Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.

Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.T he sunlit surface layer of the world'soceans functionsasagiantbiogeoch emicalmem-brane between the atmosphere and the ocean interior (1). This biome includes plank-ton communities that fix CO 2 and other elements into biological matter, which then enters the food web. This biological matter can be remineralized or exported to the deeper ocean, where it may be sequestered over ecological to geological time scales. Studies of this biome have typically focused on either conspicuous phyto-or zooplankton at the larger end of the organismal size spectrum or microbes (prokaryotes and viruses) at the smaller end. In this work, we studied the taxonomic and ecological diversity of the intermediate size spectrum (from 0.8 mmtoafew millimeters), which includes all unicellular eukary-otes (protists) and ranges from the smallest pro-tistan cells to small animals (2). The ecological biodiversity of marine planktonic protists has been analyzed using Sanger (3-5) and high-throughput (6, 7) sequencing of mainly ribosomal DNA (rDNA) gene markers, on relatively small taxonomic and/or geographical scales, unveiling key new groups of phagotrophs (8), parasites (9), and phototrophs (10). We sequenced 18S rDNA metabarcodes up to local and global saturations from size-fractionated plankton communities sampled systematically across the world tropical and temperate sunlit oceans. A global metabarcoding approachTo explore patterns of photic-zone eukaryotic plankton biodiversity, we generated ~766 million raw rDNA sequence reads from 334 plankton samples collected during the circumglobal Tara Oceans expedition (11). At each of 47 stations, plankton communities were sampled at two water-column depths corresponding to the main hydrographic structures of the photic zone: subsurface mixed-layer waters and the deep chlorophyll maximum (DCM) at the top of the thermocline. A low-shear, nonintrusive peristaltic pump and plankton nets of...

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset of 195,728 60 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (interpopulation diversity) and microdiversity (intra-population genetic variation). These patterns 65 sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models. Introduction: 70Biodiversity is essential for maintaining ecosystem functions and services (reviewed by Tilman et al., 2014). In the oceans, the vast majority of biodiversity is contained within the microbial fraction containing prokaryotes and eukaryotic microbes, which represents ~60% of its biomass (Bar-On et al., 2018). Meta-analyses looking at changes in marine biodiversity show that biodiversity loss increasingly impairs the ocean's capacity to produce food, maintain water 75 quality, and recover from perturbations (Worm et al., 2006). To date, marine conservation efforts have focused on specific organismal communities, such as fisheries or coral reefs, rather than conserving whole ecosystem biodiversity. However, emerging studies across diverse sampled, global-scale, viruses-to-fish-larvae datasets (de Vargas et al., 2015; Sunagawa et al., 125 2015;Brum et al., 2015;Lima-Mendez et al., 2015;Pesant et al. 2015;Roux et al., 2016), and help establish foundational ecological hypotheses for the field and a roadmap for the broader life sciences community to better study viruses in complex communities. Results & Discussion:The dataset. The Global Ocean Viromes 2.0 (GOV 2.0) dataset is derived from 3.95 Tb 130 of sequencing across 145 samples distributed throughout the world's oceans ( Fig. 1A and Table S3; see Methods). These data build on the prior GOV dataset (Roux et al., 2016) by increased sequencing for mesopelagic samples (defined in our dataset as waters between 150m to 1,000m) and upgrading assemblies, both of which drastically improved sampling of the ocean viruses in these samples (results below). Additionally, we added 41 new samples derived from the Tara 135Oceans Polar Circle (TOPC) expedition, which traveled 25,000 km around the Arctic Ocean in 2013. These 41 Arctic Ocean viromes were generated to represent the most significantly climateimpacted region of the ocean, and an extreme environment. N...

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.

The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterised. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria, alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of just a few bacterial and viral genes can predict most of the variability in carbon export in these regions. Guidi et al. Page 2 Nature. Author manuscript; available in PMC 2016 September 22. Europe PMC Funders Author Manuscripts Europe PMC Funders Author ManuscriptsMarine planktonic photosynthetic organisms are responsible for approximately fifty percent of Earth's primary production and fuel the global ocean biological carbon pump 1 . The intensity of the pump is correlated to plankton community composition 2,3 , and controlled by the relative rates of primary production and carbon remineralisation 4 . About 10% of this newly produced organic carbon in the surface ocean is exported through gravitational sinking of particles. Finally, after multiple transformations, a fraction of the exported material reaches the deep ocean where it is sequestered over thousand-year timescales 5 .Like most biological systems, marine ecosystems in the sunlit upper layer of the ocean (denoted the euphotic zone) are complex 6,7 , characterised by a wide range of biotic and abiotic interactions [8][9][10] and in constant balance between carbon production, transfer to higher trophic levels, remineralisation, and export to the deep layers 11 . The marine ecosystem structure and its taxonomic and functional composition likely evolved to comply with this loss of energy by modifying organism turnover times and by the establishment of complex feedbacks between them 6 and the substrates they can exploit for metabolism 12 .Decades of groundbreaking research have focused on identifying independently the key players involved in the biological carbon pump. Among autotrophs, diatoms are commonly attributed to being important in carbon flux because of their large size and fast sinking rates 13-15 while small autotrophic picoplankton may contribute directly through subduction of surface water 16 or indirectly by aggregating with larger settling particles or consumption by organisms at higher trophic levels 17 . Among heterotrophs, zooplankton such as crustaceans impact carbon flux via production of fast-sinking fecal pellets...

This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.Supplementary informationThe online version of this article (doi:10.1038/nbt.4306) contains supplementary material, which is available to authorized users.

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.