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Monitoring of Western Australia's Pearl Oyster Fishery
No full textMaintenance and Update Frequency: unknownStatement: Original record compiled for the Western Australian Marine Science Institution (WAMSI), Project 3.8, 2008. Originally sourced from WA DEC Marine Policy and Planning Branch Pilbara and Lower West Kimberley Environmental Report Library. Date range generated from citation date, limited abstract information available.<b>Credit</b><br/>W. Fletcher<b>Credit</b><br/>K. Friedman<b>Credit</b><br/>V. Weir<b>Credit</b><br/>J. McCrea<b>Credit</b><br/>R. ClarkThis record is derived from DEC Marine Policy Branch Endnote library and spatially referenced SIER Database
The Measurement of Seagrass Photosynthesis Using PAM Fluorometry - Recovery and survival of Posidonia sinuosa sprigs and plugs after transplantation
No full textMaintenance and Update Frequency: notPlannedStatement: - Sprig transplantation at Southern Flats -
This study was part of the Seagrass Research and Rehabilitation Plan, Project 3 carried out by the Marine and Freshwater Research Laboratory. Transplantation of 1.4 hectares of P. sinuosa sprigs took place on three occasions between November 2004 and February 2005. Sprigs were collected from Parmelia Bank, Western Australia (4.6 - 6.6 m depth) and were transplanted to Southern Flats (2.0 - 3.8 m) (see large thumbnail).
Suitable sprig transplant material was collected from the edge of the donor meadow by removing sections of seagrass rhizomes that had leaves and white roots attached. The transplant material was brought onto a boat and stored in seawater-filled containers, shaded by the boat's canopy. During transport to the recipient site, the sprigs were removed from the containers and the rhizomes were tied to wire staples with biodegradable twine. This process meant that the sprigs were immersed for up to fifteen minutes. The sprigs were then replaced in the water-filled containers until ready to plant. Upon arrival at the recipient site, the sprigs were moved into free-draining crates to enable transport underwater. Not all the crates could be carried at once and therefore some were left on the boat for up to one and a half hours, covered with wet calico bags until divers were ready to plant the sprigs.
Southern Flats was selected as the recipient site, based on suitable sediment and water quality characteristics. The site has been marked out with rope during preparation prior to transplantation. The rope was laid out in two adjacent 100 x 100 m grids. Each team of divers took a crate filled with sprigs and a 1 x 1 m quadrat and proceeded to plant sprigs with a spacing of 1 m. Sprigs were planted by pushing the wire staple into the sand and creating a furrow for the rhizome, approximately 10 cm deep. The rhizome and its root were covered with sand, making sure that the leaves remained exposed.
For Chlorophyll fluorescence measurement methodology see section 6.2.1.1 of thesisStatement: - Sampling protocol -
Transplantation of 1.4 hectares of sprigs took place on three occasions between November 2004 and February 2005. Each occasion consisted of four consecutive days of transplantation (November 8-11, December 6-9 and February 14-17). On each day sprigs were collected from Parmelia Bank, transported to Southern Flats and transplanted. Fluorescence measurements were made on the following:
1) in situ P. sinuosa material before removal for transplantation, Parmelia Bank,
2) collected material, once tied onto wire staples while stored in water-filled containers, during transport to Southern Flats,
3) transplanted sprigs, Southern Flats, and
4) control P. sinuosa, naturally occuring near the recipient site at Southern Flats.
On each day measurements were made as described above. In addition, the transplants planted on previous days were re-measured, in order to determine any changes in photosynthetic rates.
Transplants were revisited during March and May 2005. On each visit fluorescence measurements were made on the following:
1) transplanted sprigs, Southern Flats, and
2) control P. sinuosa, naturally occuring near the recipient site at Southern Flats
- Sampling times -
For logistical reasons, fluorescence measurements could not all be taken at the same time. Measurements were made on each day between the following times:
1) 0930 -1040 h: donor site, Parmelia Bank,
2) 1030 - 1200 h: during transport on the boat,
3) 0850 - 1640 h: transplanted sprigs, Southern Flats, and
4) 0850 - 1510 h: control P. sinuosa meadow, Southern Flats.Statement: - Plug and sprig transplantation at Woodman Point -
Three plug sizes (5, 10 and 15 cm diameter) and one set of sprigs were transplanted at Woodman Point, Western Australia, during February 2005 (see large thumbnail). Plugs and spigs were collected from the edge of a P. sinuosa seagrass meadow (2.0 m) and transplanted into an adjacent area of bare sand (1.9 m).
Ten replicate plugs of each size were collected from the edge of the donor meadow by hammering PVC plug sleeves into the seagrass. After the plug sleeves were in place, the surrounding sand was dug away to remove the plug from the sediment. A cap was placed on the bottom of the PVC plugs to prevent loss of material. Plugs were extracted and transplanted using the method described by van Keulen et. al. (2003) (see thesis references). Ten sprigs were collected by removing a section of rhizome from the edge of the meadow and tying the sprig onto wire staples underwater.
