Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

Abstract

BackgroundBiogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as “anaerobic digestion.” This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge.ResultsIn this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway.ConclusionThis study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0441-1) contains supplementary material, which is available to authorized users.

Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

“…In AD of cattle manure and sludge, some authors (Rivière et al, 2009;St-Pierre and Wright, 2014;Campanaro et al, 2016) reported, as part of the core group, also Cloroflexi, which, on the contrary, we found at 0.03% only. Maus et al (2017) also reported Firmicutes, Bacteroidetes as the main bacteria phyla in mesophyllic conditions plants with cow manure as inoculum.…”

“…Maus et al (2017) also reported Firmicutes, Bacteroidetes as the main bacteria phyla in mesophyllic conditions plants with cow manure as inoculum. The Firmicutes are important because they are implicated in several metabolic processes including carbohydrates degradation, fatty acids utilization, WoodLjungdahl pathway (WLP) (homoacetogenesis) or syntrophic acetate oxidation (SAO) as reported by Campanaro et al (2016).…”

“…Moreover, some researchers observed that the excretion of bacteriocins by Lactobacilli and Prevotella resulted in inhibitory effects of hydrogen production (Castelló et al, 2011). Negativicutes (7.3%), Candidate_division_TM7 (2.2%), and Synergistia (0.8%) are more abundant in T2 and in particular N samples, even though the latter are reported to ferment amino acids to acetate and propionate together with other species (Campanaro et al, 2016).…”

Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

“…5 The variation of the "DNA coverage" between the two time periods (before and after LCFA addition) was determined by changes in abundance of the species in the microbial community. The contribution due to variations of the genome abundance was removed from the gene expression changes; this was performed by comparing the results obtained from edgeR software determined for DNA reads and RNA reads.…”

Alkaline Pretreatment of Banana Stems for Methane Generation: Effects of Temperature and Physicochemical Changes

“…AD is the most efficient method of energy generation from biomass in terms of the energy output/input ratio (28:1) compared with other biological and thermo-chemical routes of energy production (Deublein and Steinhauser 2011). The AD process can be divided into four steps: hydrolysis, acidogenesis, acetogenesis, and methanogenesis (Campanaro et al 2016). In most cases, methanogenesis is the rate-limiting step of the whole process (Chen et al 2008); however, for lignocellulose biomasses, hydrolysis is believed to be the rate-limiting step (Azman et al 2015).…”