[St. Joseph Bay Urchin Surveys - 2016 and 2019] - Herbivorus green sea urchin counts from surveys conducted in St. Joseph Bay, Florida, USA in May 2016 and August 2019 (RAPID: Species on the Move: Tropicalization of Western Atlantic Seagrass Beds)

Summary:
The herbivorus green sea urchin (Lytechinus variegatus) was surveyed across the southern part of St. Joseph Bay at 16 sites spaced approximately 1 nautical mile apart. Initial surveys were performed in May 2016 as part of a prior study of seagrass coverage, reproduction, and herbivore intensity. Using RAPID funds, the same survey was conducted in August 2019, 11 months after Hurricane Michael, an extremely powerful category 5 tropical cyclone, made landfall nearby with devastating effects. Densities were recorded by snorkelers in 5 replicate, haphazardly thrown 0.25-m2 quadrats at each site.

Comparing pre- and post-hurricane urchin densities allows for estimates of how Hurricane Michael's passage impacted resident urchin densities. These data were collected by Dorothy Byron and Alexandra Rodriguez of the Dauphin Island Sea Lab.

cdm_data_type = Other
VARIABLES:
UID (unitless)
Year (unitless)
MMDD (unitless)
Date (unitless)
site (unitless)
planned_lat (degrees_north)
planned_long (degrees_east)
latitude (Visited_lat, degrees_north)
longitude (Visited_long, degrees_east)
surveyor (unitless)
urchin_count (number of individuals per 0.5m x 0.5m quadrat)
urchins_m2 (number of indviduals/m2)


[Stability of symbionts in corals] - Diversity, distribution, and temporal stability of coral 'zooxanthellae' on a Pacific reef evaluated with samples collected in Palau from 2013 to 2022 (Collaborative Research: Stability, flexibility, and functionality of thermally tolerant coral symbioses)

Summary:
This data set provides information about the long-term composition of symbiont populations within individual coral colonies. Diverse coral taxa (Scleractinia) from a West Indo-Pacific fore reef (Palau) were tagged and sampled at various intervals--ranging from six months to several years--over nine years' time. Symbiont identity was examined using multiple genetic markers that resolved symbiont diversity to species and individual genotypes (i.e. clonal strains). Consistent with previous colony monitoring studies, symbiont populations in a majority of colonies were dominated by one species and one strain (based on multi-locus genotyping) over multiple years. Thus, the distribution of symbiont diversity at the genus, species and clone level, comprising specific and stable partner combinations, scale predictably to reef habitat, host taxon, and individual colony.

cdm_data_type = Other
VARIABLES:
Symbiont_species (unitless)
Colony_and_Month (unitless)
Host_Genera (unitless)
Host_Species (unitless)
Genotype (unitless)
C1_22_allele_1 (base pairs (number of nucleotides))
C1_22_allele_2 (base pairs (number of nucleotides))
C1_25_allele_1 (base pairs (number of nucleotides))
C1_25_allele_2 (base pairs (number of nucleotides))
C1_24_allele_1 (base pairs (number of nucleotides))
C1_24_allele_2 (base pairs (number of nucleotides))
C1_05_allele_1 (base pairs (number of nucleotides))
C1_05_allele_2 (base pairs (number of nucleotides))
Zoa_33_allele_1 (base pairs (number of nucleotides))
Zoa_33_allele_2 (base pairs (number of nucleotides))
C1_16_allele_1 (base pairs (number of nucleotides))
C1_16_allele_2 (base pairs (number of nucleotides))
Z1_Spl_1_allele_1 (base pairs (number of nucleotides))
... (5 more variables)


[Stable C and O isotopes for Guaymas Basin and Sonora Margin sediments] - d13C and d18O isotopic data for carbonate nodules and sedimentary carbonates in Guaymas Basin and Sonora Margin sediments collected from R/V El Puma, leaving Guaymas on October 14, 2014 and returning to Mazatlan on October 27, 2014 (RAPID proposal: Site characterization cruise to document the active and extensive subsurface biosphere in the Guaymas Basin)

