Reef seawater biogeochemistry data from samples collected in the Jardines de la Reina reef-system, Cuba in November of 2017
Project
| Contributors | Affiliation | Role |
|---|---|---|
| Apprill, Amy | Woods Hole Oceanographic Institution (WHOI) | Principal Investigator |
| Kujawinski, Elizabeth | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Gray, Laura | Woods Hole Oceanographic Institution (WHOI) | Scientist, Contact |
| York, Amber D. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Abstract
Funding Description:
Dalio Foundation (now ‘OceanX’) (awarded to Amy Apprill)
National Science Foundation (OCE-1736288) (awarded to Amy Apprill)
Mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility using instruments funded by the National Science Foundation (grant OCE-1058448 awarded to Elizabeth B. Kujawinski and Melissa Kido Soule) and the Simons Foundation (Award ID #509042, awarded to Elizabeth B. Kujawinski)
Location: Jardines de la Reina reef system south of the island of Cuba; General location: 20.8333° N, 78.9167° W
Non-purgeable total organic carbon (TOC, unfiltered), dissolved organic carbon (DOC, 0.2 µm filtered), total nitrogen (TN, unfiltered), and total dissolved nitrogen (TDN, 0.2 µm filtered) concentrations were analyzed using a Shimadzu TOC-VCSH total organic carbon analyzer (Hansell & Carlson, 2001) with a TNM-1 module. Inorganic macronutrient (phosphate, nitrite + nitrate, nitrite, ammonium, silicate) concentrations were measured with a continuous segmented flow system (as used in Apprill & Rappé, 2011). Nitrite was subtracted from the nitrite + nitrate concentrations to obtain the nitrate concentrations. Concentrations of total organic nitrogen were obtained by subtracting the sum of the inorganic nitrogen species (nitrite + nitrate and ammonium) from the total nitrogen concentrations per sample. If the measured concentrations fell beneath the detection limits of the instrument (ammonium = 0.02 M, phosphate = 0.01 M, nitrite + nitrate = 0.07 M, nitrite = 0.01 M), these measurements were removed from the analysis.
A few erroneous data values related to bottle/sample misidentification were included in the publication Weber et al. (2020). The differences between values are minor. The original values in Weber et al. (2020) are listed below and the corrected values are included within the dataset published here.
Reef name: JR4B_surf
The value for PO4 was 0.18
The value for SI was 1.6
The value for NO2 was 0.04
The value for NH4 was 0.03
The value for TON was 2.83
Reef name: OR2_surf
The value for TN was 0.18
The value for TON was -0.012
Abundances of each cell type were estimated by binning populations using FlowJo (v. 6.4.7) software.
Version 1:
* 908026_v2_biogeochemistry.csv was imported into the BCO-DMO data system with values "NaN" as missing data values. This file version was submitted to BCO-DMO 2023-10-26.
* The table was renamed 908026_v1_biogeochemistry in the BCO-DMO system since it will be the first published version of this dataset.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.
* date format changed to ISO format
| File |
|---|
908026_v1_biogeochemsitry.csv (Comma Separated Values (.csv), 3.66 KB) MD5:d9d6f5abc00b30e5907da59f063e0b7c Primary data table for dataset 908026 version 1. |
Relationship Description: Data from the same study (Metabolights study id MTBLS1820). In both the biogeochemistry and metabolite datasets, water samples were collected from surface and benthic depths from the same reefs. Column "reef" in both datasets indicates the reef site identifier and reef sample depth. See methods for details of how each water sample was collected.
