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Investigation of microbial diversity in the purification processes for water containing activated mud
A conventional metagenomic approach (whole-DNA cloning in the form of large inserts and then systematic sequencing) was implemented in order to study the metabolic capacities of the microorganism flora of the Evry mesophilic anaerobic digester. The first stage was the construction of a representative genome bank (1 million fosmids) and then systematic sequencing of all the extremities of the clones.
In addition to Archaea, 40 bacterial divisions were detected, showing the great diversity of the microorganisms involved in anaerobic digestion. The metagenomic approach enabled the discovery of 2 candidate bacterial divisions, WWE1 and WWE3 (Pelletier et al., 2008; Guermazi et al., 2008) and the reconstruction of the whole genome of a hitherto uncultured representative of division WWE1 ('Candidatus Cloacamonas acidaminovorans') (Pelletier et al., 2008). Systematic analysis of the assembly (comparison with the nucleic acid and protein resources) and use of functional classification tools enabled analysis of the contigs. A detailed analysis of the 15 scaffolds of more than 1 Mb enabled us to assign a role to the principal contributors (Archaea and bacteria) in the anaerobic trophic chain (cf. figure below).
We also showed that many of the bacterial genomes of the candidate divisions were relatively small (700 to 1500 kb). This has since been confirmed (Brown et al., 2015; Giovannoni et al., 2014; Kantor et al., 2013; Wrighton et al., 2014). In the case of WWE3, analysis of the genomes showed that they all had genes considered essential with the exception of those contributing to biosynthesis of cofactors, hence the difficulty in isolating them.
Laboratory involved :
CEA is a French government-funded technological research organisation in four main areas: low-carbon energies, defense and security, information technologies and health technologies. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world.