Summary:
d13C and d18O isotopic data for carbonate nodules and sedimentary carbonates in Guaymas Basin and Sonora Margin sediments collected from R/V El Puma (the Pacific Coast research vessel of the Autonomous University of Mexico) from October 14, 2014 to October 27, 2014.\r\n\r\nData for each core include: sample identification (core No., section number, cm within section, sample type), total sediment depth in cm, and d\u00b9\u00b3C isotopic composition in permille. background = sediment around the nodule.

cdm_data_type = Other
VARIABLES:
Core_section_cm (unitless)
cm_in_core (centimeters (cm))
sample_type (unitless)
d13C (D13 C, per mil (‰))
d13C_stdev (D13 C Stdev, per mil (‰))
d18O (D18 O, per mil (‰))
d18O_stdev (D18 O Stdev, per mil (‰))


[Stable Isotope measurements – experimental animals] - Carbon and Nitrogen stable isotope measurements for experimental animals used in laboratory-based experiments collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022 (Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons)

Summary:
Carbon and Nitrogen stable isotope measurements for experimental animals used in laboratory-based experiments collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022. Laboratory experiments took place at the Fisheries and Mariculture Laboratory of the University of Texas Marine Science Institute from July 2021 to November 2022.

cdm_data_type = Other
VARIABLES:
Taxon (unitless)
Tissue_sampled (unitless)
Length (centimeters (cm))
Tank_number (unitless)
Acclimation_days (days)
Days_after_acclimation (days)
Treatment (unitless)
Diet_fed (unitless)
Notes (unitless)
Primary_check (unitless)
d13C (per mil)
percent_C (percentage)
d15N (per mil)
percent_N (percentage)


[Stable Isotope measurements – field and lab samples] - Carbon and Nitrogen stable isotope measurements for various marine samples collected from the Gulf of Mexico as well as eggs, animals, and food sources collected in the laboratory and commercial sources from 2020 to 2022. (Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons)

Summary:
Carbon and Nitrogen stable isotope measurements for various marine samples collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022 as well as eggs, animals, and food sources from the laboratory and commercial sources from 2020 to 2022.

cdm_data_type = Other
VARIABLES:
Taxon (unitless)
Common_name (unitless)
Sample_ID (unitless)
Classification (unitless)
Weight (milligrams (mg))
Date_collected (unitless)
Site (unitless)
Length (centimeters (cm))
Notes (unitless)
Primary_check (unitless)
d13C (per mil)
percent_C (percentage)
d15N (per mil)
percent_N (percentage)


[Stable Isotopes and Elemental Ratios] - C and N stable isotopes and elemental ratios of high and low molecular weight (HMW, LMW) DOM collected from the North Pacific Subtropical Gyre and Central North Atlantic determined by elemental analyzer isotope ratio mass spectrometry (EA-IRMS) (The Microbial Nitrogen Pump: Coupling 14C and Compound-specific Amino Acids to Understand the Role of Microbial Transformations in the Refractory Ocean DON Pool)

Summary:
C and N stable isotopes and elemental ratios of high and low molecular weight (HMW, LMW) DOM collected from the North Pacific Subtropical Gyre and Central North Atlantic determined by elemental analyzer isotope ratio mass spectrometry (EA-IRMS). These data were published in Broek et al. (2019) and Broek et al. (2017).

cdm_data_type = Other
VARIABLES:
location (unitless)
year (unitless)
season (unitless)
sample_type (unitless)
depth (m)
wt_pcnt_C (unitless (percent))
wt_pcnt_C_stdev (unitless (percent))
wt_pcnt_N (unitless (percent))
wt_pcnt_N_stdev (unitless (percent))
d15N (D15 N, permil (‰))
d15N_stdev (D15 N Stdev, permil (‰))
d13C (D13 C, permil (‰))
d13C_stdev (D13 C Stdev, permil (‰))
C_N_ratio (unitless)
C_N_ratio_stdev (unitless)


[Stable Isotopes in Reactive Si Pools] - Stable isotopes in reactive silica pools of Mississippi River plume sediments collected aboard the R/V Pelican in May 2017 (The biotic and abiotic controls on the Silicon cycle in the northern Gulf of Mexico)

