Daniele Iudicone

Eukaryotic plankton diversity in the sunlit ocean

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.

Structure and function of the global ocean microbiome

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.

Patterns and ecological drivers of ocean viral communities

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.

Seasonal variability of the mixed layer depth in the Mediterranean Sea as derived from in situ profiles

A new 0.5° resolution Mediterranean climatology of the mixed layer depth based on individual profiles of temperature and salinity has been constructed. The criterion selected is a threshold value of temperature from a near-surface value at 10 m depth, mainly derived by a method applied on the global (de Boyer Montegut et al., 2004 dBM04). With respect to dBM04, the main differences reside in the absence of spatial interpolation of the final fields and in the improved spatial resolution. These changes to the method are necessary to reproduce the Mediterranean mixed layers behavior. In the derived climatological maps, the most relevant features of the basin surface circulation are reproduced, as well as the areas prone of the deep water formation are clearly identified. Finally, the role of density in the definition of the mixed layers differing behaviors between the oriental and the occidental regions of the basin is presented.

Plankton networks driving carbon export in the oligotrophic ocean.

The biological carbon pump is the process by which CO2 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 uncharacterized. 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 and 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 a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Water-mass transformations in a neutral density framework and the key role of light penetration

A new formulation is proposed for the evaluation of the dianeutral transport in the ocean. The method represents an extension of the classical diagnostic approach for estimating the water-mass formation from the buoyancy balance. The inclusion of internal sources such as the penetrative solar shortwave radiation (i.e., depth-dependent heat transfer) in the estimate of surface buoyancy fluxes has a significant impact in several oceanic regions, and the former simplified formulation can lead to a 100% error in the estimate of water-mass formation due to surface buoyancy fluxes. Furthermore, internal mixing can also be overestimated in inversions of in situ data when the shortwave radiation is not allowed to be penetrative. The method examines the evolution equation of neutral density via the tendencies of potential temperature and salinity. The neutral density framework does not require the choice of a reference pressure and thus, unlike previous approaches that consider potential density, it is well suited for examining the whole open-ocean water column. The methodology is easy to implement, particularly for ocean numerical models. The authors present here its application to a long simulation made with an ice–ocean global model, which allowed the method to be validated.

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

The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.

Insights into global diatom distribution and diversity in the world’s ocean

Significance Diatoms, considered one of the most diverse and ecologically important phytoplanktonic groups, contribute around 20% of global primary productivity. They are particularly abundant in nutrient-rich coastal ecosystems and at high latitudes. Here, we have explored the dataset generated by Tara Oceans from a wide range of oceanic regions to characterize diatom diversity patterns on a global scale. We confirm the dominance of diatoms as a major photosynthetic group and identify the most widespread and diverse genera. We also provide a new estimate of marine planktonic diatom diversity and a global view of their distribution in the world’s ocean. Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

Environmental characteristics of Agulhas rings affect interocean plankton transport

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

The role of Southern Ocean surface forcings and mixing in the global conveyor

Despite the renewed interest in the Southern Ocean, there are yet many unknowns because of the scarcity of measurements and the complexity of the thermohaline circulation. Hence the authors present here the analysis of the thermohaline circulation of the Southern Ocean of a steady-state simulation of a coupled ice–ocean model. The study aims to clarify the roles of surface fluxes and internal mixing, with focus on the mechanisms of the upper branch of the overturning. A quantitative dynamical analysis of the water-mass transformation has been performed using a new method. Surface fluxes, including the effect of the penetrative solar radiation, produce almost 40 Sv (1 Sv 10 6 m 3 s 1 ) of Subantarctic Mode Water while about 5 Sv of the densest water masses ( 28.2) are formed by brine rejection on the shelves of Antarctica and in the Weddell Sea. Mixing transforms one-half of the Subantarctic Mode Water into intermediate water and Upper Circumpolar Deep Water while bottom water is produced by Lower Circumpolar Deep Water and North Atlantic Deep Water mixing with shelf water. The upwelling of part of the North Atlantic Deep Water inflow is due to internal processes, mainly downward propagation of the surface freshwater excess via vertical mixing at the base of the mixed layer. A complementary Lagrangian analysis of the thermohaline circulation will be presented in a companion paper.