Rhys grew up in Sydney, Australia where he spent every opportunity at the beach, whether it be in the surf, or checking out the rockpools for critters. He spent a few years after school soul searching and by chance he booked into a dive course in Sydney… in the middle of winter. Despite the cold, experiencing what lay underneath the waves changed everything and soon he was living in south-east asia teaching others to SCUBA dive. At the ripe age of 24, he then began a path to becoming a marine scientist in order to understand more about what was down there. After the Bachelors degree, he spent 5 years working fulltime at places like AIMS, JCU and Orpheus Island Research Station, all while completing a masters of science part time. At the completion of the Masters degree, Rhys knew it was time to get his teeth into a larger project that he could call his own so promptly applied for a PhD with AIMS@JCU with Dr Line Bay, Dr Samantha Goyen and Dr David Bourne, looking for “Phenotypic signatures of temperature tolerance (and other fitness related traits) in corals on the Great Barrier Reef”.

Phenotypic signatures of temperature tolerance (and other fitness related traits) in corals on the Great Barrier Reef

2022 to 2025

Project Description

This project will seek to find common phenotypic signatures of fitness-related traits across populations of A. millepora on the southern Great Barrier Reef using fate-tracked corals (i.e., tagged) and natural bleaching phenotypes, and rapid heat stress assays (SeaSim-in-a-box SSIAB). Currently there are 425 A. millepora genotypes geotagged across 4 sites within the Keppel Islands Group which have persisted through a bleaching event (April 2020) showing almost 100% recovery by October 2020. These populations also have known experimental heat tolerance phenotypes and samples have already been collected, providing a novel, long-term dataset to build on. This project will potential trade-offs and mechanisms of resilience of A. millepora across seasons by measuring growth, reproduction (fecundity), survival and running enzymatic activity assays. In addition, PAM chlorophyll fluorescence to determine photosynthetic efficiency and hyperspectral imaging of photopigment and chromoprotein densities and structure will be used. Both approaches act as metrics of physiological status and health. The project will also align phenotypic characteristics with NGS amplicon sequencing of the ITS region to determine Symbiodiniaceae community. This is a novel combination of complementary approaches applied over time and scale and will contribute to our understanding of adaptive variation among individual corals.

Project Importance

Improved understanding of the scope and rates of recovery, acclimatisation and adaptation of coral reef species to climate change, in order to improve forecasting ability of future coral reef status.
Using the tagged, fate-tracked A. millepora colonies at the Keppel Islands, phenotypic variability in heat stress tolerance (bleaching resistance and recovery) and fitness traits (survival, growth, reproduction) can be determined. This PhD research will build on previous bleaching history and recovery rate data collected for these populations (after a natural bleaching event) to follow these colonies across seasons and further test heat stress tolerances and adaptive capacity using experimental rapid heat stress assays. A key objective of this project will be to test for trade-offs between bleaching resilience and fitness traits (growth, survival and reproductive traits). The populations of A. millepora at the Keppel Islands showed rapid and widespread recovery from severe bleaching (April 2020) which may suggest these are resilient populations. Still to be determined is the ability of these populations to recover from warming in the future. Understanding the phenotypic variation over seasons will provide critical data for predictive models of coral adaptation and resilience under environmental change, and to better inform novel management actions. Also, gaining an in-depth understanding of these resilient populations will benefit current restoration objectives in aquaculture propagation and selective breeding.

