Gene editing technologies to understand and protect coral reefs

New tools are needed to understand the resilience of corals, the efficacy of coral seeding initiatives and their capacity to cope with rising temperatures in response to global heating trajectories.

This research seeks to harness cutting-edge gene editing technologies to build a range of tools that can help us answer a wide range of questions, informing more effective strategies for intervention and management.

Scientist at microscope — Max Moonier conducting gene editing research on corals. Image: Marie Roman

First, our research seeks to identify genes that underpin characteristics like heat resilience, bleaching tolerance, and growth, using gene editing techniques with the CRISPR/Cas9 system. By introducing precise DNA edits into corals’ DNA, we can disrupt certain genes and thus test their function under various conditions.

Second, our research investigates how inserting new genes into coral can change their function, such as increasing their heat tolerance or growth rate. This is done by adding new DNA to the coral (using synthetic gene fragments), which can make new genes that could change the corals fitness, such as making them more heat tolerant.

Third, our research seeks to develop a scalable approach to track individual corals and their offspring. By combining two novel genomic technologies, CRISPR-Cas9 gene editing and environmental DNA (eDNA) metabarcoding, we can insert unique genetic tags into coral, which are heritable over generations and detectable in seawater samples.

Microinjecting Acropora millepora eggs with CRISPR-Cas9 to induce genetic barcodes. Video: Max Moonier

Identifying genes underpinning coral function

Over the past five years, in collaboration with Prof. Cleves group at Johns Hopkins University we have developed technology to make precise changes in the coral genome using CRISPR/Cas9. This tool has been used to identify various genes that are crucial for important coral processes.

In 2018, we identified a key gene, HSF1, that controls coral tolerance to heat stress. This is the first gene to be shown to control coral survival to heat.

In 2020, we identified a gene we believe is involved in corals' ability to biomineralise their skeletons.

From 2021, we have built a database of key genes for CRISPR screens from several Acropora coral species, to increase the knowledge of the genetic basis of heat stress in corals and feed the possibilities of CRISPR screens.

In 2022 and 2023, we continued to identify genes that control survival to acute heat stress and have explored how the regulation of these genes effect survival over time and across species.

Petri dish and injector in fluorescent light — Image: Marie Roman

A multigenerational, scalable tool for tracking coral

In 2024, Max Moonier, Ryan Lister, and the team developed an approach to track corals across generations using the CRISPR-Cas9 system. To do this, we insert unique “genetic barcodes” into coral DNA, kind of like giving each coral a unique DNA tracking number. These genetic tags can be passed down to offspring and are detectable in environmental DNA (eDNA), which is DNA that has shed off the coral and can be collected in a seawater sample. Together, this means we can track individual corals simply by collecting and sequencing water samples – no tagging or handling required.

This tool directly addresses one of the biggest challenges in coral restoration: monitoring whether restored corals survive, reproduce, and contribute to the future of reefs. Early proof-of-concept experiments at AIMS’ National Sea Simulator have demonstrated that the method works, offering a powerful, non-invasive, and potentially scalable way to assess restoration success over time. This year, the team will produce many barcoded corals and grow them out long term. This approach could not only help protect Australian reefs but may also be adapted to other species and ecosystems, supporting global restoration efforts in the face of climate change.

Diagram of using eDNA to track heritable characteristics of coral — Figure: Max Moonier, illustrations by Dean Tysdale

Genetically engineering corals for resilience

This year, the team is pioneering the use of a new tool – synthetic gene fragments – to add new genes into corals. These DNA fragments act like molecular instructions that can influence how corals function. Each fragment has two main parts: a promoter, which acts like a switch telling the gene when and where to turn on, and a gene, which contains the instructions to make a specific protein. By choosing genes linked to beneficial traits, such as heat, bleaching or disease tolerance, for example, and pairing them with promoters that activate under stress, we can begin to explore how targeted genetic changes might strengthen coral resilience in a warming ocean.

The first step in this research is to identify a panel of promoters that can switch genes on and off at different strengths and times. We’ll also identify a set of reporter genes – genes that produce an easily visible signal - so we can confirm that the promotors are active. For example, by pairing a specific promoter for a gene with a fluorescent protein gene, we can make corals glow when the gene is activated. We can then investigate whether we can improve traits that enhance climate resilience of corals by adding functional genes regulated with stress-activated promotors.