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Record 2017/04 | eCat 100945

Bynoe Harbour Marine Survey 2016: GA4452/SOL6432 Post-survey report

Siwabessy, P.J.W., Smit, N., Atkinson, I., Dando, N., Harries, S., Howard, F.J.F., Li, J., Nicholas, W.A., Picard, K., Radke, L.C., Tran, M., Williams, D. and Whiteway, T.

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www.ga.gov.au

Bynoe Harbour Marine Survey 2016: GA4452/SOL6432 Post-survey report GEOSCIENCE AUSTRALIA RECORD 2017/04

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Siwabessy, P.J.W. , Smit, N. , Atkinson, I. , Dando, N. , Harries, S. , Howard, F.J.F. , Li, J. , 1 1 1 1 3 1 Nicholas, W.A. , Picard, K. , Radke, L.C. , Tran, M. , Williams, D. and Whiteway, T.

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Geoscience Australia, GPO Box 378, Canberra, ACT 2601 Department of Environment and Natural Resources, Northern Territory Government, PO Box 496, Palmerston, NT 0831 Australian Institute of Marine Science, PMB 3, Townsville MC, Qld 4810

Department of Industry, Innovation and Science Minister for Resources, Energy and Northern Australia: The Hon Josh Frydenberg MP Assistant Minister for Science: The Hon Karen Andrews MP Secretary: Ms Glenys Beauchamp PSM Geoscience Australia Chief Executive Officer: Dr Chris Pigram This paper is published with the permission of the CEO, Geoscience Australia

© Commonwealth of Australia (Geoscience Australia) 2016 With the exception of the Commonwealth Coat of Arms and where otherwise noted, this product is provided under a Creative Commons Attribution 4.0 International Licence. (http://creativecommons.org/licenses/by/4.0/legalcode) Geoscience Australia has tried to make the information in this product as accurate as possible. However, it does not guarantee that the information is totally accurate or complete. Therefore, you should not solely rely on this information when making a commercial decision. Geoscience Australia is committed to providing web accessible content wherever possible. If you are having difficulties with accessing this document please email [email protected]. ISSN 2201-702X (PDF) ISBN 978-1-925297-41-6 (PDF) eCat 100945 Bibliographic reference: Siwabessy, P.J.W., Smit, N., Atkinson, I., Dando, N., Harries, S., Howard, F.J.F., Li, J., Nicholas W.A., Picard, K., Radke, L.C., Tran, M., Williams, D. and Whiteway, T. 2016. Bynoe Harbour Marine Survey 2016: GA4452/SOL6432 – Post-survey report. Record 2017/04. Geoscience Australia, Canberra. http://dx.doi.org/10.11636/Record.2017.004

Contents

1 Introduction ............................................................................................................................................1 1.1 Background and survey aims ..........................................................................................................1 1.2 Study area ........................................................................................................................................2 1.3 Seabed mapping ..............................................................................................................................4 1.3.1 Scientific rationale ......................................................................................................................4 1.3.2 Seabed mapping approach, purpose and desired outputs ........................................................5 1.3.3 Survey aims ................................................................................................................................6 2 Methods .................................................................................................................................................7 2.1 Survey overview ...............................................................................................................................7 2.2 Sampling overview ...........................................................................................................................7 2.3 Geophysical data .............................................................................................................................8 2.3.1 Seabed mapping ........................................................................................................................8 2.3.2 Sub-bottom profiler ...................................................................................................................10 2.4 Physical sampling ..........................................................................................................................10 2.4.1 Smith-McIntyre grab .................................................................................................................10 2.4.2 Underwater photography and video .........................................................................................12 2.5 Oceanographic data.......................................................................................................................12 2.5.1 Tide...........................................................................................................................................12 2.5.2 Sound Velocity Profiles (SVP) ..................................................................................................14 3 Data summary .....................................................................................................................................15 3.1 Survey summary ............................................................................................................................15 3.2 Geophysical data ...........................................................................................................................15 3.2.1 Multibeam echosounder ...........................................................................................................15 3.2.2 Sub-bottom profiler ...................................................................................................................28 3.3 Physical Data .................................................................................................................................29 3.3.1 Sedimentology ..........................................................................................................................29 3.3.2 Geochemistry ...........................................................................................................................32 3.3.3 Biology ......................................................................................................................................33 3.4 Oceanographic data.......................................................................................................................37 3.4.1 Tide...........................................................................................................................................37 3.4.2 Sound Velocity Profile (SVP)....................................................................................................38 4 Summary and concluding remarks ......................................................................................................40 Appendix A Scientific and technical crew ...............................................................................................45 Appendix B Spatial coordinates of waypoints used to guide station selection .......................................46 Appendix C Technical report on multibeam sonar operations ...............................................................49 Appendix D Survey details for sub-bottom profiles ................................................................................56 Appendix E Survey details for Smith-McIntyre grab (GR) samples .......................................................57 Appendix F List of Smith-McIntyre grab sub-samples ............................................................................64 Appendix G Survey details for photo and video .....................................................................................70 Appendix H Survey leader daily log 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Executive Summary

A benthic sediment sampling survey (GA4452/SOL6432) was undertaken in Bynoe Harbour in the period from 2 to 27 May 2016. Partners involved in the survey included Geoscience Australia (GA), the Australian Institute of Marine Science (AIMS) and the Department of Environment and Natural Resources within the Northern Territory Government (NT DENR) (formerly the Department of Land and Resource Management (DLRM)). This survey forms part of a four year (2014-2018) science program aimed at improving knowledge about the marine environments in the Darwin and Bynoe Harbour region. The program involves the collection and collation of baseline data to create thematic habitat maps that underpin marine resource management decisions. The program was made possible through environmental offset funds provided by the INPEX-led Ichthys LNG Project (http://www.inpex.com.au/, hereafter referred to as INPEX) to NT DENR and co-investment from GA and AIMS. Under Condition 11(a) of the approval, INPEX must deliver habitat mapping for the region. The program builds upon an NT Government project (2011-2018) which will see the collection of baseline data (multibeam echosounder data, sediment samples and video transects) from inner Darwin Harbour (Siwabessy et al., 2015). The AIMS vessel RV Solander was used to obtain high-resolution multibeam sonar data to map 2 bathymetry, backscatter and water column data over 698 km of Bynoe Harbour. Physical data (including underwater video and stills, grabs, tide gauge and Sound Velocity Profiles (SVPs)) were obtained from 102 stations to characterise the seabed sediments, guide interpretations of geomorphology and seabed hardness, and improve knowledge of the water column. Initial interpretations of the newly acquired data show that the interaction of tidal currents with river outflow and storm-generated currents has created a seabed characterised by a complex network of geomorphic features and associated habitats, including: 

Complex hardgrounds (rock with shallow pits and hollows), which indicate there have been periods of subaerial exposure and erosion when sea-level was lower than the current seabed. They occur mostly in shallow water and provide suitable habitat for benthic communities;



Plains which have variable backscatter results (indicating that hardness is variable). This likely indicates that some regions have a thin sediment veneer while others have thicker accumulations of sediment over rock. Areas of veneer correspond to patchy rocky outcrops supporting locally abundant patches of octocorals and sponges.



Channels, which are typically harder-scour features with gravel sediments;



Sandwaves and ripples, of linear, dendritic and sinuous types occurred predominantly over plains and channels.

The baseline environmental data acquired in this habitat mapping program is providing new insights into the marine environment of Bynoe Harbour. The data will underpin future environmental assessments and consequently support management decisions. This report provides details of the Bynoe Harbour survey, including the area surveyed, methods used and initial results. Data from this survey will be made publically available via the Geoscience Australia website (http://www.ga.gov.au/).

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1 Introduction

This report provides the details of the activities undertaken by Geoscience Australia (GA), the Australian Institute of Marine Science (AIMS) and the Northern Territory Government Department of Environment and Natural Resources (DENR) during a seabed mapping survey (GA04452/SOL6432) of Bynoe Harbour. This project was made possible through offset funds provided by the INPEX-led Ichthys LNG Project to the Northern Territory Government DENR, and co-investment from Geoscience Australia and Australian Institute of Marine Science. This survey was completed between 3 May and 27 May 2016. Scientific results of the survey will be detailed in a final habitat mapping report that will synthesise all data collected across the habitat mapping program.

