Cinzia Alessi - AIMS@JCU

Cinzia Alessi

Recipient of an AIMS@JCU Scholarship

College of Science and Engineering

Cinzia Alessi

College of Science and Engineering
Identification of environmental and biological factors affecting survival and ecophysiology of post settled corals

Cinzia graduated with a bachelor's degree in Marine Biology and a Master's degree in Marine Ecology obtained at the University of Palermo, Sicily (Italy). After her graduation, Cinzia collected a few international research experiences working with corals. The first experience abroad was at Mote Marine Laboratory in Florida for a period of research where she tested the effects of Ocean Acidification on the physiology of corals. Following this experience, she has been selected for a scholarship at Coral Eye in Indonesia where she developed a personal project on soft corals. After a few months, she started an internship at the Indian Ocean Marine Science Centre in Western Australia, where she was in charge of a complex experiment testing the effects of pH, Light, and flow on the physiology of corals and coralline algae. At the expiration of her Visa, Cinzia had to leave Australia and she decided to move to the Maldives to work for six months as a coral biologist of an Eco-Resort in the Ari Athol where she was in charge for the coral conservation project. Her last working experience was in the Philippines, where Cinzia started to work as a coral biologist for Sulubaaï Environmental Foundation in April 2019. Her main role was to lead the coral restoration project in a small private island located in Shark Fin Bay, Palawan. She definitely enjoyed this experience and felt extremely lucky to work in the coral triangle, but she realized that she wanted to get back to studies and be more involved in marine science, so she applied for the JCU@AIMS scholarship.

Identification of environmental and biological factors affecting survival and ecophysiology of post settled corals

2020 to 2024

Project Description

Reefs are experiencing a significant decline in coral abundance and diversity due to stressors associated with climate change and other anthropogenic disturbances. The intensity and frequency of these disturbances are increasing causing the inability of damaged reef ecosystem to renew and restore themselves, prompting calls for direct intervention to assist reef recovery. Demographic processes such as coral settlement and post-settlement survival are linked to rates of coral recovery after disturbance events. Survival of corals early post-settlement is generally very low and is influenced by abiotic (e.g. light, depth, seawater temperature, salinity, flow rates) and biotic factors (e.g. competition for space, predation, and bio-erosion). Regarding the coral recruit mortality, the main stressors involved are complex and species-specific. However, mortality rates gradually reduce when corals reach size-escape thresholds (usually > 1cm). Estimates of these demographic processes improve our capacity to predict recovery trajectories following disturbance events.

Thus, this project focus on two research axes to fill the knowledge gap in post-settlement survival and resilience: (i) the role of environmental and biotic factors in facilitating juvenile coral growth and survival, across a diversity of coral taxa on the Great Barrier Reef and (ii) the physiological responses of coral early life history stages to disturbances. Physiological traits associated with coral resilience could explain which species are more resilient to stressful conditions and deepen the scientific knowledge on what drives resilience. The following points will be addressed:

• To identify how early life-history of corals are related to the local adult population and which species and habitats are best suited for coral re-seeding;
• To define the main environmental and biotic stressors involved in juvenile coral mortality;
• To test a variety of substrates to promote coral post-settlement survival;
• To assess how climate change stressors could affect the physiology (e.g. photosynthesis, respiration, and calcification) of juvenile corals to identify corals that might be resilient to future threats.

This project explores coral re-seeding using both ocean and laboratory settled coral larvae and micro-fragmentation, with a focus on early survival on the reef. This research will identify which species and habitats are best suited for re-seeding and will test the performance of a variety of substrate designs (including natural substrates) for deployment. The range of habitats and conditions available in the Keppel Islands will allow a field experimental design to evaluate how environmental and biological factors influence the growth and survival of restored corals.

The better understanding of the processes involved in coral recruit mortality should enable me to implement restoration strategies that maximize survival. That includes to predict the best locations, species and substrates for future restoration efforts, to develop best-practice guides for achieving high post-settlement survival for use in coral restoration.

Project Importance

Brief Description of the Project:
This project will assess environmental and biological conditions that result in the best survival and growth of juvenile corals to identify whether those conditions differ across species and deployment ages/sizes. It will also test the physiological response of early life stages of corals and it will identify optimal substrates for coral recruitment filling the gaps regarding which species and habitats are best suited for re-seeding. Field trials will be conducted in Keppel Islands.

