E Shelf mapping SS Final

Benthic Habitat Mapping

of the Eastern shelf of

Cockburn Sound 2004

Prepared for:

Cockburn Sound Management Council

Prepared by:

DAL Science & Engineering Pty Ltd

Coastal CRC

University of Western Australia School of Plant Biology

July 2004

Report No. 321/1

DALSE: CSMC: Benthic Habitat Mapping in Cockburn Sound 2004 i

Revisions history

Submitted to client Report Version Prepared by Reviewed by Copies Date

DRAFT 1.- S.SHUTE B.HEGGE, G.KENDRICK A.BICKERS

Disclaimer This report has been prepared on behalf of and for the exclusive use of Cockburn Sound Management Council, and is subject to and issued in accordance with the agreed terms and scope between Cockburn Sound Management Council and DAL Science & Engineering Pty Ltd. DAL Science & Engineering Pty Ltd accepts no liability or responsibility whatsoever for it in respect of any use of or reliance upon this report by any third party. Copying this report without the permission of Cockburn Sound Management Council or DAL Science & Engineering Pty Ltd is not permitted. © Copyright 2004 DAL Science & Engineering Pty Ltd

DALSE: CSMC: Benthic Habitat Mapping in Cockburn Sound 2004 ii

Contents Executive Summary .................................................................................................iii

1. Environmental setting ......................................................................................1

2. Background .......................................................................................................2

3. Methods .............................................................................................................4 3.1 Study region .......................................................................................................................4 3.2 Habitat mapping.................................................................................................................5

3.2.1 Aerial photography ..................................................................................................8 3.2.2 Sidescan Sonar.......................................................................................................8 3.2.3 Towed video groundtruthing................................................................................. 11 3.2.4 Spot dives............................................................................................................. 12

3.3 Mapping methods ........................................................................................................... 13

4. Results .............................................................................................................15 4.1 Sidescan Sonar ............................................................................................................... 15 4.2 Towed video groundtruthing ......................................................................................... 15 4.3 Spot dives ........................................................................................................................ 15 4.4 General habitats identified............................................................................................. 15 4.5 Habitat coverage ............................................................................................................. 18 4.6 Detailed habitat mapping at spot dive locations ......................................................... 20 4.7 Vegetation percentage cover......................................................................................... 21 4.8 Presence of epiphytes.................................................................................................... 22

5. Discussion.......................................................................................................23

6. References.......................................................................................................24

7. Acknowledgements ........................................................................................25

DALSE: CSMC: Benthic Habitat Mapping in Cockburn Sound 2004 iii

List of Tables Table 2.1 Areal cover of habitat types on western margin of Eastern Shelf

(study region defined in report by DALSE, 2002) ...................................2 Table 4.1 Habitat coverage within the 2004 groundtruthing survey area..............18 Table 4.2 Habitat coverage on Eastern Shelf in 2004 compared against

coverage historical mapping exercises.................................................18

List of Figures Figure 3.1 Location of Eastern Shelf of Cockburn Sound........................................4 Figure 3.2 Survey sites within the Eastern Shelf .....................................................6 Figure 3.3 Coverage of groundtruthing survey methods..........................................7 Figure 3.4 Theory behind Sidescan Sonar (From; Bickers, 2003) ...........................8 Figure 3.5 Sidescan Sonar ‘towfish’ ........................................................................9 Figure 3.6 Example of unprocessed Sidescan Sonar swathe ...............................10 Figure 3.7 Towed video system.............................................................................12 Figure 3.8 Laminated copy of SSS imagery being annotated during a dive ..........13 Figure 4.1 Habitat map of the Eastern Shelf of Cockburn Sound (2004)...............17 Figure 4.2 Habitat map of the Eastern Shelf of Cockburn Sound (2002)...............19 Figure 4.3 Detailed habitat map for spot dive sites CS1, CS2 and CS3 (2004).....20

List of Appendices Appendix A Habitat photographs .............................................................................27 Appendix B Spot dive in situ habitat notes...............................................................31 Appendix C SACFOR scale .....................................................................................34

DALSE: CSMC: Benthic Habitat Mapping in Cockburn Sound 2004 iv

Executive Summary Western Australia has high diversity of seagrasses with 10 genera and 25 species recorded. Seagrasses are widespread off the Perth metropolitan coast; found mainly in shallow sandy areas. These marine angiosperms play a significant role in coastal processes and are considered to be a particularly important indicator of good water quality, with seagrass survival dependent on clear waters. Mapping the extent of seagrasses in coastal waters is a major contribution to managing these waters Mapping the distribution of seagrasses off the coast of Perth has previously been undertaken using aerial photography and extensive video groundtruthing, but these methods are only effective in optically clear waters where the continuous distribution of vegetated habitat can be determined from the aerial photographs and species and assemblage distributions are determined from the video. Areas of relatively poor visibility, such as the Eastern Shelf of Cockburn Sound, are difficult to map with confidence using these techniques. The present survey maps seagrass and reef habitats on the Eastern Shelf, Cockburn Sound utilizing sidescan sonar and towed video together with limited spot dives. The sidescan sonar is not affected by water clarity and enabled mapping of the benthic acoustic textures that were subsequently groundtruthed with towed video and spot SCUBA dives. This report presents the findings of detailed surveys which were undertaken to: Accurately map the benthic coverage and assemblages of the Eastern Shelf, Cockburn Sound for summer 2004, using sidescan sonar and extensive groundtruthing. A broad range of habitat types were identified, and the area was found to exhibit a high degree of spatial complexity. The habitat types recorded were as follows; • Posidonia sp. seagrass beds; • Patchy Posidonia sp. seagrass beds; • Mixed seagrass and reef; • Halophila sp. seagrass beds; • High relief reef; • Pavement reef; • Cobble reef; • Wrack; • Soft sediment; and • Vegetated area (mapping from aerial photography only).