1.1 Background and program objective Darwin is Australia’s most northern capital city and the only major population centre on 5,600 km of comparatively undeveloped coastline between Perth and Cairns. It lies on Darwin Harbour, which is located on the southern shore of the Beagle Gulf in the Timor Sea (Figure 1.1) and is one of Australia’s largest deep water harbours. With ongoing development in Northern Australia and increasing coastal development in Darwin Harbour, robust baseline data and a strong scientific understanding of ecological processes are required to inform planning and management for sustainable development and multiple use of this region. The Darwin Harbour Regional Plan of Management (Darwin Harbour Advisory Committee, 2003) has identified that there is limited information on the local environmental values and attributes which could potentially be affected by coastal development. Furthermore, the plan identified that there is a lack of data on broad scale habitat and biodiversity distributions and of processes which maintain ecosystem health. This has been highlighted in environmental assessments associated with recent large development proposals. In response, the Northern Territory Government announced in December 2010 that $500 000 over two years would be allocated for a baseline habitat mapping program to ensure that the best scientific data would be available to inform sustainable development. Under this program, DENR collaborated with GA, AIMS and the Darwin Port Authority to undertake multibeam and backscatter data acquisition for inner Darwin Harbour in 2011. The survey data has been processed, analysed and interpreted to produce a series of mapping products describing the seabed characteristics to support seascape analysis of inner Darwin Harbour. In 2011, INPEX Corporation (http://www.inpex.com.au/, hereafter referred to as INPEX) and the Northern Territory Government entered into a voluntary agreement where INPEX would fund and/or deliver several environmental and social offset programs. The environmental offset programs were incorporated into conditions for the approval decision for INPEX’s Ichthys Liquefied Natural Gas proposal [2008/4208] by the Department of the Environment (DOE). Under Condition 11(a) of the approval, INPEX must deliver habitat mapping for the Darwin Harbour region (including Bynoe Harbour). The intent of this offset program is to improve knowledge of the marine habitats in the Darwin and Bynoe Harbour region through collaboration and collation of baseline data that will allow

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creation of thematic habitat maps to underpin marine resource management decisions. The four year (2014-2018) program will: 

improve knowledge of marine habitats in the Darwin Harbour region;



produce habitat maps of Darwin Harbour region and Bynoe Harbour;



improve understanding of how new future use may impact on Darwin Harbour; and



improve environmental management decisions for Darwin Harbour.

To deliver the Offset Habitat Mapping program, DENR built on previously developed relationships and established a working group in 2013, with joint partners AIMS and GA, to deliver the program’s objectives. The working group has identified four core tasks for the program: 1. Conduct seabed mapping to obtain high resolution bathymetric and backscatter data within Darwin and Bynoe harbours; 2. Examine the abiotic patterns important to benthic communities within Darwin and Bynoe harbours; 3. Characterise the seafloor fauna and flora (i.e. benthos) within Darwin and Bynoe harbours; and 4. Model species/community distribution within Darwin and Bynoe Harbours.

1.2 Study area The Darwin – Bynoe Harbour region lies in the eastern part of the Beagle Gulf, which is located between the southern shores of Melville and Bathurst Islands and the Australian mainland (Figure 1.1). This region includes Port Darwin, outer Darwin Harbour (waters between Gunn Point and Charles Point and includes Shoal Bay) and Bynoe Harbour, which is bounded by Cox Peninsula in the east 2 2 and five islands in the west. The total area of interest is about 2000 km of which 1300 km are subtidal environments. Similar to Darwin Harbour, Bynoe Harbour is a tropical estuary formed within a drowned river valley (a ria), located on the northwestern coast of the greater Joseph Bonaparte Gulf, northern Australia. Bynoe Harbour is positioned approximately 12.5° south of the equator, facing Cape Fourcroy on Bathurst Island and the Timor sea, across the intervening Beagle Gulf (Woodroffe et al., 1988; Nott, 2003). The climate is monsoon tropical. Nearby Darwin Airport receives about 1726 mm of rainfall annually, with the majority falling in the monsoon (wet) season between November and March. Riverine discharge is low as the Darwin and Bynoe harbour catchments are relatively small. Prevailing winds are seasonal with north-west monsoons in November to March giving way to southeast trade winds from May to September. During the wet season, the monsoonal conditions generate turbulent wave action and high turbidity along this coast. The annual range in sea surface temperature in the adjacent Darwin Harbour is from 23 - 34°C. Beagle Gulf is dominated by tidal currents that flow in an east to west direction, turning to northwest– southeast near the entrance to Bynoe Harbour. The tides amplify as they transit across the wide continental shelf and the currents become bidirectional as they approach the coast. Darwin and Bynoe harbours have a large tidal range (macrotidal) with a 7.9 m maximum tidal range (5.5 m mean spring range and 1.8 m mean neap range) (Woodroffe et al., 1988; Andutta et al., 2013). The tidal cycle is semidiurnal (two tidal cycles are experienced every 24 hours). Tidal currents in this region can reach up to 2 m/s (7.2 km/h) during a maximum spring tide (Andutta et al., 2013; Williams et al., 2006). As a result of the tidal energy, the harbour is considered to be a reasonably well-mixed homogenous water body that is naturally turbid but carries low nutrient loads. Turbidity values range from 5 Nephelometric

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Turbidity Units (NTU) in the dry season to in excess of 400 NTU during wet season storms. Bynoe Harbour contains one main channel. Near the harbour entrance this channel bifurcates around a single island, Indian island. Unlike Darwin Harbour, comparatively little information was available on the sediments and geomorphology of the seabed for Bynoe Harbour prior to this study. However, the near shore geology is reasonably well known. The Bynoe region is underlain by the western domain of the Pine Creek Orogen, the Litchfield Province (Pietsch and Edgoose, 1988). Deformed and intrusive Archean to Proterozoic basement rocks are overlain to the north by Cretaceous marine sediments of the Bonaparte Basin, extending offshore onto the shelf. To the south and north of Bynoe Harbour lies the Welltree Metamorphics, comprising amphibolite facies gneisses, schist, and quartzite (Pietsch, 1986, Carson et al., 2008). The Welltree Metamorphics is intruded by the post-orogenic Two Sisters Granite (Pietsch and Edgood, 1988). At the eastern end of Bynoe Harbour the Burrell Creek Formation outcrops. The metasediment is comprised of phyllite, siltstone, conglomerate and greywacke and is incised by the Anna and Charlotte rivers as they travel west into Bynoe Harbour. The Burrell Creek Formation is intruded by the Two Sisters Granite and numerous pegmatite bodies. A large number of cassiterite-rich pegmatites are located between Bynoe Harbour and Darwin Harbour th to the north and were mined for tin from the late 19 century (Ahmad, 1995). This area is commonly referred to as the "Bynoe pegmatite field", or "Bynoe Field" (Jiang and Sun, 2015). During the Last Glacial Maximum (23-19 ka BP) Bynoe and Darwin Harbours and the adjacent Beagle Gulf were subject to subaerial erosion and weathering. While Holocene sea level and sedimentary processes are well documented (Woodroffe and Grime, 1999; Woodroffe et al., 1993), less is known about the post-Cretaceous to Holocene history of this area. Several lines of evidence suggest that the greater Joseph Bonaparte Gulf region was affected by global low sea levels, similar to the last ice age, since at least the end of the mid-Pleistocene Transition (~ 650 ka BP) with buried river channels present just outside Beagle Gulf (Bourget et al., 2013; Saqab and Bourget, 2015; Nicholas et al., 2014). For the majority of this time, sea level was too low for Bynoe Harbour to be an estuary (Figure 1.1). Thus, Bynoe Harbour is a drowned river valley which has been exposed to erosion and weathering for a large proportion of the past 650 000 years. The harbour has only been intermittently connected to the sea over that time. Estuarine conditions similar to present were established some 7 to 8 thousand years ago, just as rising sea levels stabilised after the last ice age (Lewis et al., 2013).

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Figure 1.1 Location map of the area surveyed during the Bynoe Harbour Marine Survey (red outline) along with the location of areas previously surveyed and areas to be surveyed in future field seasons.

1.3 Seabed mapping 1.3.1 Scientific rationale Historically, benthic habitat maps produced from taxonomic lists and biodiversity values for a site/region were based on point sampling methods (Eleftheriou and McIntyre 2005 and references therein). However, the outputs from this approach, such as community patterns, can be limited due to insufficient knowledge about the spatial extent of physical characteristics that underpin community patterns (e.g. substrate type), and gradual shifts in species composition along environmental gradients

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(e.g. Gray 2002; Ellis and Schneider 2008; Gray and Elliot 2009).Recent advances have overcome many of these constraints. Underwater acoustic remote sensing technologies such as multibeam echo sounder (MBES) systems (Rattray et al., 2009; Huang et al., 2011; Huang et al., 2013), Geographic Information Systems (GIS) and geospatial analysis (Lund and Wilbur, 2007; Zajac, 2008; Bishop et al., 2012) provide high-resolution data to describe the physical seafloor. In addition, developments in numerical modelling of hydrodynamics (Williams et al., 2006), surface processes (Tenore et al., 2006; Pitcher et al., 2004) and biological surrogacy (Pitcher et al., 2007a) have transformed benthic habitat mapping into a complex multi-disciplinary task enabling full-coverage predictive mapping products (Pitcher et al., 2007a; Haywood et al., 2008). There are three main approaches to benthic habitat mapping (Brown et al., 2011): 1. abiotic habitat mapping; 2. benthic community mapping; 3. single species habitat mapping. Abiotic habitat mapping uses physical and chemical characteristics as surrogates for biodiversity with the underlying premise that species distribution can be predicted based on environmental data (Post et al., 2006; Gray and Elliot, 2009, ). Pitcher et al. (2007b) identified grain size distribution, carbonate, irradiance, bottom sheer stress, bathymetry, bottom-water physics, nutrients, turbidity as surrogates for mapping and characterisation of biotic and physical attributes of the Torres Strait Ecosystem. McArthur et al. (2010) concluded that sediment variables such as grain size, rugosity and compaction hold the strongest independent predictive power as a surrogate for biodiversity. Analysis of these data coupled with data derived from MBES (e.g. depth, backscatter strength, slope, aspect, benthic position index, rugosity), allows for seascape analysis and mapping of areas with similar environmental characteristics, which is of value for use in many aspects of marine spatial planning (e.g. Ierodiaconou et al., 2007; Rattray et al., 2009; Heap and Harris, 2011; Huang et al., 2011; Berkström et al., 2012; Anderson et al., 2013; Lucieer et al., 2013; Rattray et al., 2013). Further, the outputs are commonly used in gap analysis and sampling design for additional benthic community and single species sampling programs.

