51 research outputs found
The Tara Pacific expeditionâA pan-ecosystemic approach of the â-omicsâ 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 effectsâin 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 â-omicsâ 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 (2016â2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an eastâwest transect from Panama to Papua New Guinea and a southânorth 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
Open science resources for the discovery and analysis of Tara Oceans data
Le " Tara ExpĂ©ditions" organise des expĂ©ditions pour Ă©tudier et comprendre l'impact des changements climatiques sur nos ocĂ©ans.International audienceThe Tara Oceans expedition (2009â2013) 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
Basin-Scale Underway Quantitative Survey of Surface Microplankton Using Affordable Collection and Imaging Tools Deployed From Tara
International audienceWorld ocean plankton quantitative biodiversity data are still severely limited due to the high cost and logistical constraints associated to oceanographic vessels and collection/analytic devices. Here, we report the first use of an affordable and open-source plankton collection and imaging kit designed for citizen biological oceanography, composed of a high-speed surface plankton net, the Coryphaena , together with a portable in-flux automated imaging device, the PlanktoScope . We deployed this kit in December 2020 along a latitudinal transect across the Atlantic Ocean on board the schooner Tara , during the first Leg of her âMission Microbiomesâ. The citizen-science instruments were benchmarked and compared at sea to state-of-the-art protocols applied in previous Tara expeditions, i.e. on-board water pumping and filtration system and the FlowCam to respectively sample and image total micro-plankton. Results show that the Coryphaena can collect pristine micro-plankton at speed up to 11 knots, generating quantitative imaging data comparable to those obtained from total, on-board filtered water, and that the PlanktoScope and FlowCam provide comparable data. Overall, the new citizen tools provided a complete picture of surface micro-plankton composition, biogeography and biogeochemistry, opening the way toward a global, cooperative, and frugal plankton observatory network at planetary scale
An integrative assessment of the plastic debris load in the Mediterranean Sea
International audienceThe Mediterranean Sea is recognized as one of the most polluted areas by floating plastics. During the Tara Mediterranean expedition, an extensive sampling of plastic debris was conducted in seven ecoregions, from Gibraltar to Lebanon with the aim of providing reliable estimates of regional differences in floating plastic loads and plastic characteristics. The abundance, size, surface, circularity and mass of 75,030 pieces were analyzed and classified in a standardized multi-parameter database. Their average abundance was 2.60 Ă 105 items kmâ2 (2.25 Ă 103 to 8.50 Ă 106 kmâ2) resulting in an estimate of about 650 billion plastic particles floating on the surface of the Mediterranean. This corresponds to an average of 660 metric tons of plastic, at the lower end of literature estimates. High concentrations of plastic were observed in the northwestern coastal regions, north of the Tyrrhenian Sea, but also off the western and central Mediterranean basins. The Levantine basin south of Cyprus had the lowest concentrations. A Lagrangian Plastic Pollution Index (LPPI) predicting the concentration of plastic debris was validated using the spatial resolution of the data. The advanced state of plastic degradation detected in the analyses led to the conclusion that stranding/fragmentation/resuspension is the key process in the dynamics of floating plastic in Mediterranean surface waters. This is supported by the significant correlation between pollution sources and areas of high plastic concentration obtained by the LPPI
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.status: publishe
Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale
International audienceIn every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modeled at the planetary scale, biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce âPlankton Planetâ, an initiative whose goal is to engage the curiosity and creativity of researchers, makers, and mariners to ( i ) co-develop a new generation of cost-effective (frugal) universal scientific instrumentation to measure the genetic and morphological diversity of marine microbiomes in context, ( ii ) organize their systematic deployment through coastal or open ocean communities of sea-users/farers, to generate uniform plankton data across global and long-term spatio-temporal scales, and ( iii ) setup tools to flow the data without embargo into public and explorable databases. As proof-of-concept, we show how 20 crews of sailors were able to sample plankton biomass from the world surface ocean in a single year, generating the first seatizen-based, planetary dataset of marine plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. The data unveil significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems and microbiomes across the dimensions of the Earth system
Plankton Planet : âseatizenâ oceanography to assess open ocean life at the planetary scale
Abstract In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planetary scale, but biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce â Plankton Planet â, an initiative whose goal is to merge the creativity of researchers, makers, and mariners to ( i ) develop frugal scientific instrumentation and protocols to assess the genetic and morphological diversity of plankton life, and ( ii ) organize their systematic deployment through fleets of volunteer sailors, fishermen, or cargo-ships to generate comparable and open-access plankton data across global and long-term spatio-temporal scales. As proof-of-concept, we show how 20 crews of sailors (âplanktonautsâ) were abl to sample plankton biomass from the world surface ocean in a single year, generating the first citizen-based, planetary dataset of plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. This dataset has unveiled significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems across the dimensions of the Earth system
Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago
International audienc
Aerosol concentration and size distribution (0.25-32”m) measured with an optical particle counter at a 30min granularity during the Tara Pacific Expedition 2016-2018
The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide the continuous dataset originating from an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) instrument acquiring continuously during the full course of the campaign. Aerosols pumped through one of the ([MAST-PUMP]) inlets were channeled through a conductive tubing of 1.9 cm inner diameter to four parallel 47mm filter holders installed in the rear hold using a vacuum pump (Diaphragm pumpME16 NT, VACUUBRAND BmbH & Co KG, Wertheim, Germany) at a minimum flow rate of 30 lpm (20lpm prior to may 2016). Air was conducted to an optical particle counter ([EDM]; EDM180 GRIMM Aerosol Technik Ainring GmbH & Co. KG, Ainring, Germany) measuring and counting particles in the size range 0.25 - 32 ”m as a 30 minutes average, both the particle concentration (nb cm-3) together with its normalized size distribution (dN/dlogDp (nb cm-3 log(nm)-1) i.e., the concentration divided by the log of the width of the bin)
Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1
data setThe tables in this dataset associate metabarcoding sequencing files generated by Genoscope (i.e. fastq.gz files with informative filename structures; with sequencing file pairs associated to unique 'readset' identifiers; housed on their FTP server at www.genoscope.cns.fr/sadc/tarapacific/METABARCODING; with the 'METAB' sequence strategy identifier as part of the sequencing file name) with their associated 'sample-id_source' identifier; as detailed in the 'TARA-PACIFIC_samples-provenance' file part of the 'Tara Pacific samples provenance and environmental context' Zenodo publication (DOI: 10.5281/zenodo.4068292) part of the 'tarapacific' Zenodo community). The main purpose of these tables is to act as a reference to identify samples (i.e., with a single 'sample-id_source') for which sequencing replication exists, per primer set (i.e., more than one set of fastq.gz sequencing files were generated, pre primer set). In the case of replication, these tables classify the replication into three classes color coded as green (same DNA extraction, same PCR, same sequencing run, different sequencing lane), yellow (same DNA extraction, same PCR, different sequencing run) and red (different DNA extraction and/or different PCR). It should be noted that in the vast majority of cases a 'sample-id_source' associates to only one readset per primer set. For a full description of the dataset, please see the included README.</p
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