Dataset: Biogeochemistry, metabolomics, and metagenomics of Florida's Coral Reef from sampling conducted over 15 days in June 2019

Study Area: We sampled coral reef environments during a research cruise aboard the M/V Alucia between June 5 and June 19, 2019. During this time, we conducted surveys and sampled biogeochemical seawater parameters at 85 reefs across 8 zones in Florida's Coral Reef, from the North Key Largo/Biscayne Bay area, designated as Zone 1, to the Dry Tortugas National Park (Zone 8). We selected reefs based on input from the Florida Fish and Wildlife Conservation Commission and existing reefs in long-term monitoring programs (e.g., Coral Reef Evaluation and Monitoring Project, CREMP).

Sample Collection and Ship-board Processing: We conducted diver-based surveys to evaluate the prevalence of stony coral tissue loss disease (SCTLD) at each of the 85 reefs. At each site, one diver performed a 30-minute roving diver survey to determine the richness of scleractinian species, the presence or absence of stony coral tissue loss disease, and the size of all observed coral colonies. The diver assigned coral colonies to four size classes, based on diameter/length: <10 centimeters (cm), 10-25cm, 25-50cm, and >50cm. The area in square meters (m2) surveyed by each diver was estimated to calculate the density of corals at each site.

We generated 100 m2 plots at each of the 85 reefs for benthic surveys via high-resolution 2D orthophotomosaics. We analyzed 45 of these reefs for benthic composition data after determining this would sufficiently cover the observed variability in the different reefs.

We collected discrete seawater samples at all 85 reefs to measure inorganic nutrient (phosphate, ammonium, silicate, nitrite plus nitrate) concentrations, total organic carbon (TOC) and total nitrogen (TN) concentrations, and cell abundances (heterotrophic microbes (unpigmented bacteria and archaea), Prochlorococcus, Synechococcus, and picoeukaryotes). We collected samples via SCUBA with acid-washed and combusted 40-milliliter (mL) borosilicate glass vials for TOC and TN collections and 30 mL acid-washed square bottles (HDPE, Nalgene, ThermoFisher Scientific, Waltham, MA, USA) for nutrient collections, and filled both vials while at reef depth. Samples were kept on ice in a cooler for less than 4 hours prior to processing. Once on board the M/V Alucia, we processed all samples. We added 75 microliters (μL) of phosphoric acid to the 40 mL glass vials to fix the samples for TOC and TN, and kept these samples at room temperature or 4°C until laboratory analysis. We removed 1.4 mL of seawater from the nutrient bottles, mixed it with 8% paraformaldehyde (1% final concentration, Electron Microscopy Sciences), fixed it in the dark for 20 minutes at 4°C, then froze it at -80°C. We capped the 30 mL inorganic nutrient bottles and placed them at -80°C until analysis.

Metabolomic Analyses: We collected seawater for targeted and untargeted metabolomic analyses at 13 reefs across the 8 zones of Florida’s Coral Reef. At each reef, we collected seawater in 1.7L Niskin bottles via SCUBA at three distinct locations on the reef for biological replication. These Niskin bottles were kept in a cooler for less than 4 hours prior to processing on the M/V Alucia. Once back on board the M/V Alucia, we transferred seawater from the Niskin bottles into acid-washed 2L polycarbonate bottles using acid-washed PharMedBPT tubing (Masterflex, Cole-Parmer, Vernon Hills, IL, USA). These water samples were processed as described previously by Weber et al. (2020). Briefly, we prefiltered the seawater through a 47-millimeter (mm) 0.1-micrometer (μm) pore size polytetrafluoroethylene filter (Omnipore, EMD Millipore Corporation, Billerica, MA, USA) to remove all microbial biomass via peristalsis and placed the filtered seawater directly into a second acid-washed 2L polycarbonate bottle. We acidified this filtrate with 2 mL OPTIMA-grade 12 M (molar) hydrochloric acid prior to solid phase extraction (SPE). We used SPE to concentrate metabolites (primarily low molecular weight dissolved organic matter) from the filtered seawater. We used a Waters vacuum manifold to slowly pass the seawater through 1 gram per 6 cubic centimeters (g/cc) SPE cartridges (Bond Elut PPL; Agilent, Santa Clara, CA, United States) pre-conditioned with HPLC-grade methanol and weighed bottles with seawater prior to and following SPE to calculate the volume of seawater filtered. SPE cartridges were wrapped in combusted aluminum foil and frozen to -80°C prior to analysis at the Woods Hole Oceanographic Institution.

Microbial Biomass and Chlorophyll Analyses: We collected seawater for microbial biomass and chlorophyll analysis at 27 reefs across the 8 zones of Florida’s Coral Reef. At each reef, we employed a groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA) to pump seawater from just above the reef benthos into acid-washed or 10% bleach-rinsed 4L LDPE bottles (Nalgene). Samples were kept in a cooler on ice until processing less than 4 hours following collection. Once back on board the M/V Alucia, we used peristalsis to filter 2L of seawater to obtain duplicates from each reef through a 0.2 μm Supor filter (Pall, Port Washington, New York, USA) for microbial biomass housed in a 25 mm filter holder (Swinnex-25, Millipore Corporation), as described previously (Becker et al. 2020). Chlorophyll samples were obtained by filtering 2L of seawater in duplicate with the same peristalsis setup, but using a GF/F filter. We placed filters (GF/F or 0.2 μm) into 2 mL cryovials and froze them at -80°C prior to further processing at the Woods Hole Oceanographic Institution.

Coral Tissue Analyses: On reefs with active stony coral tissue loss disease, we collected coral tissue and near-coral seawater samples from apparently healthy and actively diseased coral colonies. We aimed to only sample reefs where at least three healthy coral colonies were present in addition to at least three diseased colonies. Sample collection proceeded on near-coral seawater followed by coral tissue as described previously (Becker et al. 2021). Prior to tissue collection, we collected near-coral seawater via a 60 mL syringe within 1-5 cm of the lesion margin on diseased corals or healthy tissue from apparently healthy colonies. Following near-coral seawater collections, we sampled tissue of diseased corals at the lesion margin between apparently healthy tissue and bleached and sloughing tissue or apparently healthy colonies (without any indication of disease or other affliction) randomly on the coral head. We collected tissue samples with Luer slip 10 mL syringes. Syringes were quickly placed into small Whirl-Pak bags to contain any mucus and tissue leaking from the syringe. Following the collections, all tissue and near-coral seawater syringe samples were placed on ice prior to processing. We transferred samples of coral tissue and mucus into 15 ml conical tubes and froze them at -80°C until analysis. We attached filter holders containing 25 mm 0.2 μm Supor filters to the 60 mL luer-lock syringes and depressed them by hand to capture microbial biomass on the filters. We placed filters into labeled 2 mL cryovials and placed them in a -80°C freezer until analysis.