1.3.2 Seabed mapping approach, purpose and desired outputs The seabed mapping survey will build on data collected in 2015 also under the current seabedmapping program, along with data from a previous Port Darwin seabed-mapping program, conducted in 2011 (Figure 1.1). The purpose of this task is to obtain and collate detailed full coverage acoustic datasets representing depth, seabed morphology, acoustic backscatter and sediment characteristics (e.g. grainsize and sediment chemistry, seabed mapping). The collected data will contribute towards the creation of thematic habitat maps that will, a) support the design of cost effective sampling of benthic fauna and flora; and b) make inferences about species/assemblages beyond sampling locations alone (community and species mapping). Data and GIS layers include: 

Bathymetry, acoustic backscatter and derived data products, e.g. slope, aspect, curvature, rugosity, hardness, inferred substrate types (e.g. mud, sands) and benthic position index.



Sediment characteristics (e.g. % gravel, % sand, % mud, Folk classification, percentage carbonate, sediment origin (marine vs terrestrial)).

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Sediment chemistry characteristics (e.g. TOC, TN, C isotopes, N isotopes, pore water, oxygen demand, contaminants (heavy metals)).

1.3.3 Survey aims The aim of the survey was to collect bathymetry and sediment chemistry data for Bynoe Harbour in waters deeper than 5m (LAT). The specific objectives of the survey were to: 1. Obtain high resolution geophysical (bathymetry) data for Bynoe Harbour including Port Patterson; 2. Characterise substrates (acoustic backscatter properties, sub-bottom profiles, grainsize, sediment chemistry) for Bynoe Harbour, including Port Patterson; 3. Collect GPS tidal data for the survey area.

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2 Methods

2.1 Survey overview Survey GA4452/SOL6432 was undertaken in two operational legs: Leg 1 (02/05/2016 to 16/05/2016) and Leg 2 (17/06/2016 to 27/05/2016). Operations included geophysical data acquisition (using multibeam echosounders), seabed sampling (grabs), underwater imaging and sound velocity profiling (SVP). In addition, a GPS tide gauge was deployed for the survey period.

2.2 Sampling overview We collected approximately 100 samples in water depths greater than 5m (LAT). However, prior to the survey, a total of 200 random sample locations were identified to accommodate for areas that could not be mapped once on site due to factors such as, shallow depths, difficulty in reaching the area, and lack of time (Appendix B). The following sampling design method was used and implemented in R (R Development Core Team, 2012), with sp (Pebesma and Bivand, 2005), raster (Hijmans, 2014) and spcosa (Walvoort et al., 2015) used to analyse and plot the data: 1. each area was spatially divided into 25 strata based on latitude and longitude; 2. eight sampling points were randomly selected within each stratum (random waypoints, Figure 2.1). 3. the distribution of sampling locations within each area was visually examined. The sampling design was deemed acceptable because all sampling locations were spread relatively evenly over the survey area (Figure 2.1). The sub-selection of the 100 samples was done during the survey as areas were mapped. The total initial area was divided into smaller polygons and samples were sub-selected proportionally to the size of the new area (Figure 2.1).

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Figure 2.1 The spatial distribution of 200 random waypoints. The waypoints are shown overlaid on 2.5 m resolution SPOT satellite imagery. The spatial coordinates of the 200 waypoints are summarised in Appendix B.

The water column and seabed of each waypoint was sampled, when time allowed, using the methods described below. Once a waypoint was sampled, the location was assigned a station number.

2.3 Geophysical data 2.3.1 Seabed mapping 2.3.1.1 Multibeam echosounder Continuous bathymetric data were collected within the study area and while transiting using a Kongsberg EM2040C multibeam echosounder system, mounted in the moon pool of the RV Solander in dual head configuration (Figure 2.2). Technical details of the multibeam operations can be found in Appendix C.

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The grid was divided into 13 cells which were each individually mapped to ensure that the data acquisition was undertaken in swaths that ran parallel to depth contours. However, in areas with abundant ship traffic, safety considerations meant that mapping could not follow the isobaths.

Figure 2.2 Kongsberg EM2040C multibeam sonar system installed on RV Solander, showing: (a) POS MV motion reference unit, data acquisition and processing units, and; (b) dual head mounting deployed in the moon pool.

Bathymetry The multibeam bathymetry data were processed using CARIS HIPS/SIPS v8.1.13 software. The processing included: i) applying algorithms that corrected for tide and vessel pitch, roll and heave; and ii) applying filters and visually inspecting each swath line to remove any remaining artefacts and noisy data (e.g. nadir noise and outliers). During the survey, a co-tidal solution was adopted to minimise tidal bursts. This solution used average tides from multiple tide stations weighted inversely to distance between the tide station and the point of interest available in CARIS. Study areas were divided into closed zones with designated primary tide stations of known locations, all defined in a Zone Definition File (*.zdf) in CARIS. The predicted tides were calculated for predefined locations (Section 2.5.1.1). Final high-resolution bathymetric surfaces at 1 m horizontal resolution were created within CARIS and then exported as surface grid bathymetric maps for display and analysis.

Backscatter strength Along with bathymetric data, the Kongsberg EM2040C multibeam system co-registered backscatter data. These data were processed using the multibeam backscatter CMST-GA MB Process v15.04.04.0 (64) toolbox software co-developed by the Centre for Marine Science and Technology (CMST) at Curtin University of Technology and GA (described in Gavrilov et al., 2005; Parnum and Gavrilov, 2011). The process within the toolbox involved removing system transmission loss, removing the system model, calculating the incidence angle, correcting the beam pattern, calculating the angular backscatter response within a sliding window of 100 pings with a 50% overlap in a 1° bin,

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removing the angular dependence, and restoring the backscatter strength at an angle of 25° (Daniell et al., 2010). The final processed backscatter data were then gridded to 1 m horizontal resolution and exported for display and analysis. Removing the angular dependence from the backscatter is necessary for consistent backscatter strength across the swath in various incidence angles (for a homogeneous seafloor). Here the angular backscatter response was calculated in a 1° bin of incidence angle and averaged within the sliding window. This angular backscatter response is an intrinsic property of the seafloor, illustrating that the backscatter strength changes with the angle of incidence and is dependent on substrate type.

2.3.2 Sub-bottom profiler Sub-bottom profiles were collected using an Edgetech SB-216S chirp profiler. The profiler was deployed from the stern of the RV Solander and towed about 40 m away from the stern for a total of about 53 m from the GPS antenna (Figure 2.3). The chirp signal was set up to sweep between 2 and 15 kHz and used a 20 ms pulse length. Profiles were collected mainly across the axes of the channels (Appendix D) and where multibeam backscatter suggested soft substrate (low acoustic return).

(A)

(B)

Figure 2.3 A) Edgetech SB-216S sub-bottom profiler deployed off the stern of the ship, and B) Acquisition system

2.4 Physical sampling 2.4.1 Smith-McIntyre grab 2

Unconsolidated seabed sediments were collected using a Smith-McIntyre (SM) grab (10 L, 0.1 m opening). The grab sampler was deployed from the starboard side winch of the RV Solander. The SM grab sampler is mounted on a sturdy, weighted, steel frame, with springs to force the two-jaw bucket into the sediment substrate when released. Tripping pads, positioned below the square-based frame on which the bucket is suspended, first make contact with the seabed and are pushed upward to release two latches holding the spring-loaded bucket jaws. Tension from the winch wires keeps the grab closed during retrieval. Each SM grab was subsampled for both sedimentology and geochemistry. A summary of SM grab sampling is found in Table 2.1 and Appendix Table E.1.

2.4.1.1 Sedimentology The principal aim of the sedimentology component of the survey was to determine the texture and composition of the surface sediments for seabed characterisation. Up to 100 g of bulk sediment was

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sub-sampled from the top 2 cm of the grabs. Samples were submitted to the GA sedimentology laboratory for grain-size analysis using: (i) sieve separation to determine the particle size distribution and summary statistics of the Wentworth grain-size fractions; and (ii) laser diffraction to determine the size distribution of the mud fraction using a Malvern Mastersizer 2000. Separate sample splits were used to measure carbonate content using the carbonate digestion method (Müller and Gastner, 1971).

2.4.1.2 Environmental geochemistry The principal aims of the environmental geochemistry component of the survey were: (i) to determine the geochemical composition of surface sediment for seabed characterisation; and (ii) to quantify the levels of reactive organic matter in the sediments that were due to pigments and organic matter. Sediments from the grabs were sub-sampled into seven separate containers (Appendix F) and processed aboard according to the methods described in Table 2.1. Table 2.1 Details of shipboard laboratory processing used to prepare and analyse the sub-samples. Sub-sample codes (_A1, etc.) correspond to the file extension assigned to the sub-sample types in the shipboard database. See Appendix F for a summary of all sub-samples taken during the survey. Subsample

Parameters to be measured

Shipboard processing

_A1

Grain size

Approximately the top 2 cm of sediment was spooned into a labelled bag

_B1

Porosity; Total chlorins and chlorin indices.

