0 avis
Identification de virus d’archées méthanogènes au sein de bioprocédés de digestion anaérobie par séquençage métagénomique shotgun
Archive ouverte
Edité par CCSD -
International audience. Introduction and objectivesViruses of microbes are recognized as major drivers of ecosystem functioning. However, deciphering the specificity of host-microbes interaction in communities of uncultured microbes remains an important bottleneck in microbial ecology. In this contribution, we focus on the viral diversity in anaerobic digestion (AD) plants which is still poorly characterized . We developed a laboratory-scale study based on metagenomics and stable isotope probing (SIP) to identify viruses associated to uncultured methanogenic archaeal populations.Material and methodsWe used 13C-labeled formate, a substrate for methanogenesis, to both enrich and label formate-consuming methanogens in AD microcosms. We separated cellular and viral DNAs by SIP, according to their mass density, by ultracentrifugation on a CsCl gradient. The total cellular DNA and the three cellular DNA fractions separated by SIP were sequenced by Illumina NextSeq. Shotgun metagenomic data served for the construction of Metagenome Assembled Genomes (MAGs) and of a spacer database, thanks to spacer detection in contigs. Shotgun metaviromes were also obtained. In order to identify the possible hosts of viruses, we aligned the viral contigs against the metagenome-based spacer database, as well as a public spacer database (https://crisprcas.i2bc.paris-saclay.fr/).Results and discussionWe showed by SIP and 16S rDNA metabarcoding that the microbial community had been enriched in Methanobacterium species, which were also enriched in the heavy DNA fraction.We estimate that about 15 viral contigs longer than 3 kb may originated from viruses of methanogens. Among them, three could be novel viral genomes that are not related to known viruses; according to the presence of an encoded structural protein, one of them is likely a novel spindle-shape virus, a morphotype specific for archaeal viruses which was also observed by transmission electron microscopy.ConclusionsIn this contribution, we showed the innovative use of DNA-SIP methodology to identify viral populations associated to key functional groups contributing to biogeochemical fluxes in communities of uncultured microbes. This approach should greatly develop the knowledge on the diversity of viruses of methanogens in AD ecosystems.
Consulter en ligne
Suggestions
Du même auteur
