Close-up view of bright green algae fronds
On the outer shelf of Australia’s Great Barrier Reef (GBR), meadows of live Halimeda algae provide a green coating over donut-shaped carbonate rock deposits left by generations of their predecessors. Credit: Mardi McNeil

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 and development. 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.

Bringing Bioherms into Focus

The presence of the GBR’s Halimeda bioherms has been known since the 1970s–1980s [Orme et al., 1978], but little work has been undertaken to study them until the past 5 years. Lidar bathymetry data have revealed extensive areas of unusual donut- and honeycomb-like morphologies on the seafloor in the lee of the barrier coral reefs in the northern GBR [McNeil et al., 2016]. This mysterious seafloor topography corresponds to vast buildups of Halimeda-derived sediment and living Halimeda meadows that have been interpreted as active analogues of ancient algal bioherms [Braga et al., 1996].

The high-resolution digital elevation models derived from the data collected reveal spectacular bioherm shapes and patterns not previously visible.

However, even the latest 25-meter-resolution lidar data were insufficient to reveal the bioherms in the detail required to more fully understand them [McNeil et al., 2021b]. For the 2022 survey, R/V Investigator’s state-of-the-art retractable drop keel, which is lowered beneath the ship’s hull, was mounted with a 200- to 400-kilohertz multibeam echo sounder capable of mapping shallow seafloor features to submeter resolution. The high-resolution digital elevation models derived from the data collected reveal spectacular bioherm shapes and patterns not previously visible. The echo sounder simultaneously collected acoustic backscatter data, which indicate seafloor texture and composition, yielding clues about the nature of the bioherms’ benthic habitats.

During the survey, we systematically mapped three bioherm sites and one nonbioherm site distributed across 2.5° of latitude (435 kilometers) in the northern GBR, acquiring 58 square kilometers of new multibeam coverage at 50-centimeter grid resolution (Figure 1). The effort marked the first time these interreef sections of the Great Barrier Reef Marine Park have been mapped to this level of detail, and it represents a significant advance in visualizing the complex geomorphology that forms the substrate of this unique region of seafloor.

Regional map showing locations of Halimeda bioherms amid the Great Barrier Reef off Australia, with three inset images showing seafloor topography at three bioherm sites
Fig. 1. (a) The distribution of Halimeda bioherms along the northern GBR is indicated in green in this regional map. (b)–(d) Representative 3D images based on newly collected bathymetry data display the complex bioherm morphologies at three main study sites. The black rectangle in Figure 1c represents the area shown in Figure 2. Abbreviation: mbsl = meters below sea level.

The Anatomy of a Donut

Systematic bathymetry mapping was combined with the simultaneous collection of 507 linear kilometers of acoustic subbottom profiles. These dense grids of subbottom profiles, which reveal sediment layers up to 30–40 meters below the seafloor, will allow a 3D reconstruction of the geologic foundations upon which these bioherm features are growing, their internal structure, and their relationship to their complex surface geomorphic expression (Figure 2).

Perspective view showing seafloor topography at a bioherm site, as well as a cross section of sediment layering below the surface
Fig. 2. High-resolution bathymetry and subbottom imagery of sediment layers below the seafloor, combined with precisely targeted vibrocores (red lines), reveal the 4D anatomy and evolution of the Halimeda bioherms. Patterns of steeply dipping and truncated layers as well as outcroppings at the seabed indicate the bioherms’ complex internal architecture. Credit: Victorien Paumard and Carra Williams

To study the bioherms’ internal structure and makeup more closely, we recovered 6-meter-long sediment cores along precisely targeted transects across the bioherms using a vibrocoring system. Many of the donut hollows held encrusted rocky outcrops resembling patches of reef, and these were dredged to recover surface geology and biology samples.

Early observations of the sediment cores and dredge samples have revealed diverse textures and compositions, including possible paleomangrove muds, cemented grainstones, and fossil reef deposits. More detailed analyses of sedimentary facies, together with radiocarbon dating and the marine geophysical data collected, will allow us to reconstruct the 4D development of the bioherms and provide important information about paleoenvironmental and paleoceanographic changes through the Holocene.

