Methods

Study Sites and Sampling Methods

Two pairs of high relief and low relief reefs were chosen for this study: Katrina reef (high) and Legacy reef (low) in the central Sound, and Square Handkerchief reef (high) and USM reef (low) in the western Sound (Map. 1). Due to the difficulty of sampling the reefs directly, settlement of biofouling organisms on artificial plate installations was used as a proxy for the reef community. These installations consisted of an array of plexiglass settlement plates fixed at different depths in the water column. Ten arrays were deployed at each reef during each sampling season (quarterly from July 2011 to June 2012) and allowed to soak for 4 weeks before being collected. Respiration (R) and net productivity (Pn) were measured on all 10 arrays, chlorophyll-a (chl-a) measurements were performed on half of the arrays, and biomass (B) was measured on the other half. The results were compared seasonally among depth zones and across reefs by a three-way ANOVA. Patterns in the dependent variables due to reef location within the Sound or distance from shore were also examined. In a second experiment, R, Pn, chl-a, and particulate organic matter concentrations were measured for water samples collected during the array soaking period to assess the contribution of phytoplankton to local primary production.

Sampling was conducted quarterly from August 2011 to May 2012 for a total of four sampling seasons: summer (July 28 – Aug. 19, 2011), fall (Oct. 14 – Nov. 11, 2011), winter (Jan. 27 – Mar. 9, 2012), and spring (Apr. 12 - May 14, 2012). The artificial installations were deployed at the beginning of each sampling season and retrieved after approximately four weeks, depending on weather conditions. Water samples were collected at each reef approximately two weeks after the arrays were deployed, except in the summer when water samples were collected after the array soaking period. Irradiance, salinity, and temperature were measured at each reef during array deployments, water sample collections, and array retrievals for each sampling season.

The weights were made by pouring concrete mix into 6 inch round plastic pots and placing a stainless steel eye bolt in the center to which the rope was then tied. Pexiglass tiles, 104 cm2 (16 in2) and 0.635 cm (¼ in) thick, were attached to the rope at different levels depending on the reef type. The rope was threaded through a hole drilled in the center of the tile and kept in place using small plastic zip ties threaded through the rope on both sides of the tile. In each array, the surface plate (S) was fixed at 0.31 m (1 ft) below the surface, the mid plate (M) at 0.61 m (2 ft) below surface, and the bottom plate (B) at 0.91 m (3 ft) below the surface. 

Surface water samples were collected at ten random sites at each reef during each sampling season to measure water column R, Pn, chl-a, and particulate organic matter (POM). Bottom samples were collected also during the fall and winter for comparison with surface samples. Pre-labeled BOD bottles (300 ml) were used to collect the surface water samples by dipping the bottle into the seawater just below the surface. A Niskin bottle was used to collect water samples near the bottom (about 15 cm above the sediment), which were then transferred into labeled 300 ml BOD bottles at each site. 

Primary productivity of settlement plant periphyton and water column phytoplankton samples was measured using the light and dark bottle method described in Kendrick and Lavery (2001). In this method, the photosynthetic rate is determined from the rate of oxygen exchange between an algal or plant sample and the surrounding water. The sample is placed in a gas tight chamber and the change in dissolved oxygen (D.O.) concentration is measured under dark and light conditions. Oxygen is liberated during photosynthesis, which only takes place when light is available; therefore the oxygen concentration should increase during the light period. In a sample consisting of purely autotrophic material, the change in D.O. in the light is a measure of gross photosynthesis minus plant respiration, or net photosynthesis. Net photosynthesis is a measure of the amount of primary production available to heterotrophs after the algae have satisfied their own respiratory requirements. Gross photosynthesis is a measure of total photosynthesis including the costs of plant respiration and is calculated by correcting net photosynthesis for respiration.Immediately after arriving at the lab, the BOD bottles were filled completely with artificial seawater and placed in a water bath to maintain a constant temperature of 25ºC.  A Tidbit data logger (Onset Corp.) was used to record the temperature of the water bath during the incubation. The samples were incubated in the dark for a period not exceeding 6 hours, followed by a period of light not exceeding 6 hours, but typically half as long as the respiration time. The stopping point was determined by obtaining a measurable change in D.O. (usually at least 1 mg O2 L-1), which could take very little time if a large amount of biomass was present. A Hach HQ40d meter with anIntelliCAL LBOD101 Luminescent Dissolved Oxygen (LDO) probe was used to measure changes in D.O. concentration in the BOD bottles during the incubation period.

Annual net benthic production for each reef was estimated by scaling up average settlement plate net productivity measurements for each season to the geospatially mapped surface area of the reefs and adding the four seasonal estimates together to obtain an annual estimate of net production. An annual estimate of water column net production was obtained by scaling up the average seasonal productivity measured for the water samples to the volume of water overlying the reefs. These benthic and water column annual production estimates were then added together to obtain an estimate of total habitat annual net production for each reef, which incorporated both sources of primary productivity. In addition, annual production estimates were standardized to area (m2) or volume (m3) in order to compare between reef and water column production values and determine if differences exist between reef types.