Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing

Abstract

The diversity of Archaea in anaerobic digesters was characterized by strand conformation polymorphism (SSCP) analysis and the sequencing of 16S rDNA genes. The 44 digesters sampled, located in eight different countries, treated effluents from agriculture, the food processing and petro-chemical industries, pulp and paper plant, breweries, slaughterhouses and municipal waste. All the existing processes were represented among the samples (fixed-film, fluidized bed, stirred-tank, UASB, sequential batch reactor, lagoon). Single strand conformation polymorphism analysis targeting the V3 region of 16S rDNA revealed between four to six distinct archaeal peaks per digester. The diversity of dominant Archaea in the 44 digesters was estimated as 23 different 16S rDNA sequences. Cloning of archaeal 16S rRNA genes from 11 distinct total genomic DNA, screening of clones by SSCP and the sequencing of 170 of them made it possible to characterize these SSCP peaks. All the sequences retrieved were members of the Euryarchaeaota subdomain. Furthermore, most of the sequences retrieved were very close to already known and cultivated strains or to environmental clones. The most frequent archaeal sequences were close to Methanosaeta concilii and to a 16S rDNA clone vadinDC06 located in the Methanobacterium clade (84% and 73% of digesters respectively). The other sequences were members of the Methanobacteriales and the Methanomicrobiales families. Only one sequence was far from any sequence of the database and it could be grouped with several sequences of environmental clones. Each digester harboured between two to nine archaeal sequences with only one of them corresponding to a putative acetate-utilizing species. Furthermore, the process in the digesters appeared to play a part in the distribution of archaeal diversity.

Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

“…Currently, the only genera known to use acetate for methanogenesis are Methanosarcina and Methanosaeta. However, Methanosarcina failed to inhabit in the anaerobic sewer biofilms, which is consistent with the finding that usually only one acetoclastic methanogen dominates such anaerobic environments (60). It is likely that Methanosaeta out-competed Methanosarcina due to differences in their affinities for acetate.…”

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

“…Our knowledge about the microbial consortia involved in this process is limited because of a lack of phylogenetic and metabolic data on these predominantly uncultivated microorganisms. As an alternative to culture techniques, several molecular inventories, based on the study of the 16S rRNA gene, were carried out on anaerobic environments and have shown the extent of the diversity in these complex ecosystems (Godon et al, 1997a, b;Sekiguchi et al, 1998;Leclerc et al, 2004;Chouari et al, 2005a). These studies have limitations in that they often focused on one type of process, one sample, and often only lab-scale units.…”

Comparative Analysis of Bacterial and Archaeal Communities in Methanogenic Sludge Granules from Upflow Anaerobic Sludge Blanket Reactors Treating Various Food-Processing, High-Strength Organic Wastewaters

“…According to these studies, the 16S rRNA gene clones retrieved from UASB sludges indicated the major microbial constituents to be those of the phyla Proteobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Bacteroidetes in the domain Bacteria, and those of the classes Methanomicrobia, Methanobacteria, and Thermoplasmata in the domain Archaea (47). In addition, such studies have also shown that a large number of the clones assigned to candidate phyla (known as 'clone clusters') were frequently found in such ecosystems (7,8,10,20,31,48,55). However, there are still obstacles to precisely determining and monitoring the entire microbial community of sludge because of the limited number of datasets reported so far.…”

“…So far, molecular-based community analyses have been performed for UASB granular sludges treating wastewater from a paper factory (41), a terephthalatemanufacturing plant (53), a beer brewery (13), and sucrose/ propionate/acetate-based artificial wastewater (44). In addition, the molecular characterization of UASB granules targeting specific microbial groups has also been reported (10,20,31). According to these studies, the 16S rRNA gene clones retrieved from UASB sludges indicated the major microbial constituents to be those of the phyla Proteobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Bacteroidetes in the domain Bacteria, and those of the classes Methanomicrobia, Methanobacteria, and Thermoplasmata in the domain Archaea (47).…”