In tropical reef ecosystems corals are the key habitat builders providing most ecosystem structure, which influences coral reef biodiversity and resilience. Remote sensing applications have progressed significantly and photogrammetry together with application of structure from motion software is emerging as a leading technique to create three-dimensional (3D) models of corals and reefs from which biophysical properties of structural complexity can be quantified. This enables the addressing of a range of important marine research questions, such as what the role of habitat complexity is in driving key ecological processes (i.e., foraging). Yet, it is essential to assess the accuracy and precision of photogrammetric measurements to support their application in mapping, monitoring and quantifying coral reef form and structure. This study evaluated the precision (by repeated modeling) and accuracy (by comparison with laser reference models) of geometry and structural complexity metrics derived from photogrammetric 3D models of marine benthic habitat at two ecologically relevant spatial extents; individual coral colonies of a range of common morphologies and patches of reef area of 100s of square metres. Surface rugosity measurements were generally precise across all morphologies and spatial extents with average differences in the geometry of replicate models of 1–6 mm for coral colonies and 25 mm for the reef area. Precision decreased with complexity of the coral morphology, with metrics for small massive corals being the most precise (1% coefficient of variation (CV) in surface rugosity) and metrics for bottlebrush corals being the least precise (10% CV in surface rugosity). There was no indication however that precision was related to complexity for the patch-scale modelling. The 3D geometry of coral models differed by only 1–3 mm from laser reference models. However, high spatial variation in these differences around the model led to a consistent underestimation of surface rugosity values for all morphs of between 8% and 37%. This study highlights the utility of several off-the-shelf photogrammetry tools for the measurement of structural complexity across a range of scales relevant to ecologist and managers. It also provides important information on the accuracy and precision of these systems which should allow for their targeted use by non-experts in computer vision within these contexts.

Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area) underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km²). Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i) branching coral colony (Acropora spp.); (ii) reef area (400 m²); and (iii) reef transect (2 km). At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3% ± 6% (CI). Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo). This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

Growth and contraction of ecosystem engineers, such as trees, influence ecosystem structure and function. On coral reefs, methods to measure small changes in the structure of microhabitats, driven by growth of coral colonies and contraction of skeletons, are extremely limited. We used 3D reconstructions to quantify changes in the external structure of coral colonies of tabular Acropora spp., the dominant habitat-forming corals in shallow exposed reefs across the Pacific. The volume and surface area of live colonies increased by 21% and 22%, respectively, in 12 months, corresponding to a mean annual linear extension of 5.62 cm yr⁻¹ (±1.81 SE). The volume and surface area of dead skeletons decreased by 52% and 47%, respectively, corresponding to a mean decline in linear extension of −29.56 cm yr⁻¹ (±7.08 SE), which accounted for both erosion and fragmentation of dead colonies. This is the first study to use 3D photogrammetry to assess fine-scale structural changes of entire individual colonies in situ, quantifying coral growth and contraction. The high-resolution of the technique allows for detection of changes on reef structure faster than other non-intrusive approaches. These results improve our capacity to measure the drivers underpinning ecosystem biodiversity, status and trajectory.

Assessments of the status of tidal flats, one of the most extensive coastal ecosystems, have been hampered by a lack of data on their global distribution and change. Here we present globally consistent, spatially-explicit data of the occurrence of tidal flats, defined as sand, rock or mud flats that undergo regular tidal inundation. More than 1.3 million Landsat images were processed to 54 composite metrics for twelve 3-year periods, spanning four decades (1984–1986 to 2017–2019). The composite metrics were used as predictor variables in a machine-learning classification trained with more than 10,000 globally distributed training samples. We assessed accuracy of the classification with 1,348 stratified random samples across the mapped area, which indicated overall map accuracies of 82.2% (80.0–84.3%, 95% confidence interval) and 86.1% (84.2–86.8%, 95% CI) for version 1.1 and 1.2 of the data, respectively. We expect these maps will provide a means to measure and monitor a range of processes that are affecting coastal ecosystems, including the impacts of human population growth and sea level rise.

As marine species adapt to climate change, their heat tolerance will likely be under strong selection. Yet trade-offs between heat tolerance and other life history traits could compromise natural adaptation or assisted evolution. This is particularly important for ecosystem engineers, such as reef-building corals, which support biodiversity yet are vulnerable to heatwave-induced mass bleaching and mortality. Here, we exposed 70 colonies of the reef-building coral Acropora digitifera to a long-term marine heatwave emulation experiment. We tested for trade-offs between heat tolerance and three traits measured from the colonies in situ – colony growth, fecundity, and symbiont community composition. Despite observing remarkable within-population variability in heat tolerance, all colonies were dominated by Cladocopium C40 symbionts. We found no evidence for trade-offs between heat tolerance and fecundity or growth. Contrary to expectations, positive associations emerged with growth, such that faster-growing colonies tended to bleach and die at higher levels of heat stress. Collectively, our results suggest that these corals exist on an energetic continuum where some high-performing individuals excel across multiple traits. Within populations, trade-offs between heat tolerance and growth or fecundity may not be major barriers to natural adaptation or the success of assisted evolution interventions.