Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

“…Using transcriptomes from MMETSP together with metatranscriptomes from Tara Oceans (Alberti et al, ; Carradec et al, ; Louca et al, ; Sunagawa et al, ), we could further compare the qualitative shifts in genotypes highlighted above with changes in transcriptional outputs in cyanobacteria (Figures a and b), eukaryotic phytoplankton (Figures c, d, and S5), metazoans (Figure S6 and supporting information S4), and more specifically in diatoms (Figures c, d, and S7). Importantly, ISIP levels were decreased in the leeward stations (Figures a, c, and d), and study of gene switches proposed to be responsive to ambient iron concentrations such as ferredoxin/flavodoxin, plastocyanin/cytochrome c 6 , and FBAI/FBAII (Allen et al, ; Mackey et al, ; Marchetti et al, ; Peers & Price, ; Pierella Karlusich et al, ; Thompson et al, ) revealed patterns generally consistent with increased bioavailability at Stations TARA_123–125 with respect to HNLC Station TARA_122 both in Synechococcus (Figures a and b) and in the major groups of eukaryotic phytoplankton (Figures c, d, S5, and S7).…”

“…In this study, we only used samples collected from the surface water layer. Details about genomics methods are available in Carradec et al () and in the following publications: virus metagenomes (Roux et al, ); prokaryote metagenomes (Sunagawa et al, ); eukaryote metabarcoding (de Vargas et al, ); and eukaryote metagenomes and metatranscriptomes (Alberti et al, ; Carradec et al, ). The abundance of individual genes was assessed by normalization to the total number of sequences within the same organismal group (Carradec et al, ).…”

“…Using transcriptomes from MMETSP together with metatranscriptomes from Tara Oceans (Alberti et al, 2017;Carradec et al, 2018;Louca et al, 2016;Sunagawa et al, 2015), we could further compare the For clarity we focused only on changes in 5-to 20-μm size fractions. Colors indicate the contribution of each station to the total levels.…”

Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics

“…Samples for single cell sorting were collected during the circumglobal Tara Oceans expedition (2009–2013; Karsenti et al, ) and processed as described in Alberti et al (). Flow cytometry cell sorting on cryopreserved samples and genomic DNA amplification by multiple displacement amplification (MDA) were performed at the Single Cell Genomics Center in the Bigelow Laboratory (https://scgc.bigelow.org).…”

Rare microbes from diverse Earth biomes dominate community activity

“…Samples encompass the ocean, Amazon River 15 and its plume into the ocean 16,17 , the human gut 18 , permafrost soil layers 19 , a thermokarst bog 19 , and human-engineered biogas plants 20,21 . Ocean samples span: the sunlit epipelagic [22][23][24][25][26][27][28] (0 -200 m), the dimly lit mesopelagic (200 -1,000 m), dark bathypelagic (1,000 -4,000 m), the benthic zone (near seafloor), and hydrothermal vent plumes 29,30 (Table S1). Our analysis uses database independent de novo high resolution 99% average nucleotide (ANI) contiguous assemblies that captures the entire genomic repertoire from all domains of life.…”