] - Sponge mesocosm data testing effects of temperature and dissolved oxygen on sponge filtration from experiments conducted (RAPID: Consequences of Rapid Environmental Change on Pelagic-to-Benthic Coupling by Sponges on the Continental USAs only Barrier Reef Ecosystem)

This dataset contains the data from the mesocosm experiments described in the following study description.  See the "Related Datasets" section for more datasets from this study.

Study description:

Climate change is quickly altering marine environments by increasing sea surface temperatures and decreasing dissolved oxygen (DO) levels. Although these effects have been well-studied on the declining corals, the impact of temperature and dissolved oxygen extremes on the functional roles of sponges remains primarily unexamined. This study, conducted in the Lower Florida Keys, FL (USA) had two objectives: (1) compare sponge abundance and size distributions on hardbottom before and after the summer 2023 heatwave, and (2) investigate the filtration capacity of eight common sponge species from the Florida Keys with different morphologies (tubular vs. spherical) and microbial associations (HMA vs LMA) in mesocosms that simulated elevated temperature and hypoxic conditions for ~45 minutes. Field surveys by divers at the same 24 sites in May 2023 and June 2024 revealed that the abundance and size of spheroid sponges (e.g., Speciospongia vesparium, Hippospongia lachne) declined after the heatwave, but no noticeable effects were detected among the other species surveyed. The mesocosm experiments revealed tubular and LMA sponges consistently exhibited higher filtration efficiency of high nucleic acid (HNA) bacteria than spherical and HMA sponges under most treatment conditions. Elevated temperatures (2.5 to 5°C above ambient) significantly reduced HNA bacteria filtration capacity in spherical and HMA sponges (-43.6% ± 5.1 to -21.5% ± 4.4), whereas LMA tubular sponges were unfazed (-52.3% ± 11.6% to -62.6% ± 8.8%). The findings imply that future reef communities may shift toward more sponge dominance, particularly by heat and hypoxia-resistant, fast-growing LMA species, potentially altering ecosystem functions like water quality regulation, nutrient cycling, and habitat structure.

cdm_data_type = Other
VARIABLES:
Date (unitless)
Day (days)
Table (unitless)
Tank (unitless)
... (49 more variables)


[Temperature and light perturbations] - Incomplete assimilatory nitrate reduction by LLI Prochlorococcus in response to light and temperature stress (Features and implications of nitrogen assimilation trait variability in populations of Prochlorococcus)

These data include Prochlorococcus cell density, nitrate (NO3-) and nitrite (NO2-) concentration, and fluorometry data for experiments that examined nitrite production by LLI Prochlorococcus following a pulse of nitrate under stress conditions. The conditions evaluated included light shock, and temperature shock.

cdm_data_type = Other
VARIABLES:
Experiment (unitless)
ExpSampleID (unitless)
Strain (unitless)
Rep (unitless)
ExpCondition (unitless)
N_source (unitless)
Light_Intensity (micromoles photones per square meter per second (umol photons m-2 s-1))
Light_Color (unitless)
Temperature (Degrees Celsius (°C))
Culture_ID (unitless)
ExpTime (minutes)
ISOTime (unitless)
Nitrite_Concentration (micromoles nitrite per liter (umol nitrite L-1))
Nitrite_Concentration_Notes (unitless)
Cell_Concentration_FCM (cells per milliliter (cells mL-1))
FRRF_filename (unitless)
FCM_filename (unitless)
FCM_Beads_Filename (unitless)
FCM_blank_filename (unitless)


[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)

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)

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 effects on bryozoan growth and reproduction] - Differential effects of temperature on multiple components of fitness in a modular animal (Bugula neritina) reveal how temperature affects reproductive capacity (Consequences of kin structure in benthic marine systems)

Thermal performance curves (TPCs) are important tools for predicting the sensitivity of populations to climate change. The goal of this study was to assess and compare the relationships between temperature and different life-history components in a modular animal to reveal the mechanisms underlying TPCs for fitness. We reared replicated clones of the marine bryozoan Bugula neritina across a thermal gradient (16 values) ranging from 23 to 32°C, which reflected the upper thermal range of seasonal variation in the field. TPCs were constructed for survival (measured as zooids states within a colony), growth rate, development to reproductive maturity and reproductive capacity, which were measured over much of the realized lifespan expected under field conditions (~30 days). The effect of temperature was more acute on zooid states rather than whole-colony survival, and increased temperature increased the frequency of polypide regression. Most colonies reached reproductive maturity up to ~30°C, but growth rate and reproduction decreased at temperatures beyond ~25°C. The decline in reproductive capacity over temperatures above ~25°C was then due to the decline in the production of zooids capable of brooding embryos and zooids transitioning to regressed states up until about 30°C and transitioning to dead state beyond that.

cdm_data_type = Other
VARIABLES:
colony (unitless)
genotype (unitless)
fragment (unitless)
tankID (unitless)
target_temp (degrees Celsius (°C))
realized_temp (degrees Celsius (°C))
incubator (unitless)
date (unitless)
colony_age_days (unitless)
days_since_cutting (unitless)
days_since_being_put_into_treatment (unitless)
zooids_starting (unitless)
ovicells_count (unitless)
zooids_feeding (unitless)
zooids_regressed (unitless)
zooids_dead (unitless)
zooids_total (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)

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)

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)

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)