Habitats were mapped at a scale of 1:5,000 with the margins of each habitat type clearly defined using the Sidescan Sonar (SSS) imagery. The texture and tone of the SSS imagery, together with the habitat information obtained through the towed video and spot dives, was used in the classification and mapping of the benthic habitats. The resultant map provides a level of detailed habitat information not previously available for this area. In addition, it provides an accurate baseline against which future habitat extents can be accurately compared.

DALSE: CSMC: Benthic Habitat Mapping in Cockburn Sound 2004 1

1. Environmental setting Cockburn Sound is a protected marine water to the south of Fremantle, Western Australia (Figure 1). Cockburn Sound is sheltered to the west by Garden Island and bounded to the north and south by Parmelia Banks and Southern Flats, respectively. These Banks are composed of unconsolidated carbonate sands and have formed largely from the onshore transport of sands over the past 7,500 years (DAL, 1998). Parmelia Bank is aligned in an east–west direction from Woodman Point to Carnac Island. The crest of the Bank is in a water depth of approximately 4–5 m and a variety of seagrass species occur across the Bank. The Southern Flats span the gap between Rockingham and Garden Island with depths of between 2–4 m encountered along the crest. Parmelia Bank is bisected by the Fremantle Port Authority (FPA) channel which enables shipping access into Cockburn Sound. This channel was originally dredged prior to the 1950s and maintenance dredging has been conducted occasionally since then. A causeway and bridge runs across Southern Flats linking Garden Island to the mainland and this produces a 2–3 fold reduction in the exchange of water occurring at the southern end of Cockburn Sound (DALSE, 2003).


2. Background Changes in the coverage of vegetated areas in Cockburn Sound between 1967 and 2002 have previously been assessed using aerial photography and semi-automated mapping methods (DALSE, 2002, Kendrick, et al. 2002, DAL et al., 2000). These studies provided a measure of the changes in vegetated areas over this period although the variable quality of the aerial imagery for the Eastern Shelf meant that the vegetated and unvegetated areas could only be mapped with an intermediate level of reliability. Limited groundtruth surveys indicated that seagrasses within Cockburn Sound were predominately Posidonia sinuosa meadows (DAL et al., 2000). In March and April 2002, aerial photography of the Perth metropolitan coastal waters was purpose-flown to obtain high quality imagery of the benthic habitats. This photography was georeferenced and mosaiced and provided an ideal dataset for examining recent changes in vegetated coverage. DAL Science & Engineering Pty Ltd (DALSE) were requested by the Cockburn Sound Management Council (CSMC) to use this photography to map the coverage of vegetated areas along the western margin of the Eastern Shelf of Cockburn Sound (DALSE, 2003). Following analysis of this 2002 aerial photography it was determined that approximately 27 ha of vegetated area and 994 ha of bare sand were present within the defined study region (western margin of the Eastern Shelf). Historical analysis of the aerial photography also suggested that since 1981, the area of vegetated habitat in this study region has remained at approximately 3–4% (Table 2.1).

Table 2.1 Areal cover of habitat types on western margin of Eastern Shelf (study region defined in report by DALSE, 2002)

Year Habitat class 2002 1999 1994 1981 1972 1967

Area in hectares Bare sand 993.9 991.5 977.5 996.7 711.3 146.4Vegetated 27.1 29.5 41.0 23.9 303.7 870.6Unmapped 579.0 579.0 581.5 579.4 585.0 583.0Total 1,600.0 1,600.0 1,600.0 1,600.0 1,600.0 1,600.0Percentage of total area Bare sand 62.1% 62.0% 61.1% 62.3% 44.5% 9.1%Vegetated 1.7% 1.8% 2.6% 1.5% 19.0% 54.4%Unmapped 36.2% 36.2% 36.3% 36.2% 36.6% 36.4%Percentage of mapped area* Bare Sand 97.5% 97.4% 96.0% 97.9% 69.9% 14.4%Vegetated 2.7% 2.9% 4.0% 2.3% 29.9% 85.5%

Note: ‘Unmapped’ corresponds to waters deeper than 10m along the western edge of the study region, and land area. Mapping from the 2002 aerial photography was completed using similar methods to the previous mapping study (DAL et al., 2000) to enable historical comparison. However, due to the relatively poor light penetration of the water column in the region of the Eastern Shelf, the mapping was considered to have an intermediate level of reliability. The previous groundtruth surveys on the Eastern Shelf showed that the vegetated areas in this region were either Posidonia sinuosa or reef; with a small fringe of Posidonia australis being observed at the southern edge of Parmelia Bank (DAL et al., 2000). DALSE were subsequently commissioned by the CSMC to undertake a groundtruthing survey of selected areas of the Eastern Shelf of Cockburn Sound, with the purpose of acquiring additional information on the benthic habitats in the region.