Project Methods

Phenotypic characterisation and fitness traits (growth, reproduction, survival) determination:
Phenotypic characterisation will occur through the collection of PAM chlorophyll fluorescence to determine photosynthetic efficiency, and hyperspectral imaging of photopigment, chromoprotein densities and structure. Both approaches act as metrics of physiological status and health. For each genotype, CoralWatch health scores and images will be recorded, providing bleaching health and size data. Post heat stress experiments, samples will be preserved and further analysis of these is proposed here:
Enzyme activity assays- Research to date has largely focused on reactive oxygen species and oxidative stress related proteins and lipid peroxidation due to decades of research showing the link between coral bleaching and oxidative stress. We will investigate further the relationship between the production of MAAs, GST, CAT, LPO, SOD amino acids and their role in oxidation and lipid peroxidation inhibition in corals. Beyond oxidative stress, this project will also look at other key biochemical markers of heat stress such as heat shock proteins. This analysis will utilize enzyme and protein activity assay kits. Snap frozen samples from the field will be used for these assays.
Fitness traits of growth, survival and reproduction:
For each genotype, CoralWatch health scores and images will be recorded, providing bleaching and size data. Additionally, photo-transects will be used to document survival/mortality with photographs analysed using point-count analysis. Underwater photogrammetry and three-dimensional models created from overlapping photographs can also be used to measure linear, radial and vertical extension rates. There is also potential to measure growth capacity through calcification measurements. These methods will help determine if growth rate and size are a predictor of bleaching response.
To determine the relationship between bleaching severity, the thermal gradient and fecundity/subsequent reproductive output, the % polyps fecund, average # eggs per mesentery/polyp and the length of the sterile zone can be examined.
Determination of the Symbiodiniaceae genotype:
For this analysis, samples from each site and season will be analysed for Symbiodiniaceae community composition. Next generation sequencing of marker genes, ITS region and perhaps psbAncr, SSU, LSU can be used to characterise Symbiodiniaceae-host associations. Samples will be preserved in the field in molecular grade ethanol. The DNA will be extracted using established protocols for this species, and samples will be sent to an external facility for sequencing. ITS2 data can be submitted to SymPortal for bioinformatics analysis.
Experimental-field-based methods
Field thermal stress experiments will be conducted using the state-of-the-art SeaSim in a Box system (SSIAB). This system is standardized, highly repeatable, and accurate. Samples from replicate tagged colonies will be collected and brought to the mothership. Initial fragments will be taken for ITS typing and preserved in ethanol. Fragments will then be distributed to experimental tanks to induce their thermal stress responses. Coral Bleaching Automated Stress System methods adapted to the SSIAB system. These experiments will be conducted in the Keppel Islands across seasons with potential to expand across other GBR sites and species. After treatment, the corals will be photographed with hyperspectral imagery, PAM tested for photosynthetic activity and then snap-frozen with liquid nitrogen for later physiological and genetic analysis as described above.

Project Results

1) To determine the physiological phenotypic signatures and fitness traits (growth, reproduction, survival) of tagged and fate-tracked corals (A. millepora) across seasons in the Keppel Islands. A key objective within this is to determine physiological trade-offs between bleaching response and other fitness related traits.
This relates to the priority research area: Improved understanding of the scope and rates of recovery, acclimatisation and adaptation of coral reef species to climate change, in order to improve forecasting ability of future coral reef status.
2) To determine the physiological mechanisms behind the phenotypic signatures and fitness traits observed. Understanding these mechanisms will contribute to: Improved understanding of the scope and rates of recovery, acclimatisation and adaptation of coral reef species to climate change, in order to improve forecasting ability of future coral reef status. Specifically, results from this will help to determine a phenotypic of thermal tolerance which can be applied across local and international restoration and reef resilience objectives as well as provide critical data for predictive models of coral adaptation and resilience under environmental change. If clear signatures are found across enzymatic and metabolic processes, these could then be used as a bioindicator tools for identifying heat tolerance across the GBR and more globally.
3) Using field and laboratory-based experiments to ask whether the phenotypic signatures and fitness traits observed are conserved across natural heat stress events and those simulated through experimentation and are they conserved across season. This relates to the priority research area: Improved understanding of the scope and rates of recovery, acclimatisation and adaptation of coral reef species to climate change, in order to improve forecasting ability of future coral reef status.

Keywords

Algae,
Chemical ecology,
Climate change,
Coral reefs,
Corals,
Ecology,
Field based,
Genetics,
Molecular techniques,
Ocean warming,
Tagging