A Microscale View to Coral Function in a Changing Environment

Project Information

MicroCoFE

Grant agreement ID: 101108420

DOI

10.3030/101108420

Project closed

EC signature date 7 March 2023

Start date 1 November 2023

End date 31 October 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 214 934,40

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - MicroCoFE (A Microscale View to Coral Function in a Changing Environment)

Reporting period: 2023-11-01 to 2025-10-31

Summary of the context and overall objectives of the project

Context
Coral reefs are highly valuable ecosystems that support biodiversity, coastal protection, and millions of people worldwide. However, they are rapidly declining due to climate-driven stressors such as warming, acidification, and deoxygenation. These factors disrupt coral physiology and lead to bleaching and mortality.
A major knowledge gap remains at the microscale, where corals exchange gases and nutrients with surrounding seawater. This exchange is controlled by the diffusive boundary layer (DBL)—a thin layer of water above the coral surface. Recent discoveries showed that corals actively modify this layer using epidermal cilia, which generate vortices that enhance transport. Until now, no tools existed to visualise these processes in 3D or link them to coral stress responses.

Overall Objectives

This MSCA project was designed to fill this gap by developing new optical imaging tools to understand how corals regulate their microenvironment under climate stress. The main objectives were:

- Produce the first 3D maps of oxygen and flow around corals using sensPIV.

- Develop pH-PIV, a new method to image pH and flow simultaneously.

- Determine how ciliary vortices influence coral resilience under warming, hypoxia, and acidification.

- Link external microenvironment patterns with internal tissue structure using OCT.

These goals integrate marine biology, biophysics, and advanced chemical imaging.

Scientific Impact

The project provides new mechanistic insights into how corals cope with climate stress at the microscale. The imaging tools developed allow researchers to study flow–structure–function interactions that were previously impossible to observe. These methods can also be used in other marine organisms and in biomedical systems where microscale fluid transport is important.

Societal and Environmental Impact

By identifying traits and species that better regulate their microenvironment, the project supports:

- improved reef restoration,

- better conservation planning,

- selection of stress-tolerant coral species,

- and evidence-based climate adaptation strategies aligned with EU policy goals, including the EU Biodiversity Strategy 2030 and the European Green Deal.

Given the high cost of restoration, even small increases in coral survival can create significant ecological and economic benefits.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the fellowship, major progress was achieved across all work packages, leading to new imaging tools, unique datasets, and multiple publications.

1. 3D sensPIV (T-WP1)
A fully operational 3D sensPIV system was built, calibrated, and validated, enabling the first 3D visualization of oxygen and flow dynamics above Porites lutea. This work, strengthened during the secondment, resulted in custom analysis pipelines and a published lead-author paper in Methods in Ecology and Evolution.

2. pH-PIV Development (T-WP2)
A prototype system for simultaneous pH and flow imaging was created. pH-sensitive nanoparticles were calibrated, the imaging setup modified, and analysis algorithms co-developed with Aarhus University. Preliminary pH-PIV recordings were successfully produced.

3. Environmental Stress Experiments (B-WP3)
Stress experiments (warming and low O2) were completed for P. lutea. A new in vivo cilia-dynamics platform was developed to quantify ciliary beating formation under stress. Results show how warming disrupts DBL structure and ciliary transport (manuscript submitted to PNAS) and were extended to additional coral species with collaborators in Australia and Saudi Arabia.

4. OCT–DBL Integration (B-WP4)
OCT imaging was used to map coral tissue and skeleton architecture. OCT datasets were acquired for several morphotypes and integrated with sensPIV outputs, contributing to the published Methods in Ecology and Evolution paper and to an eLife submission on coral behaviour and O2 dynamics.

5. Additional Outputs
The fellowship contributed to:

- a new frame-straddling luminescence imaging method (published in ACS Sensors),

- a second-author manuscript on 3D ciliary transport (submitted to Physical Reviews X – Life),

- several collaborative manuscripts on coral oxygen dynamics and deoxygenation stress (under review or submitted).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project significantly advanced the state of the art in coral ecophysiology and microscale imaging. Before this fellowship, no tools existed to visualize the 3D chemical and physical microenvironment around living corals or to capture ciliary-driven transport under stress. The project filled this gap and produced several breakthroughs.

1. First 3D Mapping of Coral Diffusive Boundary Layers

A new 3D sensPIV system delivered the first fully resolved 3D maps of oxygen and flow above live corals. This moves far beyond earlier 1D and 2D approaches and reveals spatial DBL heterogeneity, vortex patterns, and the role of ciliary activity in mass transfer. These datasets provide a new reference for future modelling.

2. New Platforms to Visualize Ciliary, Flow and Oxygen Dynamics Under Stress

A novel in vivo cilia-dynamics imaging platform and improved flow-through chamber now allow quantification of ciliary beating, vortex strength, and microscale flow disruption under warming and hypoxia. This reveals how cilia actively mitigate extreme conditions and directly links ciliary behaviour to coral stress tolerance.

3. Additional Innovations Beyond the Original Plan

The fellow contributed to:

- a new frame-straddling luminescence imaging method (ACS Sensors 2025),

- application of the imaging tools to new coral species,

- multiple manuscripts on internal O2 dynamics, heat-induced oxygen deprivation, and standardising deoxygenation studies.


Overview of Final Results

The project produced:

- the first 3D flow–oxygen datasets for corals,

- a new cilia-dynamics imaging platform,

- integrated OCT + DBL datasets,

- multiple publications and manuscripts,

- new algorithms and calibration workflows,

- and expanded international collaborations.

Overall, the project positions the fellow and host institution at the forefront of microscale coral physiology and provides tools with broad applications in marine science and environmental monitoring.