Summary:
Stable isotopes in reactive silica pools of Mississippi River plume sediments collected aboard the R/V Pelican in May 2017

cdm_data_type = Other
VARIABLES:
Cruise_Collected (dimensionless)
MultiCore (Multi Core, number/identification)
Station_Number (dimensionless)
Bottom_Depth (meters)
latitude (degrees_north)
longitude (degrees_east)
Date_Collected (unitless)
Time_Collected (HHMM)
Sample_Depth (centimeters)
Nominal_Depth (centimeters)
Porewater (uM)
Vapor_Phase_Carbonate (%)
POC (Particulate Organic Carbon, %)
POC_2_Stdev (dimensionless)
PON (%)
PON_2_Stdev (dimensionless)
Reactive_Pool_Treatment (unitless)
Avg_d30Si (Avg D30 Si, 0/00)
Avg_d30Si_2_Stdev (Avg D30 Si 2 Stdev, dimensionless)
Avg_Si_Released (Mass Concentration Of Silicate In Sea Water, umol/g)
Avg_Si_Released_2_Stdev (Mass Concentration Of Silicate In Sea Water, dimensionless)
Mg (ppm)
Al (ppm)
K (ppm)
Ti (ppm)
V (ppm)
... (6 more variables)


[Station AT55 Temperature mooring data] - Temperature mooring data collected at Station AT55 in Lake Michigan from August 1, 2017 to April 20, 2018. (Collaborative Research: Regulation of plankton and nutrient dynamics by hydrodynamics and profundal filter feeders)

Summary:
A fixed mooring was established to measure water column temperatures in Lake Michigan near Milwaukee, WI, from Aug 1 \u2013 Aug 17, 2017 at a 55 meters depth site and again during 2018 from April 5 \u2013 April 20, 2018. The mooring involved a large tripod to which a surface line was attached and along this line were temperature sensors at various depths.

cdm_data_type = Other
VARIABLES:
HAB_cm (centimeters (cm))
HAB_m (meters (m))
temp (Temperature, degrees Celsius)
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)
latitude (degrees_north)
longitude (degrees_east)


[Station locations] - Station locations for the global metaproteomic dataset from R/V Kilo Moana cruise KM1128, the METZYME expedition in the tropical North Pacific in 2011. (Connecting Trace Elements and Metalloenzymes Across Marine Biogeochemical Gradients)

Summary:
Station locations for the global metaproteomic dataset from R/V Kilo Moana cruise KM1128, the METZYME expedition in the tropical North Pacific in 2011.

cdm_data_type = Other
VARIABLES:
cruise (unitless)
station_ID (unitless)
station_number (unitless)
depth (m)
McLane_cast (Mc Lane Cast, unitless)
McLane_date_local (Mc Lane Date Local, unitless)
McLane_time_local (Mc Lane Time Local, unitless)
latitude (degrees_north)
longitude (degrees_east)
time (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)


[station_plans] - Broad-scale station numbers and locations from the US-GLOBEC Georges Bank project (U.S. GLOBEC Georges Bank)

Summary:
Broad-scale station numbers and locations from the US-GLOBEC Georges Bank project

cdm_data_type = Other
VARIABLES:
year (unitless)
description (n/a)
station (n/a)
lat_deg (Latitude, degrees)
lat_min (Latitude, minutes)
lat_ddmm_tt (Latitude, ddmm.tt)
lon_deg (Longitude, degrees)
lon_min (Longitude, minutes)
lon_ddmm_tt (Longitude, ddmm.tt)
latitude (degrees_north)
longitude (degrees_east)
depth_w (Depth, meters)
distance (nautical miles)
priority (n/a)


[Stegastes planiforms attack behavior towards invasive lionfish] - Experimental results describing Stegastes planiforms attack behavior towards Pterois volitans and native predators in the Cayman Islands and the Bahamas during 2011 (Mechanisms and Consequences of Fish Biodiversity Loss on Atlantic Coral Reefs Caused by Invasive Pacific Lionfish)