The priorities were to obtain additional information on the following: • Species assemblage (for example, distinguish between seagrass species, reef

areas, wrack material, mussel beds); • Vegetation percentage cover; • Presence of epiphyte material; and • Habitat information for areas deeper than 10 m or with poor water clarity.


3. Methods

3.1 Study region The present study area includes and expands upon the study region used in the recent aerial photographic analysis (western margin of the Eastern Shelf region). The study region extends from Woodman Point to James Point and covers a total area of 5148 ha. Approximately 948 ha of the study region is land and this was explicitly defined to enable future analysis of any changes in location of the shoreline (Figure 3.1).

Figure 3.1 Location of Eastern Shelf of Cockburn Sound


3.2 Habitat mapping This project for habitat mapping in the Eastern Shelf of Cockburn Sound made use of the following data: • Visual examination of the 2002 aerial imagery to define the SSS survey area

and provide indicative habitat information for areas not covered by the SSS; • Extensive Sidescan Sonar (SSS) survey across the Eastern Shelf region; • Towed underwater video to provide ground truth data and assist in the

interpretation of the SSS data; and • Spot dives in selected areas which were identified as having high habitat

complexity. Survey sites are shown in Figure 3.2 whilst a map showing the areas covered by the different survey methods is given in Figure 3.3. A detailed description of the methods employed for each of these elements is provided below.


Figure 3.2 Survey sites within the Eastern Shelf


Figure 3.3 Coverage of groundtruthing survey methods


3.2.1 Aerial photography The 2002 imagery was used as an initial guide to the extents and location of the vegetated and unvegetated areas within Cockburn Sound. Scrutiny of the imagery also allowed the identification of those areas which could not be accurately mapped from the aerial photographs (due to high water column turbidity or dater depth in excess of 10 m). This information was used to define the region of the SSS survey.

3.2.2 Sidescan Sonar High frequency Sidescan Sonar (SSS) has been popular for the mapping and visualisation of the seabed since the 1980s and provides a time and cost effective method for the delineation of habitat types in relation to their acoustic properties. Sidescan Sonars utilize two transducers which produce a fan-shaped pulse (ping) of sound energy. A towfish containing the transducers is towed behind a boat at a constant depth below the water surface, transmitting pings through the water column. As the ping interacts with the seabed, a small proportion is reflected back to sensors on the towfish (the ‘return’ signal). The energy of the return signal is amplified and recorded (Figure 3.4).

Figure 3.4 Theory behind Sidescan Sonar (From; Bickers, 2003)

A calculation, using the speed of sound through water, allows prediction of the distance of the source of each ‘reflection’ from the towfish. As the towfish moves over the seabed, subsequent lines of data are built up to form an acoustic image (swathe) of the seabed. This image is affected by the following factors: • Sonar frequency (higher frequencies give higher resolution but reduced

penetration through the water column);


• The angle between the outward ping of energy and the target (for example, a target face sloping towards the towfish will return a higher proportion of the signal than a face sloping away from the towfish); and

• Nature of the surface (texture and density). The strength of the ‘reflection’ or return signal gives an indication of the acoustic texture and hardness of the seabed. For visualization purposes, darker shades are typically allocated to substrates giving a strong return, and lighter shades to those substrates giving a weak return. For this study, an Edgetech 272T 100 kHz towfish (Figure 3.5) was utilized along with a 260TH surface unit. Return signals were routed to a computer-based data acquisition system (Sonar Wiz). Simultaneously, vessel heading and position (from differential GPS) and water depth (from echo sounder) were collected and automatically recorded on the computer (Bickers, 2003).

Figure 3.5 Sidescan Sonar ‘towfish’

The cross section of the unprocessed swathe represents the range of return times of the ping of energy. A light-shaded area exists through the centre of the image and represents the return from the water column below the towfish; the width of this region therefore provides a measure of the depth of water below the towfish (Figure 3.6). The edge of the darker imagery represents the quickest return from the seabed (i.e. the seabed directly below the towfish), and the imagery progressively further from the central line represents progressively slower returns (from the seabed further from the towfish).


Figure 3.6 Example of unprocessed Sidescan Sonar swathe

The first step in the processing of the SSS imagery is to remove the water column region and adjust the imagery (central band of imagery compressed relative to margins of imagery, due to fan shape of transmitted ‘ping’) so an accurate picture of the seabed remains and adjacent SSS ‘swathes’ can then be merged to produce a mosaiced image. This imagery can then be georeferenced and imported into a GIS package for further analysis and definition of habitat boundaries. Several features of the SSS mosaic give an indication of the substrate characteristics; • The general tone of the imagery, with soft flat sediment giving light grey tones

(low return) and reef or seagrass giving dark grey tones (high return); • The texture of the imagery can aid in the differentiation, for example, of patchy

seagrass beds from more continuous reef areas; and • The relief of the seabed, as displayed down the central line of the unprocessed

imagery, or indicated from the presence of shadows cast by tall objects. Sidescan Sonar was used to provide almost complete coverage of habitats across the Eastern Shelf of Cockburn Sound (Figure 3.3).


