Plankton networks driving carbon export in the oligotrophic ocean

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 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

The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Data - Tara Oceans, Malaspina and OSD

This Section will compile data from Marine Metagenome Initiatives such as Tara Oceans, Malaspina and OS

Assessing the magnitude and significance of deep chlorophyll maxima of the coastal eastern indian Ocean

Deep chlorophyll maxima (DCM) have the capacity to fuel substantial fractions of total water column production. The ecological importance of a ubiquitous DCM layer ranging from 50 to 120 m deep within Leeuwin Current (LC) and offshore waters of Western Australia is addressed here using data from a regional oceanographic field study conducted during the austral summer of 2000. Phytoplankton communities from surface and DCM layers were compared by examining pigments (chlorophyll a), phytoplankton carbon, photosynthetic characteristics and productivity rates estimated using 14C-based photosynthesis versus irradiance relationships. In the DCM layer, both extracted pigments (up to 0.83 mg m−3) and phytoplankton carbon (6.4–54.4 mg C m−3) were maximal, and were on average 6 and 5 times larger than in the surface layer, respectively. Sensitivity analyses were performed on production estimates using regionally relevant ranges of light attenuation (Kd=0.050–0.066 m−1) and photoinhibition (β*=0.00–0.01 mg C (mg chl a)−1 h−1 [μmol m−2 s−1]−1). These analyses provide upper and lower limits on previously reported estimates of primary production for the region, and show that small differences in light attenuation and photoinhibition can significantly affect computations of primary production and cause a shift from surface-dominated to DCM-dominated production scenarios. The contribution of the DCM layer to total water-column production ranged from a maximum of 30–70% under the scenarios examined. A regional overview of nitrate and stratification conditions in relation to the depth of the phytoplankton biomass maximum indicated that the critical balance between light and nutrients was a key factor driving DCM structure. We show that changing oceanographic conditions in both the along-shore and cross-shore directions, which included latitudinal variation in the strength of the LC, are accompanied by changes in the depth (and in turn production) of the DCM. The previously unrecognized significance of these DCM layers in the coastal eastern Indian Ocean has important implications for satellite-based estimates of production within the region

Methodology used on board to prepare samples from the Tara Oceans Expedition (2009-2013)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides methodological context about the sampling and on-board-preparation of samples during the Tara Oceans Expedition (2009-2013). For each sample, we provide details about the standard protocols (i.e. Sample Method) as well as deviations from these protocols (i.e. Sample Comment). We also provide URLs to related data, sampling logsheets, campaign summary reports, oceanographic reports, and step-by-step protocols

Systematics of a rare radiolarian— Coelodiceras spinosum Haecker (Sarcodina: Actinopoda: Phaeodaria: Coelodendridae)

International audienceWe describe a specimen of Coelodiceras spinosum Haecker 1908 [Haecker, V., 1908. Tiefsee-Radiolarien. Wissenschaftliche ergebnisse der Deutschen Tiefsee-Expedition. 14, 1-706] (Sarcodina: Actinopoda: Radiolaria: Phaeodaria: Coelodendridae) collected in a sediment trap deployed in the Indian Ocean, 300 NM WNW off Perth, Western Australia, updating Haecker's 1908 description. Our specimen was collected in the centre of a cold-core eddy at a depth of 300 m. The intact silica structure of the specimen lacked soft organic material, suggesting that the organism was dead when it entered the trap; the traps were deployed for 10 days and did not contain poison or preservative. In this paper, we expand the original description of C. spinosum by Haecker (1908) [Haecker, V., 1908. Tiefsee-Radiolarien. Wissenschaftliche ergebnisse der Deutschen Tiefsee-Expedition. 14, 1-706], using Scanning Electron Microscopy (SEM). Our specimen had three frenula and a short rhinocanna, differing from the single frenulum and long rhinocannae described by Haecker (1908) [Haecker, V., 1908. Tiefsee-Radiolarien. Wissenschaftliche ergebnisse der Deutschen Tiefsee-Expedition. 14, 1-706]

Methodology used in the lab for molecular analyses and links to the Sequence Read Archive of selected samples from the Tara Oceans Expedition (2009-2013)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides URLs to sequence read files available from samples analysed to date, along with their corresponding contextual data and sequencing methods described in details in the companion data article