Global climate change vs. coral reefs
Japanese, Israeli scientists offer genomics-based approach to restoration
Japanese and Israeli scientists recently held collaborative workshops in Okinawa, where they exchanged views on the impact that global-scale climate changes are having on coral reef ecosystems.
Jointly hosting the workshops were the Science Council of Japan, the Israel Academy of Sciences and Humanities, the Okinawa Institute of Science and Technology Graduate University, and the Japanese Coral Reef Society.
Below, I review a recent trend that has scientists taking a genomics-based approach to coral reef research in Japan and touch on topics brought up during the workshops.
About coral reefs
Coral reefs cover 0.2% of the world's ocean regions, yet they are home to 30% of all species of marine life and are some of the most biologically diverse places on Earth.
Reef-building corals, called hermatypic corals, belong to the Cnidaria phylum, which also includes jellyfish and sea anemones. The individual coral polyps depend on unicellular algae that live within their cells for the majority of their nutrients. They use the nutrients provided by these symbiotic algae to form their skeletons, made of calcium carbonate, from the seawater. Over time, these stony frameworks have accumulated to become the massive, complicated structures in the oceans that we call coral reefs.
These reefs nurture a wide variety of marine organisms. By serving as a natural breakwater, they also protect human activity from the tall waves caused by typhoons and other natural events.
However, rising seawater temperatures and other global-scale environmental changes are disrupting the symbiotic relationship between the coral polyps and the algae. Coral bleaching is becoming more frequent, and in 2016 coral reefs around the world, including those off Okinawa, suffered devastating damage. Japan's Environment Ministry reported that bleaching affected 90% of the Sekisei Lagoon, located between Ishigaki Island and Iriomote Island. It is Japan's largest coral reef, and 70% of it is dead.
Worldwide, one-third of reef-building corals are said to be in danger of extinction. When coral reefs collapse, the many marine organisms that live on the reefs lose their habitats, and biodiversity is lost.
Corals are essential to marine ecosystems in tropical and subtropical waters. But most biological research on coral has centered on ecology. Until around 2010, there was little information about the genetics of the corals and their symbiotic algae. There is still much to learn about the phenomenon of coral bleaching, the nature of coral diseases, and the mechanism of the symbiosis between the coral polyps and the algae.
To help advance the biological study of corals, I worked with colleagues to decode the complete genome of Acropora digitifera, which is a species of coral commonly found in the waters of Okinawa. It was the first reported whole genome sequencing of a coral. Using a next-generation sequencer, we decoded the full 420-megabase genome of the coral and identified approximately 23,700 genes.
In analyzing the genome we made five main findings:
- The lineage to the modern reef-building corals goes back further than the fossil record suggested;
- the Acropora genus, which is susceptible to bleaching, lacks the enzyme needed to synthesize cysteine and may depend on its algal symbiont for this amino acid;
- the coral has the independent ability to synthesize mycosporine-like amino acids that absorb ultraviolet radiation;
- the coral has complex innate immune system-related genes;
- and the coral has a number of coral-specific genes related to calcification.
Once we decoded the complete genome of a species of coral, the next step was to decode the genome of a species of algae that has a symbiotic relationship with the coral. So that is what we did, sequencing Symbiodinium minutum.
Previously, chlorella was the only other animal-symbiont algae to have been sequenced, so an analysis of the genomic structure of this coral-symbiont algae proved surprising. Highlights include the findings that this genome incorporates both prokaryotic and eukaryotic families of genes, and that unidirectionally aligned genes are found throughout the genome.
Further research should shed light on how the peculiarities of the genome affect the algae's symbiotic relationship with the coral, and whether the symbiotic relationship is what led to this unique genomic structure.
Reef conservation, restoration
Efforts are currently underway in a number of places to preserve and restore coral reefs. Below is an introduction to how the techniques of genomics can be harnessed for this effort.
To restore and sustainably maintain coral reefs through anthropogenic intervention requires the creation of environments that are as close to the natural settings as possible. This requires not only an accurate understanding of the natural state of coral reefs but also concern for the preservation of genetic diversity and biodiversity, and attention to the risk of genetic destabilization of corals. For example, if the plans call for the transplantation of coral, it is important to collect the coral that will serve as the 'seedlings' from a location of genetic exchange. That, in turn, requires information about genetic exchanges between coral assemblages both within regions and between regions.
Our decoding of the whole-genome sequence of Acropora digitifera coral made it possible to identity a great many single nucleotide polymorphisms, or SNPs, which are places in the genome where the DNA sequence differs by a single base pair.
We used this genomewide SNP information to conduct a high-resolution analysis of the population structure of Acropora digitifera around Okinawa. Our findings suggest that coral dispersal is limited and the range of inhabitation widens only slowly. This means that once a coral reef has been lost, its recovery could take much longer than previously thought.
Furthermore, a recent ecological study around the main Okinawa Island found neighboring coral reefs might have a large contributory effect on recovering coral reefs (reported in a talk by Kazuhiko Sakai, director of the University of the Ryukyus Tropical Biosphere Research Center).
Taken together, this suggests that coral reef conservation efforts in the waters off Okinawa require the protection of coral reefs in each region, and not just those places that are rich in corals.
Although many coral reefs exist in relatively shallow waters (in depths of less than 10 meters), recent reports tell of rich and varied coral reefs in mid-depth waters of 30 meters to 150 meters (reported in a talk by associate professor Saki Harii of the University of the Ryukyus Tropical Biosphere Research Center).
The coral bleaching that took place on a massive scale last summer occurred mainly among corals living at shallow depths. The deeper waters -- where changes in sunlight, water temperature and other environmental factors are less pronounced -- serve as refugia from bleaching. These safe-haven coral communities may play an important role in the preservation and restoration of communities, and they have become a subject of attention in recent years.
One method employed to restore coral reefs is to plant coral fragments, and the most common way to mass-produce these fragments is to clone one fragment to create many in a process of asexual propagation.
However, there are a number of problems associated with asexual propagation. Even if the plantings take hold and the corals produce eggs, they may not survive into a second generation because clones cannot fertilize one another. Also, with clones, there is a risk that all of the corals could suffer the same fate when exposed to an environmental stressor.
By instead planting a variety of coral fragments with different individual characteristics, you can restore the coral reef in a form that can flexibly respond to environmental variations and survive to create progeny.
Because it is extremely difficult to differentiate coral based on their external appearance, methods of DNA testing and profiling need to be developed.
DNA testing methods are typically designed to be used on just the species they have been developed for, but by analyzing genomic information from Acropora digitifera and a second Acropora species belonging to a distant clade, a method has been developed that might possibly be applied to more than 100 corals in the Acropora genus.
This opens the door to the use of DNA profiling for the majority of the coral fragments used for replanting, and the restoration of coral reefs that are just as genetically diverse as a natural coral reef.
In fact, this technology is being utilized in Okinawa Prefecture's coral reef conservation and restoration initiatives in order to restore the coral with biodiversity in mind.
The availability of whole genome sequence data for coral and their symbiotic algae promises to dramatically advance the study of coral biology and help to answer questions and detail how coral coexist with algae and how coral respond to global warming and other environmental changes
This genome information will also help conserve and restore coral reefs more effectively and more efficiently.
The impact of climate change is hitting coral reefs hard, but hopefully these irreplaceable environments of rich biodiversity will persevere.
Chuya Shinzato is associate professor at Atmosphere and Ocean Research Institute's Department of Marine Bioscience of the University of Tokyo. This article was first published in the March 2017 issue of the monthly magazine Trends in the Sciences, edited with the cooperation of the Science Council of Japan, and later translated into English by the Nikkei Asian Review.