Publications by authors named "J Poulain"

152 Publications

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients.

ISME J 2021 Jun 8. Epub 2021 Jun 8.

Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.

Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.
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http://dx.doi.org/10.1038/s41396-021-01021-wDOI Listing
June 2021

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection.

Anim Microbiome 2021 May 7;3(1):35. Epub 2021 May 7.

Ifremer, IRD, Institut Louis-Malardé, Univ Polynésie Française, EIO, F-98719 Taravao, Tahiti, Polynésie Française.

Background: Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154 provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host-pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model.

Results: We showed that the infection of the host is characterised by an enhancement of functions associated with antibiotic and glucans catabolism functions but a reduction of sulfate assimilation process in T. maritimum. The fish host concurrently displays a large panel of immune effectors, notably involving innate response and triggering acute inflammatory response. In addition, our results suggest that fish activate an adaptive immune response visible through the stimulation of T-helper cells, Th17, with congruent reduction of Th2 and T-regulatory cells. Fish were, however, largely sensitive to infection, and less than 25% survived after 96 hpi. These surviving fish showed no evidence of stress (cortisol levels) or significant difference in microbiome diversity compared with controls at the same sampling time. The presence of T. maritimum in resistant fish skin and the total absence of any skin lesions suggest that these fish did not escape contact with the pathogen, but rather that some mechanisms prevented pathogens entry. In resistant individuals, we detected up-regulation of specific immune-related genes differentiating resistant individuals from controls at 96 hpi, which suggests a possible genomic basis of resistance, although no genetic variation in coding regions was found.

Conclusion: Here we focus in detail on the interplay between common fish pathogens and host immune response during experimental infection. We further highlight key actors of defence response, pathogenicity and possible genomic bases of fish resistance to T. maritimum.
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http://dx.doi.org/10.1186/s42523-021-00097-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106148PMC
May 2021

Complete Genome Sequences of Two Species Isolated from Marine Environments of the Pacific Ocean.

Microbiol Resour Announc 2021 Apr 22;10(16). Epub 2021 Apr 22.

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France

YsY11 and T9AD were both isolated from marine environments of the Pacific Ocean. Here, we report the whole-genome sequences of these two organisms. YsY11 consists of a single 4.77-Mb chromosome, and T9AD consists of a 5.57-Mb chromosome and a 2.8-kb plasmid.
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http://dx.doi.org/10.1128/MRA.01062-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063651PMC
April 2021

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA.

Sci Rep 2021 Apr 12;11(1):7856. Epub 2021 Apr 12.

Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280, Plouzané, France.

Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1-V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
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http://dx.doi.org/10.1038/s41598-021-86396-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041860PMC
April 2021

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding.

Mol Ecol Resour 2021 Apr 9. Epub 2021 Apr 9.

MARBEC, University of Montpellier, Ifremer, IRD, CNRS, Sète, France.

Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on read correction with DADA2 allowing analysing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster amplicon sequence variants (ASVs) into operational taxonomic units (OTUs) with swarm, a network-based clustering algorithm, and the option to curate ASVs/OTUs using LULU. Finally, taxonomic assignment was implemented via the Ribosomal Database Project Bayesian classifier (RDP) and BLAST. We validated this pipeline with ribosomal and mitochondrial markers using metazoan mock communities and 42 deep-sea sediment samples. The results show that ASVs and OTUs describe different levels of biotic diversity, the choice of which depends on the research questions. They underline the advantages and complementarity of clustering and LULU-curation for producing metazoan biodiversity inventories at a level approaching the one obtained using morphological criteria. While clustering removes intraspecific variation, LULU effectively removes spurious clusters, originating from errors or intragenomic variability. Swarm clustering affected alpha and beta diversity differently depending on genetic marker. Specifically, d-values > 1 appeared to be less appropriate with 18S for metazoans. Similarly, increasing LULU's minimum ratio level proved essential to avoid losing species in sample-poor data sets. Comparing BLAST and RDP underlined that accurate assignments of deep-sea species can be obtained with RDP, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific databases.
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http://dx.doi.org/10.1111/1755-0998.13398DOI Listing
April 2021