Summary:
Experimental results describing Stegastes planiforms attack behavior towards Pterois volitans and native predators in the Cayman Islands and the Bahamas during 2011

cdm_data_type = Other
VARIABLES:
location (unitless)
latitude (degrees_north)
longitude (degrees_east)
bottle_treatment (unitless)
damsel_number (unitless)
charge (unitless)
nip (unitless)
butt (unitless)
continuous_attack (unitless)


[Stegastes planiforms attack rate towards invasive lionfish] - Experimental results describing Stegastes planiforms attack rates towards Pterois volitans and native predators in the Cayman Islands and the Bahamas during 2011 (Mechanisms and Consequences of Fish Biodiversity Loss on Atlantic Coral Reefs Caused by Invasive Pacific Lionfish)

Summary:
Experimental results describing Stegastes planiforms attack rates towards Pterois volitans and native predators in the Cayman Islands and the Bahamas during 2011

cdm_data_type = Other
VARIABLES:
location (unitless)
latitude (degrees_north)
longitude (degrees_east)
bottle_treatment (unitless)
habitat (unitless)
habitat_type (unitless)
damsel_number (unitless)
distance (centimeters)
attack_rate (count)


[Stegastes planiforms attacks by predator] - Experimental results indicating which predators were attacked by Stegastes planiforms in the Cayman Islands and the Bahamas during 2011 (Mechanisms and Consequences of Fish Biodiversity Loss on Atlantic Coral Reefs Caused by Invasive Pacific Lionfish)

Summary:
Experimental results indicating which predators were attacked by Stegastes planiforms in the Cayman Islands and the Bahamas during 2011

cdm_data_type = Other
VARIABLES:
location (unitless)
latitude (degrees_north)
longitude (degrees_east)
bottle_treatment (unitless)
habitat (unitless)
damsel_number (unitless)
attack (unitless)


[Stillwater Cove temperature time series] - Temperature time-series data from 4 depths in the Central California kelp forest, measured at the Stillwater Cove Mooring from 2010-2012 (Climate Change Kelp project) (Effects of ocean climate change on recruitment of kelp populations)

Summary:
Temperature data from 4 depths at the study site in the giant kelp forest habitat of the Central California Coast. Temperature was recorded every 5 minutes from June 2010 to October 2012.

cdm_data_type = Other
VARIABLES:
site (text)
site_descrip (text)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
depth_comment (Depth, text)
year_local (unitless)
month_local (unitless)
day_local (unitless)
time_local (unitless)
temp (Temperature, degrees Celsius)
yrday_local (dimensionless)
ISO_DateTime_Local (ISO Date Time Local, unitless)


[STING I and STING II extracted chlorophyll a and pheophytin] - Chlorphyll a and pheophytin from two cruises performed as part of the STING project from R/V Atlantic Explorer AE2305 (Sting I cruise) and R/V Endeavor EN704 (Sting II cruise) in the Gulf of Mexico near Florida from February to July 2023 (Collaborative Research: Linking iron and nitrogen sources in an oligotrophic coastal margin: Nitrogen fixation and the role of boundary fluxes)

Summary:
These data include the average (n=3 replicates per measurement) measured chlorphyll a and pheophytin from two cruises performed as part of the STING project.  STING I (AE2305) was aboard the R/V Atlantic Explorer from 2023-02-20 to 2023-03-06. STING II (EN704) was aboard the R/V Endeavor from 2023-07-01 to 2023-07-12.

cdm_data_type = Other
VARIABLES:
Cruise (unitless)
Station (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
Date (unitless)
STING_ID (unitless)
Collection (unitless)
Type (unitless)
Chla (micrograms/liter (ug/l))
Pheophytin (micrograms/liter (ug/l))


[STING macronutrient concentrations] - Dissolved Macronutrient Concentrations from Depth Profiles and Incubation Experiments from STING I Cruise AE2305 on R/V Atlantic Explorer in the Gulf of Mexico from February to March 2023 (Collaborative Research: Linking iron and nitrogen sources in an oligotrophic coastal margin: Nitrogen fixation and the role of boundary fluxes)

Summary:
Concentrations of inorganic dissolved macronutrients, including phosphate, nitrate plus nitrite (N+N), silicic acid, and nitrite, from phytoplankton shipboard incubation experiments and depth profiles collected on STING I cruise AE2305 on R/V Atlantic Explorer in the Gulf of Mexico from February to March 2023.