Project Methods

Field experiments will be developed in the Keppel Islands, where “permanent sites” across a range of depths and reef-zones habitat (shallow fringing reefs, bommies, and patch reefs), wave exposure, and water quality gradient will be selected. Abiotic data will be collected using loggers (e.g. light, temperature, and pH) and sediment traps to quantify sedimentation rate and grain-size distributions. Flow rates, turbidity, salinity, and nutrient levels will be quantified during each visit.

Biological data (e.g. corallivore density, herbivore and grazer density, benthic community composition (% cover), coral species assessment) and structural complexity (e.g. rugosity) will be described using visual census methods found in AIMS fieldwork procedures (e.g. AIMS Long Term Monitoring Program standard operating procedures; AIMS LTMP SOPs). The benthic cover will be estimated from photomosaics of each site, with stratified randomized points in Coral Point Count (

Broadcast spawning corals colonies will be collected before the mass-spawning events, while brooding species will be collected according to their reproductive cycle from the Keppel Islands region and transported at the National Sea Simulator. Coral spawning behavior will be recorded, and corals will be spawned, reared and settled onto three different kinds of substrates (coral skeletal tiles, terracotta plugs, and SECORE devices) under controlled conditions. After the spawning, adults will be micro-fragmented (1-2 polyps) and attached to terracotta plugs. Coral recruits and micro-fragmented colonies will be monitored in the aquarium, where post-settlement survivorship, growth rates, and health conditions will be recorded and documented using time series photography. Approximately 1 month after settlement, juveniles and micro-fragmented corals will be transported back to the Keppel Island field sites for deployment, where growth rates and survival will be quantified every 3 months for 18-24 months, through photogrammetry with ImageJ and using UV light. The growth and survival rates of field-deployed corals will be compared with the conditions at each field site to tease apart the relative influence of each environmental and biological predictor.

A subset of corals will be maintained in the lab to assess the physiological response to the main stressors identified at the collection sites. Incubation chambers will be run to test stressors in isolation and/or in combination within 2 or more levels for each stressor, to define the effect of the stressors on photosynthesis (via photosynthetic efficiency), respiration, and calcification.

Statistical analysis: “Permanent sites” across a range of depths, current exposition, tide rugosity, shelf and reef zones will be selected throughout the region. Partial and full canonical correspondence analysis (pCCA and CCA) will be used to identify the correlation between site descriptors (e.g. depth, exposition, tide, rugosity, shelf) and patterns of coral distribution. Community cover will be quantified by classifying the substrate under 100 random plots using CPCe, categories will be defined as sand, rock, CCA, turf algae, macroalgae, other (soft corals, sponges and invertebrates), and live corals. Data will be plotted using multidimensional scaling (MDS) and will be analysed using ANONISM, based on Bra-Curtis dissimilarity matrix. Regression models will be also used to define the best species-substrate-habitat combinations to identify the optimal candidate substrates for restoration. Relationships between environmental (temperature, light, flow rates, depth etc) and biological variables (soft corals, sponges, and invertebrates) and coral growth and survival will be analysed with generalized linear mixed effects (GLME) models to identify the strongest predictors of growth and survival. Non-linear boosted regression tree models (machine learning technique) will be used to pinpoint threshold values in the strongest predictors, above (or below) which, survival increases. This project will also employ powerful machine learning which uses algorithms modelling techniques to tease apart the complex relationships among coral recruit dynamics and environmental and biological drivers, which are usually non-linear, sometimes correlated, and often exhibit threshold responses. In tandem, automated image analysis and 3D modelling will be used in the lab to measure the surface area of coral recruits. The best species-substrate-habitat combinations will be used to define the optimal candidate substrates and sites for restoration and an index will be developed to evaluate future candidate restoration sites. Two-Way ANOVA with a post hoc comparison will be used to test the physiological response to the interaction of stressors (e.g. temperature Vs sedimentation). All statistical models will be developed using the statistical freeware R (R Core Team) and PRIMER v6 software.

Project Results

Outcomes of this work will enable to produce best-practice guides for achieving high post-settlement and post-deployment survival for use in coral restoration.


Climate change,
Coral reefs,
Marine planning,
Natural disturbance,
Quantitative marine science