The plugs and sprigs were moved underwater to the recipient site. Plugs were planted in a 2 x 5 configuration, with a spacing of 15 - 35 cm between them. Sprigs were planted by pushing the wire staple into the sand and creating a furrow for the rhizome, approximately 10 cm deep. The rhizome and roots were covered with sand, making sure the leaves remained exposed. Sprigs were planted in a 2 x 5 configuration, with a spacing fo 25 cm between them.
For Chlorophyll fluorescence measurement methodology see section 6.2.2.1 of thesisStatement: - Sampling protocol -
Transplantation of plugs and sprigs took place on three days during February 2005. On each day, ten plugs of the appropriate size (5, 10 or 15 cm diameter) were transplanted and on one of the days sprigs were also transplanted. Fluorescence measurements were made on the following:
1) in situ P. sinuosa material before removal for transplantation
2) transplant material after the PVC plug sleeve had been hammered into the meadow, but before removal from the substrate,
3) collected transplant material while still in the plug sleeve at the recipient site before transplantation
4) transplanted P. sinuosa plugs, and
5) transplanted P. sinuosa sprigs.
Plugs and sprigs were revisited once a week for four weeks and then periodically until 5 July 2005. On each revisit, fluorescence measurements were made on the following:
1) 5 cm diameter plugs
2) 10 cm diameter plugs
3) 15 cm diameter plugs
4) sprigs, and
5) control P. sinuosa meadow naturally occuring adjacent to the recipient sand patch.
- Sampling times -
For logistical reasons, fluorescence measurements could not all be taken at the same time. Measurements were made between the following times:
1) 1020 - 1110 h: 5 cm plugs,
2) 0800 - 1010 h: 10 cm plugs,
3) 0800 - 0948 h: 15 cm plugs,
4) 0800 - 1040 h: sprigs, and
5) 0840 - 1135 h: control meadow.<b>Credit</b><br/>Seagrass Research and Rehabilitation Plan, Project 3 - Marine and Freshwater Research Laboratory<b>Purpose</b><br/>To improve transplantation of seagrass.Data was collected on the photosynthetic rates of Posidonia sinuosa plugs (shoots with sediment intact) and sprigs (shoots with bare roots) before, during and after transplantation from Parmelia Bank to Southern Flats, Cockburn Sound, W.A. and from Woodman Point to Woodman Point, W.A. between November 2004 to February 2005
RAN CTD Profile Data - HMAS MERMAID ProjectID: HI521MER_M From: 2012-06-22 To: 2012-08-07
No full textStatement: Initial Processing
Incoming data undergoes gross range checks and removal of any corrupted or unrealistic data. Some CTD data is subject to a pressure offset error generally less than 1 decibar. A pressure offset error occurs when the pressure sensor does not read 0 dbar in air. In cases where the pressure offset error was observed before the CTD cast the pressure readings have been corrected for the offset which is stored in the global netCDF attribute named 'CTD_pressure_offset'.
Salinity on the PSS-78 scale is computed from conductivity, temperature and pressure using the UNESCO (1983) algorithm with temperature corrected from the ITS-90 scale to the ITS-68 scale used by the algorithm.
For this CTD model the response time (time constant) of the temperature sensor (100 ms) is slower than the conductivity cell (25ms). This leads to a phenomenon called 'salinity spiking' in the salinity data. Spiking is caused by the fact that calculated salinity is a function of conductivity, temperature and pressure [S=f(C,T,z)]. The temperature response lags the conductivity response resulting an error in the calculation of salinity. This is evident as noticeable spikes in the salinity profiles especially at depths where temperature is rapidly changing e.g in the ocean thermocline. The spiking was reduced reduced by applying a 2.5 sample time shift (0.1 s) to the temperature values and using the shifted temperature value in the re-computation of the salinity. An array of raw pressure, temperature and de-spiked salinity is then passed to the next processing stage.
The raw CTD data contains a non-monotonic sequence of pressures due to up/down motion of ship/winch. A sequence of unique monotonic pressures up to the maximum value is extracted and then linearly interpolated to 1 decibar pressure levels with the corresponding interpolated temperature and salinity. Finally the interpolated files are converted to a set of netCDF files ready for QC.
Quality Control
Quality control (QC) involves viewing location of the data on a map, visual inspection of each profile of temperature and salinity and comparison with nearest neighbours and climatology. CTD profiles are checked for any density inversions i.e. density decreasing with depth by computing sigma-t density. A density inversion may indicate unrealistic salinity and/or temperature values. QC flags are applied to indicate whether data is good, suspect, bad or not tested. QC flags may apply at the 'whole profile' level or individual pressure levels.
