Seabed Biodiversity on the Continental Shelf of the Great Barrier Reef World Heritage Area 2003 - 2006 (CRC Reef, CSIRO)

This very large study is published in Pitcher et al. (2007). Its purpose was to quantify patterns in seabed biodiversity and inter-reefal environmental conditions throughout the GBR.

The study had three aims: (1) Assessment of seabed biodiversity on the continental shelf of the Great Barrier Reef World Heritage Area, and assessment of the use of biophysical data as environmental correlates of biodiversity and benthic communities; (2) Mapping bycatch and seabed benthos assemblages in the GBR Region for environmental risk assessment and sustainable management of the Queensland East Coast Trawl Fishery, and (3) Assessment of the performance of acoustic remote sensing for seabed mapping and as a surrogate for biodiversity on the continental shelf of the GBR.

It contains several large data sets, based on >600 km of towed video, ~100,000 photos, 1150 baited remote underwater videos, echograms, ~14,000 benthic samples, ~4,000 seabed fish samples, and ~1,200 sediment samples.

The eAtlas has processed the Towed video data into a shapefile [1 MB] for dataset visualisation. This processing was done by combining the start and end tow events from the VESSEL_TASKS_ALL table to create a shapefile (GBR_CSIRO-AIMS_Seabed-biodiversity-2003-2006_DropCam.shp) and CSV (GBR_CSIRO-AIMS_Seabed-biodiversity-2003-2006_DropCam.csv) with a line feature for each tow. The information from tables VESSEL_VIDEO_BIOHABITAT and VESSEL_VIDEO_SUBSTRATUM were added as attributes of the line features based on the matching SITE_ID. 


Format:

The processed data from this study is stored in an Access Database (77 MB). The eAtlas summarised the tow video data into a shapefile [1MB] and CSV files (290 KB). Note the attribute names in the shapefile were truncated to 10 characters due to the limitation of shapfiles. These names are provided in the Data Dictionary below.


Data Dictionary:

The following are descriptions of all the attributed in the tables of the Access Database. Each section corresponds to a table in the database.

SITE_DATA:

- SITE_ID: site ID number
- GRD_ID: 0.01 degree gridcell ID number
- GRD_LAT: latitude centre of GRD_ID grid cell (GDA94)
- GRD_LON: longitude centre of GRD_ID grid cell (GDA94)
- STRATUM_ID: biophysical stratification membership number
- SNDR_DEPTH: site echosounder depth (metres)
- GBR_ASPECT: derived aspect from GBRMPA 15 second bathymetry
- GA_CRBNT: % carbonate of sediment samples, processed by Geoscience Australia
- GA_GRAVEL: % gravel grainsize fraction of sediment samples, processed by Geoscience Australia
- GA_SAND: % sand grainsize fraction of sediment samples, processed by Geoscience Australia
- GA_MUD: % mud grainsize fraction of sediment samples, processed by Geoscience Australia

VESSEL_TASKS_ALL:

- SITE_ID: site ID number
- VESSEL_ID: vessel ID code: LB=Lady Basten (AIMS), GM=Gwendoline May (QDPI)
- DTTM_EST: date/time (EST) of task event on vessels
- LATITUDE: latitude of task event, decimal degrees
- LONGITUDE: longitude of task event, decimal degrees
- DEPTH: depth of task event (m), recorded from vessel echosounder
- EVENT_1: drop camera deployment & recovery task events
- EVENT_2: drop camera transect start & end task events
- EVENT_3: 1.5m epibenthic sled tow start & end task events
- EVENT_4: BRUVS deployment task events
- EVENT_5: research trawl (8 fathom Florida Flyer) tow start & end task events

VESSEL_TASKS_BRUVS:

- SITE_ID: site ID number
- VESSEL_ID: vessel ID code: LB=Lady Basten (AIMS)
- DTTM_EST: date/time (EST) of BRUVS deployment event on vessel
- LATITUDE: latitude of BRUVS deployment event, decimal degrees
- LONGITUDE: longitude of BRUVS deployment event, decimal degrees
- DEPTH: depth of BRUVS deployment event (m), recorded from vessel echosounder
- BRUV_ID: ID number of BRUVS deployed

VESSEL_TASKS_DROPCAM:

- SITE_ID: site ID number
- VESSEL_ID: vessel ID code: LB=Lady Basten (AIMS)
- DTTM_EST: date/time (EST) of DROPCAM transect start event on vessel
- LATITUDE: latitude of DROPCAM transect start event, decimal degrees
- LONGITUDE: longitude of DROPCAM transect start event, decimal degrees
- DEPTH: depth of DROPCAM transect start event (m), recorded from vessel echosounder
- DURATION: duration of DROPCAM transect tow (minutes)
- LENGTH: length of DROPCAM transect tow (metres)

VESSEL_TASKS_SAMPLING:

- SITE_ID: site ID number
- VESSEL_ID: vessel ID code: LB=Lady Basten (=>SLED), GM=Gwendoline May (=>TRAWL)
- DTTM_EST: date/time (EST) of sampling tow start event on vessel
- LATITUDE: latitude of sampling tow start event, decimal degrees
- LONGITUDE: longitude of sampling tow start event, decimal degrees
- DEPTH: depth of sampling tow start event (m), recorded from vessel echosounder
- DURATION: duration of sampling tow (minutes)
- LENGTH: length of sampling tow (metres)
- AREA_HA: swept area of sampling tow (hectares)

VESSEL_SAMPLES:

- SITE_ID: site ID number
- SAMPLE_ID: sample ID number
- VESSEL_ID: vessel ID code: LB=Lady Basten (AIMS), GM=Gwendoline May (QDPI)
- SAMPLE_DATE: sampling date (EST)
- CLASS: preservation class for sampled biota
- DATA_RECORDER: name of data recorder on vessel
- CONTAINER_ID: container ID number for storage of samples preserved on vessel
- LABORATORY: destination laboratory for sorting of specimens
- PRESERVATION: type of preservation
- SAMPLE_TOTAL_WT: total weight of sample before any sub-sampling
- SAMPLE_RETAINED_WT: weight of sample after any sub-sampling, retained for lab sorting
- COMMENTS: comments

LAB_SPECIMEN_TAXA:

- OTU_ID: operational taxonomic unit ID number, nominal species equivalent
- KINGDOM: taxonomic kingdom name
- PHYLUM: taxonomic phylum name
- CLASS: taxonomic class name
- ORDR: taxonomic order name
- FAMILY: taxonomic family name
- GENUS: taxonomic genus name
- SPECIES: taxonomic species name, if identified - otherwise alpha taxonomy applies
- DESCRIPTION: specimen description 
- LOCATION: location of OTU, note synonymous OTUs may reside in other labs
- SITE_ID: site ID number
- SAMPLE_ID: sample ID number
- OTU_ID: operational taxonomic unit ID number, nominal species equivalent
- LAB_WT: weight (g) of specimens where measured (negative = not weighed)
- LAB_CNT: count of specimens where distinct (negative = not countable)

BRUVS_SPECIES_CAAB:

- CAAB_CODE: species Codes for Australian Aquatic Biota www.marine.csiro.au/caab/
- KINGDOM: taxonomic kingdom name
- PHYLUM: taxonomic phylum name
- CLASS: taxonomic class name
- ORDER: taxonomic order name
- FAMILY: taxonomic family name
- GENUS: taxonomic genus name
- SPECIES: taxonomic species name, if identified

BRUVS_maxN_DATA:

- SITE_ID: site ID number
- BRUV_NUM: BRUV Station ID number within Site
- CAAB_CODE: species Codes for Australian Aquatic Biota www.marine.csiro.au/caab/
- MAXN: maximum count of species in any single video frame recorded at station

VESSEL_VIDEO_SUBSTRATUM:

Note the names in brackets correspond to the attribute name in the shapefile.
- SITE_ID(SITE_ID): site ID number
- SoftMud(SoftMud): percentage of Soft Mud observed along video transect
- Silt(Sandy-Mud)(Silt): percentage of Silt (Sandy-Mud) observed along video transect
- Sand(Sand): percentage of Sand observed along video transect
- CoarseSand(CoarseSand): percentage of Coarse Sand observed along video transect
- SandWaves/Dunes(SandDunes): percentage of Sand Waves / Dunes observed along video transect
- Rubble(5-50mm)(Rubble): percentage of Rubble (5-50mm) observed along video transect
- Stones(50-250mm)(Stones): percentage of Stones (50-250mm) observed along video transect
- Rocks(>250mm)(Rocks): percentage of Rocks (>250mm) observed along video transect
- Bedrock/Reef(Bedrock): percentage of Bedrock / Reef observed along video transect

VESSEL_VIDEO_BIOHABITAT:

Note the names in brackets correspond to the attribute name in the shapefile.
- SITE_ID(SITE_ID): site ID number
- NoBiohabitat(NoBiohabit): percentage of seab with No Biogenic habitat observed along video transect
- Bioturbated(Bioturbate): percentage of Bioturbated seabed observed along video transect
- AlcyonariansSparse(AlcyonSpar): percentage of Sparse Alcyonarians observed along video transect
- AlcyonariansMedium(AlcyonMed): percentage of Medium Alcyonarians observed along video transect
- AlcyonariansDense(AlcyonDens): percentage of Dense Alcyonarians observed along video transect
- WhipGardenSparse(WhipGaSpar): percentage of Sparse Whip Garden observed along video transect
- WhipGardenMedium(WhipGaMed): percentage of Medium Whip Garden observed along video transect
- WhipGardenDense(WhipGaDens): percentage of Dense Whip Garden observed along video transect
- GorgonianGardenSparse(GorgonSpar): percentage of Sparse Gorgonian Garden observed along video transect
- GorgonianGardenMedium(GorgonMed): percentage of Medium Gorgonian Garden observed along video transect
- GorgonianGardenDense(GorgonDens): percentage of Dense Gorgonian Garden observed along video transect
- SpongeGardenSparse(SpongeSpar): percentage of Sparse Sponge Garden observed along video transect
- SpongeGardenMedium(SpongeMed): percentage of Medium Sponge Garden observed along video transect
- SpongeGardenDense(SpongeDens): percentage of Dense Sponge Garden observed along video transect
- HardCoralGardenSparse(HardCoSpar): percentage of Sparse Hard Coral Garden observed along video transect
- HardCoralGardenMedium(HardCoMed): percentage of Medium Hard Coral Garden observed along video transect
- HardCoralGardenDense(HardCoDens): percentage of Dense Hard Coral Garden observed along video transect
- LiveReefCorals(LiveReefCo): percentage of Live Reef Corals observed along video transect
- Flora(Flora): percentage of Flora observed along video transect
- Algae(Algae): percentage of Algae observed along video transect
- Halimeda(Halimeda): percentage of Halimeda observed along video transect
- Caulerpa(Caulerpa): percentage of Caulerpa observed along video transect
- Seagrass(Seagrass): percentage of Seagrass observed along video transect
- BivalveShellBeds(BivalShBed): percentage of Bivalve Shell Beds observed along video transect
- SquidEggs(SquidEggs): percentage of Squid Eggs observed along video transect
- TubePolychaeteBeds(TubePolBed): percentage of Tube Polychaete Beds observed along video transect

LAB_VIDEO_HABITAT_DATA:

- SITE_ID: site ID number
- FRAME_NO: transect video segment frame number
- HABITAT_TYPE: habitat category type: Biological, Sediment, Physical
- FEATURE: habitat feature descripor within category type
- DESCRIPTOR1: first descriptor of habitat feature, if applicable
- DESCRIPTOR2: secondary descriptor of feature, if applicable
- PERCENT_COVER: percent cover of frame by feature of given descriptor
- VERTICAL_SCALE: vertical scale of feature (cm), if recorded
- HORIZONTAL_SCALE: horizontal scale of feature (cm), if recorded


Reference:

Pitcher, C.R., Doherty, P., Arnold, P., Hooper, J., Gribble, N., Bartlett, C., Browne, M., Campbell, N., Cannard, T., Cappo, M., Carini, G., Chalmers, S., Cheers, S., Chetwynd, D., Colefax, A., Coles, R., Cook, S., Davie, P., De'ath, G., Devereux, D., Done, B., Donovan, T., Ehrke, B., Ellis, N., Ericson, G., Fellegara, I., Forcey, K., Furey, M., Gledhill, D., Good, N., Gordon, S., Haywood, M., Hendriks, P., Jacobsen, I., Johnson, J., Jones, M., Kinninmoth, S., Kistle, S., Last, P., Leite, A., Marks, S., McLeod, I., Oczkowicz, S., Robinson, M., Rose, C., Seabright, D., Sheils, J., Sherlock, M., Skelton, P., Smith, D., Smith, G., Speare, P., Stowar, M., Strickland, C., Van der Geest, C., Venables, W., Walsh, C., Wassenberg, T., Welna, A., Yearsley, G. (2007). Seabed Biodiversity on the Continental Shelf of the Great Barrier Reef World Heritage Area. AIMS/CSIRO/QM/QDPI CRC Reef Research Task Final Report. 320 pp.

Tags: marine
Organization: Commonwealth Scientific and Industrial Research Organisation (CSIRO)