Four sampling stations were established in the lagoon at Davies Reef in February 1986. Two stations were located in the shallow zone, immediately behind the reef flat, and two stations were located the deeper zone in the centre of the lagoon. The stations were sampled on four occasions during 1986: Summer (February); Autumn (May); Winter (August); and Spring (November).
At each station, samples were collected using cylindrical PVC corers pushed manually to a depth of 200 to 250 mm into the sediment. Smaller infauna were sampled from 4 sets of five 55 mm diameter cores. Each set of cores was collected over an area of 1 m² and sets of cores were spaced about 4 m apart. Larger infauna were sampled in a similar manner using 4 sets of six 143 mm diameter corers. At one of the deeper sites, 8 contiguous series of samples, consisting of seven to sixteen 55 mm cores were also taken through Callianassid shrimp mounds.
After separation from the sediment, animals were identified to family level, counted and grouped into 6 categories (macrophagous polychaetes, microphagous polychaetes, crustaceans, bivalves, gastropods and other taxa) and assigned to 2 size classes (small, 0.5-2.0 mm; large, >2 mm). Ash-free dry weight (AFDW) was calculated for each group after decalcification of those specimens with calcareous skeletons or shells. Published allometric relationships were used to estimate respiration rates, secondary production and consumption of organic material.
Two sets of paired sediment traps were deployed for 2 to 4 consecutive days at mid-depth in the water column at each sampling station. Collecting jars were replaced every 24 hours by divers and the samples filtered onto pre-ashed GF/F filters and frozen. In the laboratory samples were dried at 60°C, weighed, decalcified, reweighed and analysed using a Perkin Elmer CHN analyser.
Oxygen flux, a measure of rates of benthic community metabolism was measured in cylindrical chambers, enclosing a portion of the sediment. Each perspex chamber had a volume of 3.4 litres, a base area of 283 cm² and two sampling ports sealed with rubber stoppers through which water samples could be extracted with a syringe. Six chambers were deployed at each site. Duplicate samples were extracted over a four hour period from 10:00 to 14:00 hrs and at night and the oxygen concentration measured using a polarographic oxygen probe. Gross primary production and respiration rates were then calculated.
Bacterial abundance was determined by direct counts of acridine-orange-stained cells and epifluorescence microscopy. Three sediment cores (0.5 cm inner diameter, 1 cm deep) were collected at each site and preserved in 4% formalin-seawater. The sediments were treated with 10% acetic acid (v/v in distilled water) overnight to dissolve the carbonate sediment, then homogenised for 3.5 min with a laboratory disperser (Ystral, Germany). Cell biovolumes were determined by microscopy. Carbon content was assumed to be 220 fg C/µm³.
Bacterial production rates were measured as the incorporation of tritiated thymidine into DNA. Five 0.6 cm³ sediment samples were collected at each sampling site. Each core was incubated in a tube with 48 µl of 16 Ci/mmol [methyl-³H] thymidine for 10 min at in situ temperature. Incubations were terminated with 10 ml 90% ethanol. A conversion factor of 1x10^18 cell divisions/mol thymidine incorporated was used in calculating bacterial production.
Protozoa were extracted from five replicate cores (1.1 cm inner diameter, 1 cm deep) using the silica gel Percoll. Each core was centrifuged at low speed (490 x g) for 20 min in a 30 ml centrifuge tube containing 10 ml of a Percoll-sorbitol mixture. The procedure was repeated three times. Ciliates and flagellates (>=20 µm) were counted in a petri dish with the glass bottom marked into 1 cm² grids.
Chlorophyll and phaeopigments were estimated from three to five replicate cores of sediment (1.1 cm inner diameter, 1 cm deep) per site by extraction with acetone (90% v/v with water). After extraction in the dark overnight at 0°C, samples were centrifuged to remove particulates. Absorbance of the extracts before and after acidification was measured at 665 and 750 nm on a Varian spectrophotometer.
Total organic carbon and nitrogen were measured from three replicate sediment cores per site. Sediments were dried at 60°C to constant weight, then ground to a powder. Total nitrogen was determined by combustion of sediments in a Perkin Elmer CHN analyser. Total organic carbon was measured on a Beckman TOC analyser.
Grain size analyses were carried out on two replicate cores of surface sediments collected at each site. Percent silt and clay were estimated by sieve and pipette analysis. The sand fraction was dry-sifted and weighed to determine particle size distribution.