Abstract:
This study contains assessment data of oyster habitat and trophic interactions in Matagorda Bay obtained from 2020-01-24 to 2022-02-01. Such data includes location and date of sampling, water quality measurements, oyster population sampling, fauna and flora biomass, analysis of oyster mantel tissue for dermo, tidal flat assessment, sediment porosity of sampled tidal flats, and stable isotope concentrations of a portion of samples.
Suggested Citation:
Beseres Pollack, J., A. Outhwaite, T.A. Palmer, and N.J. Breaux. 2023. Assessment data of oyster habitat and trophic interactions in Matagorda Bay obtained from 2020-01-24 to 2022-02-01. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n58d8qry
Data Parameters and Units:
Sta_metadata
Variable Name Description Units
Bay Bay samples were taken in
Sta Name of station that was sampled
Substa Specific area within a sampling station
Sta_alt Alternative station name
Habitat/ Sample Type Type of habitat for each station or the type of sample taken at the station
Latitude Latitude of station/substation decimal degrees
Longitude Longitude of station/substation decimal degrees
Comments
Samples When and where samples were taken
Variable Name Description Units
Date Sample date(s) ddMMMyyyy
Sta Sample station name(s)
Station Type Alternate station name
Hydro Hydrographic measurements taken Y/N
Oyster Quadrat m2 Benthos sampled for oysters m2
Motile fauna m2 Benthos sampled for motile fauna m2
SPOM Chla & SI Water sampled for chlorophyll-a and Suspended Particulate Organic Matter Stable Isotopes Y/N
Reef SSOM Chla & SI Sediment near reef sampled for chlorophyll-a and Stable Isotopes Y/N
Marsh SSOM Chla & SI Marsh sampled for chlorophyll a and Stable Isotopes Y/N
Dermo Oysters sampled for dermo disease Y/N
Infauna SI Infauna sampled for Stable Isotopes Y/N
Marsh Plants SI Marsh plants sampled for Stable Isotopes Y/N
MPB Microphytobenthos sampled for Stable Isotopes Y/N
Oyster Biomass Oyster biomass sampled Y/N
OSOM SI Oyster shell organic matter sampled for Stable Isotopes Y/N
Barnacle & Mussel Biomass Barnacle & mussel biomass sampled Y/N
Cyanobacteria mat Cyanobacteria mat sampled Y/N
Soft Sediment SSOM Chla & SI Soft sediment sampled for chlorophyll-a concentrations and Soft Sediment Organic Matter Stable Isotopes Y/N
Comments
Hydro Hydrographic/water quality measurements
Variable Name Description Units
Date Date that hydrographic measurement was taken ddmmmyyyy
Time Time that hydrographic measurement was taken hh:mm (24 hr)
Sta Sampling station name
Sta_alt Alternative station name
Cloud Cover (%) Cloud cover %
Wind Speed Wind Speed knots
Wind Direction Wind Direction
Position Top or bottom of water column top, bottom
DOCal Dissolved Oxygen saturation in air %
Secchi Water transparency measured by secchi disc m
Depth Depth sample was taken m
Temp Water temperature °C
DO_pct Dissolved Oxygen saturation of water %
DO_mgl Dissolved oxygen concentration in water mg L-1
SpCond Specific conductivity mS cm-1
Sal Salinity
pH pH
Turb Turbidity NTU
TotDepth Total depth of bottom m
Comments additional remarks
Oyster Oyster population sampling
Variable Name Description Units
Date Date that sample was taken ddMMMyyyy
Time Time that sample was taken hh:mm (24 hr)
Sta Sampling station name
Sta_Alt Alternative station name
Sample_Type Sampling method type quadrat
Area Size of sampling area m2
Rep Replicate number
Spat Estimated number of oyster spat None(0), Few(1-10), Many(11-100), Abundant(>100)
Barnacles Estimated number of barnacles None(0), Few(1-10), Many(11-100), Abundant(>100)
Mussels Estimated number of mussels None(0), Few(1-10), Many(11-100), Abundant(>100)
n_Live Number of live oysters n
Vol_Live Volume of live oysters L
n_Dead Number of dead oysters n
Vol_dead Volume of dead oysters L
Height height of oyster from bill to hinge mm
