Background: The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. Results: Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus ‘Ca. Villigracilis’. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. Conclusion: Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.

The anammox (anaerobic ammonium oxidation) process has been used to remove nitrogen from wastewaters and is considered a promising approach due to its advantages over conventional processes (nitrification and denitrification). The development of molecular biology tools has allowed for great advances in describing the microbial communities in anammox reactors, which is important to understand the complex reactions and interactions that occur inside these systems. This study presents a review of the microbial diversity studies in anammox reactors. Several researchers have investigated the microbial community composition in anammox reactors, in order to elucidate the roles that the different microbial groups (besides the anammox bacteria) play in these systems. The microbial communities of anammox reactors appear to be affected by several factors, such as the configuration of the reactors, the biomass growth mode inside of the reactors, operational conditions and type of inoculum used for start-up. However, independent of reactors characteristics, some microbial groups such as Proteobacteria and Chloroflexi have always been found with Planctomycetes in anammox reactors. Moreover, other microbial groups such as Chlorobi, Acidobacteria and Bacteroidetes are often detected in these systems. Identifying the roles and interactions of such microorganisms inside anammox reactors is a great challenge for future studies.