| Parameter | Description | Units |
| reef | sample name of reef (site identifier and sample depth; "surf" for surface or "benthic" for reef depth). | unitless |
| site | Site identifier | unitless |
| date | Date of water sample collection in ISO 8601 format | unitless |
| latitude | sample site latitude | decimal degrees |
| longitude | sample site longitude | decimal degrees |
| depth | depth of sampling | meters (m) |
| biome | general habitat description | unitless |
| sampling_depth | Descriptive term for sampling depth; "surf" for surface or "benthic" for reef depth. | unitless |
| grouping | general geographic grouping of reef sites | unitless |
| DOC | Dissolved organic carbon | micro molar (uM) |
| DN | Dissolved nitrogen | micro molar (uM) |
| TOC | Total organic carbon | micro molar (uM) |
| TN | Total nitrogen | micro molar (uM) |
| Pro | Prochlorococcus cell abundance | cells per mL |
| Syn | Synechococcus cell abundance | cells per mL |
| Pico | Picoeukaryote cell abundance | cells per mL |
| Hbact | Unpigmented cell abundance | cells per mL |
| Totalcells | Summation of all cell types | cells per mL |
| PO4 | Phosphate | micro molar (uM) |
| SI | Silicate | micro molar (uM) |
| NO2 | Nitrite | micro molar (uM) |
| NO3 | Nitrate | micro molar (uM) |
| NH4 | Ammonium | micro molar (uM) |
| DON | Dissolved organic nitrogen | micro molar (uM) |
| TON | Total organic nitrogen | micro molar (uM) |
| Temp | Seawater temperature | degrees Celsius |
| pH | pH | pH scale |
| Sal | salinity | parts per thousand (ppt) |
| DO | Dissolved oxygen | mg per L |
| Tchl | Total chlorophyll a | micrograms per L |
| TchltoPhaeo | Ratio of total chlorophyll a to phaeophytin concentrations | unitless |
| Dataset-specific Instrument Name | Altra flow cytometer |
| Generic Instrument Name | Flow Cytometer |
| Dataset-specific Description | To obtain cell counts, flow cytometry was conducted using a collinear analyses method and a UV wavelength of 488 nm on an Altra flow cytometer at the University of Hawaii. Each sample was divided so that pigmented, fluorescent cells and unpigmented cells could be run separately. |
| Generic Instrument Description | Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) |
| Dataset-specific Instrument Name | Shimadzu TOC-VCSH total organic carbon analyzer (Hansell & Carlson, 2001) |
| Generic Instrument Name | Shimadzu Total Organic Carbon Analyzer TOC-VCPH |
| Dataset-specific Description | Non-purgeable total organic carbon (TOC, unfiltered), dissolved organic carbon (DOC, 0.2 µm filtered), total nitrogen (TN, unfiltered), and total dissolved nitrogen (TDN, 0.2 µm filtered) concentrations were analyzed using a Shimadzu TOC-VCSH total organic carbon analyzer (Hansell & Carlson, 2001) with a TNM-1 module. |
| Generic Instrument Description | The Shimadzu Total Organic Carbon Analyzer TOC-VCPH is a PC-controlled, total organic carbon analyzer (high-sensitivity model), designed to measure total carbon (TC), inorganic carbon (IC), total organic carbon (TOC), and non-purgeable organic carbon (NPOC); an optional accessory enables the measurement of particulate organic carbon (POC) and total nitrogen (TN) as well. The instrument uses the 680 degrees Celsius combustion catalytic oxidation method to analyze aqueous samples, and optionally solid and gas samples. |
| Dataset-specific Instrument Name | Lambda 18, Perkin Elmer, Waltham, MA, USA |
| Generic Instrument Name | Spectrophotometer |
| Dataset-specific Description | Acetone (90%) was used to extract Chlorophyll a and phaeophytin and the optical density (OD) values were measured on a calibrated spectrophotometer using standard optics (Lambda 18, Perkin Elmer, Waltham, MA, USA). |
| Generic Instrument Description | An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. |
| Dataset-specific Instrument Name | YSI Exo Sonde (Xylem Inc., Yellow Springs, OH, USA) |
| Generic Instrument Name | YSI EXO multiparameter water quality sondes |
| Dataset-specific Description | At each reef, CTD casts were completed (YSI Exo Sonde, Xylem Inc., Yellow Springs, OH, USA) to measure the physicochemical properties of the water column. |
| Generic Instrument Description | Comprehensive multi-parameter, water-quality monitoring sondes designed for long-term monitoring, profiling and spot sampling. The EXO sondes are split into several categories: EXO1 Sonde, EXO2 Sonde, EXO3 Sonde. Each category has a slightly different design purpose with the the EXO2 and EXO3 containing more sensor ports than the EXO1. Data are collected using up to four user-replaceable sensors and an integral pressure transducer. Users communicate with the sonde via a field cable to an EXO Handheld, via Bluetooth wireless connection to a PC, or a USB connection to a PC. Typical parameter specifications for relevant sensors include dissolved oxygen with ranges of 0-50 mg/l, with a resolution of +/- 0.1 mg/l, an accuracy of 1 percent of reading for values between 0-20 mg/l and an accuracy of +/- 5 percent of reading for values 20-50 mg/l. Temp ranges are from-5 to +50 degC, with an accuracy of +/- 0.001 degC. Conductivity has a range of 0-200 mS/cm, with an accuracy of +/-0.5 percent of reading + 0.001 mS/cm and a resolution of 0.0001 - 0.01 mS/cm. |
Signature exometabolomes of Caribbean corals and influences on reef picoplankton (Coral Exometabolomes)
NSF Award Abstract:
Coral reefs are some of the most diverse and productive ecosystems in the ocean. Globally, reefs have declined in stony (reef-building) coral abundance due to environmental variations, and in the Caribbean this decline has coincided with an increase in octocoral (soft coral) abundance. This phase shift occurring on Caribbean reefs may be impacting the interactions between the sea floor and water column and particularly between corals and picoplankton. Picoplankton are the microorganisms in the water column that utilize organic matter released from corals to support their growth. These coral-picoplankton interactions are relatively unstudied, but could have major implications for reef ecology and coral health. This project will take place in the U.S. territory of the Virgin Islands (USVI) and will produce the first detailed knowledge about the chemical diversity and composition of organic matter released from diverse stony coral and octocoral species. This project will advance our understanding of coral reef microbial ecology by allowing us to understand how different coral metabolites impact picoplankton growth and dynamics over time. The results from this project will be made publically accessible in a freely available online magazine, and USVI minority middle and high school students will be exposed to a lesson about chemical-biological interactions on coral reefs through established summer camps. This project will also contribute to the training of USVI minority undergraduates as well as a graduate student.
Coral exometabolomes, which are the sum of metabolic products of the coral together with its microbiome, are thought to structure picoplankton communities in a species-specific manner. However, a detailed understanding of coral exometabolomes, and their influences on reef picoplankton, has not yet been obtained. This project will utilize controlled aquaria-based experiments with stony corals and octocorals, foundational species of Caribbean reef ecosystems, to examine how the exometabolomes of diverse coral species differentially influence the reef picoplankton community. Specifically, this project will capitalize on recent developments in mass spectrometry-based metabolomics to define the signature exometabolomes of ecologically important and diverse stony corals and octocorals. Secondly, this project will determine how the exometabolomes of these corals vary with factors linked to coral taxonomy as well as the coral-associated microbiome (Symbiodinium algae, bacteria and archaea). With this new understanding of coral exometabolomes, the project will then apply a stable isotope probe labeling approach to the coral exometabolome and will examine if and how (through changes in growth and activity) the seawater picoplankton community incorporates coral exometabolomes from different coral species over time. This project will advance our ability to evaluate the role that coral exometabolomes play in contributing to benthic-picoplankton interactions on changing Caribbean reefs.
RAPID/MRI: Acquisition of a Triple-Quad Mass Spectrometer for Quantitative Identification of Dispersants and Water-Soluble Oil in the Gulf of Mexico (RAPID Mass Spec for Dispersants)
The PI's request MRI RAPID funding to acquire a triple-quad Mass Spectrometer for quantitative identification of dispersants and water-soluble oil in the Gulf of Mexico. Dispersants were applied to the leak at the bottom of the ocean. Preliminary results using the PI's Fourier-transform ion cyclotron resonance (FT) mass spectrometer show that is possible identify the active ingredient of this dispersant in samples collected during research cruises in the Gulf of Mexico. Components of the dispersant have even been found in samples taken from within the underwater oil plume deep below the ocean's surface (~1100 m). Now the PI's would like to quantify this compound in order to assess its environmental fate in this environment.
In order to quantify these marker compounds, a mass spectrometer designed for sensitive and accurate quantification of targeted compounds is required. The PI's have identified a triple-quadrupole mass spectrometer (triple-Q-MS) as the most appropriate instrument for their needs. With the help of the EPA, the PI's now have the appropriate method ready and have been running samples on a triple-Q-MS in a colleague's lab. The increased sensitivity and quantitative accuracy of the triple-Q-MS will allow them to quantify dispersant components and other target compounds at lower concentrations, thus providing important constraints on modeling and predictive efforts underway in other research groups.
Broader Impacts
This research has the potential to provided unprecedented data on the environmental fate of both petroleum and dispersant components as they interact with the extant biological, chemical, and physical processes of the Gulf of Mexico. Beyond the immediate needs of the Gulf oil spill the development of the methods described in the proposal will have broad applications not only in oil spill research but also in marine organic matter characterization and its interactions with biological, chemical and physical processes. The instrument will be available for Gulf oil spill related research in a timeframe consistent with the intent of the RAPID funding mechanism.
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) | |
| NSF Division of Ocean Sciences (NSF OCE) |
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