CTD cast positions and times undergo a land and ship speed check. Casts with position on land or unrealistic speed between casts are flagged as failed position or time. Temperature and salinity profiles are then visually compared against a 3 standard deviation envelope from the CSIRO-CARS (2009) atlas. Profiles or segments of profiles with data outside the envelope are flagged as doubtful or failed. Profiles are also checked for consistency or doubtful features by comparing with previous/next casts (buddies) and also by comparison with historical CTD casts taken in the same area and season.<b>Credit</b><br/>Royal Australian Navy Hydrography and Metoc Branch<b>Purpose</b><br/>Part of the long term ocean monitoring program.This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 105 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI521MER_M from HMAS MERMAID.<br/><br/>The CTD was manufactured by Applied Microsystems Limited and is the "Micro CTD" model. This CTD type is referred to operationally as the MVP200_CTD. This CTD is fitted with a 4 electrode platinized conductivity cell, thermistor temperature sensor and a semiconductor strain gauge pressure sensor.<br/><br/>The CTD sensors are calibrated at the manufacturer Applied Microsystems Limited on a 12-18 month schedule. The CTD temperature sensor is calibrated against 'Hart' temperature standards. The pressure sensor is calibrated using 'Budenburg Deadweight' standards. The conductivity sensor is calibrated using 'Hart' temperature standards and seawater samples of known conductivity.<br/><br/>The CTD sensors are mounted to a fish-shape probe. The probe is controlled by an electric winch (MVP200 type). For downcasts the fish is allowed to free-fall (winch is in 'free-wheel' mode) under its own weight at about 2-3 ms-1 and then is winched back. Data is recorded in downcast and usually in upcast direction at a sampling rate of 25 Hz. The downcast data is of higher quality because sensors encounter undisturbed seawater that flows through the nose of the fish. On the upcast the fish is flipped around (tail first) and the sensors in the nose encounter disturbed flow from the fish tail.<br/><br/>This type of CTD is prone to a phenomenon called 'salinity spiking' caused by a mismatch between the response times of the temperature and conductivity sensor. Data undergoes a salinity de-spiking routine to correct for this. See the history metadata for further details on the salinity de-spiking process.<br/><br/>Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts
Aggregations of common holothurians on reef flats of Coral Bay, Ningaloo Reef, North Western Australia
No full textMaintenance and Update Frequency: notPlannedStatement: -Distribution analysis-
The geographic position of individual sea cucumbers was determined using a modification of the manta tow - a rapid quantitative survey technique used to determine the abundance and/or densities of marine organisms. In this study manta tows were conducted in the traditional sense; however, instead of counting individual specimens, the position of each was recorded as a single global positioning system (GPS) way-point. To record geographic information relevant to individual species, two operators each holding a hand held GPS entered the postion of sea cucumber when the appropriate signal was given by the diver. In this case, the diver signaled the presence of one species by raising a green glove, or similarly the presence of another by raising a red glove. In situations where animals were too numerous to record individually, the GPS way-point was noted and the diver estimated the number of specimens according to the following categories: <10; <20 or <30 animals. This was typically the case for S. chloronotus which tended to maintain a concentrated pattern of distribution relative to H. whitmaei and H. atra. For geographic information software (GIS) purposes, an appropriate number of way-points were entered, so that on the aerial photographs the animals appear as a group of tightly clustered points.Statement: Surveys conducted between August 2002 and April 2003, encompassed all sections of the inner-reef, including broadly defined habitats such as the inner lagoon (including open sand), the reef-flat (inner and outer), the inner reef slope and, where possible, the reef-crest. Certain sections including the deeper zones adjacent to Pt. Maud and the area west of the reef crest were not included in the surveys. Each of the areas included in the distribution surveys were determined prior to embarking and marked in the field with floating reference buoys. Within the zone identified by the buoys, parallel manta tow transects were conducted approximately every 30 to 50 m. This stratified sampling design enabled the survey to cover all habitats within an area encompassing approximately 750 ha of coral reef habitat.
On return to the laboratory, each of the way-points was plotted on a digitally recified aerial photograph to determine the extent and range of the distribution of the sea cucumber species.Statement: -Population densities-
Traditional manta tow surveys consisting of 9 to 10 transects were conducted in three pre-determined locations between September 2001 and January 2002 (prior to the GPS modified surveys). Manta tows were conducted on the reef flat adjacent to Lotty's Lagoon, the outer reef at Glass Botton Boats (GBB) and adjacent to the reef crest at Pt. Maud. Each of the areas included in the survey were initially chosen based on the preferred habitats of H. whitmaei but nevertheless included habitats occupied also by H. atra and S. chloronotus. Each of the three species were surveyed (by manta tow) over distances of approximately 240 to 300 m, depending on the shape of the habitat under investigation. The area included in the final density estimates was calculated as the length of the transect by the width of the viewing area i.e. 1.5 m either side of the tow line to give a total width of 3 m.