Comments additional remarks
Motile fauna
Variable Name Description Units
Date Date that sample was taken ddMMMyyyy
Sta Sampling station name
Sample_Type Sampling type used: quadrat, sweep net, core tube quad, sweep, core
Area Size of sampling area m2
Rep Replicate number
Taxa Name of taxa
Taxa Group Higher-level taxonomic grouping
n Number of individuals in sample n
Pan wt Weight of pan mg
Pan+Dry Wt Weight of pan + dried biomass sample mg
Dry Wt Dry biomass mg
Comments
Dermo Analysis of oyster mantle tissue for dermo disease/Perkinsus marinus infection
Variable Name Description Units
Sta Sampling station name
Sta_alt Alternative station name
Collected Date oysters were collected in field ddMMMyyyy
Cultured Date oystes were incubated with thio broth and antibiotic ddMMMyyyy
Thio Date thioglycollate batch was made ddMMMyyyy
Antibiotic Date antibiotic batch was made ddMMMyyyy
Size_Class oyster sizeclass: sub-market (<76 mm), market (>76 mm) Sub-Market, Market
Tissue Type of oyster tissue analyzed Mantle
Oyster Oyster identification number numeric
Height Height of oyster from bill (=lip) to hinge mm
Bill Description of bill condition: sharp, regressed
Condition Condition Index: ranges from 1-9, numerical condition code according to Quick and Mackin (1971) (Table 1).
Intensity Based on the number or coverage of enlarged P. marinus hypnospores observed in the tissue using the scale in Table 2.
Examined Date the cultured sample was examined under the microscope ddMMMyyyy
Comments
Entered Data entry person's initials, and date
Depth_Loggers Deployment of HOBO pressure loggers to estimate changes in water level at tidal flats
Variable Name Description Units
Bay Bay sampled
Sta Sampling station name
Start Date Date loggers began logging ddMMMyyyy
Start Time Time that loggers began logging hh:mm (24 hr)
Instrument ID ID of depth logger
In water Date Date when logger was placed in water ddMMMyyyy
In water time Time of when logger was placed in water hh:mm (24 hr)
Deploy Depth Depth that logger was placed m
Total Depth (m) Total depth of water m
Out water Date Date logger was collected ddMMMyyyy
Out water time Time logger was removed from water hh:mm (24 hr)
Retrive Depth (m) Depth at which logger was retrieved m
Total Depth (m) Total water depth at time of retreival m
Comments
Flat_assessment Basic assessment of wind tidal flats
Variable Name Description Units
Date Date that sample was taken ddMMMyyyy
Sta Sampling station name
Depth (m) Depth of water m
Time Time data were collected hh:mm (24 hr)
Algal coverage % Estimated spatial coverage by cyanobacteria mat %
Distance from edge (m) Distance of stationl from the transistion edge between tidal flat and marsh m
Comments
Sed_porosity Sediment porosity in tidal flats
Variable Name Description Units
Date Date that sample was taken ddMMMyyyy
Sta Sampling station name
Sed Depth Depth of sediment sampled (from surface of sediment) cm
Taken below cyanobacteria mat If sediment sample was taken below cyanobacteria mat Y/N
Rep Sampling replicate
Full bag wt Weight of sediment and bag g
Empty dish wt Weight of empty petri dish g
Dish + wet sed wt Weight of petri dish and wet sediment g
Wet sed wt Weight of wet sediment ("Dish + wet sed wt" - "Empty dish wt") g
Dish + dry sed wt Weight of petri dish and dried sediment g
Dry sed wt Weight of dry sediment ("Dish + dry sed wt" - "Empty dish wt") g
Porosity Porosity of sample (("Wet sed wt" - "Dry sed wt")*100) %
Flora_biomass Plants were sampled by BioWest from 11-21 May 2020 and brought to HRI from 15-21 May 2020
Variable Name Description Units
Date Date that sample was taken. NB. Samples were actually taken over a range of dates and the recorded dates represent the midpoints. 13May2020 = (11-15May2020), 19May2020 = (18-21May2020) ddMMMyyyy
Sta Sampling station name
