Dr Mike McWilliam was awarded the 2024 Maple-Brown Family Foundation Fellowship, funding postdoctoral research conducted at Lizard Island Research Station in October – November 2024. The primary aims of Mike’s project were to explore the relationship between coral reef habitat structure and primary productivity using benthic metabolic chambers. Following successful data collection, the results revealed that habitat geometry is a fundamental driver of carbon fixation rates on coral reefs, uncovering a deep quantitative link between reef geometry and reef energetics. The project has brought about numerous benefits, including improved knowledge of reef functioning, career progression for the primary researcher, and educational and career development for student researchers involved in data collection and project writeup. A peer-reviewed publication reporting the results of this research is currently in an advanced stage of review in the journal Nature Ecology and Evolution. Mike’s final report to the Lizard Island Reef Research Foundation follows:
Background: Primary production is the entry point for energy into the Earth’s biosphere and is the driving force for ecosystem growth and development. Shallow-water coral reefs are among the most productive of all ecosystems, capturing multiple kilograms of carbon per square meter per year. These high rates of productivity can be partly attributed to the tropical climate where reefs grow. However, productivity can also be enhanced by ‘habitat geometry,’ including the geological features of the local area and the size, shape, and abundance of habitat-building organisms (e.g., corals). In particular, dense coral thickets can provide highly effective 3D light-traps and act as ‘energy generators’ for reefs. This fixed carbon is the driving force for a range of reef processes, including organic biomass accumulation, calcification, and reef development. Similar research linking habitat structure to productivity has been undertaken in temperate forests, boreal forests, phytoplankton communities, and estuaries. Nevertheless, two of the most prominent features of reefs, their intricate habitat complexity and high primary productivity, have never been quantifiably linked. There are currently no tests of the relationship between 3D habitat geometry and primary production in open reef ecosystems, and uncertainty remains about the importance reef geometry relative to other influences such as the local environment or the specific organisms present.
Aims: This project aimed to understand the role of habitat geometry in regulating coral reef productivity and energetic dynamics. Funding from the Maple-Brown Family Foundation Fellowship enabled us to directly test the relationship between habitat structure and primary productivity on reefs around Lizard Island using specially constructed chambers (Figs. 1-2). The project design facilitated new measurements of the strength, consistency, and predictability of the relationship between habitat structure and primary production, ultimately improving our knowledge of how shifts in 3D habitat structure can modify reef productivity and the possible consequences for ecosystem functions such as biomass accumulation and reef growth.
Figure 1: Location of two metabolic chambers used to quantify reef productivity on shallow reef patches in the Lizard Island Lagoon. The chambers are indicated by red arrows and are shown next to two divers. Photo: Norbert Rapolthy.
Field methodology: The project utilised a simple and cost-effective design for metabolic chambers (Fig 2) to quantify the productivity and habitat complexity of small reef patches. These chambers were designed independently by the researchers of this project, but similar chamber designs have been employed elsewhere by other researchers across the world. The chamber is constructed of basic materials, and require two probes to measure oxygen concentrations, light and temperature within the chambers. Chambers were deployed at various locations around Lizard Island, with preference given to shallow reef patches in protected areas of the Lagoon (Figs. 1-2). Each chamber requires approximately 1.5 hours to collect information on photosynthesis, respiration, and habitat complexity.
Figure 2: Design of metabolic chambers used to measure primary productivity (left) and location of chamber deployment sites across Lizard Island (right).
Habitat complexity was subsequently measured using Structure-from-motion photogrammetry, which enabled us to create 3D mosaics of reef structure (Figure 3). This method requires a camera to take 200-300 images of a small reef patch along with scaled targets for processing, and software to The primary measure of habitat structure we were interested in was rugosity, which measures the ratio between 3D surface area of a reef and the 2D area it occupies, and thereby captures the 3D complexity of the reef patch.
Figure 3: Examples of 3D mosaics of reef patches constructed using 3D photogrammetry. Habitat complexity metrics (e.g., Rugosity) were directly quantified from these 3D models for use in the analysis of the geometry-productivity relationship.
A wide range of habitats across the shallow reefs of Lizard Island were purposefully targeted for this study to capture maximum variability in reef environments. Measuring different reef patches with different dominant organisms helped us to validate the consistency of the geometry productivity relationship in a highly variably reef setting. Habitats targeted included patches dominated by live coral, patches dominated by algal turf (including recently dead coral or rubble), soft coral habitats, and patches of shallow seagrass growing in the Lizard Island Lagoon (Figure 4). Control sites with only sand included within chambers were also sampled.
Figure 4: Examples locations where chambers were deployed, including (a) control deployments with sand only, (b) coral-dominated plots, (c) plots in which up to three chambers were deployed in a single dive, (d) dead coral patched colonised by turfs, (e) patches of seagrass, (f) plots which included a self made battery powered underwater pump to test for the effects of water flow on productivity readings.
Figure 5: The core result– strong quantitative relationships between habitat rugosity (x-axis) and gross primary production (y-axis). Black points indicate data collected on Lizard Island, while red points indicate data collected previously in Hawai’i. The plot is extracted from Figure 1 of the publication in review.
Key findings: The core result of this work is that two prominent features of reefs, intricate habitat complexity and high primary productivity, are closely related. Specifically, we find that:
- Habitat complexity is the strongest predictor of local-scale production in an open reef setting, exceeding the influence of local environmental variation such as temperature, light, and benthic composition.
- High habitat complexity generates more excess carbon for reef development, with greater surplus energy for consumption by other organisms or export across reef environments
- Reefs with higher habitat complexity have proportional allocation to respiration, potentially indicating greater biomass of cryptic fish and invertebrates, each of which can alter the energetic dynamics of high-complexity reefs.
- When combined with similar data from Hawai’i (collected prior to Lizard Island), the results indicate that the relationships between habitat complexity and geometry transcends taxonomic and biogeographic boundaries, meaning they are potentially widespread across the worlds reefs.
Outcomes:
- Knowledge gained: The research has enhanced our collective ability to understand and forecast reef energetics and functioning. Since the research reports that energetic fluxes can be predicted by reef geometry, it is hoped that the results of this research will generate future research efforts to quantify the relationship at longer timescales and across larger areas, and explore the consequences of the relationship for reef functions such as calcification and biomass accumulation.
- Publications: A manuscript which directly reports these results is currently in second stage of review at the journal Nature Ecology and Evolution. Given the generally positive reviews, is expected (though not guaranteed) that the publication will be released in mid-2026. Both the Maple-Brown Family Foundation Fellowship and Australian Museum’s Lizard Island Research Station are acknowledged in the publication for their support for this research. Other publications arising from this project are at an early stage of conceptualisation.
- Career Progression: The grant has been a highly valuable addition to the career progression of the early-career researcher/principal investigator (Mike McWilliam), allowing me to demonstrate independent fieldtrip coordination and research, and providing excellent opportunities to develop leadership skills on a remote expedition involving boating and diving.
- Education: The project would not have been possible without two student researchers (Emily Washington and Norbert Rapolthy). The project has also helped them in their education and careers, providing fieldtrip, research, and manuscript-writing experience, and will provide a valuable early co-authored publication during their PhD years. One student (Norbert Rapolthy) subsequently undertook seven month’s employment at Lizard Island Research Station as Station Officer, with this field trip providing experience needed to secure and succeed in the position.
Figure 6: Project personnel. The project was made possible by two student volunteer researchers, Emily Washington and Norbert Rapolthy