Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis

Abstract

Methanogenesis from the biomass in the anoxic biogas reactors is catalyzed by syntrophic cooperation between anaerobic bacteria, syntrophic acetogenic bacteria and methanogenic archaea. Understanding of microbial community composition within the biogas reactors may improve the methane production from biomass fermentation. In this study, methanogenic archaea diverity of a biogas reactor supplied with swine feces as mono-substrate under mesophilic conditions was investigated. Community composition was determined by analysis of methyl coenzyme reductase subunit A gene (mcrA) clone library consisting of 123 clones. Statistical analysis of mcrA library indicated that all major groups of methanogens from our biogas reactor were detected. In the library, 57.7% clones were affiliated to Methanobacteriales, 34.2% to Methanomicrobiales, 2.4% to Methanosarcinales and about 5.7% clones belonged to unclassified euryarchaeota. Over 90% of the methanogenic archaea from our biogas reactor were postulated to be hydrogenotrophic methanogens. Comparing with other previous studies reporting that hydrogenotrophic methanogens are dominant species in the biogas plants, this study firstly reported that Methanobacteriales instead of Methanomicrobiales are the most predominant methanogenic archaea in the biogas reactor fed with swine feces as sole substrate.

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

“…Stoichiometric modeling (56,57) and measurements of natural methanogenic systems (58) have been used to predict acetate accounts for ϳ70% of methane production, and a meta-analysis of anaerobic digester studies found that the acetoclastic genus Methanosaeta accounted for 55% of archaea (although a large proportion of sequences were unclassifiable to genus) (5). However, several studies of biogas reactors have identified a dominance of hydrogenotrophic methanogens, though the relative proportions of Methanobacteriales and Methanomicrobiales vary (41,42,46). In the present study, mcrA-based taxonomic classification suggested the SWH and YL digesters had large or dominant populations of acetoclastic Methanosarcinales, while GZ and ST were dominated by hydrogenotrophic Methanomicrobiales.…”

“…However, OTU mcrA richness was also high relative to comparable studies using the 97% sequence similarity threshold. For example, a study of 118 mcrA sequences from an anaerobic batch reactor identified 21 OTU mcrA at an estimated 90% coverage of total richness (20), whereas a study of 123 mcrA clones from an anaerobic biogas reactor identified 28 OTU mcrA at 89% estimated coverage (42). It is therefore possible that the digesters selected for the present study are more diverse than others previously reported on.…”

“…However, the taxonomic identity of the methanogen groups involved and their community composi- tion under different operating conditions are still not well understood (5,6). Although the 16S rRNA gene is a common target for community analysis, the mcrA gene has been used for the taxonomic classification of methanogens either independently (41,42) or in concert with the 16S rRNA gene (14,20). In the present study, pyrosequencing of both genes was applied to investigate the community composition of methanogens from four different anaerobic digesters.…”

“…Previous investigations mainly relied on Sanger sequencing of 16S rRNA gene clone libraries (16,20,41,42), which can underestimate richness and diversity due to lack of sequencing depth. The development of high-throughput pyrosequencing has expanded our view of the diversity, abundance and structure of microbial communities in many environments (43).…”

Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

“…Several recent studies have found that the hydrogenotrophic pathway and the Methanoculleus genus were predominant in reactors fed with liquid swine manure (46,47) or with manures mixed with other agricultural wastes (48,49). Not only are Methanoculleus spp.…”