The SSS imagery is georeferenced using a differential GPS to record the position of the survey vessel. The layback distance of the towfish from the vessel is calculated by running perpendicular tracks across a discrete seabed feature and comparing the positions given within each swathe. The spatial accuracy of the resultant SSS mosaic was compared with digital navigational charts and was found to have an accuracy of ±10m. The data obtained was of high quality and was especially valuable for the deeper habitats (>10 m) along the western margin of the Eastern Shelf, which are difficult to identify from the aerial imagery.

3.2.3 Towed video groundtruthing Despite the wealth of data provide by the SSS imagery on the hardness, texture and relief of the substrate, groundtruthing is still essential in enabling benthic habitats to be confidently and accurately defined. The first component of the ground truth surveys was completed using towed underwater video. An underwater video camera (Figure 3.7) was towed behind the survey vessel at speeds of 1.5–2.5 knots and the resultant digital signal was supplied to an onboard video recorder and screen. The depth of the camera was controlled manually to ensure that it remained an optimal distance (<0.5 m) from the seabed for identification of the benthic habitats. The camera, at this height above the seabed, records benthic habitat across an approximately 1m wide transect. The underwater video was used to examine features of interest identified from the SSS imagery and to identify habitat types which corresponded to the different tones and textures obtained in the SSS imagery. This was done by recording the position of boundaries between the different habitat types identified as well as recording habitat characteristics at fixed intervals through the video footage within each habitat type. This allowed the classification of the SSS imagery.


Figure 3.7 Towed video system

3.2.4 Spot dives Spot dives were used to examine areas of high habitat complexity following the initial analysis of the SSS imagery and video footage. These spot dives assisted in the determination of the composition and small-scale variability present in these complex areas. The dives also allowed more detailed descriptions of each habitat type to be made. Dives were carried out at five separate locations, chosen to cover a range of habitat types as determined by the analysis of the SSS imagery. The location of each dive site was determined using a DGPS and the divers annotated laminated copies of the SSS imagery with information on habitat composition (Figure 3.8).


Figure 3.8 Laminated copy of SSS imagery being annotated during a dive

3.3 Mapping methods The boundaries of the habitat types were defined visually from the SSS data at a scale of 1:5,000. In areas where SSS coverage was not obtained, the 2002 aerial photography was employed. This mapping was undertaken using ArcView to create a single coverage of benthic habitat types. The habitat polygons were identified based on visual interpretation of the SSS imagery (and aerial photography) using pre-defined mapping control rules. The previous (2002) habitat mapping from aerial photography distinguished habitat classes: bare sand, vegetated and land. In the absence of groundtruth survey data for 2002, it was not possible to distinguish between seagrass and reef, and both were classified as vegetated. Consistency in the mapping of these habitat types was maintained through the use of the following control rules (Kendrick et al., 2000) which were implemented using the semi-automated Spann-Wilson segmentation method: 1. Vegetated patches, that were isolated and less than 30 m2, were not mapped. 2. Vegetated patches, that were greater than 30 m2 and less than 100 m2, were

mapped as separate patches when the distance between one patch and another was greater than the diameter of the patch.

3. Vegetated patches, that were greater than 30 m2 and less than 100 m2, were mapped as a single meadow when the distance between one patch and another was less than the diameter of the patch.

4. Vegetated patches greater than 100 m2 were mapped separately. Unvegetated regions within these patches, with areas greater than 100 m2

, were mapped as bare sand.


For the present study, the mapping control rules were modified to more closely reflect the resolution of the groundtruthing methods employed as follows: 1. Isolated habitat features of less than 200 m2 were not mapped. 2. Seagrass patches mapped individually if clearly distinguishable from

surrounding patches on SSS imagery (at scale 1:5,000). 3. All habitat features greater than 200 m2 were mapped from the SSS imagery at

a scale of 1:5,000. 4. Areas covered by a combination of seagrass and reef structures, in which the

two habitats were indistinguishable in the SSS imagery (at scale of 1:5,000), were classified as mixed habitats.

5. In areas for which detailed habitat data from spot dives was available, separate mapping using greater detail was carried out.

For the present study, the habitat classes were expanded to enable more detailed mapping of the broad range of benthic habitats identified. The habitat classification of each polygon was determined from an examination of the underwater video and spot dive information. Whilst the soft sediment habitat corresponds directly to the old unvegetated habitat classification, additional habitat types have been added to more accurately describe the range of vegetated habitats present. These habitat classes are described in detail in Section 4.4. The resolution of the mapping depended upon the types of survey coverage achieved within each area (Figure 3.3). For those areas solely covered by the 2002 aerial imagery, mapping resolution was low, with only bare substrate areas and vegetated areas (areas consisting of seagrass, wrack or reef) being mappable. For those areas covered by SSS, the extents of the habitats could be more accurately defined, and more detailed classification of habitat types made. Areas covered by SSS and towed video could be mapped at a higher resolution still, with habitat boundaries and habitat types more accurately mapped. Those areas covered by SSS and spot dives (and sometimes towed video) could be mapped at an even higher resolution, with the production of highly detailed habitat maps possible (Figure 4.3).