In addition to the density measures obtained by traditional manta tow, densities based on the results of GPS modified surveys were estimated using ESRI ArcView 3.3 at two habitat scales: i) within areas of species aggregation (identified by Kernal Home Range analysis in Animal Movement), and ii) over the full extent of the habitats occupied.The distribution of three sea cucumbers (H. whitmaei (Bell 1887), H. atra (Jaeger 1933) and S. chloronotus (Brandt 1835) in the vincinity of Coral Bay, Ningaloo Reef, Western Australia was measured. There was an emphasis on factors that may contribute to the heterogeneous distribution of H. whitmaei within broadly defined habitats and reasons for variable density estimates reported in the literature
Parent record: Owner advantage in the fiddler crab, Uca mjoebergi: Investigating why owners win more contests?
No full textMaintenance and Update Frequency: notPlannedStatement: A standard set of data was collected for each fight. For each fight the date, time, the type of floater, and winner were recorded. Additionally, all crabs were measured, and fighting phases as well as fight duration were recorded. The winner is the male that owns the territory at the end of a fight. The loser is the crab which walks away at the end of the fight. A fight was considered over when: a) the loser walked >30cm away, b) travelled past two other males territories, c) entered another burrow, or d) started another fight.
Parameters: Date, ltidet (time of diurnal low tide), hightideht (high tide height of the tide which follows the diurnal low tide), rtimet (time of the fight), tsltide (number of minutes since low tide), ctype (condition, NF=natural floater, RF=removed floater, RO=removed owner, TE=owner within a plot with food added, TN=owner within a plot which is natural i.e. no food added, OB=owners burrows blocked, OUB=control-owners burrows not blocked), winner, cara (intruder carapace width - mm), chel (inturder cheliped / claw length - mm), ocara (owner carapace width - mm), ochel (owner cheliped / claw length -mm), actions observed (P=push, B=burrow, G=grapple, F=flick, D=dig, Pi=pinch, TB=true burrow fighting), dura (duration of fight - seconds), digdura (dig duration - seconds), sizediff (size difference between owner and intruder claws - mm).<b>Credit</b><br/>Funded by The Australian Research Council (ARC)<b>Credit</b><br/>Funded by The Ecological Society of Australia<b>Credit</b><br/>The Australian National University (ANU)<b>Purpose</b><br/>To determine how the owner advantage persists (manifests) itself in the fiddler crab, Uca mjoebergi.
To determine which asymmetries contribute to the owner advantage by comparing 'natural' fights to fights with the asymmetry experimentally reduced or enhanced.Resource owners generally win contests against intruders, a phenomenon referred to as the 'Owner Advantage' (OA). Uca mjoebergi is a typical fiddler crab that is highly sociable, territorial and lives in mixed sex colonies on intertidal mudflats. Burrows are used in territory defence, for mating, and as refuge from predators and environmental stresses. Fights are common between owners and floating males who battle for ownership of the territory and burrow. <br/><br/>Experiments were conducted from 28th Sept - 30 Dec 2006 at the lower reaches of Ludmilla Creek within East Point Reserve, 5km North of Darwin, NT. The series of experiments was run to assess which asymmetries between owner-floater contribute to the owner advantage. <br/><br/>The studies reveal that in Uca mjoebergi the OA is >90%. Floaters were found not to be poorer fighters, performing just as well as owners of the same size in standardised treatments. This meant that asymmetries other than fighting ability were contributing to the substantial OA. Mechanical advantage was found to be highly significant providing advantage to owners during fights. At low tide owners are more motivated than intruders based on their investment in territory. As the tide rolls in it was expected that floaters-owners experience motivational symmetry, however this was found not to reduce owner fighting success. In fact, when motivation was heightened to symmetric, owners won more contests. The effects of high quality territories on contests and owner motivation were weak. Although owners in high quality territories won more contests this was not a significant difference. The results also indicate there was a trend for owner fighting success to increase with an increase in the investment in neighbour relations
Serpent Project Enfield 6 - measuring megafaunal abundance, diversity and distribution.
No full textStatement: END02 is approximately 13 m away from END01 so there was some overlap in drill spoil.