6.5 mL of surface sediment (0-2 cm) was syringed into pre-weighed plastic container. The samples were wrapped in Al-foil and frozen.

_C1

Sediment oxygen demand

Bulk sub-sample (6.5 ml) of surface sediment (0-2 cm) incubated in filtered (0.5μm) seawater in Biological Oxygen Demand (BOD) bottles for ~24 hrs in the dark at approximately sea surface temperatures (SST). Dissolved oxygen concentrations (and saturation values) were measured at the start and finish of the incubations.

_C2

Total sediment metabolism

Salinity, temperature and pH were measured on pore waters extracted from sub-samples C_D1. These pore waters were then filtered (0.45 µm) into 3 ml gas-tight vials (pre-charged with 25 μL HgCl2) within 1 hr of collection (T=0). The procedure was repeated on pore waters from an additional bulk sample collected as per C_D1 and incubated for ~24 hrs at SST (T=1). All samples were refrigerated prior to laboratory analysis for dissolved inorganic carbon (DIC). Samples taken at core incubation stations only.

_C3

CO2 production and consumption rates; total oxygen uptake rates

Two 5 cm diameter cores of surface sediment overlain by 0.153L of filtered (0.5μm) and UVtreated seawater was incubated in the dark for ~6 o hours at ~25 C after a ~3 hour pre-incubation period. Dissolved oxygen levels were measured at ~30 minute intervals. Samples for DIC analysis were taken at the start and finish of each of the incubations. Blank cores (seawater only) were run intermittently throughout the survey period. Core incubations were undertaken at 46 stations only. At 10 of these stations additional samples were taken for N2 and dissolved nutrients at the start and finish of the incubations.

_D1

Major, minor, trace and rare earth elements; Bulk

Surface sediment (0-2 cm) was syringed into falcon vials. Pore waters were removed within 20 minutes

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Subsample

Parameters to be measured

Shipboard processing

carbonate of collection (see C_C2). Residual sediment was Specific surface area; TOC, TN and C & N isotopes frozen for transport to the laboratory. _S1

Major, minor, and trace and rare earth elements

Notation used to denote solid specimens from grabs. The specimens were placed in plastic bags and refrigerated

2.4.2 Underwater photography and video Epifauna and broad-scale sedimentology and topography of the seabed were surveyed by underwater video cameras (GoPro ©) attached to the Smith-McIntyre grab. Underwater video and still cameras captured the deployment of the grab to the seafloor. High-resolution still images (12 MP and 1080p video resolution, captured every 1 second during the grab deployment) were used in conjunction with the video footage to assist identification of the biota. Upon retrieval of the cameras, the still images were downloaded and renamed by station and sequential image number. These images were then sorted into usable images for seafloor classification. Images of interesting or representative habitat and biota were singled out for further analysis and description.

2.5 Oceanographic data 2.5.1 Tide Tidal data acquisition was over 30 days, a full spring – neap tidal cycle. The tides for the period recorded at the national tide reference station at Fort Hill wharf are shown in Figure 1.1. AIMS services two moorings for the Integrated Marine Observing System (IMOS) network and these are located at the entrance to Darwin Harbour and in the middle of the Beagle Gulf. Another mooring had been deployed to the east of the survey area and collected data for a period of 24 days during the survey. A two-dimensional finite element hydrodynamic model was developed for the area to simulate tidal elevations and currents. The boundary conditions for the model are harmonics derived from observations from Tapa Bay to the west and Cape Hotham to the east. These harmonics are available from the Australian Hydrographic Office national electronic tide predictions (AHO, 2015). The model was run to include all periods of mooring observations. The model calibrates well to observed tides. An example of modelled output and observed data is shown in Figure 2.4. The model performs equally well against all moored data.

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Figure 2.4 Observed (blue line) versus modelled (orange line) tidal elevation for Beagle Gulf.

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2.5.2 Sound Velocity Profiles (SVP) Sound velocity profiles (SVP) are required to correct for refraction on multibeam depth readings due to changing sound speed within the water column. Local oceanographic conditions dictate how often the SVP measurement is required. At each SVP station, a Valeport Mini SVP was deployed by hand with rope concurrently with the sediment sampling (Figure 2.5). After being submerged at approximately 1 m below the sea surface for approximately 1 minute, the Valeport Mini SVP was lowered through the water column, and then raised back to the ship. The data was downloaded immediately using a serial connection to a dedicated laptop running the Valeport software. Using the SVP editor available in the multibeam acquisition software called Seafloor Information System (SIS), the data were examined and formatted to the required format and then applied to the SIS. The downcast data was always used.

Figure 2.5 The Valeport Mini SVP.

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3 Data summary

2

The study area, covering 698 km of seabed across water depths ranging from 3 to 51 m, was mapped using the multibeam sonar (Figure 3.1; Figure 3.2; Table 3.1). The final mapped area also included a patch of data 28 km west of Bathurst Island to investigate and map a potential unidentified shipwreck for the Northern Territory Department of Lands, Planning and the Environment Heritage Branch (Figure 3.3). Multibeam water column data were also collected over the entire surveyed area. A total of 102 Smith-McIntyre grabs, 104 underwater camera drops, 29 sub-bottom profile lines and 34 sound velocity profiles were collected during the survey (Table 3.1). A summary of the data collected and preliminary observations for each dataset are presented in this section.

3.1 Survey summary Table 3.1 Summary of data acquired during GA4452/SOL6432 survey. Data Type

Sample Total

Units

Multibeam

698

km

Smith McIntyre grab

102

no.

Underwater camera drops

104

no.

Sub-bottom profiles

112

km

Sound velocity profiles

34

no.

GPS tide

1

no.

2

3.2 Geophysical data 3.2.1 Multibeam echosounder Bathymetry The high-resolution bathymetry mapping revealed a seabed dominated by a large drowned braided river-valley, and (potential) lake with adjacent shoreline platforms (Figure 3.1; Figure 3.2). Along the western boundary of the outer harbour a large number of rocky reefs were mapped in detail. Depths in the survey area ranged from 3 m near the coast and offshore islands to up to 50 m in the deepest sections of the channel. While large parts of the mapped area and channel are exposed bedrock, unconsolidated sediment dominates other areas and is found in a variety of morphological features, including ripples, flat plains, sediment lobes, hummocks, furrows and various types of dunes. The interaction of strong tidal currents with river outflow and storm-generated currents has given rise to this diversity of sedimentary depositional features, examples of which are described below (Figure 3.2; Table 3.1).

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Figure 3.1 Hillshaded bathymetry gridded at 1 m resolution along with the location of the Smith-McIntyre grab sampling stations. For more information on grab locations see Appendix Table E.1

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Figure 3.2 Location of seabed features of interest identified from multibeam data and summarised in Table 3.2

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Table 3.2 Description and representative examples of seabed features identified from multibeam data. For the location of these representative examples see Figure 3.2. Name

Bathymetry

Backscatter

Representative Profile

Description

Channel

This channel morphology is characterised by generally enclosed, long and narrow bathymetric lows on the seafloor indicated by laterally converging contours of increasing depth and relatively steep flanks. Channels typically have a higher backscatter response as they are generally scoured features with finer/softer material being transported elsewhere.

Complex bedform

This morphology is characterised by widely spaced (600-750 m) large bedforms that are up to 2 m high. Smaller bedforms and dunes are superimposed on these larger features (15-30 m spacing, variable height but up to 2 m) The backscatter indicated that these bedforms are composed of coarser material than the surrounding seabed. The smaller bedforms are likely the consequence of tidal reworking of the underlying (relict) bedform features.

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Name

Bathymetry

Backscatter

Representative Profile

Description

Complex hardground

The broad shallow pits in the seabed are most likely solution hollows, and indicative of periods of subaerial exposure and erosion when sea-level was lower than the modern seabed, the most recent interval being either during the last glacial (18-23 ka BP), or slightly later (Lewis, et al., 2013).

Dune (sinuous)

This dune morphology is characterised by slightly asymmetric, sinuous, crests. The dunes have wave heights of 3-5 m and a period of 700-800 m. The slight asymmetry of these sandwaves suggests that the likely flow direction, for these dunes, at the seabed is from west to east. Backscatter values indicate that these dunes are composed of coarser material than the surrounding seafloor.

Dune (trochoidal)

This morphology is characterised by fields of dunes that are trochoidal in cross-section. Dunes are up to 5 m high and 100 - 350 m wavelength. Trochoidal dunes typically indicate bidirectional flow, with one direction slightly preferred to the other. The slight asymmetry of these dunes suggests that the flow direction, for these features, at the seabed is towards the south-southeast (i.e. inshore).

