Rule-based semi-automated tools for mapping seabed morphology from bathymetry data

Seabed morphology maps and data are critical for knowledge-building and best practice management of marine environments. To facilitate objective and repeatable production of these maps, we have developed a number of semi-automated, rule-based GIS tools (Geoscience Australia’s Semi-automated Morphological Mapping Tools - GA-SaMMT) to operationalise the mapping of a common set of bathymetric high and bathymetric low seabed Morphological Features. The tools have a graphical user interface and were developed using Python scripts under the widely-adopted proprietary ArcGIS Pro platform. The utility of these tools was tested across nine case study areas that represent a diverse range of complex bathymetric and physiographic settings. Overall, the mapping results are found to be more consistent than manual mapping and allow for capture of greater detail across a range of spatial scales. The mapping results demonstrate a number of advantages of GA-SaMMT, including: 1) requirement of only a bathymetry grid as sole data input; 2) flexibility to apply domain knowledge to user-defined tool parameters, or to instead use the default parameter settings; 3) repeatability and consistency in the mapping outputs when using a consistent set of tool parameters (user defined or default); 4) high-degree of objectivity; and 5) efficiency in mapping a large number (thousands) of seabed morphology features in a single dataset. In addition, GA-SaMMT can comprehensively quantify the characteristics of individual seabed bathymetric high and low features, respectively generating 34 and 46 metrics for each type of feature. Our results indicate that attribute metrics are invaluable in the interpretation and modelling of mapped Morphology Features and provide insights into their formative processes and habitat potential for marine communities

Spatial and temporal evolution and internal sedimentary architecture of Holocene Halimeda bioherms; northern Great Barrier Reef

This research investigates the initiation and growth of Holocene Halimeda algal limestone build-ups in the Great Barrier Reef. Legacy sediment samples and newly acquired analytical data were combined to explain inter-reef Halimeda bioherm origins, temporal growth and development, spatial distribution, geomorphology, carbonate volume, nutrient source, and habitat significance. Halimeda bioherms are much more complex than previously thought. The project contributes a significant new understanding of the Halimeda bioherm geological and ecological system in space and time, elevating the importance of Halimeda bioherms as Holocene sedimentary archives and modern inter-reef benthic habitats

Tracing nitrate sources using the isotopic composition of skeletal-bound organic matter from the calcareous green algae Halimeda

The nitrogen (N) isotopic composition (δ15N) of water column nitrate (NO3−) reveals important information about the source(s) of N, and/or the transformation processes occurring during N transport, to a particular environment. However the physical collection of samples for δ15N–NO3− determination can be logistically challenging and does not address questions about historical δ15N–NO3−. Here we adapt the persulphate/denitrifier protocol, previously developed for scleractinian corals, to analyse the δ15N of organic material in the skeletons of the calcareous macroalgae Halimeda (hereafter referred to as δ15N-SOM). Using the newly established protocol, we show that the Halimeda δ15N-SOM can be used as a proxy for the δ15N of water column NO3−. Based on aquarium and field measurements we show that the maximum offset between the Halimeda δ15N-SOM and the δ15N of water column NO3−, as a result of fractionation during uptake, is 1‰. However this was only tested at low NO3− concentrations (−1). Our results demonstrate that in low-nutrient environments, Halimeda skeletal material, including historical material obtained from sediment cores, can provide a reliable proxy record of δ15N–NO3− at the base of the food web. This technique holds much promise for reconstructing spatial and temporal patterns of N supply to coral reef systems worldwide

Making Sense of the Great Barrier Reef's Mysterious Green Donuts

On the outer shelf of Australia’s Great Barrier Reef (GBR), under 20–50 meters of water, lies a broad expanse of giant green “donuts.” These seafloor circles, each several hundred meters across, aren’t the result of a rogue offshore baking experiment. Rather, they consist of the remnants of countless generations of green calcareous algae from the Halimeda genus. The green color comes from the current generation of Halimeda living atop these bioherms, as scientists call this type of mounded deposit with a sunken center.The actively accumulating Halimeda bioherms on the northern GBR shelf cover more than 6,000 square kilometers and are the most extensive of such deposits in the world [Whiteway et al., 2013; McNeil et al., 2016]. These globally significant bioherms have complex morphologies that are not yet explained, and compared with the adjacent coral reef systems, little is known about the fundamental processes that control their distribution anddevelopment. Much also remains unknown about the biogeochemical cycling associated with the bioherms, their role as key habitats for benthic (bottom-dwelling) species between the coral reefs and the Australian coast, and how they may be affected by climate change. In August and September 2022, we were part of a multidisciplinary team of scientists that set out on a research voyage on Australia’s R/V Investigator to better understand these enigmatic structures by mapping and sampling them in breathtaking detail. The mission of Project HALO (Halimeda Bioherm Origins, Function and Fate) was to illuminate how the bioherms formed over the past 12,000 or so years (i.e., the Holocene) and their importance in biogeochemical nutrient cycling and as modern habitats amid one of Earth’s most critical but vulnerable biodiversity hot spots