Baited traps were deployed both within and outside of the drill spoil to attract mobile megafauna. Traps were examined every 24 hrs and video taped for 5 minutes. Large numbers of shrimp were seen on this mission whereas previous missions in this field failed to collect shrimp. Shrimp and amphipods from within the spoil (8m from blow-out converter (BOP)) and shrimp, amphipods, hagfish and isopods outside of the spoil (100 m from BOP) were collected for heat shock protein analysis. Traps were re-deployed every 24 hrs and collection repeated. In a second experiment, isopods outside of the spoil (100m from BOP) were collected and re-deployed within the drill spoil and outside of the drill spoil. Controls were brought to the surface and frozen and procedural controls were re-immersed down to the sea bed (attached to back of ROV garage) and brought back to surface.<b>Credit</b><br/>Woodside Energy Ltd<b>Credit</b><br/>Transocean Inc<b>Credit</b><br/>Subsea 7<b>Credit</b><br/>Katie Robertson, The University of Sydney (USYD)<b>Purpose</b><br/>The science goals for this project are to expand on baseline environmental surveys carried out in the area on behalf of Woodside. We conducted detailed ROV megafaunal video surveys to provide quantitative data on megafaunal ecology; particularly abundance, diversity and distribution in this area. In addition we conducted a series of experiments to quantify the expression of heat shock proteins on deep sea organisms from within and outside of drill spoil including an in situ deployment to determine the effects of drilling mud on heat shock protein expression.SERPENT - Scientific and Environmental remotely operated vehicle (ROV) Partnership using Existing iNdustrial Technology. A highly successful mission resulted after 5 days of ROV operations. Eight video transects were completed, for megafaunal abundance, diversity and distribution in the area. Transects were conducted every 450m and extend to 100m from the drill site. Videos will be analysed for megafaunal diversity and habitat mapping during 2006. <br/><br/>There is only one habitat type at END01 which is soft bottom. There is no evidence of any rock formations or hard bottom of any type. This will be accounted for when analysing video transects. Preliminary analysis indicates a high density and diversity of megafauna. The main component of the megafaunal community is consistent with soft bottom communities and includes echinoderms (asteroids, echinoids) a host of crustaceans (prawns and large isopods), eels that live in the sediment and some bottom dwelling fish. Unlike at ENC03, there were no large sponge beds only sparsely scattered sponges. <br/><br/>A variety of prawns, crabs, hagfish, amphipods, isopods and fish were attracted to the bait traps (first experiment). Initial examination of the data suggests that there is a difference in the diversity of organisms that visit the traps (inside vs outside the drill spoil). Isopods and hagfish only appeared to visit traps outside of the drill spoil. Further analysis will validate any trends in the data.<br/><br/>Species collected for determining the level of heat shock protein expression (second experiment):<br/><br/>* 5 isopods outside of the drill spoil <br/>* 5 isopods outside of the drill spoil re-deployed within the drill spoil <br/>* 5 isopods outside of the drill spoil re-deployed outside of the drill spoil<br/>* 5 isopods outside of the drill spoil caged and attached to ROV garage, immersed to seabed and brought to surface again<br/>* 23 isopods outside of the drill spoil<br/>* 20 isopods outside of the spoil used for re-deployment experiment <br/>* 40 shrimp outside of the drill spoil<br/>* 57 amphipods outside of the drill spoil<br/>* 3 hagfish outside of the drill spoil<br/>* 20 shrimp within the drill spoil<br/>* 8 amphipods within the drill spoil<br/>* 1 sea cucumber within the drill spoi
RAN CTD Profile Data - SMB DUYFKEN ProjectID: HI446(C)DUY_H From: 2009-02-12 To: 2009-02-23
No full textStatement: Initial Processing
Incoming data undergoes gross range checks and removal of any corrupted or unrealistic data. Some CTD data is subject to a pressure offset error generally less than 1 decibar. A pressure offset error occurs when the pressure sensor does not read 0 dbar in air. In cases where the pressure offset error was observed before the CTD cast the pressure readings have been corrected for the offset which is stored in the global netCDF attribute named 'CTD_pressure_offset'. In some cases there is a separate recording for the downcast and upcast. The downcast data were selected as priority for better quality data. In rarer cases only an upcast was available so it is used by default.
Salinity on the PSS-78 scale is computed from conductivity, temperature and pressure using the UNESCO (1983) algorithm with temperature corrected from the ITS-90 scale to the ITS-68 scale used by the algorithm.
The raw CTD data contains a non-monotonic sequence of pressures due to up/down motion of ship/winch. A sequence of unique monotonic pressures up to the maximum value is extracted and then linearly interpolated to 1 decibar pressure levels with the corresponding interpolated temperature and salinity. Finally the interpolated files are converted to a set of netCDF files ready for QC.
Quality Control
Quality control (QC) involves viewing location of the data on a map, visual inspection of each profile of temperature and salinity and comparison with nearest neighbours and climatology. CTD profiles are checked for any density inversions i.e. density decreasing with depth by computing sigma-t density. A density inversion may indicate unrealistic salinity and/or temperature values. QC flags are applied to indicate whether data is good, suspect, bad or not tested. QC flags may apply at the 'whole profile' level or individual pressure levels.
