Oceans cover over 70 percent of the Earth’s surface and regulate the planet’s weather, climate, and atmospheric composition. They sustain a large proportion of the planet’s biodiversity and contain substantial quantities of living and non-living resources. However, many regions remain unexplored and many of their basic biological and chemical processes are poorly understood. Less than 20 years ago the study of oceans was restricted to studies of organisms that could be grown in the laboratory. However, with advent of new molecular tecnnologies, a new field named ocean genomics has emerged in the last couple of years. Especially one technique, high-throughput sequencing, has revolutionized the way we study life in the world ocean. In contrast to most terrestrial habitats, life in the sea is dominated, both in terms of biomass and metabolism, by microorganisms from all three domains of life. Therefore, ocean genomics is mostly related to the study of these small organisms. Studies in this field have changed the way we understand the diversity of life in oceans. This new field has been pioneered by Craig Venter. With a somewhat brute force approach, they collected large volumes of water from the ocean, filtered out the microbes and decoded the genomic make-up of these single-cell organisms. Chamberlin and Dickey 2008 have revealed that the DNA of different organisms at different depths of the ocean are unique and revealed an entirely different world in the ocean. Their work has provided a new understanding of metabolic pathways. We now realise that we know even less about the microbial processes that are very important, for example, for governing carbon cycle, productivity of the ocean for food.
MOTIVATION - Why ocean genomics?Edit
With its huge biomass, oceans provide a great opportunity to estimate true biodiversity on earth. Massive sequencing techniques allow us to explore such a biodiversity at genomic level. Its study is expected to help us in problems such as: * The origin of life * Discovery of new species As an example, through the Global Ocean Sampling Expedition, metagenomic samples have been collected from different places around the world. All of these samples are sequenced using shotgun sequencing, in hopes that new genomes (and therefore new organisms) would be identified. A pilot project, conducted in the Sargasso Sea, found DNA from nearly 2000 different species, including 148 types of bacteria never seen before (Venter et al, 2004.) * Discovery of alternative metabolic pathways, genetic codes and specific adaptations. * Gene transfer across species
Practical ecological understandingEdit
Ocean genomics also represents an opportunity to study the extent of biodiversity under different and very diverse ecological niches. These niches probably accommodate habitats for very diverse set of species interactions, including different types of symbiosis. Understanding the human impact on aquatic ecosystems will also allow us to estimate its consequences at mid- and long- term.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment. Nowadays the advance of technology makes it possible to access the genomes of every ecosystems including the ones of the oceans.
Early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get (mostly) unbiased samples of all genes from all members of sampled communities.
Beginning in 2003, Craig Venter, leader of the privately-funded parallel of the Human Genome Project, has led the Global Ocean Sampling Expedition, circumnavigating the globe and collecting metagenomic samples throughout. All of these samples are sequenced using shotgun sequencing, in hopes that new genomes (and therefore new organisms) would be identified. The pilot project, conducted in the Sargasso Sea, found DNA from nearly 2000 different species, including 148 types of bacteria never before seen. As of 2009, Venter has circumnavigated the globe and thoroughly explored the West Coast of the United States, and is currently in the midst of a two-year expedition to explore the Baltic, Mediterranian and Black Seas. Another dimension is studied by comparing the genomes in function of the depth where the sample was collected.
Hypothesis driven experimentsEdit
This is the more classical approach in science. One hypothesis is formulated and the experiment is designed based on it. It can be focused in the life cycle of a living organism, a particular biochemical pathway or a complete ecosystem.
For example, there was a particular study focused on the change of the environment in the Gulf of Mexico after the oil disaster. Scientists analyzed how did some species adapt to the new dramatic conditions and did they manage to continue their life cycles.
There are a couple of porjects focusing on ocean genomics. They include but are not limited to the following: *Global Ocean Sampleing Project: http://www.jcvi.org/cms/research/projects/gos/overview/ *The Marine Genomics Project: http://www.marinegenomics.org/ *Marine Biodiversity and Ecosystem Functioning EU Network of Excellence: http://www.marbef.org/ *Microbial Genome Sequencing Project: http://camera.calit2.net/microgenome/ *Marine Microbial Genomic Sequencing Project: http://giovannonilab.science.oregonstate.edu/marine-microbial-genome-sequencing-project
European Commision marine biodiversity, genomics networks
Origin of our understanding.Edit
Starting with Miller’s "prebiotic soup" experiment (Miller 1953, Miller-Urey experiment) which produced amino acids, essential to life, studying ocean genomics allow us to understand better chemistry on the building blocks of life. Among these are the synthesis of nucleotides, polymerization of nucleotides to oligonucleotides, incorporation of a self-copying gene into simple ‘cells’ upon which natural selection could act, and the origin of homochirality of amino acids and sugars. Gattering and placing together the original puzzle pieces of life from beginning to current gives scientific assumption of our origin of life more plausible.
Comprenhending anthropological disturbances. Refining our understanding of biology.Edit
With current anthropogenic disturbances (climate change driving ocean warming, oil spills, coastal disturbances, current radiation issues, over fishing/illegal fishing, run off pollution, run off fertilizer, etc...) we can use societal ignorance and its effects on the ocean, and in turn the planet, to further our comphrension of how drastic and disturbing our presence effects these areas. The field of ocean genomics can be implemented from an extremely conservationist and preventionist point of view, using it to further our understanding on how these effected organisms are adjusting to our presence and to our invasion and disturbance to their environments as well as precautionary guidelines to preserve vunerable species, our oceans, and in longterm ourselves. The strategies and techniques for marine conservation can combine theoretical disciplines, such as population biology, with practical conservation strategies, such as setting up protected areas, as with marine protected areas or Voluntary Marine Conservation Areas.
Pushing forward our knowledge.Edit
But in the future, coastal disturbances, over fishing/illegal fishing, run off pollution and fertilizers, won’t be the worst thing stripping the oceans of oxygen, as global warming’s effects could leave the seas deprived of oxygen for thousands of years. Carbon dioxide accumulates in Earth's atmosphere, warming the planet, the oceans warm in response. Already, oxygen levels in the world's seas have been declining for decades as the water has, on average, become warmer. This warming in turn alters the chemistry of the ocean, specifically, decreasing the waters' ability to hold oxygen. Several studies in recent years have shown this relationship. (Andrea Thompson, 28 Jan 2009)