Variations in Mid- to Late Holocene Nitrogen Supply to Northern Great Barrier Reef Halimeda Macroalgal Bioherms

The northern Great Barrier Reef (GBR) Halimeda bioherms have accumulated on the outer continental shelf from calcium carbonate algal sediments over the past ∼10,000 years and cover >6,000 km2 of shelf area. As such, Halimeda bioherms play a key role in the shallow marine carbon cycle over millennial timescales. The main source of nitrogen (N) to these bioherms is thought to be westward transport of upwelled NO3--rich water from the Coral Sea. However, the primary N source has not been traced geochemically, and we have no understanding of any temporal variation. Here, we reconstruct patterns of N supply to Halimeda bioherms in the GBR since the mid-Holocene using the 15N/14N ratio of skeletal-bound organic N (δ15N-skeletal organic material [SOM]) in modern and fossil Halimeda sediment cores. Average Halimeda skeletal δ15N-SOM was 6.28 ± 0.26‰, consistent with δ15N-NO3- from western tropical South Pacific (WTSP) thermocline waters. Thus, geochemically validating shelf-break upwelling of an oceanic N source that regulates bioherm spatial distribution. Halimeda δ15N-SOM decreased by 1‰–2‰ from 5,000 to 2,000 cal. yr BP, reaching a minima of 5.5‰ that persisted for almost 1,000 years. The Halimeda δ15N-SOM variation reflects mid- to late Holocene changes in regional climate and intensified El Niño activity that likely facilitated elevated N2 fixation in the WTSP, thereby lowering thermocline δ15N-NO3-. Thus, Halimeda skeletal material provides a valuable high-resolution geochemical archive of past oceanographic and climatic processes over centennial to millennial timescales, complementing existing paleoclimate proxy records.</p

Age determination of Halimeda bioherm sediment deposits from the Great Barrier Reef, Australia, using 14C AMS from cores collected in 1983

The inter-reef Halimeda bioherms of the northern Great Barrier Reef (GBR) have accumulated up to 25 m of positive relief throughout the Holocene. Covering > 6000 km2, the Halimeda bioherms represent a significant contribution to the development of the northeast Australian continental shelf geomorphology, neritic carbonate factory, and sedimentary archive of post-glacial environmental changes. Previously, the chronological record of initiation and development of the Halimeda bioherm carbonate factory was poorly constrained and based on very few age data points. A comprehensive new age dataset is presented, comprising sixty-three AMS radiocarbon measurements of Halimeda and foraminifera grains, mollusc shells and bulk soil from twelve inter-reef sediment cores, and ten previously published Halimeda ages that are newly calibrated. Radiocarbon measurements were undertaken at the ANSTO Centre for Accelerator Science in 2018, 2019 and 2020 from cores collected by the Bureau of Mineral Resources in 1983. Halimeda growth had established by 11,143 +237/-277 cal. yr BP, just ~450 years after the marine transgression commenced and approximately 1000 years earlier than previous inferred estimates. The outer-shelf carbonate factory was initially dominated by benthic foraminifera, then Halimeda was productive for at least 2100 years prior to the turn-on of Holocene coral reefs in the study area. Inter-reef Halimeda bioherm sediments including foraminiferal communities, might record a >10,000-year near-continuous geochemical record of northeast Australian Holocene oceanographic and climatic changes, potentially filling spatial and temporal gaps not covered by coral and other marine sediment proxies

Evolution of the inter-reef Halimeda carbonate factory in response to Holocene sea-level and environmental change in the Great Barrier Reef