This project investigates how groundwater discharge delivers important nutrients to the coastal ecosystems of the West Florida Shelf. Preliminary studies indicate that groundwater may supply both dissolved organic nitrogen (DON) and iron in this region. In coastal ecosystems like the West Florida Shelf that have very low nitrate and ammonium concentrations, DON is the main form of nitrogen available to organisms. Nitrogen cycling is strongly affected by iron availability because iron is essential for both photosynthesis and for nitrogen fixation. This study will investigate the sources and composition of DON and iron, and their influence on the coastal ecosystem. The team will sample offshore groundwater wells, river and estuarine waters, and conduct two expeditions across the West Florida Shelf in winter and summer.

cdm_data_type = Other
VARIABLES:
EVTNBR (unitless)
time (Iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)
DATE_UTC (unitless)
TIME_UTC (unitless)
DATE_GMT (unitless)
TIME_GMT (unitless)
latitude (degrees_north)
longitude (degrees_east)
PLATFORM (unitless)
CASTNBR (unitless)
STNNBR (unitless)
BTLNBR (unitless)
depth (m)
PO4 (micromoles per liter (uM))
... (20 more variables)


[Stress bands bleaching] - Comparison of bleaching data to stress bands in Porites corals on Palau reefs (Constraining Thermal Thresholds and Projections of Temperature Stress on Pacific Coral Reefs Over the 21st Century: Method Refinement and Application)

Summary:
Comparison of bleaching data to stress bands in Porites corals on Palau reefs.

cdm_data_type = Other
VARIABLES:
site (unitless)
reef_type (unitless)
latitude (degrees_north)
longitude (degrees_east)
year (unitless)
num_cores (unitless)
pcnt_stress_bands (unitless (percent))
pcnt_stress_bands_SE (unitless (percent))
mean_pcnt_bleaching (unitless (percent))
mean_pcnt_bleaching_SE (unitless (percent))


[Stress bands Jarvis] - Stress bands in coral cores collected at Jarvis Island between 2008 and 2016 (Skeletal Records of Coral Reef Bleaching in the Central Equatorial Pacific)

Summary:
The dataset contains historical coral reef bleaching events on Jarvis Island reconstructed from stress bands in Porites coral cores. Samples are collected between 2008 and 2016.

cdm_data_type = Other
VARIABLES:
core_id (unitless)
date_collected (unitless)
latitude (degrees_north)
longitude (degrees_east)
depth (m)
sb_1965_1966 (unitless)
sb_1972_1973 (unitless)
sb_1975_1976 (unitless)
sb_1982_1983 (unitless)
sb_1987_1988 (unitless)
sb_1992_1993 (unitless)
sb_1997_1998 (unitless)
sb_2002_2003 (unitless)
sb_2009_2010 (unitless)
sb_2015_2016 (unitless)


[Submarine groundwater discharge on conspecific interactions] - Coral physiologic response data from study of conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology in Mo'orea, French Polynesia in 2021 (RUI: Collaborative Research: Defining the biogeochemical context and ecological impacts of submarine groundwater discharge on coral reefs)

Summary:
This dataset reports physiological metrics of corals, including chlorophyll content, endosymbiont density, photosynthesis, and respiration rates, collected during experiments examining the effects of conspecific interactions and submarine groundwater discharge on coral health.

