Open science resources for the discovery and analysis of Tara Oceans data

Pesant, Stéphane; Not, Fabrice; Picheral, Marc; Kandels‐Lewis, Stefanie; Bescot, Noan Le; Gorsky, Gabriel; Iudicone, Daniele; Karsenti, Eric; Speich, Sabrina; Troublé, Romain; Dimier, Céline; Searson, Sarah

doi:10.1038/sdata.2015.23

Cited by 895 publications

(441 citation statements)

References 72 publications

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“…While recent oceanographic efforts such as Tara Oceans (Pesant et al, 2015) and Malaspina (Duarte, 2015) expeditions have generated a staggering wealth of novel observational data on plankton distribution and diversity (Figure 1), these same data have revealed the extent of our ignorance of marine ecosystem structure and function. A large fraction of plankton diversity recorded in recent surveys cannot be assigned to known taxonomic groups (de Vargas et al, 2015), highlighting how profoundly our knowledge of the planktonic world is biased toward the taxa sampled or cultured.…”

Section: Introductionmentioning

confidence: 99%

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

et al. 2017

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With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the "Impact of climate change on the distribution of plankton functional and phylogenetic diversity" (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: (1) What can we learn about plankton communities from the new wealth of high-throughput "omics" data? (2) What is the link between plankton diversity and ecosystem function? (3) How can species distribution models be adapted to represent plankton biogeography? (4) How will plankton biogeography be altered due to anthropogenic climate change? and (5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way.

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Section: Introductionmentioning

confidence: 99%

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

et al. 2017

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“…http://dx.doi.org/10.1101/053090 doi: bioRxiv preprint first posted online May. 12, 2016; 46 . These included samples from a range of depths: surface, deep chlorophyll maximum, bottom of mixed layer when no deep chlorophyll maximum was observed (Station 123, 124, and 125), and mesopelagic samples.…”

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confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

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et al. 2016

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Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

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“…Sample collection and preparation were described previously (Logares et al, 2014;Pesant et al, 2015;Sunagawa et al, 2015). The current analysis focuses on 139 DNA samples from the two smallest size fractions (0.2-1.6 μm and 0.2-3 μm).…”

Section: Samplingmentioning

confidence: 99%

Global genetic capacity for mixotrophy in marine picocyanobacteria

et al. 2016

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The assimilation of organic nutrients by autotrophs, a form of mixotrophy, has been demonstrated in the globally abundant marine picocyanobacterial genera Prochlorococcus and Synechococcus. However, the range of compounds used and the distribution of organic compound uptake genes within picocyanobacteria are unknown. Here we analyze genomic and metagenomic data from around the world to determine the extent and distribution of mixotrophy in these phototrophs. Analysis of 49 Prochlorococcus and 18 Synechococcus isolate genomes reveals that all have the transporters necessary to take up amino acids, peptides and sugars. However, the number and type of transporters and associated catabolic genes differ between different phylogenetic groups, with lowlight IV Prochlorococcus, and 5.1B, 5.2 and 5.3 Synechococcus strains having the largest number. Metagenomic data from 68 stations from the Tara Oceans expedition indicate that the genetic potential for mixotrophy in picocyanobacteria is globally distributed and differs between clades. Phylogenetic analyses indicate gradual organic nutrient transporter gene loss from the low-light IV to the high-light II Prochlorococcus. The phylogenetic differences in genetic capacity for mixotrophy, combined with the ubiquity of picocyanobacterial organic compound uptake genes suggests that mixotrophy has a more central role in picocyanobacterial ecology than was previously thought.

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Open science resources for the discovery and analysis of Tara Oceans data

Cited by 895 publications

References 72 publications

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Global genetic capacity for mixotrophy in marine picocyanobacteria

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