The inter-reef Halimeda bioherms of the northern Great Barrier Reef (GBR) have accumulated up to 25 m of positive relief and up to four times greater volume of calcium carbonate sediment than the nearby coral reefs during the Holocene. Covering >6000 km2, the Halimeda bioherms represent a significant contribution to the development of the northeast Australian continental shelf geomorphology, neritic carbonate factory, and sedimentary archive of post-glacial environmental changes. However, the geochronological record of initiation and development of the Halimeda bioherm carbonate factory was poorly constrained and based on very few datapoints. A comprehensive age dataset is presented, comprising sixty-three new AMS radiocarbon measurements of Halimeda and foraminifera grains, mollusc shells and bulk soil from twelve inter-reef sediment cores, and ten previously published Halimeda ages. Facies transitions and environmental changes are recorded from lithological and palynological analyses spanning Last Interglacial Halimeda deposits, Last Glacial Maximum terrestrial palaeosols, transgressive mangrove vegetated shorelines, and the turn-on of the Halimeda bioherm carbonate factory. Mangrove pollen and coral records from the study area provide additional spatial, temporal and environmental context.Halimeda had established by 11.1 cal kyr BP, just 450 years after transgressive shelf inundation and approximately 1000 years earlier than previous inferred estimates. The outer-shelf carbonate factory was initially dominated by benthic foraminifera, then Halimeda was productive for at least 2100 years prior to the turn-on of Holocene coral reefs in the study area at 8.9 cal kyr BP from Boulder Reef (15.4°S, 145.4°E). Inter-reef Halimeda bioherms play a major role in carbon and nutrient cycling and potentially preserve a near-continuous geochemical record of northeast Australian Holocene oceanographic and climatic changes, filling spatial and temporal gaps not covered by coral and other marine sediment proxies.</p

New constraints on the spatial distribution and morphology of the Halimeda bioherms of the Great Barrier Reef, Australia

Halimeda bioherms occur as extensive geological structures on the northern Great Barrier Reef (GBR), Australia. We present the most complete, high-resolution spatial mapping of the northern GBR Halimeda bioherms, based on new airborne lidar and multibeam echosounder bathymetry data.\ud \ud Our analysis reveals that bioherm morphology does not conform to the previous model of parallel ridges and troughs, but is far more complex than previously thought. We define and describe three morphological sub-types: reticulate, annulate, and undulate, which are distributed in a cross-shelf pattern of reduced complexity from east to west.\ud \ud The northern GBR bioherms cover an area of 6095 km², three times larger than the original estimate, exceeding the area and volume of calcium carbonate in the adjacent modern shelf-edge barrier reefs. We have mapped a 1740 km² bioherm complex north of Raine Island in the Cape York region not previously recorded, extending the northern limit by more than 1° of latitude.\ud \ud Bioherm formation and distribution are controlled by a complex interaction of outer-shelf geometry, regional and local currents, coupled with the morphology and depth of continental slope submarine canyons determining the delivery of cool, nutrient-rich water upwelling through inter-reef passages.\ud \ud Distribution and mapping of Halimeda bioherms in relation to Great Barrier Reef Marine Park Authority bioregion classifications and management zones are inconsistent and currently poorly defined due to a lack of high-resolution data not available until now.\ud \ud These new estimates of bioherm spatial distribution and morphology have implications for understanding the role these geological features play as structurally complex and productive inter-reef habitats, and as calcium carbonate sinks which record a complete history of the Holocene post-glacial marine transgression in the northern GBR

The first in situ observation of the Ram's horn squid Spirula spirula turns 'common knowledge' upside down

[Excerpt] The ram's horn squid Spirula spirula (Linnaeus, 1758) is the only extant cephalopod with an internal calcareous, chambered shell that is coiled, making it the sole living representative of the once speciose order Spirulida. As also supposed for its Cenozoic and Cretaceous ancestors, the function of the septate, many-chambered shell of Spirula has been considered as primarily for buoyancy. Behavioral observations of this species have been confined to those made in aquaria involving freshly net-caught specimens. Invariably, during those aquaria observations, the posterior end containing the open planispiral shell pointed towards the top of the tank, while the upward-oriented terminal fins moved with a rapid "waving or fluttering motion", presumably attempting to keep the animal submerged. A large photophore is present between the two fins on the posterior end of the body, and this has been observed to emit a "pale, yellowish-green light" that can glow "uninterruptedly for hours". We report here the first in situ observations of S. spirula in its natural habitat, illustrating the importance of such observations for a correct understanding of the ecology of deep-water organisms