Transect BioWest transect name within a site. NB, exact locations are not recorded
Plot BioWest plot name taken along the transect
Rep Replicate sample number integer (1,2,3)
Community General plant community composition description
Taxa Name of plant taxa
Area Area sampled m2
Whole/Sub Sample were given in large paper bags. Some samples were too large to dry everything. In these cases a subsample (Sub) was dried. When samples were small the Whole sample was dried. Sub, Whole
Bag# Some replicates were split into multiple bags because of their large size. This column indicates which bag out of a total number of bags per replicate # of #
Bag wt Weight of bag g
Wet wt w/bag Weight of the whole sample including the bag g
Wet wt Wet weight of whole sample ("Wet wt w/bag" - "Bag wt")
Subsamp wet wt w/ bag Weight of subsample and bag when a subsample was taken, or weight of whole sample and bag when the whole sample was used g
Subsamp wet wt Wet weight of subsample with no bag g
Subsamp dry wt w/ bag Weight of dry subsample or sample and bag combined g
Subsamp dry wt Weight of dry subsample or sample ("Dry wt w/bag" - "Bag wt") g
Dry wt Dry weight of whole sample. If whole sample was dried = "Subsamp dry wt". If a subsample was taken ="Subsamp dry wt"/"Subsamp wet wt" * "Wet wt" g
DW gm2 Dry weight per square meter ="Dry wt"/ "Quadrat size" g m-2
In Oven Time sample went into drying oven hh:mm
Out Oven Time sample was removed from oven and weighed hh:mm
Drying time Time sample was dried in drying oven days
Comments
Water_chl Chlorophyll concentration of water
Variable Name Description Units
Bay Bay sampled
Sta Sampling station name ddmmyyyy
Type Type of sample (OSOM, SPOM, MPB)
Analysis Analyiss that sample was used for: chlorophyll-a (chl), Isotopes (C,N,S)
Rep Sampling replicate
Vol water Volume of sample filtered mL
Vol solvent Volume of sovent (acetone) used to extract chlorophyll from filter mL
Prelim Chla Chorophyll concentration without accounting for procedural blank ug L-1
Blank Procedural blank chlorophyll concentration (only acetone) ug L-1
Chla Chlorophyll concentration of water = "Prelim Chla" - "Blank" ug L-1
Comments
Sediment_chl Chlorophyll concentration of surface sediments
Variable Name Description Units
Date Date that sample was taken ddmmyyyy
Sta Sampling station name
Area Habitat type in which the core was taken: Tidal flats have Marsh, Edge, and Flat; Reef for oyster reef; Benthic for bay bottom Reef/Marsh/Benthic/ Edge/ Flat
Rep replicate
Sed Depth depth to which the core was taken: 2(top 2 cm), 2-5, 2-10, 5-12 cm
Wet Sed wt w/bag Weight of bag and wet sediment sample g
Shell w/bag Weight of bag + shell hash, detritus, and other material that was retained after sieving on a 500 µm sieve g
Wet sed wt The wet weight of the sediment sample - the empty bag and shell material g
Dish wt Weight of empty petri dish g
Subsamp wet wt w/ dish Weight of dish filled with wet sediment subsample g
Subsamp dry wt w/ dish Weight of dish filled with freeze-dried sediment subsample g
Subsamp wet wt Weight of wet sediment subsample = "Subsamp wet wt w/ dish" - "Dish wt" g
Subsamp dry wt Weight of dry sediment subsample = "Subsamp dry wt w/ dish" - "Dish wt" g
Tube wt Weight of test tube to be used for chlorophyll-a analyses g
Subsamp chl dry wt w/ tube Weight of dish filled with dried sediment subsample and test tube g
Subsamp dry chl wt Weight of dry chlorophyll subsample = "Subsamp chl dry wt w/ tube" - "Tube wt" g
Prelim Chla RFU Chorophyll concentration of dried sediment without accounting for procedural blank RFU
Blank RFU Procedural blank chlorophyll concentration (only acetone) RFU
Sed Chla RFU Chlorophyll concentration of dried sediment = "Prelim Chla (RFU)" - "Blank (RFU)" RFU
Vol solvent Volume of solvent (acetone) used to extract chlorophyll from sediment mL
Dilution Dilution volume after 1 mL of sample was added to 9 mL of solvent integer