Study description:

Land-based inputs, such as runoff, rivers, and submarine groundwater, can alter biological processes on coral reefs. While the abiotic factors associated with land-based inputs have strong effects on corals, corals are also affected by biotic interactions, including other neighboring corals. The biological responses of corals to changing environmental conditions and their neighbors are likely interactive; however, few studies address both biotic and abiotic interactions in concert. In a manipulative field experiment, we tested how the natural environmental gradient created by submarine groundwater discharge (SGD) affected holobiont and symbiont metabolic rates and endosymbiont physiology of Porites rus. We further tested how the effect of SGD on the coral was mediated by intra and interspecific interactions. SGD is a natural land-sea connection that delivers nutrients, inorganic carbon, and other solutes to coastal ecosystems worldwide. Our resus show that a natural gradient of nutrient enrichment and pH variability as a result of acute SGD exposure generally benefited P. rus, increasing gross photosynthesis, respiration, endosymbiont densities, and chlorophyll a content. Conspecifics in direct contact with the a neighboring coral, however, altered the relationship between coral physiology and SGD, lowering the photosynthetic and respiration rates from expected values when the coral had no neighbor. We show that the response of corals to environmental change is dependent on the types of nearby neighbor corals and how neighbors alter the chemical or physical environment around the coral. Our study underscores the importance of considering biotic interactions when predicting the physiologic responses of corals to the environment.

cdm_data_type = Other
VARIABLES:
PlateID (unitless)
FragmentID (unitless)
Treatment (unitless)
... (32 more variables)


[Substrate Coverage] - Percent coverage along a transect or subsample of each of four substrate types recorded during emergent and rapid emergent surveys conducted in the subtidal zone of northern California, Sonoma and Mendocino counties, from 1999 to 2023 (Collaborative Research: The effects of marine heatwaves on reproduction, larval transport and recruitment in sea urchin metapopulations)

Summary:
The Kelp Forest Monitoring data record span surveys across 24 years from 1999 through 2023 at 20 locations on the Sonoma-Mendocino Coast, Northern California, and span the major marine heatwave of 2014-2016. Years without data, inclusive: 2002, 2020, 2021. These surveys are ongoing and are conducted by the California Department of Fish and Wildlife dive team with participation from dive program partners at UC Davis, UC Santa Cruz, Cal Poly Humboldt, Sonoma State and other dive programs and volunteers. Not all sites were surveyed in all years. Surveys prior to 2003 were not conducted by the same teams or with the same methods except that all surveys were done using Scuba along 30 x 2m transects randomly placed in the subtidal zone in rocky habitats dominated by bull kelp, Nereocystis luetkeana, forests. These randomly placed band transects surveys were stratified by depth (A=0-15, B=16-30, C=31-45, D=46-60 ft) as we know sea urchin and abalone populations differ by depth.

Data collected include the number of live, dying (in some years during the mass mortality events), and sea urchins (red-Mesocentrotus franciscanus and purple-Strongylocentrotus purpuratus), red abalone (Haliotis rufescens), pinto abalone (H. kamtschatkana), flat abalone (H. walallensis), as well as empty abalone shells (again in some years). Additional data collected (if scuba bottom time and/or air allowed): red abalone size, numbers or presence of associated species such as sea stars and predators, algal group quantification, and presence of bull kelp, substrate type. Data on algae and associated species differed depending on the year and the focus of the studies in response to ecosystem conditions but all years quantified sea urchins and abalones.

This dataset provides in situ estimates of the coverage of the substrate along each survey transect as a percentage of four substrate types: reef, boulder, cobble, and sand.

cdm_data_type = Other
VARIABLES:
Survey_Num (unitless)
DFW_short_code (unitless)
SiteName (unitless)
latitude (degrees_north)
longitude (degrees_east)
... (16 more variables)


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

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

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


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

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

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


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

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

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


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

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

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

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


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

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

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


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

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

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

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

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

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


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

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

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


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

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

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


[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.)

Summary:
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)

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

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


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

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

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


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

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

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


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

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

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


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

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

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

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


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

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

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


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

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

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

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

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


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

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

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


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

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

These data are\u00a0associated with the corresponding paper:

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

Other datasets related to this paper:

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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

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


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

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

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

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


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

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

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

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


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

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

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

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


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

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

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


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

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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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


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

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

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


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

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

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


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

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

Study description:

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

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

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

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


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

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

Study description:

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

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

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

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


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

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

Study description:

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

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

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

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


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

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

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


[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)

Summary:
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)

Summary:
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)

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

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


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

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

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


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

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

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


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

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

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


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

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

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