Dataset: Effects of sponge excurrent seawater on coral reef picoplankton composition in the Florida Keys January 2022

Incubation experiments were set up with sponge excurrent water, coral exudates, sponge excurrent and coral exudates, or surface reef water as media and with reef surface picoplankton as inoculum to compare microbial growth over 48 hours. Excurrent seawater samples of three sponge species (Verongula rigida, Xestospongia muta, and Niphates digitalis) were collected at Looe Key Reef in the Florida Keys, U.S.A. at approximately 10m depth (24.54605, -81.40610). The exhalent seawater was collected using acid-rinsed glass syringes with a three-way valve and PharMed BPT tubing (Cole-Parmer, USA) connected to 1L FlexFoil Plus sampling bags (SKC, Pittsburgh, PA, USA). Water was drawn in at about 2 mL per minute, which is slower than the pumping rate of the sponges. The exhalent seawater was collected the day before the experiment and filtered (0.2 µm, Omnipore, Millipore Sigma, USA) prior to storage at 4°C. Coral exudates were collected by incubating four fragments each of Acropora cervicornis and Orbicella faveolata were incubated in aquaria containing 0.2 µm filtered (Omnipore) seawater from Mote Marine laboratory seawater intake which pulls from the nearby seawater canal. The aquaria was placed in flowthrough seawater raceway in the sunlight under one layer of shade cloth (~23 – 262 µE s-1 with a mix of sun and clouds) for 6.5 hrs. The coral exudate seawater was then filtered 0.2 µm filtered and stored at 4°C.

Surface seawater over Looe Key Reef was collected the morning of the experimental setup and was used for both the inoculum of bacterioplankton and for background seawater control medium (0.2 µm filtered to create the ambient seawater medium). The sponge excurrent seawater was combined in a 1:1:1 ratio from the three sponge species. Then four different mediums were created: coral exudate water, sponge exhalant water, sponge exhalant water plus coral exudates (1:1 ratio of each medium), and ambient seawater. Coral reef surface picoplankton, served as inoculum and was added to the media in a 1:3 ratio of inoculum to medium. An initial ‘soup’ was made for each treatment in 5L acid-cleaned polycarbonate food grade containers and the total volume of the initial soup was 3900 mL for treatments with microbial inoculum and 2900 mL for control treatments without inoculum. From the initial soup, three T0 samples of seawater (1400 mL) were taken for chemical and microbial analyses. The rest of the experimental seawater with inoculum was then distributed into 2L acid-cleaned polycarbonate bottles (1L per bottle) and incubated in a flow through seawater table in the dark for 48 hours. There were five replicate bottles for each treatment (coral, sponge, sponge + coral, ambient seawater) and three replicate bottles for each no-inoculum control corresponding to each treatment. Nutrients and the bacterioplankton community composition and abundance were assessed at the start of the experiment (T0) and after 48hrs (T48).

Seawater sampled from the incubation ‘soup’ or bottles was used for multiple nutrient analyses and DNA extraction. Prior to filtration, 1 mL of seawater was preserved in 500 µL of paraformaldehyde (0.5% final concentration), which were stored in the refrigerator for 1-2 hours and then stored at -80°C until shipped to the University of Hawai’i for flow cytometry analysis. Also prior to filtration, approximately 30 mL of sample was poured into acid and milliQ water rinsed and combusted glass amber EPA vials with acid cleaned septa and lids. These 30 mL samples were acidified to pH ~2 with concentrated HCl and stored at room temperature until analysis for total organic carbon (TOC) and total nitrogen (TN) at Woods Hole Oceanographic Institution. The rest of the seawater was filtered through an Omnipore 0.2 um filter using a peristaltic pump and acid and milliQ water rinsed Pharmed BP tubing and Teflon filter holders. The filter was stored at -80C until DNA extraction, while the filtrate was poured into acid and milliQ water rinsed: 1) HDPE bottles (~20 mL) for inorganic nutrient analysis at the University of Oregon, 2) polycarbonate bottles (~500 mL) for extraction of dissolved organic matter (DOM).  Filtered seawater was processed using PPL solid phase extraction following the protocol by Dittmar et al. 2008. Extracts were dried to nearly completeness, leaving a small viscous drop in the vial. These extracts were then shipped to WHOI for metabolomics analysis.