CTD cast positions and times undergo a land and ship speed check. Casts with position on land or unrealistic speed between casts are flagged as failed position or time. Temperature and salinity profiles are then visually compared against a 3 standard deviation envelope from the CSIRO-CARS (2009) atlas. Profiles or segments of profiles with data outside the envelope are flagged as doubtful or failed. Profiles are also checked for consistency or doubtful features by comparing with previous/next casts (buddies) and also by comparison with historical CTD casts taken in the same area and season.<b>Credit</b><br/>Royal Australian Navy Hydrography and Metoc Branch<b>Purpose</b><br/>Part of the long term ocean monitoring program.This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 11 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI446(C)DUY_H from SMB DUYFKEN. <br/><br/>The CTD was manufactured by Falmouth Scientific and is the "2-inch Micro CTD" model. This CTD type is referred to operationally as the HS_CTD. This CTD is fitted within an inductive type conductivity cell, a platinum thermometer and silicon pressure sensor.<br/><br/>The CTD temperature sensor is calibrated on the ITS-90 temperature scale against a master CTD using a controlled temperature bath. The pressure sensor is calibrated using a Druck Pressure Calibrator. The conductivity sensor is calibrated in a temperature controlled bath against seawater samples of known conductivity.<br/><br/>The HS_CTD is lowered and raised by a hand winch sampling at a rate of 1.83 Hz. Data files were recorded in the downcast and upcast direction but most data is from downcasts due to higher quality. Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals and converted to netCDF format files. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts
WAMSI Node 3.2.1 - Diversity, abundance and habitat utilisation of sharks and rays - Summary
No full textStatement: SPECIES COMPOSITION
*Lagoon and reef edge surveys*
Snorkel and SCUBA underwater visual surveys were conducted as part of four field trips to Ningaloo in April and June 2007 and August and December 2008. The June and August surveys were restricted to the reef edge on SCUBA, while the April and December surveys were mainly on snorkel and in the lagoon. While the original intention was to provide coverage through the different seasons, poor weather conditions coincided with most of the planned fieldwork (including Cyclone Nicholas) resulting in re-scheduling of some trips.
*Offshore surveys*
Longline fishing was used to survey elasmobranchs outside the reef and was carried out from the Western Australia Fishery Department vessel RV ‘Naturaliste’. Longlines comprised 1 km of 12 mm diameter mainline with (usually) 50 hooks. Snoods were 8–10 m apart and each snood was 2 m long and had an 11/0 or 12/0 J hook baited with mullet. About 250 hooks were set per day, as between one and five separate lines. Lines were generally set for periods of between 2.4 h and 5.2 h (mean of 3.6 h) over the dawn period but 10 lines (set over 2 days) were set at dusk and retrieved at dawn the following day (mean soak time of 15.2 h).
*Comparison with historic research data*
The Western Australian Department of Fisheries has conducted longline research cruises with RV ‘Naturaliste’ throughout NMP and beyond since November 2001.
*Data analysis*
The number of shark sightings (dive surveys) and catch rates (longline surveys) were compared between sanctuary and non-sanctuary zones with a one-way Analysis of Variance (ANOVA).
Further details are in the final reportStatement: SPATIAL DYNAMICS
*Acoustics*
Elasmobranchs were tagged with acoustic tags and subsequently monitored with acoustic receivers (Vemco VR2, VR2W and VR3) moored on the seabed that constitute the Ningaloo Reef Ecosystem Tracking Array (NRETA). This array is part of the nationwide network of marine acoustic monitoring, the Australian Acoustic Tagging and Monitoring System (AATAMS).
A total of 96 acoustic receivers are deployed at Ningaloo Reef between Coral Bay and Tantabiddi. These are deployed as three curtains (Tantabiddi, Norwegian Bay, Coral Bay), three arrays (Mangrove Bay, Coral Bay, Stanley Pool), and three points of interest (Coral Bay). Arrays were deployed in November and December 2007, whereas curtains were deployed in February 2008.
The Tantabiddi curtain comprises 7 receivers (10–96 m), the Norwegian Bay curtain 13 receivers (95–160 m) and the Coral Bay curtain 12 receivers (7–66 m). The array at Mangrove Bay consists of 50 receivers (1–47 m) and the Coral Bay array consists of 14 receivers (2–34 m).