4. Results

4.1 Sidescan Sonar Sidescan Sonar was used to provide coverage of 1925 ha (46%) of benthic habitats within the Eastern Shelf of Cockburn Sound (Figure 3.23). This imagery provided detailed information on the distribution of hard and soft substrates, and of seagrass beds, within the Eastern Shelf of Cockburn Sound. The data greatly increases the detail in which the boundaries benthic habitats can be mapped (over aerial photography) and provides information not previously available on the high spatial complexity of the habitat distributions within this area. The differentiation of some habitats (on the basis of the SSS imagery alone) was, however, difficult since similar tones and textures from the SSS were obtained from different habitats. The distinction of pavement reef areas, patchy cobble reefs and patchy Posidonia sp. beds was found to be particularly difficult. This was due to each of these habitat types containing features of high return (exposed bedrock, concentrations of cobbles/boulders and dense seagrass patches respectively) as well as features of low return (areas of sand either overlying the reef structures or being present between the seagrass patches). Thus a similar texture from the SSS was obtained from each of these habitat types.

4.2 Towed video groundtruthing The towed video footage provided detailed information on the species assemblages and substrate characteristics along the towed transect. This detailed information greatly aided the classification of the different tones and textures obtained within the SSS imagery. High variability within the Posidonia sp. beds was recorded from the towed video survey; however, this was not evident from SSS imagery. In particular, in several locations, the towed video recorded discrete patches of Posidonia australis within predominantly Posidonia sinuosa beds and sparse clump of Posidonia coriacea around the edge of some Posidonia sinuosa beds.

4.3 Spot dives The five spot dives provided detailed information on the species assemblages and densities as well as the substrate types present within each area surveyed. This data was used in the broad classification of habitats from the SSS imagery. However, due to the relatively small number of sites dived, and the high spatial variability identified within each habitat type, caution should be exercised in extrapolating this information to other areas. The highly detailed habitat information available for three of the dive locations (CS1, CS2 and CS3) is presented separately (Figure 4.3). Dives at sites CS4 and CS5 were carried out as rapid transect swims and therefore highly detailed habitat information covering the surrounding area was not obtained. In situ observations on sediment type and representative species at all of the dive sites are given in Appendix B.

4.4 General habitats identified A range of seagrass, reef and soft substrate habitats were identified within the 2004 study area. Both patchy and continuous seagrass beds composed of Posidonia spp. and Halophila spp. were identified. A variety of reef structures were also recorded,


ranging from low relief pavement reef, often covered by a thin veneer of sand, to cobble reef and high relief reef. Soft substrate, consisting of fine silty sand or poorly sorted medium/coarse sand, was found over much of the study area. A complex mosaic of habitats was found in some areas, with several habitat types in close association with eachother. The habitat types identified, together with a short description, are given below; • Posidonia sp.

Areas covered by continuous Posidonia sp. bed

• Patchy Posidonia sp. Areas covered by patches of Posidonia sp.

• Mixed seagrass and reef

Areas covered by a combination of seagrass and reef structures. • Mixed seagrass and reef

Areas covered by a combination of seagrass and reef structures. • Halophila sp.

Areas covered by continuous Halophila sp. bed or by patches of Halophila sp.

• Soft sediment Unvegetated areas in which soft sediments were dominant.

• Pavement reef

Low lying (average height <0.5 m above surrounding seabed) limestone pavement reef, often covered by a thin veneer of soft sediment.

• High relief reef

Natural limestone reef outcrops characterised by high relief (average height >0.5 m above surrounding seabed).

• Cobble reef

Reef structure predominantly composed of cobbles or boulders of either natural or anthropogenic origin.

• Vegetated area

Habitat identified from the aerial imagery as being vegetated. Distinction between seagrass bed, reef or wrack material could not be made from this imagery

• Wrack material

Areas covered by a dense cover of unattached seagrass leaves and algae


Figure 4.1 Habitat map of the Eastern Shelf of Cockburn Sound (2004)


4.5 Habitat coverage Soft sediment was found to be the dominant habitat type within the 2004 study area (76.9% of total area)(Table 4.1). Halophila sp. seagrass beds formed the next most extensive habitat type followed by Posidonia sp. seagrass beds.

Table 4.1 Habitat coverage within the 2004 groundtruthing survey area

Habitat type Area (ha) Percentage Soft sediment 3957.4 76.9 Land 947.8 18.4 Halophila sp. 67.9 1.3 Posidonia sp. 61.6 1.2 Vegetated area 39.3 0.8 Cobble reef 30.3 0.6 Pavement reef 25.9 0.5 Patchy Posidonia sp. 8.4 0.2 Wrack 7.6 0.1 Mixed seagrass & reef 1.4 0.0 High relief reef 0.5 0.0 Total 5148 100

Comparison of the extent of habitats mapped within the 2002 study area (Table 4.2) shows that vegetated habitats (including reef and seagrass habitats and wrack material as these could not be separated from the historic aerial imagery) were mapped over a larger proportion of the area in 2004 than between 2002 and 1981. This marked difference is, however, likely to be due to the identification and mapping of a larger number of vegetated habitat areas, due to the more effective survey methods employed during this study. The difference in the coverage and classification of mapped habitats between the 2002 mapping study (DALSE, 2002) and this study can be seen from examination of the habitat maps produced from each project (Figure 4.1; Figure 4.2).

