Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Abstract

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation.

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

“…Combining metaproteomic analyses and isotopic, chemical and molecular approaches, the present study provides one of the most comprehensive views of expressed biological functions during cellulosic waste methanisation, complementing the information gained from previous metagenomic or metatranscriptomic studies (for example, Krause et al, 2008;Schluter et al, 2008;Jaenicke et al, 2011;Rademacher et al, 2012;Zarkzewski et al, 2012). Using the complete UniprotKB database, over 500 protein functions were identified.…”

“…Isotopic labelled substrates were exploited to identify the functional microbial groups catalysing the methanisation of cellulose using stable isotope probing (Li et al, 2009). Several metagenomic studies shed light on the identity of the functional groups and provided an extended catalogue of the catalytic potential (Krause et al, 2008;Schlü ter et al, 2008;Jaenicke et al, 2011;Rademacher et al, 2012). However, these approaches do not generate direct information on the expressed genes and associated metabolic processes.…”

Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure

“…One explanation might be that our co-fermentation system was not at optimal condition. Some studies showed that hydrogenotrophic pathway prevailed in the co-digesters of agricultural waste (Jaenicke et al 2011). Acetoclastic methanogenesis may be a major pathway in some systems (Supaphol et al 2011), or both pathways were utilized for methanogenesis ).…”

The effects of initial substrate concentration, C/N ratio, and temperature on solid-state anaerobic digestion from composting rice straw

“…Six genera of methanogens, Methanosarcina, Methanosaeta, Methanoculleus, Methanosphaera, Methanobrevibacter, and Methanobacterium, were found in the SS-AD. Certain studies showed that a hydrogenotrophic pathway prevailed in the digesters of agricultural waste (Jaenicke et al, 2011). Acetoclastic methanogenesis may be a major pathway in certain systems, or both pathways were utilized for methanogenesis (Li et al, 2013).…”