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Name

Bathymetry

Backscatter

Representative Profile

Description

Straightcrested Dunes with secondary ripples

This morphology is characterised by straight crested, slightly asymmetric transverse sandwaves. Crests are oriented east-west and are overprinted by rippled seabed. The slight asymmetry of sandwaves suggests that the dominant flow direction at the seabed is from southeast to northwest here (i.e. offshore). The large dunes would have formed in moderately high energy conditions, while the smaller ripples would form in lower energy environments.

Furrows with ripples

This morphology is characterised by linear, sub-parallel 20 m wide channels up to 1 m deep. The channels are up to 1.5 km in length. Backscatter values indicate that sediment within the channels is softer than the surrounding seabed. Commonly the base of the furrow has ripples present, aligned orthogonal to the channel axis. Ripples have wave heights of ~20 cm wavelengths of ~7 m.

Hummock

Numerous mounds are present on the seabed where sediment texture is gravellymuddy-Sand (gmS). The mounds commonly have diameters of 10-25 m, rising 15-45 cm above the surrounding seafloor. The distance between mounds is approximately 30 m or more, giving the seabed a dimpled appearance. Many mounds appear to have a linear to sub-linear crest, suggesting formation by traction. Backscatter values indicate that the mounds have a slightly weaker backscatter response than the surrounding seabed. These are probable storm deposits.

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Name

Bathymetry

Backscatter

Representative Profile

Description

Ledge (cf. small terraces)

This morphology is characterised by a flat or gently sloping area with a steep rise on one margin and a steep drop on another margin. The rise and drops are between 0.5-3 m in elevation difference. These features occur on hard seabed and possibly represent bedding planes, and/or different layers in the partly lithified sediment.

Plain

This morphology is largely flat and smooth with depth gradually increasing away from the present coastline. Despite having a simple morphology and appearance in the bathymetry, plains can have quite variable backscatter values (Figure 3.5) which likely indicates that some regions consist only of a thin sediment veneer while others are composed of thicker accumulations of sediment.

Reef

This morphology is characterised by exposed hard substrate, raised above the surrounding seabed. In this example the reef rises approximately 7-10 m above the adjacent and comparatively flat plain.

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Name

Bathymetry

Backscatter

Representative Profile

Description

Sandwaves

This morphology is characterised by slightly sinuous sandwaves with heights of 0.25-1 m and wavelengths of 10-15 m. The slight asymmetry of the sandwaves indicates a direction of sediment transport at this location, at the seabed, is from north to south (i.e. onshore).

Sandbank/S ediment lobe

This sandbank is up to 12 m thick, approximately 4 km long and oriented eastnorth east to south-southwest. The asymmetry of the sandbank, and the morphology of dunes on its surface indicates a direction of sediment transport at the seabed towards the west. Backscatter values indicate the middle of the sediment lobe appears composed of softer material than at its margin.

Weathered bedrock

At this location a very thin veneer of sediment overlies cemented or sedimentary rock, which has a distinctive surface typical of subaerial exposure and weathering. The most recent interval of time when significant weathering may have occurred here is the Last Glacial Maximum (last ice age, 18-23 ka BP) or intervals of time immediately before or after when sea levels were below the level of the seabed here (Lewis, et al., 2013). Backscatter values support this interpretation as do the presence of hummocks overlying the rugose morphology.

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Tiwi Wreck At 8:18 pm on 26 May 2016 the RV Solander mapped an unidentified wreck, referred to as the Tiwi wreck, at -11.7694° 129.7636° approximately 28 kilometres west of Bathurst Island (Figure 3.3a). Mapping was undertaken at the request of an officer at the Northern Territory Department of Land, Planning and Environment, who provided coordinates and a sidescan sonar image of a potential unidentified wreck. Mapping was completed by 9.56 pm, 2 May 2016. The wreck was mapped using both 300 kHz and 400 kHz frequency settings. The soundings were then converted, examined, manually cleaned and gridded at 30 cm resolution using Caris v8 software.

Figure 3.3 Unidentified wreck, referred to as the Tiwi wreck.

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The Tiwi wreck can be seen lying on its starboard side in 60-62- meters of water on generally flat and featureless seabed (Figure 3.3b and c). The wreck is 27 m long, 7.5 m wide and is shallowest at 58 m – rising ~5 m above the surrounding seafloor (Table 3.3). Off the port side in the middle of the wreck there is potential evidence of a mast, rigging or some other part of the vessel that has fallen off (Figure 3.3c). However, a lot of noise and ringing of soundings off the hull was noted (Figure 3.4) and this feature could just be produced by noisy soundings. The ringing soundings likely indicate the vessel is composed of a highly reflective material such as steel. Table 3.3 Summary characteristics of the Tiwi wreck. Length (m)

27

Width (m)

7.5

Shallowest point (m)

58

Deepest point (m)

63

Figure 3.4 Image of all soundings collected around the Tiwi Wreck. Ringing and noisy soundings are clearly visible. Noisy soundings were manually excluded from the final product (Figure 3.3).

Backscatter intensity Backscatter strength varies between seabed features (Table 3.2). High backscatter strength is typically associated with elevated features including reefs due to hard substrate, while low backscatter is associated with soft sediments e.g. within plains (Figure 3.5). Among the seabed features listed in Table 3.2 weathered bedrock and reef are among those having the highest backscatter values. Theoretically, backscatter strength increases with the sediment grain size. However, this was not always the case here. In some cases, the same grain sizes observed on the same plain (Table 3.2) are associated with low and high backscatter values (bimodal) (Figure 3.6).

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The difference in backscatter strength between areas with high backscatter values and areas with low backscatter values within the same plain along the profile line A-B (Table 3.2) is 4 dB (Figure 3.6). The higher backscatter values of the plain are at the same level of the backscatter value of the weathered bedrock (Figure 3.6). This suggests the presence of a sand veneer over cemented sediment or other harder seabed materials in the area. The complex bedform (Table 3.2) also has a bimodal distribution of backscatter values (Figure 3.6). The higher backscatter values of the complex bedform peak at -21.5 dB, associated with the dune crest whereas the lower backscatter values of the complex bedform peak at -31 dB, associated with flat areas between dunes. This difference may indicate the difference of grain size of the sediment between the dune crest and the areas in between. In addition, higher backscatter values of the complex bedform are comparable to the lower backscatter values of the plain (Figure 3.6). Many sandwave/dune type seabeds show a pattern of alternating high and low backscatter values which coincide with the crests and troughs. Some have troughs associated with higher backscatter values whereas crests associated with lower backscatter values. In contrast, others such as the one observed in the furrows with ripples (Figure 3.7) have troughs associated with lower backscatter values and crests associated with higher backscatter values. The hummock (Table 3.2) is another interesting morphological feature showing an interesting backscatter pattern associated with mounds and their surrounding seabed. The hummock is characterised by lots of rounded mounds (10-25 m in diameter) rising 15-45 cm above the surrounding seafloor. These rounded mounds have backscatter values about 0.25 to 1 dB lower than the surrounding (Figure 3.7).

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Figure 3.5 Hillshaded backscatter data gridded at 1 m resolution and the location of sub-bottom profiler (SBP) lines. For more information of SBP lines see Appendix D.

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0.35 Complex bedform Plain Weathered bedrock

0.3

-17.5 dB

Probability

0.25

0.2 -21 dB-17.5 dB

0.15

-31 dB

0.1

-21.5 dB

0.05

0 -50

-45

-40

-35

-30 -25 -20 Backscatter [dB]

-15

-10

-5

0

Figure 3.6 Histograms of complex bedform, plain and weathered bedrock along corresponding profile line A-B shown in Table 3.2.

A

B

Depth (m)

(A) -16

-18

-20

-22

0

100

200

300

400

500

600

0

100

200

300 Distance (m)

400

500

600

Backscatter (dB)

(B) -24

-26

-28

-30

Figure 3.7 (A) Water depth and (B) backscatter intensity for a cross section of furrows with ripples A-B (see Table 3.2 for location) showing a pattern of alternating high-low backscatter associated with crests and troughs.

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A

B

Depth (m)

(A) -13

-14

-15

-16

0

100

200

300

400

500

600

0

100

200

300 Distance (m)

400

500

600

Backscatter (dB)

(B) -16 -18 -20 -22 -24

Figure 3.8 (A) Water depth and (B) backscatter intensity for a cross section of hummock A-B (see Table 3.2 for location) showing mounds characterised by a subtly weaker backscatter response than the surrounding seabed.

3.2.2 Sub-bottom profiler Sub-bottom profiles reveal up to 20 m penetration and at least 7 distinct acoustic facies (Table 3.4). The facies characterise features such as bedforms (AF1), channel infills (AF3), sediment lobes (AF5), and anomalies such as, gas masking (AA1). Table 3.4 Representative examples and characteristics of the different acoustic facies observed in the sub-bottom profiler data. Acoustic Facies

Reflection Characteristics

AF1

Reflection-free facies with distinct continuous sharp top reflector and absence of bottom reflector

AF2

Reflection-free facies with distinct continuous sharp top reflector, and discontinuous, weak bottom reflector

28

Example

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Acoustic Facies

Reflection Characteristics

AF3

Sigmoidal and parallel reflections with distinct continuous sharp top reflector and often overlaying reflection free with diffractions facies. The facies infills depressions

AF4

Parallel and continuous reflections, in places, dipping and truncated by the distinct continuous sharp top. The facies drape the bottom reflector.