Table 4.2 Habitat coverage on Eastern Shelf in 2004 compared against coverage historical mapping exercises

Year Habitat class 2004 2002 1999 1994 1981 1972 1967

Area in hectares Bare sand 1,485.5 993.9 991.5 977.5 996.7 711.3 146.4Vegetated 98.1 27.1 29.5 41.0 23.9 303.7 870.6Unmapped 16.4 579.0 579.0 581.5 579.4 585.0 583.0Total 1,600.0 1,600.0 1,600.0 1,600.0 1,600.0 1,600.0 1,600.0Percentage of total area Bare sand 92.8% 62.1% 62.0% 61.1% 62.3% 44.5% 9.1%Vegetated 6.1% 1.7% 1.8% 2.6% 1.5% 19.0% 54.4%Unmapped 1.0% 36.2% 36.2% 36.3% 36.2% 36.6% 36.4%Percentage of mapped area Bare Sand 93.8% 97.5% 97.4% 96.0% 97.9% 69.9% 14.4%Vegetated 6.2% 2.7% 2.9% 4.0% 2.3% 29.9% 85.5%

Ref: Req165~Fig2_r165.mxd

MGA94 Coordinates

Rev 2.0

Figure 4.2: Habitat map for2002 for Southern Flats

and Eastern Shoal

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Note: Coastline is based on the Department of Land Administration's digitalcoastline(1995). Bathymetry digitised from the Department of Marine andHarbours 1:75,000hydrographic chart WA001 Edition 8 (April 1997) andR.A.N. Hydrographic Serv

Mapping: Matt Aylward (Digital Envi)Interpretation: Dr Gary Kendrick (Department of Botany, University of Western Australia) Dr Bruce Hegge (DAL Science & Engineering Pty Ltd)Presentation: NGIS Australia

Legend

Encloses 2002 mapping area (1999 coverage shownfor remaining areas)Mapping Boundary

Land

Unmapped

Bare sand

Vegetated


4.6 Detailed habitat mapping at spot dive locations The high degree of spatial complexity at the dive site locations can be seen from the detailed habitat mapping (Figure 4.3). In particular, the mapping of isolated cobble and high profile reef outcrops within predominantly seagrass habitats presented a challenge, with such differentiation of habitats only possible due to the use of spot dives within areas of high habitat complexity as identified from the SSS imagery. The presence of both continuous Posidonia sp. beds and extensive patchy Posidonia sp. beds was thought to be due to changes in the depth of soft sediment available for rhizome establishment. It was noted at dive site CS3 that in many areas not covered by Posidonia sp., the depth of soft sediment was less than 0.1 m, with underlying pavement reef or ancient seagrass rhizome structures present.

Figure 4.3 Detailed habitat map for spot dive sites CS1, CS2 and CS3 (2004)


4.7 Vegetation percentage cover The percentage cover of each type of seagrass bed was estimated from the towed video footage. The percentage cover of seagrass was recorded at fixed intervals through the video footage captured across each habitat type. Posidonia sinuosa beds were generally found to be highly dense (percentage cover >80%), with isolated sand patches. For example, along the western margin of the Eastern Shelf, directly west of Southern Harbour (video tow 3)(Figure 3.2), the percentage cover ranged from 100% to 0% (reef patch), with the average percentage cover being 86% (from 22 equally spaced observations along the video track). Similarly towards the southern end of the western margin of the Eastern Shelf (video tows 10 and 11)(Figure 3.2) the modal percentage cover within seagrass patches was 100%. Posidonia coriacea was recorded within the towed video footage as discrete plants generally around the margins of P.sinuosa beds, while Posidonia australis was recorded at low densities within P.sinuosa beds. On spot dives we did not find any P. angustifolia. At dive site CS1, Posidonia australis was found to constitute less than 20% of the total Posidonia sp. cover, with the remainder being Posidonia sinuosa. At dive site CS3, Posidonia australis made up less than 10% of the total Posidonia spp. coverage. The separation of these three Posidonia species from the SSS imagery was not possible and therefore all Posidonia beds have been classed as Posidonia sp., although the majority is considered to be Posidonia sinuosa (as this was by far the dominant species within the towed video footage, and was recorded as the dominant Posidonia sp. recorded during the spot dives). Halophila sp. beds were found to be generally less dense although still displaying a high degree of patchiness. Towards the centre of the Eastern Shelf, west of Southern Harbour (video tow 2), the percentage cover of Halophila sp. ranged from <1% to 90%, with an average of 40% cover. Similarly in the far north of the study area (video tow 8) the mean percentage cover varied from 0% to 75%, with a mean value of 43%. Extensive beds of Halophila decipiens were recorded at deeper depths than Posidonia sp. in the north of the study area as well as in the south, towards both the western and eastern margins of the Eastern Shelf (spot dive sites CS2, 3 and 4)(Appendix A, Appendix B), although the vast majority of Halophila sp. recorded from the towed video was Halophila ovalis. As the differentiation of these species is not possible from the SSS imagery a ‘Halophila sp.’ classification has been used to cover both species. Both high relief reef and cobble reef structures were found to be heavily colonized by a range of sessile epibenthos, particularly sponges, bryozoans and ascidians. Algae species, in particular Sargassum sp., were relatively abundant on the upper horizontal surfaces of some reef structures.