*Satellite tagging*
Two types of platform transmitter terminals (PTTs) were used, Wildlife Computers (Redmond, USA) smart position or temperature transmitting tag (SPOT4 or SPOT5) and SPLASH tags. SPOT tags provide ARGOS locations together with water temperature reported as time-at- temperature histograms in user defined bins. SPLASH tags provide ARGOS locations together with depth and temperature reported as time-at-depth and temperature histograms in user defined bins. Depth is recorded down to 980 m (resolution = 0.5 m; accuracy +-1 m 0–100 m, 1% 100– 1000 m), temperature is measured from –40 degrees C to +60 degrees C, with a resolution of 0.2 degree C and accuracy +- 1 degree C. Tags were attached by two 5 mm diameter bolts which passed through the first dorsal fin and were secured on the other side by two washers and nuts. Tags were secured so that the antenna extended out of the water when the fin broke the surface. Transmissions were detected and processed by the ARGOS data collection and location system The accuracy of ARGOS position estimates is coded by location class (LC) 3, 2, 1, 0, A or B, with LC3 being the most reliable with a root mean square error of <150 m. The other numeric LC codes decline in reliability and can be within several kilometres of true (ARGOS, 2008). Sharks were caught by longline and, depending on size, either landed on deck for tag attachment or held in a sling at the stern of the vessel while the tag was attached.
Further details are in final report<b>Credit</b><br/>JD Stevens, PR Last, WT White (CSIRO Marine & Atmospheric Research, Hobart) RB McAuley (Department of Fisheries, Government of Western Australia, Perth) MG Meekan (Australian Institute of Marine Science, Perth)<b>Purpose</b><br/>The main objectives of this project were to investigate the elasmobranch faunal composition of the Ningaloo Marine Park (NMP), determine the distribution and abundance of species, and examine the habitat utilisation, movement patterns and activity space of selected key species.From April 2007 to June 2009, six field trips were undertaken to investigate the elasmobranch faunal composition of the Ningaloo Marine Park (NMP), determine the distribution and abundance of species, and examine the habitat utilisation, movement patterns and activity space of selected key species. Dive and longline surveys, passive acoustic telemetry and satellite tracking were used to collect data.<br/><br/>Of interest to management, was whether existing sanctuary zones were effective for elasmobranchs as well as the location and timing of aggregation sites reported for some species
RAN CTD Profile Data - HMAS MELVILLE ProjectID: HI470MEL_H From: 2009-11-16 To: 2009-11-16
No full textStatement: Initial Processing
Incoming data undergoes gross range checks and removal of any corrupted or unrealistic data. Some CTD data is subject to a pressure offset error generally less than 1 decibar. A pressure offset error occurs when the pressure sensor does not read 0 dbar in air. In cases where the pressure offset error was observed before the CTD cast the pressure readings have been corrected for the offset which is stored in the global netCDF attribute named 'CTD_pressure_offset'. In some cases there is a separate recording for the downcast and upcast. The downcast data were selected as priority for better quality data. In rarer cases only an upcast was available so it is used by default.
Salinity on the PSS-78 scale is computed from conductivity, temperature and pressure using the UNESCO (1983) algorithm with temperature corrected from the ITS-90 scale to the ITS-68 scale used by the algorithm.
The raw CTD data contains a non-monotonic sequence of pressures due to up/down motion of ship/winch. A sequence of unique monotonic pressures up to the maximum value is extracted and then linearly interpolated to 1 decibar pressure levels with the corresponding interpolated temperature and salinity. Finally the interpolated files are converted to a set of netCDF files ready for QC.
Quality Control
Quality control (QC) involves viewing location of the data on a map, visual inspection of each profile of temperature and salinity and comparison with nearest neighbours and climatology. CTD profiles are checked for any density inversions i.e. density decreasing with depth by computing sigma-t density. A density inversion may indicate unrealistic salinity and/or temperature values. QC flags are applied to indicate whether data is good, suspect, bad or not tested. QC flags may apply at the 'whole profile' level or individual pressure levels.
CTD cast positions and times undergo a land and ship speed check. Casts with position on land or unrealistic speed between casts are flagged as failed position or time. Temperature and salinity profiles are then visually compared against a 3 standard deviation envelope from the CSIRO-CARS (2009) atlas. Profiles or segments of profiles with data outside the envelope are flagged as doubtful or failed. Profiles are also checked for consistency or doubtful features by comparing with previous/next casts (buddies) and also by comparison with historical CTD casts taken in the same area and season.<b>Credit</b><br/>Royal Australian Navy Hydrography and Metoc Branch<b>Purpose</b><br/>Part of the long term ocean monitoring program.This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 1 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI470MEL_H from HMAS MELVILLE. <br/><br/>The CTD was manufactured by Falmouth Scientific and is the "2-inch Micro CTD" model. This CTD type is referred to operationally as the HS_CTD. This CTD is fitted within an inductive type conductivity cell, a platinum thermometer and silicon pressure sensor.<br/><br/>The CTD temperature sensor is calibrated on the ITS-90 temperature scale against a master CTD using a controlled temperature bath. The pressure sensor is calibrated using a Druck Pressure Calibrator. The conductivity sensor is calibrated in a temperature controlled bath against seawater samples of known conductivity.<br/><br/>The HS_CTD is lowered and raised by a hand winch sampling at a rate of 1.83 Hz. Data files were recorded in the downcast and upcast direction but most data is from downcasts due to higher quality. Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals and converted to netCDF format files. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts
RAN CTD Profile Data - HMAS LEEUWIN ProjectID: HI444LEE_M From: 2007-07-05 To: 2007-09-02
No full textStatement: Initial Processing
Incoming data undergoes gross range checks and removal of any corrupted or unrealistic data. Some CTD data is subject to a pressure offset error generally less than 1 decibar. A pressure offset error occurs when the pressure sensor does not read 0 dbar in air. In cases where the pressure offset error was observed before the CTD cast the pressure readings have been corrected for the offset which is stored in the global netCDF attribute named 'CTD_pressure_offset'.
