The ABYSS project aims at describing deep-sea benthic biodiversity spanning several branches of the tree of life with eDNA metabarcoding tools. To accommodate both micro- and macro biologists, we designed a bioinformatic pipeline based on Illumina read correction with Dada2 allowing analysing metabarcodes from prokaryotic and eukaryotic life compartments.

The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly under target of resource-extraction industries although being drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased towards describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on DNA metabarcoding biodiversity inventories targeting prokaryotes (16S-V4V5), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed towards small fragments, we evaluated the effect of removing short DNA fragments via size-selection and ethanol reconcentration using DNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by DNA and RNA co-extracted from 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using environmental RNA (eRNA). With ribosomal loci, RNA, while resolving similar spatial patterns than co-extracted DNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to over-abundance of rRNA and RNA release. With the mitochondrial locus, RNA detected lower metazoan richness and resolved less spatial patterns than co-extracted DNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (≥10 g) for accurately surveying eukaryotic diversity. We conclude that DNA should be favoured over RNA for logistically realistic, repeatable, and reliable surveys, and confirm that large sediment samples (≥10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns. The data associated to this work can be found following the link below, with raw sequencing data in the data/dna-sequence-raw folder, taxonomic assignment databases in the data/sequence-set-nucleic-acid folder, and all analyses outputs can be found in the /operation folder. The bioinformatic scripts can be downloaded from: https://gitlab.ifremer.fr/abyss-project

The project was designed to explore biological rhythms in the hydrothermal vent mussel Bathymodiolus azoricus. The experiment provides the first high-resolution temporal transcriptomes of an hydrothermal species, both in situ and in the laboratory.

This study aimed to optimize the sampling strategy for environmental DNA (eDNA) metabarcoding targeting prokaryote, protistan, and metazoan life compartments in deep-sea sediment and aboveground water samples. For sediment, we evaluated the effect of sieving sediment to separate size classes and avoid biomass biases, and compared results to inventories obtained through DNA directly extracted from 10 g of sediment. For water, we evaluated the performance of two sampling devices: 7.5 L sterile sampling boxes and a newly developed high-throughput in situ pump. We applied these four sampling methods on a deep-sea site and evaluated resulting biodiversity inventories targeting metazoans (18S V1-V2, COI), but also prokaryotes (16S V4-V5) and unicellular eukaryotes (18S V4). The data associated to this work can be found following the DOI link below, with raw sequencing data in the data/dna-sequence-raw folder, taxonomic assignment databases in the data/sequence-set-nucleic-acid folder, and all analyses outputs can be found in the /operation folder. The bioinformatic scripts can be downloaded from: https://gitlab.ifremer.fr/abyss-project

We explored the whole digestive gland transcriptome in the Pacific oyster Crassostrea gigas using Illumina sequencing technology and compare the expression patterns obtained in: i) oysters exposed experimentally at environmentally-realistic concentration to Alexandrium minutum Daoulas1257 strain isolated from the Bay of Brest in France producing only PSTs; ii) AM89BM strain, isolated from the Bay of Morlaix in France producing both PSTs and BECs; iii) CCMI1002 strain, isolated from Irish waters producing only BECs; and iv) control oysters fed with the non-toxic dinoflagellate Heterocapsa triquetra.