Hot Spots of Biodiversity

Recent research established that the bioherms host distinct biologic communities and are hot spots of biodiversity relative to adjacent interreef areas not associated with bioherms.

Recent research established that the bioherms host distinct biologic communities and are hot spots of biodiversity relative to adjacent interreef areas not associated with bioherms [McNeil et al., 2021a]. However, this earlier work was based on legacy data collected without an understanding of the geomorphic complexity of the bioherms; thus, key features of the bioherms may have gone unsampled. Guided by our new high-resolution mapping, we could sample the bioherms’ biota systematically, using precisely targeted drop camera imagery, sediment grabs, box cores, and multicores to characterize these benthic habitats.

We collected more than 1,000 biological specimens from the surface Halimeda meadows and sediments, which support a trove of epifaunal (surface-dwelling) and infaunal (burrowing) invertebrates (Figure 3). A great diversity of marine annelid worms called polychaetes made up most of the infauna collected. On the bioherm surfaces, nestled among Halimeda fronds, were juvenile sea urchins and brittle stars, indicating that this area is an important recruitment and nursery habitat for these animals. The juvenile sea urchins included Tripneustes gratilla and Echinometra species, which are ecologically important algal grazers on coral reefs and excavators of reef structure. The brittle stars included Ophionereis, Ophiocoma, and Ophiothrix species, which are among the most abundant tropical marine invertebrates. Small sea stars in the family Asterinidae were also observed and are likely undescribed species.

Multipanel image showing various invertebrates that inhabit Halimeda bioherms, such as urchins, sea stars, nudibranchs
Fig. 3. A diverse collection of invertebrates such as urchins, sea stars, nudibranchs, and others inhabits the Halimeda bioherms. The presence of abundant juvenile invertebrates suggests that the bioherms are important nursery habitats. Credit: Matthew Clements, Stefano Borghi, Monique Webb, and Maria Byrne

Populations of the solitary coral Heteropsammia cochlea were a conspicuous feature of the Halimeda habitat. These unusual “walking corals” provide habitat for crabs and worms that move the coral around and keep its surface free of sediment. From drop camera images at 40-meter depth, our team observed the bêche-de-mer sea cucumber (Holothuria fuscogilva), which is listed as highly endangered by the Convention on International Trade in Endangered Species. We also saw the crown-of-thorns sea star (Acanthaster sp.). The crown-of-thorns is the most important coral predator, and when its populations increase, it can have devastating impacts on coral reef functional and species diversity [Deaker and Byrne, 2022].

How Halimeda Bioherms Are Fed

The Coral Sea is an oligotrophic (low-nutrient) region, which favors the presence of the tropical corals forming the GBR. However, Halimeda needs abundant nutrients to thrive, especially to construct these large bioherms [Wolanski et al., 1988]. Previous work in the central GBR has suggested that during summer, nutrients upwell from the subsurface layers (~150-meter depth) of the Coral Sea and flow through interreef passages onto the shelf, possibly providing a source of nutrients for the Halimeda [Benthuysen et al., 2016; Wolanski et al., 1988]. But what about in winter?

The 2022 Project HALO cruise collected detailed oceanographic and nutrient data for the first time from three areas of Halimeda bioherms in the northern GBR, as well as from a shelf site with no bioherms. The preliminary data suggested that in August (late austral winter), nutrient levels overlying the bioherms are very low, which would indicate that there is no external source of nutrients at this time of year. We also collected live Halimeda and underlying sediments with a multicorer to conduct light/dark incubation experiments (Figure 4). Preliminary evidence of elevated nutrient levels in the incubation experiments suggested that nutrient recycling from sediments may maintain the Halimeda in the absence of external nutrient influxes during austral winter.

