Based on research by the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report, by the end of the century, sea surface temperature and carbon dioxide (CO2) levels are expected to rise along with increased acidification and salinity in ocean water. Climate changes that impact other continents are exacerbated in Africa where the temperatures escalate at a higher rate that accelerate desert creep and the impact on the oceanic ecosystem.

To determine what will happen to fish in such a changing climate scenario, the Integrative Systems Biology Lab (ISBL) is conducting innovative research. ISBL is part of the KAUST Environmental Epigenetics Program in the Division of Biological and Environmental Sciences & Engineering, at the King Abdullah University for Science and Technology (KAUST), located at Thuwal, Kingdom of Saudi Arabia.

According to Dr. Timothy Ravasi, KAUST Professor of Marine Sciences, “Since the post-industrial revolution, the earth’s climate is changing faster than before due to anthropogenic disturbances. Climate simulations predicted that by the end of this century, the ocean’s temperature could increase up to 3 degrees Celsius and the oceans will become more acidic due to the uptake of CO2 from the atmosphere. If this scenario is correct, we need to ask the question, what will happen to marine life in this new environment? Are fish populations able to survive, reproduce or can they adapt to the changes? Answers to these questions are important not only for marine life but this will have an impact on fishing industry, in particular in developing countries, where fishing is the sole means nutrition.”

A major question of the ISBL research is learning about the ability of fish in the Red Sea to adapt to warmer ocean temperatures, changes in water acidity and increased salinity. The ISBL research seeks to determine if the fish survive the changes and answer the question of how they do it. Ravasi and his team are using genomic and epigenomic approaches in the research to determine how epigenome changes get passed down through generations of fish.

According to Ravasi, “Tools used in the ISBL research are crucial to the success of systems biology, an approach that aims to understand biological systems as more than merely the sum of their parts. Our team is also using a genomics approach based on Massively Parallel Genomes Sequencing to explore the biodiversity of Coral Reef Ecosystems focusing how climate change impacts the evolution of Coral Reef fish.”

The team uses high performance computing (HPC) systems and developed large-scale, computer-aided models of biological signaling, transcription regulatory networks, and regulatory pathways in the research. Ravasi states, “Next-Generation Sequencing techniques produce an enormous amount of sequences that need to be assembled, analyzed and visualized to create models of the genomics and epigenomics mechanisms that underline fish response to climate changes. Supercomputers such as the KAUST Shaheen II are necessary in order to handle this large amount of data (Big Data analysis). Parallelization is required to substantially reduce the time needed for this type of analysis.”

Using a Laboratory Setting to Study Climate Change Scenarios

The ISBL research began six years ago in a laboratory setting by collecting wild pairs of fish (F0 group) and placing them in laboratory tanks with increased water temperature and lowered pH. Measurements were made of phenotypic traits and genome-wide measurements. Research found that oxygen demand increased with warmer water temperatures leaving the fish with less to use for growth and reproduction. The study is now on the third generation of fish (F3 group) using Next-Generation Sequencing techniques such as transcriptomes, genomes and epigenomes sequencing to measure the responses and adaptation capabilities of coral reef fish during exposure to near future climate conditions such as higher water temperature, lower water pH and high salinity. “These techniques allow us to capture and measure those molecular processes which underline fish responses to climate changes. For example, using these approaches, we observed that higher temperature induces a metabolic phenotype while lower pH induces a behavioral impairment where fish are not able to recognize predators anymore. However, we also observed that these fish adapt very fast (one generation) to these new climate conditions if their parents already experienced them,” according to Ravasi.

Figure 1 shows an ISBL transgenerational experiment designed to test the responses of coral reef fish to end of the century ocean temperatures. This is a large collaborative project between the ISBL at KAUST and the ARC Special Research Center for Coral Reef studies at the James Cook University in Australia. The collaborative ISBL research identified several molecular pathways that allowed the fish to better adapt to the higher water temperatures and decreased pH values in the second (F2) generation of fish.


