Process Study 2 was undertaken between 20-22 September 2005 in the Huon Estuary offshore from Hideaway Bay. During this Process Study, two sediment traps were deployed at each of two sites (near sites P3 and P4 from the spatial survey) on the bottom for 24 hours.Prior to the deployment of the traps surface sediment samples were collected with a benthic grab from each site. Each sediment trap consisted of three collection tubes, material from each tube was filtered on 47 mm GFF filters, with several filters required to filter all of the particualte matter from each tube. Combined filters from each of two tubes labeled A and B (typically 3 filters for each tube) were extracted for lipid analysis. Tube C was used either for isotopes or Fauna indent.

Process Study 3 was undertaken between 03-05 October 2006 in North West Bay. Sediment traps were deployed and sediment samples taken at five sites in NWB. The primary aim was to investigate the composition of material being deposited to the sediments from the water column at these times and to compare this organic matter with that found in the sediments at the same sites. Additionally, we wished to see whether any organic matter of obvious fish farm origin could be detected. One sediment trap was deployed at each North West Bay (NWB) site in water varying in depth from 10 m (site 9) to 20 m (site 2). The trap sites were numbered 2, 4, 5, 7, and 9. Traps were deployed at their respective sites and left for at least one hour before the caps were removed in order to eliminate sediment re-suspended during deployment from entering the traps. The traps were left in place for 48 hours and then retrieved, capped and returned to Hobart for recovery of the samples. Each trap had 3 tubes, each of these tubes was split into three. One litre was taken and filtered for lipids using pre-weighed 47 mm GFF filters, one litre for pigments and the rest was split in two and stored in 500ml bottles, one for zooplankton analysis and the other for microalgal samples. Several filters were required to filter the lipid sample depending on the amount of particles in the tube. Selected filters were then analysed for lipid biomarkers. Organic matter from selected filters was also analysed for stable isotope 13C and 15 N values and carbon content. The contents of one tube from each trap was inspected for identification of zooplankton remains and faecal pellets using light microscopy. Sediments were collected at each of the above trap sites using a Wilco box corer.

Process Study 1 was undertaken between 12-14 April 2005 in the Huon Estuary offshore from Hideaway Bay. During this Process Study, two sediment traps were deployed at each of two sites (near sites P3 and P4 from the spatial survey) on the bottom for 24 hours.Prior to the deployment of the traps surface sediment samples were collected with a benthic grab from each site. Each sediment trap consisted of three collection tubes, material from each tube was filtered on 47 mm GFF filters, with several filters required to filter all of the particualte matter from each tube. Combined filters from each of two tubes labeled A and B (typically 3 filters for each tube) were extracted for lipid analysis. Tube C was used either for isotopes or Fauna indent.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Process Study 1 was undertaken between 12-14 April 2005 in the Huon Estuary offshore from Hideaway Bay. Prior to each microheterotroph grazing experiment, a CTD cast was performed at site P3 using the Seaboard 4550 to determine the depth of the fluorescence maximum. Water for a grazing experiment was collected from a depth of 20m (12 April) and 5m (13 April).

