Program 1 - Metabolic response to thermal stress: Increase our knowledge about fundamental cellular metabolism and estimate acclimatization status to the local thermal environment

Program 2 - Thermal adaptive potential: Quantitatively determine temperature resilient reefs and genotypes using Coral Bleaching Automated Stress System

Program 3 - Seascape genomics: A study of coral reef population structure, dynamics, and adaptive potential

Program 4 - Quantification of reefs composition: Scalable, reproducible and low-cost 3D-mapping and annotation of shallow coral reefs with machine learning

Program 5 - Determination of benthic communities: A novel approach to estimate coral species assemblages using environmental DNA (eDNA) metabarcoding

Program 6 - Systematic sampling for water quality: Assessing plastic and trace-metal pollution quantification and the impact on corals

Program 7 - 3D-mapping: Scalable, reproducible and low-cost quantification of the abundance and health of reefs using machine learning

Corals in the Gulf of Aqaba have extraordinarily high bleaching tolerance limits approaching 7°C above their summer thermal maxima, and therefore representing a unique coral climate change refugium. To better understand the mechanisms underpinning such tolerance, and assess the status of thermal adaptation of corals to their local environment, this program compares bleaching tolerances and thermal acclimatization/adaptation strategies of conspecific coral populations across a wide latitudinal range in the Red Sea region, coupled with metabolic performance markers studied at the scale of individual coral colonies. This program is thus closely linked with the Seascape Genomics program described above.

The variability in resilience to ocean warming is critical to reef persistence, yet the scientific community lacks any standardized diagnostics to rapidly assess bleaching severity or resilience across different corals and locations. Using a newly developed portable experimental system that allows temperature manipulation in small volumes (termed the Coral Bleaching Automated Stress System, CBASS), the program aims to i) determine empirical temperature thresholds for a range of Red Sea coral species through a series of acute in situ experiments, ii) examine the consistency of the exceptional thermal tolerance of coral species in the Red Sea across their latitudinal gradient, and iii) integrate these results into a thermal resilience map as a resource for the governments and to guide additional scientific investigations. This program is thus closely linked with the Seascape Genomics program described below.

The goal of this program is to investigate coral adaptation to the seascape conditions using a seascape genomics approach. This method combines remote sensing of seascape conditions using satellite data that are used to identify reefs exposed to contrasted conditions (e.g., high vs. low thermal stress). Next, the sampling campaign will be carried out at selected sites to collect corals samples that undergo genomic characterization. The goal of the analysis is to find genomic variants that correlates with environmental gradients and that might therefore underpin adaption to environmental variability.

The primary result of this analysis is a model of adaptation that can be used to predict the adaptive potential of different coral species at the scale of an entire reef system. In addition, satellite data also allows to describe how different reefs are connected by seawater currents. By comparing the genomic similarity between corals with their physical distance, it is possible to define a model of dispersal that classifies reefs into expected ‘sources’ or ‘sinks’ of coral propagules.

Biodiversity and species abundance play a critical role in the assessment of the health-state of marine ecosystems. However, adequate sample collection remains a challenging issue. The emerging field of environmental DNA (eDNA) is transforming our approach to assess biological diversity and ecosystem function. eDNA relies on DNA samples readily available from the environment, e.g. through shedding/secretory processes such as sloughing of skin, scales, mucus, eggs, sperm, blood, or defecation. These sources of DNA are non-invasive, less biased, and can be sampled directly from a boat.

In combination with next-generation sequencing of suitable marker genes, eDNA promises to provide a wealth of information for studies of biodiversity, species abundance, food web dynamics, environmental and invasive species monitoring. Careful establishment and curation of a reference database is critical to standardize results obtained with eDNA approaches. This project is thus closely linked with the Seascape Genomics project described above. Furthermore, in combination with ship-based sequencing, e.g. through ultra-portable sequencing platforms, results can be produced on site in collaboration with local scientists and stakeholders, supporting exchange of knowledge and minimizing permission paperwork.

This program will develop and use eDNA methods through sampling combined with cutting-edge metabarcoding and next-generation sequencing to assess the biodiversity and relative species abundance of corals (and other species) along the Red Sea coasts. Water collected and filtered for DNA will be analyzed to provide information of the visible and cryptic biodiversity of these reefs. This program will be combined with a program of visual census of coral reef diversity for the same sites (see 3D-mapping program below) and with the Seascape Genomics projects, to provide ‘ground truth’ underpinning the pioneering eDNA data.

Despite this, the levels of microplastic pollution in Red Sea coastal waters are largely unknown. Microplastic concentrations and geographic distributions are highly variable and the lack of methodological standards hamper comparable quantifications. First studies on microplastics along the Mediterranean coast showed the presence of a large variety of plastic debris in marine sediments, but baseline surveys on plastic pollution of the Gulf of Aqaba and Red Sea coasts are unavailable in the scientific literature.

Surveys of trace metals along these coasts suggest that coral reefs along the western Red Sea are likely affected by plastic pollution. In addition, hydrodynamic patterns of water currents indicate that plastic debris become trapped within the Red Sea basin and the Gulf of Aqaba due to limited transport out of the Red Sea system, and may accumulate rapidly along its shores. Baseline surveys of plastic pollution in coral reefs along the Red Sea coasts are therefore strongly needed.

This program will conduct comprehensive baseline surveys of plastic pollution in Red Sea coral reefs to identify important sites for management and protection of this economically important ecosystem. It will combine i) a visual census of macroplastic pollution in coral reefs, ii) sediment sampling for quantification of microplastics in coral reef environments, and detection and quantification of environmental pollutants (trace metals and persistent organic pollutants), and should ideally be combined with (iii) stony coral and sponge tissue sampling to quantify microplastic effects on coral reef organisms. The sampling of animal tissues (coral and sponges) in this program is important to confirm the ecological footprint on organisms and to estimate the potential long-term effects on Red Sea coral reef ecosystems.

Scalable and reproducible quantification of the abundance and health of reefs is crucial to monitor coral reef ecosystems over time, but conventional methods are limited in their scalability; i.e., they tend to require significant manual effort such as diving time, positioning of reference items, e.g. transect lines, and analysis of transects by experts. Moreover, these manual components also make different studies performed by different humans difficult to compare.The aim of this program is to develop an approach with which entire shallow reefs can be mapped using low-cost consumer electronics and substantially reduced manual labor, therefore guaranteeing comparability over different sampling sites and dates. In particular, the program will use recent advances in machine-learning powered computer vision to construct a digital twin of large (relatively shallow) reef segments. By using deep learning, this digital twin is automatically enriched with information about coral abundance, as well as the relevant types of corals and their health. This annotated digital twin can then be used to help understand the complex interplay of coral colonies with structural attributes (bathymetry) and the broader relation to the seascape environment.Furthermore, as the digital twin can objectively be compared to subsequent mappings of the same area, i.e., time-series analysis, it enables detection of change at high spatial resolutions. In the future, the digital twins could be matched to drone or satellite imagery by means of GPS, potentially serving as ground-truth data for large-scale remote sensing campaigns.