DNA from the Omnipore filters was extracted using a commercial kit and the 16S rRNA gene was amplified using the modified earth microbiome primer set for the V4 region (515F and 806R, Apprill et al. 2015). PCRs were sent to Middle Tennessee State University for library construction and sequencing on an Illumina MiSeq, producing FASTQ files as output.

Targeted Metabolite Analysis by UPLC-MS:

DOM extracts were reconstituted in 200 μl MilliQ water with 50 ng/ml isotopically-labeled injection standards d2 biotin, d6 succinic acid, d4 cholic acid, and d7 indole 3 acetic acid. We used ultra-performance liquid chromatography (Accela Open Autosampler and Accela 1250 Pump, Thermo Scientific) coupled to a heated electrospray ionization source (H-ESI) and a triple quadrupole mass spectrometer (TSQ Vantage, Thermo Scientific) operated under selected reaction monitoring (SRM) mode. We performed chromatographic separation with a Waters Acquity HSS T3 column (2.1 × 100 mm, 1.8 μm) equipped with a Vanguard pre-column and maintained at 40°C. We eluted the metabolites from the column with (A) 0.1% formic acid in water and (B) 0.1% formic acid in acetonitrile at a flow rate of 0.5 mL min-1, according to the gradient: 0 min, 1% B; 1 min, 1%B; 3 min, 15%B; 6 min, 50%B; 9 min, 95%B; 10 min, 95%B; 10.2 min, 1%B; 12 min, 1%B (total run time = 12 min). Settings for source gases were 55 (sheath), 20 (auxiliary) and 0 (sweep), and these settings are presented in arbitrary units. The heated capillary temperature was 375 °C and the vaporizer temperature was 400 °C. For positive and negative modes, we performed separate autosampler injections of 5 μL each.

Inorganic nutrients: 

Inorganic nutrients included phosphate, nitrate+nitrite, nitrite, ammonia, and silicic acid. The phosphate method is a modification of the molybdenum blue procedure of

Bernhardt and Wilhelms (1967), in which phosphate is determined as reduced phosphomolybdic acid employing hydrazine as the reductant. The nitrate + nitrite analysis uses the basic method of Armstrong et al. (1967), with modifications to improve the precision and ease of operation.  Sulfanilamide and N-(1-Napthyl)ethylenediamine dihydrochloride react with nitrite to form a colored diazo compound. For the nitrate + nitrite analysis, nitrate is first reduced to nitrite using an OTCR and imidazole buffer as described by Patton (1983). Nitrite analysis is performed on a separate channel, omitting the cadmium reductor and the buffer. The method is based on that of Armstrong et al. (1967) as adapted by Atlas et al. (1971).  Addition of an acidic molybdate reagent forms silicomolybdic acid which is then reduced by stannous chloride. This indophenol blue method is modified from ALPKEM RFA methodology which references Methods for Chemical Analysis of Water and Wastes, March 1984, EPA-600/4-79-020, "Nitrogen Ammonia", Method 350.1 (Colorimetric, Automated Phenate) A detailed description of the continuous segmented flow procedures used can be found in Gordon et. al.  (1994). 

Flow cytometry: 

Samples were preserved and stored at -80°C until later batch analysis at the University of Hawaii SOEST Flow Cytometry Facility (www.soest.hawaii.edu/sfcf). Microbial cells were enumerated using flow cytometry (Selph, 2021). In brief, samples (0.1 mL) were thawed in batches, stained with the DNA dye Hoechst 34580 (1 µg/mL final), then run at 30 µL min-1 on a Beckman-Coulter CytoFlex S flow cytometer, using lasers emitting at 375 nm (to detect Hoechst), 488 nm (for scatter and chlorophyll parameters), and 561 nm (for phycoerythrin). Resulting listmode files (FCS 3.0) were analyzed using FlowJo software (Becton Dickinson, v. 10.8.2) to distinguish microbial populations based on their fluorescence signals (chlorophyll, phycoerythrin, DNA), as well as forward and right-angle light scatter.  Heterotrophic bacteria were distinguished from phytoplankton by their DNA signature and absence of pigment.  Prochlorococcus and Synechococcus were separated from larger eukaryotic phytoplankton by their light scatter signatures, as well as their characteristic pigment and DNA signatures.  Other phytoplankton (eukaryotes, mostly 2-20 µm pico- and nano-sized cells given the small volume analyzed) had higher light scatter and more chlorophyll fluorescence per cell. >