AF5

Discontinuous sigmoidal reflections with distinct continuous sharp top reflector and discontinuous bottom reflector

AF6

Discontinuous parallel reflections with distinct continuous sharp top reflector and discontinuous parallel bottom reflector

AA1

Acoustic anomaly masking the stratified facies AF4. The upper reflector bounding the mask area is strong and mainly continuous

Example

3.3 Physical Data 3.3.1 Sedimentology The sampled seabed sediment is composed of material similar to that of the adjacent Darwin Harbour (Siwabessy et al., 2015) with sand and gravel in Bynoe Harbour composed to a large degree of shell grit and iron-rich sediment grains. In particular, the iron-rich sediment grains commonly occur as nodules of coffee-coloured sedimentary rock ("Coffee rock"; cf. pisoliths, but without typical pisolitic banding). Coffee rock is pre-existing sediment that is commonly cemented by hydrated oxides of Fe and sometimes Al which originate from weathering of soils and/or igneous and metamorphic rock, giving coffee rock the dark brown colour. At least one sample of this lithology was recovered from an area of rugose seabed, either having been broken from either a much larger rock, or more likely broken off from in-situ bedrock.

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Of the samples analysed, thirty-six percent are composed of gravelly muddy Sand (gmS, having a sand to mud ratio ranging between 1 and 9, (Folk, 1980) (Figure 3.9). Most of the samples with gmS textures were recovered from the seabed where mounds are present, and indicate mixed sediment. Sixteen percent of samples have muddy sandy Gravel (msG) textures (gravel = 30-80 % of total). Of the remainder, five samples have a Mud (M) texture, and one sample is Sand (S). These data indicate that the sediments sampled are largely mixed, both in grain size and in composition. In general, Mud and mud-rich sediment appears to be primarily located away from rugose seabed and away from high energy shallower areas (Figure 3.10). If, as is the case onshore, that the underlying geology is exposed and partly consolidated at the seabed, it is likely that a small proportion of these samples may represent some in-situ lithologies. However most samples have textures that suggest mixed composition and size ranges, indicative of reworking. A single sample of iron-indurated sediment was retrieved from station 71, broken from either a larger piece of rock, or more probably from in-situ rock. This is the only gravel texture (G) in these samples.

Figure 3.9 Folk textural classes for samples recovered from Bynoe Harbour on a ternary diagram with separate symbols for each textural class. Sediment proportions based on weight percent are dominated by sand, with 5-50 % of the remainder of each sample composed of gravel.

Sampling stations with muddy sediment had a lower average backscatter value (-29.04 dB, n = 13) than either sand (-19.09 dB, n = 60) or gravel (-16.57 dB, n = 24). The range of backscatter values was found to overlap between sandy, muddy and gravelly sampling stations (Figure 3.11).

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Figure 3.10 Sediment textures derived from visual inspection of seabed samples from survey SOL6187. Samples are dominated by sand and mud, with five samples dominated by gravel. Sandy samples were generally recovered from seabed with prominent sedimentary structures; while mud dominated sediment was recovered seabed with low relief.

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Figure 3.11 Preliminary box plots of backscatter data for mud, sand and gravel-dominated sediments for survey station point locations (Figure 3.10). The red line indicates the median, values in the box indicate the first and third quartile, and the tails of the distribution indicate the minimum and maximum.

3.3.2 Geochemistry -2

-1

In this study, total oxygen uptake (TOU) rates were higher in Bynoe Harbour (-19.5 ±8.7 mmol m d ) -2 -1 than in Outer Darwin Harbour (-12.2 ±6.1 mmol m d ) (Siwabessy et al., 2016). There was a broad decline in TOU in a southwest to northwest direction although low rates were also observed in the innermost part of the Harbour (Figure 3.12).

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Figure 3.12 The spatial predictions of total oxygen uptake (TOU) using inverse distance squared (IDS). IDS was preferred than ordinary kriging (OK) because no reliable variogram could be produced for OK. The sites designated as "enhanced" had samples taken to calculate nutrient fluxes as well as TOU.

3.3.3 Biology 3.3.3.1 Underwater photography and video Seabed habitats and benthic macro-organisms were surveyed at 101 stations using underwater videos and still imagery. In total 2:49 hours of useful video was collected from 31 stations and 475 still images from 47 sites across water depths of 9m to 35m (Appendix G). Benthic habitats throughout the surveyed areas were broadly classified where possible, based on video and still imagery observations into three main categories (see Appendix G; Przeslawski et al., 2011; Carroll et al., 2012):

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1. Barren sediments: Sediment is flat with little evidence of infaunal (bioturbation) or epifaunal activity (20 individuals over the transect; up to 15 individuals per 15 seconds estimated over the course of the video). 3. Mixed patches (octocorals and sponges): Patchy rocky outcrops supporting locally abundant patches of octocorals and sponges (that occupy a proportion of at least 20% of the transect - up to 25 individuals per 15 seconds), interspersed with areas of soft sediment and low epifaunal cover. Rocky outcrops may be covered with a thin veneer of sediment; however, epibenthic growth of sessile organisms indicates that a hard substratum is present. Preliminary classifications of benthic habitats consist of predominantly barren habitats (12 stations), bioturbated habitats (11 stations), mixed patches (9 stations) and 69 stations which were unable to be classified. Observed benthic epifauna generally filter feeders from the subclass Octocorallia (sea whips, hydroids) and Tunicates (Stalked solitary ascidians), and Phylum porifera (sponges) (Figure 3.13). Only 32% of the sites were able to be broadly described and it is likely that some seabed habitats were not adequately represented due to turbidity and/or lack of lighting in deeper stations (Figure 3.14). The lack of useable video/images is caused by the fact that the video and stills were taken opportunistically, with no consideration for tidal, turbidity and light conditions. A more appropriately designed epibethic survey will be scheduled for the second half of 2017.

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Figure 3.13 Still underwater photographs showing benthic habitats (a-f). a) Mixed patches with occurrences of sponges and ascidians, SOL6452_074CAM074, b) Mixed patches with sponges and bioturbation, SOL6452_065CAM065, c) Bioturbated, SOL6452_005CAM005, d) Bioturbated, SOL6452_061CAM061, e) Barren muddy sandy Gravel sediment SOL6452_058CAM058, f) Barren muddy sand SOL6452_057CAM057.

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Figure 3.14 Benthic habitat classifications derived from underwater video and still imagery from survey SOL6452 (Appendix Table G.1).

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3.4 Oceanographic data 3.4.1 Tide The tidal model, described in Section 2.5.1, was run for the entire survey period to produce a network of tidal nodes for the tide elevation corrections required for the bathymetric survey. These modelled nodes are summarised in Table 3.5. Modelling showed some differences in tides between all nodes used in this survey (Figure 3.15). The amplitude and phase differences are observed in SW-NE direction, e.g. on 05/05/2016 20:24 the difference is 0.5 m in amplitude and 15.8 minutes in phase. Table 3.5 Modelled nodes for tidal elevation corrections. Node

Easting

Northing

Latitude

Longitude

12658

682910.4

8631014.8

-12.378513

130.682412

12823

671805.8

8634311.2

-12.349327

130.580121

12829

657107.9

8632462.2

-12.366793

130.445066

12491

643026.4

8632082.9

-12.370879

130.315588

12623

654405.5

8623880.5

-12.444505

130.420635

12621

660853.6

8623358.9

-12.448902

130.479975

12722

664504.3

8626440.8

-12.420856

130.513395

12572

668486.9

8622742.6

-12.45408

130.550223

12479

668866.3

8616484.1

-12.510635

130.55405

12397

664883.6

8614113.5

-12.532274

130.517533

12439

661043.2

8616436.8

-12.511469

130.482075

12485

650422.8

8618760

-12.490987

130.384245

12366

646866.9

8615583.4

-12.519871

130.351678

12180

650944.3

8601264.7

-12.649125

130.389893

12235

654689.9

8604583.7

-12.618939

130.424209

12234

657439.8

8604963

-12.615374

130.449502

12328

659288.9

8609656.8

-12.572849

130.466281

12204

660663.9

8602734.6

-12.635356

130.479294

12158

666400.8

8602592.3

-12.636344

130.532111

12227

666969.8

8608044.8

-12.587025

130.537054

12086

671047.3

8596665.7

-12.689668

130.57521

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4 3

Elevation (m)

2 1 0 -1 -2 -3 -4

125

130

135 Julian Day

140

145

Figure 3.15 Predicted tide at nodes given in Table 3.5.

3.4.2 Sound Velocity Profile (SVP) Thirty-four casts were conducted over the entire survey duration, (Table 2.1) with a subset of 23 applied in SIS during acquisition. Between 1 and 3 casts were conducted per day. The sound speed variation between all SVP casts is around 3 m/sec (Figure 3.16). Depending on the intermediate result during the post-processing process, sound velocity corrections using all available SVP data may or may not be re-applied.

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Sound speed [m/s] 1540 0

1541

1542

1543

1544

1545

1546

1547

1548

1549

1550

5

Depth [m]

10

15

20

25

30

35

Figure 3.16 All SVP data applied to the multibeam acquisition system during the survey.

