DNA and RNA viromes from anaerobic digesters. DNA and RNA viromes

Viruses are the most abundant biological units on the planet and in waste water treatment plants they are detected at higher concentrations than in any other aquatic environment. Despite viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Up to now viruses have received very little attention compared to the microbial population in this specific habitat. Therefore, as a first step toward the characterisation of viral assemblages we have optimised a virus enrichment protocol from the anaerobic sludge, including reactors fed with waste water, agricultural residues and solid municipal waste plus agricultural residues. Afterwards we assessed the main viral morphotypes by means of transmission electron microscopy and we studied the DNA and RNA viromes by a metagenomic approach. Electron micrographs showed a high number of morphologically distinct viruses, and metagenomic analyses demonstrated huge and previously unknown viral genetic diversity in methanogenic reactors. While the DNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant-infecting viruses. Interestingly, less than 2 % of contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct from nearly 30 other environments already studied, including human gut, fermented food, deep sea sediments and other aquatic habitats.