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Prior to the three microheterotroph grazing experiments, a CTD cast was performed at site PE3 to determine the depth of the fluorescence maximum. Water for the three grazing experiments was collected simultaneously from a depth of 7m. For all three experiments, the sample water was filtered through a 200µm mesh as usual. For the second experiment, 10 mesozooplankton were added to the sample water in each incubated bottle. In the third experiment 30 additional mesozooplankton were added to the sample water in each incubated bottle. The additional mesozooplankton were removed from the incubated bottles at the close of the experiment, before filtration. Samples were incubated for 24 hours with subsamples collected at times T0 and T24 for phytoplankton and microheterotroph counts, nutrient analysis and pigment concentration and composition. Grazing and growth rates were calculated.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Monthly Monitoring 1 (MM1) was undertaken in the D'Entrecasteaux Channel by CMAR and in the Huon River by TAFI from 10 January 2002 until 31 March 2003. During MM1 samples were collected monthly from 12 sites in the D'Entrecasteaux Channel by CMAR for the analysis of nutrients, phytoplankton species identification, and chlorophyll a; samples were collected for salinity calibration and dissolved oxygen approximately four times a year from 3 sites. In December 2002, samples were collected for HPLC pigment analysis from 5 sites. Samples were collected monthly from 4 sites in the Huon River by TAFI for phytoplankton species identification, nutrients, spectrophotometric chlorophyll a and dissolved oxygen. This metadata record refers to the Monthly Monitoring 1 data collected by CMAR in the D'Entrecasteaux Channel. Two depths were sampled (0 and 1 m from the bottom) for the nutrient analyses, chlorophyll a analysis and dissolved oxygen. A 12 m integrated water column sample was collected for phytoplankton species identification and additionally for chlorophyll a analysis in the first 12 months of the monitoring. In December 2002, samples were collected from surface and bottom from 5 sites for HPLC pigment analysis. At each site prior to the collection of the samples a CTD profile to near bottom was collected using the SBE19-0605 and the Secchi depth measured. PLEASE NOTE - The phytoplankton results were updated in June 2012 with a correction. The original biovolume unit in column L and M was incorrect and should have been µL/L. The values in column M and L have been divided by 1000 and the unit mL/L left unchanged. Other values are not affected including CPL and Group CPL.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Process Study 2 was undertaken between 21-22 September 2005 in the Huon Estuary offshore from Hideaway Bay. Prior to each microheterotroph grazing experiment, a CTD cast was performed at site P3 using the Seaboard 4550 to determine the depth of the fluorescence maximum. Water for a grazing experiment was collected from a depth of 2 m on the 21 September 2005 Samples were incubated for 24 hours with subsamples collected at times T0 and T24 for phytoplankton and microheterotroph counts, nutrient analysis and pigment concentration and composition. Grazing and growth rates were calculated.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Monthly monitoring 2 (MM2) was undertaken in the Huon River and D Entrecasteaux Channel from 20 September 2004 until 19 October 2005, except that there was no sampling in May or July 2005. During MM2 samples were collected monthly from 11 sites for the analysis of nutrients, phytoplankton species identification, chlorophyll and carotenoid pigments and turbidity; samples were collected approximately every second month from 3-4 sites for dissolved oxygen (TAFI). Two depths were sampled (0 and 1 m from the bottom) for the nutrient analyses, dissolved oxygen and spectrophotometric chlorophyll (TAFI) and two depths were sampled for turbidity (1m and 5m). A 12 m integrated water column sample was collected for the CMAR HPLC pigment analysis and phytoplankton species identification. At each site prior to the collection of the samples a CTD profile to near bottom was collected using the SBE19-4550 and the Secchi depth measured. PLEASE NOTE - The phytoplankton results were updated in June 2012 with a correction. The original biovolume unit in column L and M was incorrect and should have been µL/L. The values in column M and L have been divided by 1000 and the unit mL/L left unchanged. Other values are not affected including CPL and Group CPL.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). Process Study 2 was undertaken between 3-5 October 2006 in the North West Bay. Prior to the three microheterotroph grazing experiments, a CTD (Seacat 4550) cast was performed at site NWB2 to determine the depth of the fluorescence maximum. Water for the three grazing experiments was collected simultaneously from a depth of 15m. For the first experiment, the sample water was filtered through a 200µm mesh. For the second experiment, no screening was used for the sample water. In the third experiment approximately 100 ml of water containing microzooplankton, which had been previously screened through a 1mm-mesh, was added to the sample water. Samples were incubated for 24 hours with subsamples collected at times T0 and T24 for phytoplankton and microheterotroph counts, nutrient analysis and pigment concentration and composition. Grazing and growth rates were calculated.

The Aquafin CRC Salmon Project is being undertaken by CSIRO Marine and Atmospheric Research (CMAR) and Tasmanian Aquaculture and Fisheries Institute (TAFI). The huon microheterotroph grazing experiments were undertaken on 23 September 2003 (HG01), 18 November 2003 (HG02), 24 February 2004 (HG03) and 26 July 2004 (HG04). Sampling took place in Hideaway Bay in the Huon Estuary. Prior to each microheterotroph grazing experiment, a CTD cast was performed at site P3 using the SBE19-0605 to determine the fluorescence profile. Water for the grazing experiments was collected from 5-7m, i.e. at about 50% of surface light level and below any surface freshwater runoff layer. Samples were incubated for 24 hours with subsamples collected at times T0 and T24 for phytoplankton and microheterotroph counts, nutrient analysis and pigment concentration and composition. Grazing and growth rates were calculated.