Beck and La Peyre: Effects of oyster harvesting activities on Louisiana reef habitat and resident nekton communities 
331 
Figure 3 
The modified sample tray used for sampling resident communities of oyster reefs in 2010 in coastal Louisiana, showing 
(A) the mesh drawstring as it would be when deployed and (B) the mesh drawstring pulled for tray retrieval. 
at each station with a 250-mL, opaque Nalgene bottle, 
placed on ice, taken to the laboratory, and immediately 
analyzed for chlorophyll-a (measured in micrograms 
per liter) (Arar 5 * * * * * ) and total particulate matter (TPM; 
measured in milligrams per liter) (Rice et ah, 2012). 
Isotope samples 
Sample collection Resident organisms used for stable 
isotope analyses were taken from tray samples. For 
each species found across all sites, only organisms of 
similar size were used in order to remove any effects 
of ontogenetic dietary shifts; organisms had to be com- 
bined across stations to obtain adequate numbers of 
each species from each site. Organisms collected in- 
cluded the eastern oyster, hooked mussel, the flatback 
mud crab ( Eurypanopeus depressus ), grass shrimp 
(. Palaemonetes spp.), the naked goby ( Gobiosoma bosc), 
the freckled blenny ( Hypsoblennius ionthas), and the 
skilletfish ( Gobiesox strumosus). Adductor muscle tis- 
sue was used for eastern oysters, and the entire or- 
ganism was used for hooked mussels (excluding their 
shells), flatback mud crabs, and grass shrimp. Tail por- 
tions were used for naked goby and skilletfish samples, 
and epaxial muscle tissue was used for freckled blenny. 
Samples of basal food sources were collected at each 
site: fine particulate organic matter (FPOM; <200 pm, 
pelagic source) and dominant marsh plants (nonpelag- 
ic, detrital source). For FPOM samples, a 1-L bottle of 
water was collected from each station (3 samples per 
5 Arar, E. J. 1997. Method 446.0: In vitro determination of 
chlorophylls a\, b\, c\ + C 2 and pheopigments in marine and 
freshwater algae by visible spectrophotometry, rev 1.2, 26 p. 
National Exposure Research Laboratory, Office of Research 
and Development, U. S. Environmental Protection Agency. 
[Available at website.] 
site), filtered through 200-pm mesh, and placed on ice. 
Three samples clipped from the stems of the marsh 
plant (Spartina spp.) were collected (20 m apart from 
each other) from each site and placed on ice. Coarse 
particulate organic matter (CPOM; >200 pm) was col- 
lected with a ring-net plankton tow (3-string bridle, 50- 
cm diameter) fitted with 200-pm mesh, pulled at each 
station for 2 min at a speed of 2.6 m/s (5 kn). Plank- 
ton tow contents were placed in a 1-L opaque bottle 
after visible detritus were removed and these bottles 
were placed on ice and taken to the laboratory for con- 
tent analysis. FPOM and CPOM samples were filtered 
through Whatman glass microfiber filters (GF/F, pre- 
combusted for 3 h at 450°C) until flow was obstructed, 
and the filters with the filtrate were frozen at -20°C. 
Sample preparation and analyses 
All samples were dried to a constant weight at 60°C, 
they ground to a powder, and treated to remove lipids. 
Inorganic carbonates were removed from shrimp, crabs, 
FPOM, and CPOM through treatment with minute 
quantities of IN hydrochloric acid until the reaction 
ceased (Jacob et al., 2005). Lipids were extracted in 2 
separate 24-h decantations with hexane at room tem- 
perature (Fry et al., 2003). Once they were treated for 
lipids and inorganic carbonates, samples were placed 
back into a drying oven at 60°C until they reached a 
constant weight. Faunal tissue samples of 1 mg (stan- 
dard error [SE] 0.2) and plant tissue samples of 2-3 
mg were weighed for stable isotope analyses. For fil- 
tered FPOM and CPOM samples, a small portion cut 
from the center of the filter was used for analyses. All 
samples were analyzed for 8 15 N and 8 13 C by the Uni- 
versity of California Stable Isotope Facility with a PDZ 
Europa ANCA-GSL elemental analyzer (Sercon, Ltd., 