Salinity on the PSS-78 scale is computed from conductivity, temperature and pressure using the UNESCO (1983) algorithm with temperature corrected from the ITS-90 scale to the ITS-68 scale used by the algorithm.
For this CTD model the response time (time constant) of the temperature sensor (100 ms) is slower than the conductivity cell (25ms). This leads to a phenomenon called 'salinity spiking' in the salinity data. Spiking is caused by the fact that calculated salinity is a function of conductivity, temperature and pressure [S=f(C,T,z)]. The temperature response lags the conductivity response resulting an error in the calculation of salinity. This is evident as noticeable spikes in the salinity profiles especially at depths where temperature is rapidly changing e.g in the ocean thermocline. The spiking was reduced reduced by applying a 2.5 sample time shift (0.1 s) to the temperature values and using the shifted temperature value in the re-computation of the salinity. An array of raw pressure, temperature and de-spiked salinity is then passed to the next processing stage.
The raw CTD data contains a non-monotonic sequence of pressures due to up/down motion of ship/winch. A sequence of unique monotonic pressures up to the maximum value is extracted and then linearly interpolated to 1 decibar pressure levels with the corresponding interpolated temperature and salinity. Finally the interpolated files are converted to a set of netCDF files ready for QC.
Quality Control
Quality control (QC) involves viewing location of the data on a map, visual inspection of each profile of temperature and salinity and comparison with nearest neighbours and climatology. CTD profiles are checked for any density inversions i.e. density decreasing with depth by computing sigma-t density. A density inversion may indicate unrealistic salinity and/or temperature values. QC flags are applied to indicate whether data is good, suspect, bad or not tested. QC flags may apply at the 'whole profile' level or individual pressure levels.
CTD cast positions and times undergo a land and ship speed check. Casts with position on land or unrealistic speed between casts are flagged as failed position or time. Temperature and salinity profiles are then visually compared against a 3 standard deviation envelope from the CSIRO-CARS (2009) atlas. Profiles or segments of profiles with data outside the envelope are flagged as doubtful or failed. Profiles are also checked for consistency or doubtful features by comparing with previous/next casts (buddies) and also by comparison with historical CTD casts taken in the same area and season.<b>Credit</b><br/>Royal Australian Navy Hydrography and Metoc Branch<b>Purpose</b><br/>Part of the long term ocean monitoring program.This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 371 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI444LEE_M from HMAS LEEUWIN.<br/><br/>The CTD was manufactured by Applied Microsystems Limited and is the "Micro CTD" model. This CTD type is referred to operationally as the MVP200_CTD. This CTD is fitted with a 4 electrode platinized conductivity cell, thermistor temperature sensor and a semiconductor strain gauge pressure sensor.<br/><br/>The CTD sensors are calibrated at the manufacturer Applied Microsystems Limited on a 12-18 month schedule. The CTD temperature sensor is calibrated against 'Hart' temperature standards. The pressure sensor is calibrated using 'Budenburg Deadweight' standards. The conductivity sensor is calibrated using 'Hart' temperature standards and seawater samples of known conductivity.<br/><br/>The CTD sensors are mounted to a fish-shape probe. The probe is controlled by an electric winch (MVP200 type). For downcasts the fish is allowed to free-fall (winch is in 'free-wheel' mode) under its own weight at about 2-3 ms-1 and then is winched back. Data is recorded in downcast and usually in upcast direction at a sampling rate of 25 Hz. The downcast data is of higher quality because sensors encounter undisturbed seawater that flows through the nose of the fish. On the upcast the fish is flipped around (tail first) and the sensors in the nose encounter disturbed flow from the fish tail.<br/><br/>This type of CTD is prone to a phenomenon called 'salinity spiking' caused by a mismatch between the response times of the temperature and conductivity sensor. Data undergoes a salinity de-spiking routine to correct for this. See the history metadata for further details on the salinity de-spiking process.<br/><br/>Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts