A Holistic Approach to Marine Eco-Systems Biology

With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system. Viruses, bacteria, archaea, protists, and planktonic metazoans form the bulk of biomass throughout the oceans and drive the global biogeochemical cycles that regulate the Earth system [6],[9],[10]. For instance, marine microbes produce nearly as much oxygen through primary production as land plants [11]. This system is driven by a complex ecological network of autotrophic, heterotrophic, and mixotrophic organisms, where trophodynamics and biogeochemical interdependencies are determining factors for primary production rates in marine systems. In addition, ocean viruses modulate primary production by inducing organism mortality and by encoding core photosynthesis genes that are expressed during infection [12]–[14]. Therefore, only an ecosystem-wide approach, from viruses to metazoans, will enable us to start disentangling the functioning of the Earth system. This approach ranges from mapping organismal diversity across scales spanning five orders of magnitude to developing empirical datasets that inform conceptual models about the complex interplay between organisms driving fluxes of energy, biogeochemical, and molecular “currencies” in ocean ecosystems [15]. A global-scale study of morphological, genetic, and functional biodiversity of plankton organisms in relation to the changing physico-chemical parameters of the oceans [8],[16]–[18] is now critical to understanding and managing our fragile oceans. Specifically, such a dataset will improve our understanding of the principles governing marine ecosystems and the evolution of life in the ocean, thus enhancing our capacity of assessing ecosystem services and enabling a better prediction of fish stock distribution and impacts of global climate variations [19]. Planktonic organisms are also an enormous but largely untapped source [8],[20] of bio-active compounds for the pharmaceutical, food, and cosmetics industries, as well as metabolic pathways that may provision our future energy needs [21]. In this context, the Tara Oceans consortium was founded, which embarked on a 3-year research cruise across the worlds' oceans. Tara Oceans is not the first group to explore global ocean biodiversity. For example, previous global initiatives include satellite-based chlorophyll measurements, the Census of Marine Life, long-term observation sites, and arrays of remote sensors on floats that provide physical, chemical, and biological data [15]. Other global genomics studies have been launched, e.g., Global Ocean Sampling (GOS) expedition [22] and the Earth Microbiome [23] project, as well as integrative projects focusing on specific biomes (e.g., Malaspina, http://www.expedicionmalaspina.es/). However, Tara Oceans takes such investigations one step further by integrating the genetic, morphological, and functional diversity in its environmental context at global ocean scale and at multiple depths (Figure 1), from viruses to fish larvae. While such a “study it all” approach is not novel (e.g., NSF Long Term Ecological Research sites), it has remained science fiction until technology and informatics became enabling. Now, high throughput sequencing, quantitative imaging methods, dedicated bio-informatics and modeling tools are poised to assess the complexity of the global ocean systems. To achieve such integration, Tara Oceans is driven by researchers with expertise in biological and physical oceanography, ecology, microbiology, systematics, molecular, cellular and systems biology, bioinformatics, data management, and modeling. Figure 1 The Tara Oceans cruise. Pragmatically, to accomplish such an ambitious goal, Tara Oceans consortium scientists have necessarily been intimately involved in every aspect of the expedition. This includes planning, preparation, and running of the on-board sampling protocols, as well as the development of sample analysis and bioinformatics pipelines, data management, and modeling projects. This involvement ensures a coherent worldwide data collection and analysis strategy, which is reinforced through regular workshops. The consortium has an open access policy concerning the data that will be made available to the scientific community as soon as possible after validation. Finally, a significant outreach effort is made to show life on board of Tara as well as translate results to the broader public (see http://oceans.taraexpeditions.org/ and http://www.planktonchronicles.org).