Three-panel image showing (top left) algae on the seafloor and (bottom left and right) scenes from laboratory incubation experiments
Fig. 4. Halimeda algae are seen here (a) living on the bioherm seafloor and (b) and (c) in multicore incubation experiments conducted to understand geochemical cycling. Credit: Figure 4a, CSIRO, CC BY 3.0; Figures 4b and 4c, Helen Bostock

The sediments from the multicores and water samples collected from the incubation experiments are currently being analyzed to better understand the sources and sinks of the various geochemical fluxes (nitrogen, carbon, and oxygen) and their influence on Halimeda productivity, bioherm development, and the adjacent coral reefs.

Seascapes of the Great Barrier Reef

A crucial unanswered question about the bioherms is why they do not form in a 130-kilometer-long section in the middle of their vast distribution.

A crucial unanswered question about the bioherms is why they do not form in a 130-kilometer-long section in the middle of their vast distribution (Figure 1). An important component of the recent survey was to investigate and compare conditions at adjacent seascapes: interreef passages, paleochannels, and offshore submarine canyons that connect the shallow GBR shelf to the deep offshore basin at localities with and without bioherms. The water masses that flow along and between these features transport energy, sediments, and nutrients between shelf and offshore systems, and they may hold the key to understanding the main drivers of Halimeda bioherm formation.

The 50-centimeter-resolution bathymetry grid we collected revealed complex paleochannels incising the GBR shelf to depths of roughly 100 meters, likely the result of successive downcutting by ancient rivers during periods of lower sea levels. This paleochannel bathymetry will be integrated with regional bathymetry data sets to model oceanographic influences on the shelf and try to understand the absence of bioherms in the 130-kilometer section.

Offshore, we used R/V Investigator’s giant piston coring system to acquire targeted sediment cores up to 10 meters long from submarine canyons on the continental slope. These cores potentially represent archives of sediment transport from the shelf to the deep ocean floor; they also may record paleoceanographic changes spanning the past 500,000 years.

We will also analyze conductivity, temperature, and depth measurements and water samples collected along a transect across a canyon axis to reconstruct a snapshot of the water masses, including their geochemical fingerprints, moving through the canyon between the shelf and offshore basin systems.

More Mysteries to Investigate

The observations from the Project HALO cruise last year revealed a stunning new picture of the Halimeda bioherms of the GBR and the unique, diverse ecosystems that thrive amid these seafloor donuts. Following our preliminary analyses, the project team is now diving into the collected observations in more detail, focusing on a variety of topics. These topics include investigating the 4D growth structure and development of the bioherms, characterizing potential new species found, and revising assessments of the bioherms’ biodiversity.

We will also quantify the nutrient cycling in the bioherms using water and sediments from the onboard incubation experiments, investigate the wealth of physical and chemical oceanographic data collected, and reconstruct novel high-resolution Holocene paleoenvironmental records from the bioherms [McNeil et al., 2019]. There is much work to do, and we welcome collaboration with the wider scientific community.

Project HALO will contribute to the World Heritage Convention’s Outstanding Universal Value designation of the Great Barrier Reef Marine Park by describing the bioherms’ extent, geomorphology, and habitats in unprecedented detail. These observations enable a better understanding of why these fascinating features occur where they do, they provide a more holistic understanding of these interreef habitats, and they contribute to improving the future management of these habitats.


We thank the entire HALO science team, Commonwealth Scientific and Industrial Research Organisation (CSIRO) support staff, and the captain and crew of R/V Investigator for their outstanding work on the voyage. The project was supported by a grant of sea time on R/V Investigator from the CSIRO Marine National Facility, part of Australia’s national science agency. We thank Victorien Paumard and Carra Williams for assistance with Figure 2. We also acknowledge funding support from the National Geographic Society and the Ian Potter Foundation.


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Author Information

Jody Webster (, University of Sydney, NSW, Australia; Mardi McNeil, Geoscience Australia, Canberra; Helen Bostock, University of Queensland, Brisbane, Australia; Luke Nothdurft, Queensland University of Technology, Brisbane, Australia; and Maria Byrne, University of Sydney, NSW, Australia

Citation: Webster, J., M. McNeil, H. Bostock, L. Nothdurft, and M. Byrne (2023), Making sense of the Great Barrier Reef’s mysterious green donuts, Eos, 104, Published on 9 March 2023.
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