The Ocean as a unique laboratory
Spanning billions of years of evolution and the entire Tree of Life, marine organisms - as individuals, as cells and as biochemichal systems - carry the secrets to understanding how life originated and how it continuously changes.
- 1 CELL BIOLOGY
- 2 EVOLUTIONARY DEVELOPMENTAL BIOLOGY
- 3 ECOSYSTEM GENOMICS
- 4 GENOMICS OF STRESSED AND EXTREME ENVIRONMENTS
- 5 References
The cell is the basic unit of all living organisms, which have originated on several occasions during evolution. Almost all fields of cell biology attract interest of marine cell biologists. Post-genomic techniques such as functional genomics, transcriptomics and proteomics have increased our understanding of how cellular components function, interact and are regulated.
EVOLUTIONARY DEVELOPMENTAL BIOLOGY
Our view of how the development of multicellular organisms proceeds has changed significantly with the arrival of molecular genetics and more recently genomics. As most higher terrestrial organisms are unique or have ancestral representatives in the ocean, marine evo-devo (evolution/development) is a fully fledged field embedded in marine research. There are tight correlations between sequence identity and conservation of gene order. As an example humans have kept quite a few genes from the the slowly evolving marine worm Platynereis.
Such information may help decipher the relationships between animal phyla, that evolves at the same time some 600 million years ago. The closest relative of the vertebrates remains a contentious issue, with most evidence pointing to a cephalochordate ancestor. Comparative developmental research on the sea urchin Strongylocentrotus and the tunicate Oikopleura contribute novel insights in immunology, segmentation and genome duplication.
Despite the large effective population sizes of marine populations and the apparent lack of physical barriers between populations in the ocean, genetic variation between marine populations is huge. As an example, the adaptation of wild Atlantic salmon to salt, brackish and fresh water has been detected at the genetic level. If this adaptating ability is mirrored in more “open” oceanic fish populations, then populations may not interbreed. This has major repercussions for the potential for recolonisation or adaptation to shifting baselines. Natural variation linked to habitat is hard to detect, but clearly progress is being made and this represents a major progress towards understanding evolution and adaptation.
Evolutionary and Ecological Functional Genomics
Until recently a major obstacle to gaining a better understanding of how organisms function in an ecosystem, was due to the lack of appropriate DNA data and relevant model organisms. Now however, we have the ability to perform large-scale screening of both species and populations giving rise to: Evolutionary and Ecological Functional Genomics (EEFG – Feder & Mitchell-Olds 2003). EEFG incorporates functional information encoded in DNA to explain evolutionary and ecological observations. Crucial here is the access to key «ecological» models. This is now being addressed via genomics on species such as the marine microbes: cyanobacteria and coccolithophores, diatoms and multicellular organisms such as tunicates, sea urchins, fish, seagrass, and macroalgae. Processes such as plant-herbivore interactions, host-pathogen interactions, temperature acclimation, life-history traits and behavioural ecology are slowly revealing their secrets. The significance of such research is exemplified in the documentation of the fast evolution of organisms involved in exotic invasions, recovery from pollution and climate shifts. Community genomics: a new discipline An ecosystem is more than the sum of its individual components and their environment and there is a growing interest in the integration of genomics in community ecology. This represents a huge challenge, given the complex link between the outward appearance and behaviour of an organism and its interaction with the environment. An example is the modelling of ecosystems and the significance of the biological pump. Also the impact of invasive species on the native community, for example in the Eastern Mediterranean basin, can be monitored and understood with genomics. Especially those species and populations already at risk due to low population numbers, restricted or patchy habitats, limited climatic ranges, and specific ecosystem services are concerned.
The impact of overfishing
Fisheries have reduced fish biomass in many cases by as much as 90%, an effect compounded by the current climate shift. The impact is felt through a loss of species diversity, a decrease of the averagefood chain length and ecosystem stability. The lossof top predators such as whales, tuna and cod has a measurable effect on smaller sized fishes which become more abundant. Small fishes prey upon zooplankton whose densities decrease, and which in turn reduces cropping of phytoplankton whose biomass increases leading to algal blooms. The effect is monitored at higher trophic levels with a measurable loss of adaptive genetic diversity. In the North Sea cod stocks have experienced massive depletions in numbers with a migration from traditional spawning grounds to colder latitudes. The stocks of the marbled rockcod and the mackerel icefish have yet to recover from collapses that occurred in the 1970s. These may not be European fish species, but European fisheries were involved in their overfishing. In the global economy, we have to take responsibility for world fisheries, not only those stocks on our doorstep.
GENOMICS OF STRESSED AND EXTREME ENVIRONMENTS
Extreme environments abound in the ocean. At great depths there are pressure effects and unique chemical environments found close to warm and coldwater seeps. In coastal region with high levels of evaporation, areas may become hypersaline, and where temperatures soar, oxygen solubility drops. in polar regions the ice traps marine life, and in isolated basins anoxia may rule. It is striking that all levels of marine life have adapted to these circumstances. The discovery of a deep-sea hydrothermal vent in the Galapagos Rift in the Pacific Ocean in 1977 at a depth of 2,600 meters, introduced a paradigm shift in our thinking about physiological processes and evolutionary adaptation. Suddenly, life was possible at the most extreme conditions of pressure, temperature, acidity, ion concentration and oxygen. Previously undocumented symbiotic associations between bacteria and a range of undescribed animals were discovered. Another example is provided by «black smokers». With limited input from solar energy and at temperatures ranging from 360°C to 0°C in the surroundings, black smokers fuel a diverse and productive ecosystem of microorganisms and even some species of worms, mussels and crabs.
At the other extreme of the temperature range, in Antarctica, biodiversity is also very rich. 17% of the world’s sea spiders, 12% of polychaete worms, 10% of sea cucumbers and 9-10% of amphipods live in the Southern Ocean. These species are over-represented when considering the area and volume of the ocean, compared to the rest of the planet . Genomic studies on these animals are in their infancy even though these stenothermal species are potential sentinels of climate change, in addition to being sources of biotechnology products, such as antifreezes and cold-adapted proteins. With improved access to DNA sequencing facilities, we are now able to compare these extremophiles with their better known temperate water relatives and determine what makes them unique and able to survive in such extreme environments. Extremophile biology has become a mature field with novel developments in enzymology, polymer and carbohydrate chemistry.