4.8 Presence of epiphytes The abundance of epiphytes was found to vary across the survey area and between seagrass species. Posidonia sp. along the western margin of the Eastern Shelf to the north and south of the study area (video tows 3 and 11) were found to have negligible epiphytic cover whereas the plants towards the centre of the western margin of the Eastern Shelf (video tow 19, dive site CS1) were found to be relatively heavily colonized by small filamentous algae (Appendix A). This site was also found to be heavily silted. Halophila ovalis was generally found to be colonized by few epiphytes. Within some beds, however, relatively large plants of the tufted brown alga (Hincksia mitchelliae) were recorded on a small proportion of the leaves (Appendix A).


5. Discussion The present habitat mapping project has significantly enhanced the habitat information for the Eastern Shelf of Cockburn Sound. The area had a high degree of spatial variability with a complex series of habitats occurring in often close association with one another. The detailed descriptions of the habitat types present, along with their accurate mapping, provides a baseline data set not previously available, against which future changes within Cockburn Sound can be measured. The dominant habitat type within the study area was soft sediment (Figure 4.1). Towards the north of the study area Posidonia sp. and Halophila sp. seagrass beds were identified. Areas of pavement reef and wrack material were also found within this region. Running south down the western margin of the Eastern Shelf, a number of discrete Posidonia sp. seagrass beds and pavement reef structures were mapped, with isolated cobble reef and high relief features also recorded. Inshore of the western margin the largest area of vegetated habitat corresponded to a historic gypsum disposal area, approximately 4 km north of James Point. The habitats within this area were composed of Halophila sp. seagrass beds, cobble reef and pavement reef. The majority of the rest of the Eastern Shelf was covered by soft substrate. The sidescan sonar provided a time and cost efficient method for the mapping of subtidal habitats, particularly in areas for which the capture of high quality aerial photographs could not be achieved. The imagery allowed delineation of the boundaries of the vegetated and unvegetated areas and permitted textural interpretation of the composition of the habitats present. However, detailed groundtruth survey data was required to allocate habitat types to the SSS imagery. Limestone bedrock was found to cover a relatively large area of the Eastern Shelf, often covered by a thin veneer of loose sand and therefore not always detectable with the SSS or visible from the towed video. The existence of this limestone was often evidenced by the presence of ascidians or algae visible in the video footage. The extents of some of the Posidonia sp. beds within the survey area were thought to be limited by the presence of a sufficient depth of sediment to allow their settlement and persistance. Areas of limestone pavement reef were also identified adjacent to several Posidonia sp. beds (along video tows 3, 5, 10, 11, 19, 35 and 42)(Figure 3.2, Figure 4.1) and within gaps between patches of seagrass at dive site CS3. In other areas Halophila sp. was identified as growing within a thin layer of soft sediment which was overlying bedrock. In these areas it is likely that only Halophila sp. could settle and remain since the larger flat-leaved seagrasses would require a deeper root system to avoid being uprooted by currents.


6. References Bickers, A.N. 2003. Cost effective marine habitat mapping from small vessels using

GIS, Sidescan Sonar and Video. Coastal GIS 2003: an integrated approach to Australian coastal issues. Woodroffe, C.D. and Furness, R.A. (Eds). Wollongong Papers on Maritime Policy, 14.

Connor, D.W., Allen, J.H., Golding, N., Lieberknecht, L.M., Northen K. O. and

Rejer, J.B. (2003). The National Marine Classification for Britain and Ireland. Version 03.02. JNCC, Peterborough. ISBN 1 86107.

DAL (1998). Historical Review of water quality in Cockburn Sound. Report prepared

for Kwinana Industries Council, Report No. 97/052/1. DAL, UWA, Alex Wyllie & Associates, NGIS Australia & Kevron Aerial Surveys

(2000). Seagrass Mapping Owen Anchorage and Cockburn Sound. Report prepared for Cockburn Cement Ltd, Department of Environmental Protection, Department of Commerce and Trade, Department of Resources Development, Fremantle Port Authority, James Point Pty Ltd, Kwinana Industries Council, Royal Australian Navy, Water Corporation of Western Australia and Water and Rivers Commission. Report No. 94/026/S3/2.

DALSE (2002). Benthic Habitat Mapping for 2002 of selected areas of Cockburn

Sound. Report prepared for Cockburn Sound Management Council. Report No. 273/1.

DALSE. (2003). The Influence of Garden Island causeway on the environmental

values of the southern end of Cockburn Sound. Report prepared for the Cockburn Sound Management Council, Report No. 02/247/2.

Embley, B (2003). Seafloor mapping. In;

http://oceanexplorer.noaa.gov/explorations/02fire/background/seafloor_mapping

Kendrick, G.A., Aylward, M.J., Hegge, B.J., Cambridge, M.L., Hillman, K., Wyllie,

A. and Lord, D.A. (2002). Changes in seagrass coverage in Cockburn Sound, Western Australia between 1967 and 1999. Aquatic Botany, 73: 75-87.


