Increasingly frequent and severe climate-driven warming events are one of the main drivers of change on tropical coral reefs. However, the degree to which disturbance events affect ecological communities is not uniform across space and varies across environmental gradients. Similarly, the extent to which the structure and function of benthic communities within shallow water habitats (<30 m) vary and respond to recurring thermal stress across different depth gradients remains unclear. Most assessments of bleaching and degradation are carried out at depths <10 m, limiting our understanding of the depth variability in the changes in benthic assemblages and vertical zonation in response dynamics. This disproportionate focus of coral reef studies at shallow depths further limits our understanding of the zonation in vital geo-ecological functioning such as primary framework production on rapidly changing coral reefs under current climate trends. Importantly, increasing evidence of bleaching and mortality reported within both shallow (<30 m) and mesophotic reef zones (30–150 m) currently requires the review of the Deep Reef Refugia Hypothesis, which suggests that coral reefs at depth can escape the impacts of thermal stress events.

Using benthic community data from the Chagos Archipelago, a relatively remote reef system in the Central Indian Ocean, this thesis aims to provide an understanding of the depth zonation patterns of recent past climate change impacts on contemporary shallow coral reefs. In the absence of direct anthropogenic impacts, the uninhabited atolls of the Chagos Archipelago can be used as an ecological baseline to measure the extent of future thermal stress events on dynamics and geo-ecological functioning of shallow coral reef benthic communities across depths. Importantly, isolated reefs provide the opportunity to understand the natural ecological limits of coral reef ecosystems, which can be used to inform important management and conservation strategies to preserve coral reefs. Whilst there is natural variation in the ecology of benthic communities with depth, it is expected that the change in community assemblages and ecological functions following thermal anomalies will cause additional variation across depth zones, with larger changes at shallower depths due to more dynamic environmental conditions and greater compositional variability across reefs. By assessing community assemblages across multiple depth gradients (5–25m) this thesis: (1) examined the variation in depth zonation in benthic communities within and among different reef sites; (2) assessed the response of benthic communities across depth to recurring warming events; and (3) analysed the variation in coral carbonate production across depth gradients.

Depth zonation in benthic forereef slope communities prior to the back-to-back bleaching events in 2015–2017 was assessed and compared in shallow (5–10 m) and deep (20 –25 m) benthic community assemblages among and within atolls (Chapter 2). Whilst within-atoll comparisons revealed distinct differences between shallow and deep forereef slope communities, the variation in both major functional groups and hard coral assemblages varied with depth among atolls. These results suggest that the spatial variation in depth zonation of benthic communities may be driven by biophysical processes that concomitantly vary across depths and atolls.

The response of different benthic lifeforms was then measured across a 5–25 m depth gradient following successive marine heatwaves in 2015–2017 (Chapter 3). There was an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge, and reef pavement. By assessing the effects of initial and repeated thermal stress, variable benthic community response to elevated seawater temperatures was observed across depths: the loss in hard coral assemblage was associated with initial thermal stress compared to soft coral cover loss that was better predicted by repeated thermal stress, with greater changes in benthic group cover at shallow (5–15 m) than at deeper (15–25 m) reef zones following successive warming events. Despite reduced changes in benthic group cover with increasing depth, the findings in this thesis revealed that repeated bleaching impacted benthic communities at depths up to 25 m.

Finally, the zonation in primary framework production was examined using a dataset 6-7 years following the 2015–2017 warming events, through an assessment of coral carbonate production rates across shallow (10m) and moderate (17.5 m) forereefs, and the importance of coral morphotypes and colony size classes on the spatial variation in carbonate production rates was evaluated (Chapter 4). Results revealed consistently higher coral cover and coral carbonate production on shallow reefs than at moderate reefs, which significantly varied among atolls. Coral morphotypes that significantly contributed to production processes on shallow reefs included small, medium, and large colonies of branching Acropora and massive Porites as well as other large branching corals. In contrast, higher occurrence of encrusting and foliose corals of all size classes largely contributed to carbonate production rates at moderate depths. Comparing two census-based approaches, the ReefBudget method provided a more realistic estimate of carbonate production rates compared to CoralNet, which employs an area-normalised scaling technique and Monte-Carlo simulation, which predicts the probability of coral carbonate production rates based on an estimated range of taxa-specific coral colony sizes and calcification rates., Slower recovery of branching and tabular corals at shallow depths at one out of four atolls, indicate the likely impacts of recurrent bleaching during the 2015–2017 warming events on the depth-homogenisation of coral community and carbonate production.

This thesis develops understanding of depth zonation patterns in benthic community changes and geo-ecological functions within contemporary shallow reef systems. It indicates heterogenous vertical zonation of benthic communities and highlight the potential ecological consequences of shifts in benthic community assemblages and primary framework production across depths. This research highlights the on-going threats of climate change on coral reef benthic communities and underline the importance of measuring how the impacts of disturbances vary across depth gradients. The overall results from this thesis have important implications for understanding long-term dynamics of vertical structuring of shallow coral reef benthic communities and ecosystem function, especially in the face of the Deep Reef Refugia Hypothesis debate and under the predicted increase in climate-induced warming events.