Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

Abstract

The microbial consortium involved in anaerobic digestion has not yet been precisely characterized and this process remains a 'black box' with limited efficiency. In this study, seven anaerobic sludge digesters were selected based on technology, type of sludge, process and water quality. The prokaryotic community of these digesters was examined by constructing and analysing a total of 9890 16S rRNA gene clones. Libraries were constructed using primers specific for the Bacteria and Archaea domains for each digester, respectively. After phylogenetic affiliation, the libraries were compared using statistical tools to determine the similarities or differences among the seven digesters. Results show that the prokaryotic community of an anaerobic digester is composed of phylotypes commonly found in all anaerobic digesters sampled and also of specific phylotypes. The Archaea community is represented by an equilibrium among a restricted number of operational taxonomic units (OTUs). These OTUs are affiliated with Methanosarcinales, Methanomicrobiales and Arc I phylogenetic groups. Statistical analysis revealed that the Bacteria community can be described as a three component model: one-third making up a core group of phylotypes common to most of the digesters, one-third are phylotypes shared among a few digesters and another one-third are specific phylotypes. The core group is composed of only six OTUs affiliated with Chloroflexi, Betaproteobacteria, Bacteroidetes and Synergistetes. Its role in anaerobic degradation appears critical to investigate. This comparison of anaerobic digester populations is a first step towards a future understanding of the relationship among biodiversity, operating conditions and digester efficiency.

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

“…This study also constructed much more complete genomes of Pseudothermotoga, Mesotoga, Caldiserica 31q06 and Cloacimonetes. Moreover, this effort generated genomes for taxa that our previous study could not address, including uncultivated phyla Atribacteria, Hydrogenedentes, Marinimicrobia and WS1; poorly understood phyla Armatimonadetes and Chloroflexi; and other uncultivated phylogenetic branches of novel Caldisericia sister clade, Syntrophus-related clade, Spirochaetes SA-8, Synergistetes TTA-B6, Planctomycetales-related clade and Phycisphaerae-related cluster WPS-1 (Chouari et al, 2005;Riviere et al, 2009;Yamada and Sekiguchi, 2009 Tables S1 and S2.…”

“…Hydrogenedentes' (formerly NKB19): a lipolytic glycerol degrader Hydrogenedentes is often associated with methanogenic environments (Riviere et al, 2009;Narihiro et al, 2014), but its ecological role has remained enigmatic. While the genomic technology available for our previous study was insufficient for metagenomically capturing Hydrogenedentes, implementing modern sequencing platforms allowed construction of a Hydrogenedentes pangenome and transcriptome.…”

“…Syntrophs specifically form obligate mutualistic interactions with methanogens to metabolize organic compounds whose degradation otherwise rapidly becomes thermodynamically unfavorable (DG40) as by-products accumulate (Schink, 1997;Schink and Stams, 2006). Despite such low-energy conditions, engineered and natural methanogenic environments harbor a wide diversity of uncharacterized microorganisms from known phyla and candidate phyla without cultivated representatives (microbial dark matter; Rinke et al, 2013; also see Juottonen et al, 2005;Nemergut et al, 2008;Griebler and Lueders, 2009;Riviere et al, 2009;Glockner et al, 2010;Kong et al, 2010;Kim et al, 2011;Lykidis et al, 2011;Nelson et al, 2011;Rinke et al, 2013). Their presence indicates many undiscovered microbial niches and interactions.…”

Effect of reclaimed water effluent on bacterial community structure in the Typha angustifolia L. rhizosphere soil of urbanized riverside wetland, China

“…A higher relative abundance of γ-Proteobacteria, Firmicutes and Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria sequences was detected at the downstream site compared to the upstream site. The higher proportion of Firmicutes and Chloroflexi sequences reflects the impact of RWTP effluent, because some members of these phyla have been proposed as indicators of fecal pollution, and they were commonly abundant in anaerobic wastewater treatment systems (Riviere et al, 2009). Previous studies have also demonstrated that the class Clostridia, which was dominant among the Firmicutes at the downstream point, has frequently been detected within urban wastewater systems (Vierheilig et al, 2013).…”

Effect of Bacillus spp. direct-fed microbial on slurry characteristics and gaseous emissions in growing pigs fed with high fibre-based diets

“…DFM on microbial interactions was difficult to analyse (Figure 4). The main identified microbial groups, for example Bacteroidetes, Bacilli, Clostridia encompass most of known fermentative bacteria in pig manure (Peu et al, 2006) as well as in anaerobic digesters (Liu et al, 2009;Riviere et al, 2009). …”