7. Acknowledgements This study was funded by the following members of the Cockburn Sound Management Council: Department of Industry and Resources, LandCorp and Fremantle Ports. This report was prepared by Spencer Shute (DAL Science & Engineering) and reviewed by Drs Bruce Hegge (DAL Science & Engineering) and Gary Kendrick (UWA). Mapping figures were produced by Dr Karen Holmes (UWA). The fieldwork was completed by Spencer Shute and Helen Astill (DAL Science & Engineering), Dr Gary Kendrick, Dr Marion Cambridge, Andy Bickers, Brenton Chatfield, Dr Karen Holmes and Simon Grove (UWA). The data analysis was carried out by Spencer Shute (DAL Science & Engineering), Dr Gary Kendrick, Andy Bickers, Dr Karen Holmes and Simon Grove (UWA). Formatting of the report was completed by Katy Rawlings (DAL Science & Engineering).


Appendix A

Habitat photographs


Appendix A Habitat photographs

Posidonia sinuosa P.sinuosa & P.australis

Favia sp. Herdmania momus

Sargassum sp. Octopus tetricus

Dive site CS1 – Representative species


Halophila ovalis H.ovalis & H.decipiens

Phoronis australis Cavernularia sp.

Dofleina armata Peronella lesueuri

Schizoporella subsinuata Heterodontus portusjacksoni

Dive site CS2 – Representative species


Posidonia sinuosa Posidonia sinuosa & wrack

Posidonia australis Posidonia coriacea

Cercodemas anceps & sponges Pinna bicolour Dive site CS3 – Representative species


Appendix B

Spot dive in situ habitat notes


Appendix B Spot dive in situ habitat notes

Site Sediment Seagrass species Characteristic species Abundance Comments CS1 Poorly sorted m/c sand with bivalve fragments.

Boulders (O) and cobbles (F). P. sinuosa & P. australis Epifauna/flora on reef

Ascidians (including H. momus) Bryozoans (including Triphyllozoan moniliferum & Schizoporella subsinuata) Grey sponge indet Hydroid indet

Sargassum sp.

F R S O C

15cm depth of soft sediment

CS2 Silty fine sand

H. ovalis O H. decipiensO

Fauna associated with soft sediment Seapens (Cavernularia sp.) Sand dollar (Peronella lesueuri) Anemone (Dofleina armata) Horseshoe worm (Phoronis australis) Epifauna / fauna on boulders/cobbles Sponges indet Ascidians indet Hippocampus sp.

Blue manna crab (Portunus pelagicus)

F O-F R R A A R R


Site Sediment Seagrass species Characteristic species Abundance Comments CS3 At Shotline;

Poorly sorted clean m/c sand with shell fragments Away from shotline; M/c sand with shell fragments overlying pavement reef (15cm deep). Ancient seagrass rhizomes also present in patches.

P. sinuosa. P. australis (individual patches) P. coriacea (individual plants) Halophila decipiens in reproductive state

Fauna associated with soft sediment Sand dollars (Peronella lesueuri)

F

CS4 Fine silty sand H. decipiens / H. ovalis mix CS5 Fine silty sand H. decipiens in linear beds


Appendix C

SACFOR scale


Appendix C SACFOR scale

SACFOR abundance scale used for both littoral and sublittoral taxa from 1990 onwards. (Superabundant/Abundant/Common/Frequent/Occasional/Rare) NB. Read notes below prior to use of scale

Growth form Size of individuals/colonies

% cover Crust/meadow Massive/Turf <1cm 1-3 cm 3-15 cm >15 cm Density

>80% S S >1/0.001 m2

(1x1 cm) >10,000 / m2

40-79% A S A S 1-9/0.001 m2 1000-9999 / m2

20-39% C A C A S

1-9 / 0.01 m2

(10 x 10 cm) 100-999 / m2

10-19% F C F C A S 1-9 / 0.1 m2 10-99 / m2

5-9% O F O F C A 1-9 / m2

1-5% or density

R O R O F C

1-9 / 10m2

(3.16 x 3.16 m)

<1% or density R R O F

1-9 / 100 m2

(10 x 10 m)

R O

1-9 / 1000 m2

(31.6 x 31.6 m)

R <1/1000 m2

(Source: Connor et al., 2003)

Use of the MNCR SACFOR abundance scales The MNCR cover/density scales adopted from 1990 provide a unified system for recording the abundance of marine benthic flora and fauna in biological surveys. The following notes should be read before their use:

1. Whenever an attached species covers the substratum and percentage cover can be estimated, that scale should be used in preference to the density scale.

2. Use the massive/turf percentage cover scale for all species, excepting those given under crust/meadow.

3. Where two or more layers exist, for instance foliose algae overgrowing crustose algae, total percentage cover can be over 100% and abundance grade will reflect this.

4. Percentage cover of littoral species, particularly the fucoid algae, must be estimated when the tide is out.

5. Use quadrats as reference frames for counting, particularly when density is borderline between two of the scale.


6. Some extrapolation of the scales may be necessary to estimate abundance for restricted habitats such as rockpools.

7. The species (as listed above) take precedence over their actual size in deciding which scale to use.

When species (such as those associated with algae, hydroid and bryozoan turf or on rocks and shells) are incidentally collected (i.e. collected with other species that were superficially collected for identification) and no meaningful abundance can be assigned to them, they should be noted as present (P).

Documents

E Shelf mapping SS Final