Slope A slope constant derived during fluorometer calibration used to convert ugL to ug/g
Sed Chla µg/L Chlorophyll concentration per sediment dry volume = "Chla (RFU)" * "Slope" µg L-1 dry volume
Sed Chla µg/g Chlorophyll concentration per sediment dry weight = "Sed Chla (ug/L)" * "Vol solvent"/1000 * "Dilution" / "Subsamp dry chl wt" µg g-1 dry weight
Dry sed wt Dry weight of whole sample ="Subsamp dry wt"/"Subsamp wet wt" * "Wet sed wt" g
Dry chl wt Weight of chlorophyll in sample = "Dry sed wt" * "Sed Chla (ug/g)" µg
Area Area of surface sediment sampled (core area) m-2
Chl µg/m2 Quantity of chlorophyll per square meter = "Dry chl wt"/"Area" µg m-2
Chl mg/m2 Quantity of chlorophyll per square meter = "Chl µg m2" * 1000 mg m-2
Est C/Chla ratio An estimated literature-based constant of how much carbon is in a sample of pure chlorophyll-a (Cifuentes et al. 1988)
Est C mg/m2 Estimated quantity of carbon per square meter = "Chl mg m2" * "Est C/Chla ratio" mg m-2 dry weight
Sed C µg/g Measured concentration of carbon in sediment µg g-1 dry weight
Actual C/Chla ratio Actual carbon / chlorophyll-a ratio = "Sed C µg/g" / "Sed Chla µg/g"
Actual C mg/m2 Actual quantity of carbon per square meter = "Chl mg/m2" *"Actual C/Chla ratio" mg m-2
Taken below cyanobacteria mat If sediment sample was taken below cyanobacteria mat Y/N
Comments Relevant comments including seagrass cover in quadrat (%) and water depth (ft)
SI Stable isotope concentrations of many types of samples
Variable Name Description Units
ID Unique sample identifier
Project Project that sample was analyzed for Oyster reef, Tidal flat, Bay
Date Date that sample was taken ddmmyyyy
Sta Sampling station name
Rep Replicate number
Animal/Producer Type of organism analyzed Animal, Producer
Taxa/Type Taxa name or sample type
Code Abbreviated code refering to each taxa or type of sample
Acidified Was sample acidifed? Y/N
d15N δ15N (ratio of the two stable isotopes of nitrogen, 15N:14N) ‰
d13C δ13C (ratio of the two stable isotopes of carbon, 13C:12C) ‰
Element Element(s) analyzed for stable isotopes C, N or both
Sed Depth Depth of sediment (sediment samples only) cm
Comments Relevant comments about sampling or sample processing
Feeding Modes Feeding modes of benthic invertebrate taxa
Variable Name Description Units
Taxa Taxa name, usually species name
Feeding Mode Feeding mode, e.g., deposit feeder, suspension feeder, predator/scavenger, unknown
Encrusting_abundance metadata, Encrusting_per_shell metadata, Encrusting_biomass metadata, Sediment_grain_size metadata
Methods:
Sampling of oyster reefs was conducted on a quarterly basis from 2020-01-24 to 2022-02-01 on four oyster reefs in the eastern part of Matagorda Bay, Texas. During each sampling event, 1.0 m2 throw traps with 1 mm mesh sides and a modified 7.6 cm metal skirt were pressed securely into each reef to collect fauna. Live and dead oysters were collected from a 0.25 or 0.07 m2 subset of the enclosed area, counted, and measured for live oyster size and volume. Another subset of 0.25 m² was excavated to a depth of 0.1 m, and the collected material was sieved over a 500 µm mesh to collect infauna. All motile fauna were preserved using buffered formalin and later identified, counted, and weighed after drying in the laboratory. Also, in the laboratory, shells from the 0.25 or 0.07 m2 subset of live oysters were weighed, and the total number of barnacles and mussels were recorded when less than ten of each encrusting fauna was present. To estimate total abundance when more than ten of each encrusting fauna were present, a subset of individual oyster shells was weighed, and barnacles and mussels were counted. To estimate biomass of encrusting fauna, a subset of ten barnacles and mussels from each reef in each season were weighed after drying.
During each oyster reef sampling event, samples were also collected for stable isotope analyses of Carbon and Nitrogen: Surface sediment organic matter (SSOM), suspended particulate organic matter (SPOM), and oyster shell organic matter (OSOM) were collected at each oyster reef using benthic coring, bottom-water samples, and oyster shells, respectively. Fauna were collected using an additional throw-trap, and representative vegetation samples were gathered from adjacent shorelines. Microphytobenthos were collected from the reef adjacent shoreline by scraping the top millimeter of sediment. Samples were processed in the laboratory, including sieving, deionized water-rinsing, freeze-drying, and grinding/ homogenization. For fauna samples, 24-hour evacuation of gut contents or excision of tissues were performed. OSOM was removed from oyster shells using a light-brushing; MPB was extracted from sediment using methods described by Riera & Richard (1996), modified by Herlory et al. (2007). For samples to be analyzed for δ13C and percent organic carbon, carbonates were removed by HCl addition (sediments and fauna), or fuming (filters for SPOM, OSOM, and MPB).
During all sampling events, water temperature, salinity, dissolved oxygen concentration, and pH were measured at each site concurrently with fauna and stable isotope sampling using a YSI Pro DSS multiparameter instrument. Surface sediment and suspended particulate organic matter were collected for chlorophyll a analysis via replicate benthic cores and bottom water collections, respectively. Chlorophyll a was extracted from filters and sediments using a non-acidification technique and measured using a Turner Trilogy fluorometer.
Field sampling was conducted on wind-tidal flats along the backside of the Matagorda peninsula in spring and summer of 2021. Two wind-tidal flats with adjacent marsh habitat were used; transects from marsh to algae mat were established, and habitat surveys conducted. Benthic macrofauna community composition was assessed using replicate core samples (38.5 cm2 area to a depth of 5 cm) at five stations along the transect.
Additional sediment cores were collected from each location for analysis of chlorophyll a in the sediment and stable isotopes analyses. The top of each core was gently scraped to remove the algal mat. Cyanobacterial mats were rinsed to remove sediment before processing for stable isotopes. Sediment was otherwise processed as described above. Nearby water quality, suspended particulate organic matter, chlorophyll a, and microphytobenthos were collected and processed as described above.
In August 2020, additional sediment cores were collected across the southern portion of Matagorda Bay. Water quality and suspended particulate organic matter were collected and processed as described above. Sediment was collected from benthic habitats and seagrass beds using 38.5 cm2 and 63.6 cm2 cores, respectively. Microphytobenthos was extracted from additional sediment collections at sites across the bay for stable isotope analysis, and processed as described above. Additional oyster collections for isotope analyses were made using a dredge over various subtidal reefs in the bay.
Provenance and Historical References:
Herlory, O., Richard, P. & Blanchard, G.F. Methodology of light response curves: application of chlorophyll fluorescence to microphytobenthic biofilms. Mar Biol 153, 91–101 (2007). https://doi.org/10.1007/s00227-007-0787-9
Riera, Pascal and Pierre Richard. Isotopic Determination of Food Sources ofCrassostrea gigas Along a Trophic Gradient in the Estuarine Bay of Marennes-Ol éron. Estuarine Coastal and Shelf Science 42 (1996): 347-360. https://doi.org/10.1006/ecss.1996.0023
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