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4 Summary and concluding remarks

The primary objectives of this survey were to characterise the seabed and associated biota in order to provide baseline information and underpin marine resource management decisions. The survey provided insight to the Bynoe Harbour region, where limited seabed information was previously 2 available. This marine survey mapped a total of 698 km using a high-resolution Kongsberg EM2040C multibeam echosounder in dual head configuration. The mapping included bathymetry, backscatter and water column data. Investigations at pre-defined waypoints were undertaken with physical and visual sampling (including underwater video and still, grab, tide gauge, and SVP) at a total of 102 stations. Key preliminary observations from the survey include: 

The seabed of Bynoe Harbour is characterised by a complex network of geomorphic features. Sandwaves and dunes observed in the area may help understand the hydrodynamic conditions of the area. Numerous complex hardgrounds located in mostly shallow waters provide support for benthic communities.



Gravelly muddy sand textures, indicating mixed composition, as well as particularly common in the gravel fraction, are dominant. At four stations mud was the sole component, all other samples consisted of gravel, sand and mud. At this stage, there is no obvious relationship between geomorphology and sediment texture.



Useable imagery from drop down cameras and video show that barren and bioturbated sediments dominate the area. However, in comparison to Darwin Harbour a larger number of mixed patches of suspension feeders (e.g. sponges, octorcorals, ascidians) were found in the survey area, which may reflect the more diverse habitats sampled within outer and inner Bynoe Harbour.



There was not a strong spatial pattern of total oxygen uptake, though the parameter declined approximately from west to east.



In areas where soft sediment is present at the seabed, sediment thickness reaches up to 20 m. Channel migration and gas masking are observed in the sub-surface throughout the area.

Integration of this newly acquired data with existing data will provide new insights into the geology and benthic habitat of the Bynoe Harbour area. This work will contribute to the Northern Territory Government’s Darwin Harbour Habitat Mapping Program by providing key seabed environmental and geological data and producing thematic habitat maps to underpin marine resource management decisions. Datasets, imagery, and related research products from this survey will be made available via the Geoscience Australia website (http://www.ga.gov.au/).

40

GA4452/SOL6432 – Post-survey report

Acknowledgements

The Bynoe Harbour Marine Survey was made possible through offset funds provided by INPEX-led Ichthys LNG Project to Northern Territory Government Department of Environment and Natural Resources (DENR), and co-investment from Geoscience Australia (GA) and Australian Institute of Marine Science (AIMS). The authors wish to thank the Master and crew of the RV Solander for the highly professional conduct of the survey. We also thank the Engineering and Applied Scientific Services (EASS) staff at GA for their logistical support and contributions, including Matt Carey, Craig Wintle and Andrew Hislop. Thanks to Matt Carey and Craig Wintle from the EASS for design of new core incubation set-up. We’d like to acknowledge those from the NT Government, AIMS and GA who were involved in the survey planning and advice during the survey. We would like to thank Dan Rawson from the Production and Promotions team for producing this record. We gratefully acknowledge Dr Rachel Przeslawski and Dr Stephanie McLennan at GA for their valuable reviews of this report. This record is published with the permission of the Chief Executive Officer of Geoscience Australia and the Australian Institute of Marine Science.

GA4452/SOL6432 – Post-survey report

41

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Pitcher CR, 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 GK. 2007a. Seabed Biodiversity on the Continental Shelf of the Great Barrier Reef World Heritage Area. CSIRO Marine Research, Cleveland, Qld, Auatralia. Pitcher CR, Haywood M, Hooper JNA, Coles R, Bartlett C, Browne M, Cannard T, Carini G, Carter A, Cheers S, Chetwynd D, Colefax A, Cook S, Davie P, Ellis N, Fellegara I, Forcey K, Furey M, Gledhill D, Hendriks P, Jacobsen I, Johnson J, Jones M, Last P, Marks S, McLeod I, Sheils J, Sheppard J, Smith G, Strickland C, Van der Geest C, Venables W, Wassenberg T, Yearsley GK. 2007b. Mapping and characterisation of key biotic and physical attributes of the Torres Strait ecosystem. CRC-TS task number: T2.1 Final Report. CSIRO Marine and Atmospheric Research, Cleveland, Qld 4163, Australia. Post AL. 2006. Physical Surrogates for Benthic Organisms in the Southern Gulf of Carpentaria, Australia: Testing and Application to the Northern Planning Area. Record 2006/009. Geoscience Australia, Canberra. Przeslawski R, Daniell J, Nichol S, Anderson T, Barrie JV. 2011. Seabed Habitats and Hazards of the Joseph Bonaparte Gulf and Timor Sea, Northern Australia. Record 2011/040. Geoscience Australia, Canberra. R Development Core Team. 2012. A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. Rattray A, Ierodiaconou D, Laurenson L, Burq S, Reston M. 2009. Hydro-acoustic remote sensing of benthic biological communities on the shallow South East Australian continental shelf. Estuarine, Coastal and Shelf Science 84: 237-245. Rattray A, Ierodiaconou D, Monk J, Versace VL, Laurenson LJB. 2013. Detecting patterns of change in benthic habitats by acoustic remote sensing. Marine Ecology Progress Series 477: 1-13. Tenore KR, Zajac RN, Terwin J, Andrade F, Blanton J, Boynton W, Carey D, Diaz R, Holland AF, López-Jamar E, Montagna P, Nichols F, Rosenberg R, Queiroga H, Sprung M, Whitlatch RB. 2006. Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach. Journal of Experimental Marine Biology and Ecology 330: 392-402. Saqab MM, Bourget J. 2015. Controls on the distribution and growth of isolated carbonate build-ups in the Timor Sea (NW Australia) during the Quaternary. Marine and Petroleum Geology, 62, 123-143. Siwabessy PJW, Tran M, Huang Z, Nichol SL, Atkinson I. 2015. Mapping and Classification of Darwin Harbour Seabed. Record 2015/018. Geoscience Australia, Canberra. http://dx.doi.org/10.11636/Record.2015.018 Walvoort, D.J. Brus, D.J.J., de Gruijter, J.J. 2015. Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata. R package version 0.3-6. http://CRAN.Rproject.org/package=spcosa. Williams D, Wolanski E, Spagnol S. 2006. Hydrodynamics of Darwin Harbour The Environment in Asia Pacific Harbours. Springer Netherlands, pp 461-476. Woodroffe C D, Bardsley KN, Ward PJ, Hanley JR. 1988. Production of mangrove litter in a macrotidal embayment, Darwin Harbour, N.T., Australia. Estuarine, Coastal and Shelf Science, 26, 581-598. Woodroffe C D, Grime D. 1999. Storm impact and evolution of a mangrove-fringed chenier plain, Shoal Bay, Darwin, Australia. Marine Geology, 159, 303-321. Woodroffe CD, Mulrennan ME, Chappell J. 1993. Estuarine infill and coastal progradation, southern van Diemen Gulf, northern Australia. Sedimentary Geology, 83, 257-275. Zajac RN. 2008. Macrobenthic biodiversity and sea floor landscape structure. Journal of Experimental Marine Biology and Ecology 366: 198-203

44

GA4452/SOL6432 – Post-survey report

Appendix A Scientific and technical crew

Appendix Table A.1 Role and affiliation of personnel on leg 1 of survey GA4452/SOL6432, 3–15 May 2015. Name

Principal Role

Agency

Responsibility

David Williams

AIMS voyage leader, Oceanographer

AIMS

AIMS voyage leader, tide gauge and other oceanographic device operations, and multibeam acquisition support

Neil Smit

NT Government scientist, Marine ecologist

DENR

NT Gov. science representative, sediment sample acquisition, benthic ecology sampling, underwater camera operations and shipboard database

Justy Siwabessy

GA chief Scientist, Seabed acoustician

GA

Science leader, multibeam acquisition support, processing, data management and GA daily report

Lynda Radke

Geochemist

GA

Geochemical sample acquisition and analysis, and shipboard database

Ian Atkinson

Senior multibeam specialist

GA

Multibeam operations and all technical support

Nick Dando

Multibeam Specialist

GA

Multibeam operations and all technical support

Kim Picard

Seabed acoustician

GA

Multibeam operations and all technical support, sub-bottom profile operations

Appendix Table A.2 Role and affiliation of personnel on leg 2 of survey GA4452/SOL6432, 16–28 May 2016. Name

Principal Role

Agency

Responsibility

Simon Harries

AIMS voyage leader

AIMS

AIMS voyage leader, Multibeam acquisition support

Neil Smit

NT Government scientist, Marine ecologist

DENR

NT Gov. science representative, sediment sample acquisition, benthic ecology sampling, underwater camera operations and shipboard database

Justy Siwabessy

GA chief Scientist, Seabed acoustician

GA

Science leader, multibeam acquisition support, processing, data management and GA daily report

Lynda Radke

GA Geochemist

GA

Geochemical sample acquisition and analysis, and shipboard database

Nick Dando

Multibeam Specialist

GA

Multibeam operations and all technical support

Floyd Howard

Multibeam processor

GA

Multibeam acquisition support and processing

GA4452/SOL6432 – Post-survey report

45

Appendix B Spatial coordinates of waypoints used to guide station selection

Appendix Table B.1 The spatial coordinates of 200 waypoints. The coordinate system is UTM Zone 52 South. No.

