Extracellular reef seawater metabolite accession numbers, sample information, and biogeochemistry data and from samples collected the in the Jardines de la Reina reef-system, Cuba

Website: https://www.bco-dmo.org/dataset/843270
Version: 1
Version Date: 2021-03-03

» Signature exometabolomes of Caribbean corals and influences on reef picoplankton (Coral Exometabolomes)
» 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)
Apprill, AmyWoods Hole Oceanographic Institution (WHOI)Principal Investigator
Kujawinski, ElizabethWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Weber, LauraWoods Hole Oceanographic Institution (WHOI)Contact
York, Amber D.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Reef depth and reef surface seawater samples were collected fro reefs in Jardines de la Reina and subjected to targeted and untargeted liquid chromatography mass spectrometry (LC-MS) methods in addition to a suite of biogeochemical measurements (inorganic and organic nutrient concentrations, microbial cell abundances, chlorophyll a concentrations, and physicochemical properties). Raw and .mzML data files from the LC-MS methods are located at MetaboLights database, using accession number MTBLS1820. The link is: https://www.ebi.ac.uk/metabolights/MTBLS1820/. These data were published in Weber et al. (2020).

Dataset Description

Funding description:

Dalio Foundation (now ‘OceanX’) (award to Amy Apprill)
National Science Foundation (OCE-1736288) (award to Amy Apprill)
National Science Foundation (grant OCE-1058448 to Elizabeth B. Kujawinski and Melissa C. Kido
1363 Soule)
Simons Foundation (Award ID #509042, Elizabeth B. Kujawinski)

Acquisition Description

Location: Jardines de la Reina reef system south of the island of Cuba; General location: 20.8333° N, 78.9167° W

Sampling and analytical procedures: 


Reef seawater microbial biogeochemistry and extracellular metabolite compositions were surveyed at nine, shallow (6 – 14 m in depth) forereef sites during a cruise to Jardines de la Reina (JR), Cuba in November of 2017. Seawater was also collected from two surface ‘off reef’ sites (800 – 1600 m depth). 


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. Seawater samples were collected from surface and reef depth to enumerate the number of microbial cells (1 mL samples), assess macronutrient concentrations (30 mL for inorganic macronutrient and 40 mL for organic carbon and total nitrogen samples) using a submersible groundwater pump. Seawater samples (4L) were collected from reef depth and off reef samples for chlorophyll and phaeophytin analysis. 

Samples collected for total organic carbon and nitrogen analyses were acidified with 75 µL of concentrated phosphoric acid, capped, and stored at room temperature. Surface and reef depth seawater samples collected for analyses of inorganic macronutrient concentrations (30 mL) were immediately frozen. Seawater, collected for enumeration of Prochlorococcus, Synechococcus, picoeukaryotic cells, and unpigmented cells (heterotrophic bacteria and archaea) was fixed with paraformaldehyde (1% final volume), incubated at 4 °C in the dark for 30 minutes, frozen at -50 °C on the research vessel, and then stored at -80 °C prior to analysis.

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. 

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).  The concentration ratios of chlorophyll a to phaeophytin were calculated and incorporated into the analyses. 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. Unpigmented cells were stained with Hoechst stain at a final concentration of 1 µg mL-1. Abundances of each cell type were estimated by binning populations using FlowJo (v. 6.4.7) software.

Surface and reef depth seawater samples were also collected to quantity the concentrations of known metabolites and survey trends in untargeted metabolite feature composition using liquid chromatography mass spectrometry. Detailed methods are included on the MetaboLights project page (Project MTBLS1820) and within the open access paper.

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Related Publications

Weber, L., Apprill, A. (2020) MTBLS1820: Extracellular reef metabolites across the protected Jardines de la Reina, Cuba reef-system. MetaboLights Database. Released 2020-11-30. Available at https://www.ebi.ac.uk/metabolights/MTBLS1820/
Weber, L., Armenteros, M., Kido Soule, M., Longnecker, K., Kujawinski, E. B., & Apprill, A. (2020). Extracellular Reef Metabolites Across the Protected Jardines de la Reina, Cuba Reef System. Frontiers in Marine Science, 7. doi:10.3389/fmars.2020.582161

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Parameters for this dataset have not yet been identified

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Project Information

Signature exometabolomes of Caribbean corals and influences on reef picoplankton (Coral Exometabolomes)

Coverage: U.S. Virgin Islands

NSF 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)

Coverage: Gulf of Mexico

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.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)

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