Figure 1. Genomic testing in three generations of coral reef fish. Courtesy of KAUST ISBL

Studying Arabian Pupfish Adaptation to High Salinity

Part of the ISBL research studied the apparent ability for Arabian killifish (pupfish) to adapt to high salinity. The team studied fish from Saudi Arabian coastal lagoons as well as desert ponds. The research discovered that after only six hours in water with reduced pH and increased salinity, the gills’ transcriptional program of desert pond fish resembles those of the fish from the Red Sea lagoon that are adapted to high salinity. We found a set of genes in the gills of the fish that are required to have a specific expression profile in order for the fish to adapt and survive to the high salinity water of the Red Sea.

Research Methods Used in the ISBL Research

The ISBL research used a variety of research methods including:                                                                                

  • PacBio SMRT sequencing (180x coverage)
  • Scaffolded into chromosomes with Hi-C chromosome contact maps (Phase Genomics)

– Scaffold N50 of 45.1 Mb

– 24 chromosomes

  • 800 RNA-Seq based transcriptomes across 5 tissues in temperature and CO2 contests from F0 to F3
  • 90 Genome-wide methylomes in the temperature study
  • 100 Illumina-based re-sequenced genomes in the CO2 study
Figure 2. Genetic Adaptation of Desert Pond fish to increased salinity. Students Lucrezia Bonzi and Celia Schunter from KAUST gathered fish and are responsible for the pictures. Courtesy of KAUST ISBL.

Hardware used in the ISBL Research  

The ISBL team performs their research on the Shaheen II supercomputer, a Cray XC40 delivering over 7.2 Pflop/s of theoretical peak performance. With 5.536 Pflop/s of sustained LINPACK performance, Shaheen II is the 20th fastest supercomputer in the world according to the November 2017 TOP500 list.

The system has 6,174 dual sockets compute nodes based on 16 core Intel Xeon® processors running at 2.3GHz. Each node has 128GB of DDR4 memory running at 2300MHz. Overall, the system has a total of 197,568 processor cores and 790TB of aggregate memory.

KAUST ISBL Makes their Databases Available to Other Researchers

The KAUST ISBL team generates in house computational pipelines for the assembly, analysis and visualization of the genomics and epigenomics datasets.

Figure 4 shows a snapshot of the NemoGenome web browser where people have access to the genome and transcriptome sequences and annotation of the iconic clownfish Amphiprion percula, which in popular culture, is known as Nemo from the Walt Disney movie “Finding Nemo”.

Figure 3. Specification of Cray XC40 Shaheen II. Courtesy of KAUST HPC Lab.

Challenges for Future Climate Change Research

The extensive ISBL research provides encouraging results about the ability of fish to adapt to difficult climate changes and even pass genetic adaptive traits to future generations. However, ISBL performed tests in a controlled laboratory environment. Many questions remain about whether the ability might be true for other fish species as well as if it could occur in a real ecosystem.

Ravasi states, “Despite the fact that in our experiments to date we have used ‘real fish populations’ collected in a real ecosystem, we still create a kind of artificial environment when we put the fish in aquaria. The natural next step is to study the responses of fish to climate change directly in their natural ecosystems without removing them.

For the temperature effect, we were able to collect nine species of coral reef fish over a period of four time points during a coral mass bleaching event that occurred in 2016 in the Great Barrier Reef in Australia. This bleaching event was caused by a thermal anomaly (high water temperature compared to the annual average) caused by the El Nino weather pattern. Now by studying the transcriptomes of these fish, we should be able to see if fish collected in their natural ecosystem react to ocean warming in a similar way we saw in the aquaria experiment.

For ocean acidification, we gained access to natural volcanic CO2 seeps in Milne Bay, Papua New Guinea. In these seeps, CO2 bubbles out of intense volcanic vents in the reef. The excess CO2 dissolves into the surrounding seawater, making water more acidic as we would expect to see in the future. We now plan to sample fish populations living around these seeps and again perform a genomics and epigenomics study to see if the behavioral impairment observed in the aquaria experiments is also seen in a natural ecosystem. Future ocean climate change work will continue to require HPC systems that allow researchers to assemble, analyze and visualize the research data”.

Figure 4. Main page of NemoGenome database website. Courtesy of KAUST ISBL.



Linda Barney is the founder and owner of Barney and Associates, a technical/marketing writing, training and web design firm in Beaverton, OR. 

This article was produced as part of Intel’s HPC editorial program, with the goal of highlighting cutting-edge science, research and innovation driven by the HPC community through advanced technology. The publisher of the content has final editing rights and determines what articles are published.