Easting

Northing

No.

Easting

Northing

1

637421

8615470

101

654479

8626117

2

637517

8626068

102

654777

8604287

3

637759

8616098

103

654903

8629570

4

638151

8620694

104

654964

8620050

5

638868

8616121

105

654997

8606453

6

638926

8623510

106

655034

8635832

7

639034

8615385

107

655139

8628108

8

639106

8610712

108

655714

8633048

9

639203

8607292

109

655983

8627802

10

639240

8611235

110

656008

8631179

11

639456

8618321

111

656081

8634261

12

639497

8628378

112

656212

8608734

13

639548

8613472

113

656484

8624659

14

639710

8626090

114

656754

8626524

15

640175

8630992

115

656818

8631412

16

640212

8612669

116

657296

8623950

17

640291

8620022

117

657615

8606737

18

640592

8614769

118

657846

8634961

19

640608

8634500

119

658120

8633897

20

640653

8619782

120

658140

8623920

21

640719

8628629

121

658324

8622206

22

640817

8607902

122

658632

8608899

23

640863

8623149

123

658941

8631094

24

640880

8636741

124

659096

8619211

25

641108

8635210

125

659115

8620010

26

641202

8627715

126

659195

8610428

27

641443

8622818

127

659310

8616618

28

641496

8629245

128

659767

8623004

29

641715

8613225

129

659928

8625231

30

641839

8621788

130

659941

8627418

31

641853

8625271

131

660083

8608936

32

641899

8635897

132

660143

8625378

46

GA4452/SOL6432 – Post-survey report

No.

Easting

Northing

No.

Easting

Northing

33

642041

8604395

133

660215

8613787

34

642153

8632574

134

660229

8602513

35

642229

8632405

135

660283

8635176

36

642249

8631429

136

660409

8618798

37

642537

8621431

137

660655

8604008

38

642782

8630585

138

661072

8628866

39

642917

8634698

139

661133

8617946

40

642926

8602326

140

661388

8636679

41

643302

8603309

141

661445

8629171

42

643828

8633863

142

661638

8632887

43

644119

8626913

143

661693

8632346

44

644185

8601743

144

661739

8611264

45

644285

8628668

145

661781

8627600

46

644427

8636077

146

661822

8602466

47

644473

8630075

147

662062

8615844

48

644800

8626126

148

662159

8615346

49

644938

8625145

149

663302

8619042

50

645009

8624691

150

663394

8635694

51

645135

8623366

151

663645

8619156

52

645240

8631125

152

663684

8619473

53

645569

8629657

153

663739

8624152

54

645774

8613544

154

664142

8628120

55

646014

8616396

155

664248

8624958

56

646140

8629257

156

664574

8629210

57

646166

8627338

157

664610

8616235

58

646284

8614387

158

664773

8615500

59

646476

8632460

159

664773

8634330

60

646483

8617441

160

664826

8631052

61

646537

8619063

161

664920

8632164

62

646648

8624028

162

664963

8635803

63

646701

8635148

163

665008

8597497

64

646823

8621647

164

665190

8612203

65

647039

8617135

165

665222

8615196

66

647094

8626715

166

665880

8609298

67

647362

8625926

167

666134

8602554

68

647533

8621637

168

666331

8607011

69

647667

8627168

169

666420

8623121

70

647721

8628612

170

666492

8634596

GA4452/SOL6432 – Post-survey report

47

No.

Easting

Northing

No.

Easting

Northing

71

647772

8620569

171

666816

8609666

72

647795

8616217

172

667116

8635039

73

647806

8631731

173

667162

8634943

74

647919

8627450

174

667377

8610932

75

648660

8622946

175

667717

8611133

76

648676

8616632

176

668156

8623293

77

648723

8634107

177

668310

8600025

78

648740

8622779

178

668362

8630911

79

648981

8623763

179

668385

8611159

80

648993

8623011

180

668496

8614909

81

649259

8600208

181

668538

8607897

82

649858

8636035

182

668651

8625127

83

650701

8636299

183

668702

8620430

84

650822

8634715

184

668828

8623541

85

650872

8632959

185

668849

8615277

86

650932

8621406

186

668927

8598817

87

651157

8597137

187

668932

8616978

88

651470

8631553

188

669060

8623213

89

651846

8628256

189

669584

8619239

90

652117

8624726

190

669765

8621130

91

652286

8635233

191

669818

8623178

92

652298

8602728

192

669825

8619776

93

652722

8632509

193

670164

8617902

94

653213

8603139

194

673393

8632317

95

653245

8625005

195

673593

8631352

96

653733

8630316

196

674392

8631169

97

653997

8634632

197

674623

8595658

98

654005

8622057

198

675903

8595246

99

654026

8602974

199

677246

8596081

100

654112

8627451

200

678991

8595699

48

GA4452/SOL6432 – Post-survey report

Appendix C Technical report on multibeam sonar operations

C.1 Introduction C.1.1 System overview Vessel – The survey was conducted on the Australian Institute of Marine Science Vessel RV Solander. The RV Solander is 35 m long and equipped with a moon pool through which the multibeam sonar heads could be raised and lowered on a mounting system. Multibeam unit - The multibeam sonar was a dual head Konsberg EM 2040C with a frequency range of 200 - 400kHz. Multibeam data was acquired at 300 kHz for comparison with the inner harbour survey backscatter data. Outer beams (> 70°) on the port head were detrimentally affected by the ship’s echo sounder (over various frequencies) which was turned off for all multibeam collection. Motion referencing unit - Applanix PosMV 320 V5 using the integrated Marinestar (a.k.a Omnistar) correction for GPS and GLONASS navigation systems. Sound Velocity Profiler – Sound velocities were measured using a Valeport Mini SVS at the sonar heads to aid in beam forming, and profile casts using a Valeport Mini SVP (sound velocity profiler) which was battery powered and deployed on rope. Locations of the casts are presented in Appendix Table B.2 below. Time and position All times are UTC. 1PPS from the PosMV V5 was used to sync the Mutlibeam Sonar. All data acquisition PC’s were also synchronised to UTC. All positions are derived from the Global Navigational Satellite System and referenced to the World Geodetic System 1984 (WGS84)

C.2 Technical Notes C.2.1 Multibeam System Components C.2.1.1 Dual sonar head Transducers with Dual CBMF Card slimline PU EM2040C Port Head Serial No: 1106 EM2040C Starboard Head Serial No: 1338 Looking up angle set during operation varied between 75-83°. "Auto" coverage mode was used with maximum swath width in metres or degrees, in an attempt to keep to keep swath widths consistent. EM2040C heads were run in high density equidistant mode, 400 beams per head (800 total). The Ping rate varied between 7-14Hz.

GA4452/SOL6432 – Post-survey report

49

Seafloor Information Software (SIS) system display, control and logging: 4.3.0 Processing Unit and sonar head software versions as follows: PU - serial 1106: 

CPU: 2.1.7 151119DDS: 4.60 140106DSV: 3.1.8 141125VxWorks 6.9 SMP Build 1.09.01 Nov 23 2015 13:05:13CBMF: 1.08 13.09.18

Sonar Head (Port) - serial 1106 

TX: 1.01 Feb 3 2014 RX: 1.00 Sep 28 2012

Sonar Head (Stb) - serial 1338 

TX: 1.01 Feb 3 2014 RX: 1.00 Sep 28 2012

Installation Components of the multibeam (Sonar Heads, IMU, GNSS antennas) were installed in their specified mounting locations. The offset between the measurement points of the components was calculated using results from a vessel survey conducted in July 2014. The sonar heads were installed on GA’s dual head 40° mounting system on the moon pool trolley and lowered into place. A stern facing Valeport sound velocity sensor is mounted immediately above the plates to provide real time sound velocity for beam-forming accuracy. The system was setup in a moon pool on a trolley system and winched down the moon pool shaft and locked into position; the locked position being precise, extremely rigid and secure. The IMU was installed with a mounting plate on a stainless plate forward and above the moon pool well. The primary (port) and secondary (starboard) antennas for the PosMV System were installed on dedicated brackets on the rigid awning on the roof deck. Antenna and equipment cables were routed from these locations to the Dry lab were the PU, PosMV, HWS and networking equipment are located. Offsets to the measurement centres of the GNSS antennas, IMU and Sonar heads are entered into the PosMV system, which provides positioning values to SIS/PU at midpoints between the sonar heads. Roll, pitch and yaw angular offsets calculated from installation and calibration are entered into the Kongsberg SIS software.

C.2.1.2 Motion Referencing System: Applanix PosMV 320 V5 using the integrated Marinestar (a.k.a. OmniStar) correction for GPS and GLONASS positioning systems: 

Inertial Measurement Unit (IMU) 



50

Model: IMU type 27 200Hz

Processing unit; incorporating two GNSS receivers connected to two separate Applanix system GNSS antennas with a 2 m spacing. 

GNSS boards BD982, v.00490, Omnistar license 1487797



Model: MV V5



Serial: 5810

GA4452/SOL6432 – Post-survey report

 

Firmware: POS MV320 V5 8.46

Manufacturers Specifications: 

Roll, Pitch accuracy:



Heave accuracy:



Heading accuracy:



Position accuracy: