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The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders.  Bacteria  dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though,  Fungi  and  Archaea  comprised 5 phyla, the  Fungi  were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities.  Clostridiales  and  Bacteroidales , the most prevalent guilds, metabolize organic macromolecules. The identified  Cytophagales ,  Alteromonadales ,  Flavobacteriales ,  Fusobacteriales ,  Deferribacterales ,  Elusimicrobiales ,  Chlamydiales ,  Synergistales  to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore,  δ-Proteobacteria ,  Gloeobacteria  and  Clostridia  affiliates syntrophically regulate  P   H2   and reduce metal to provide reducing equivalents.  Methanomicrobiales  and other  Methanomicrobia  species were the most prevalence  Archaea , converting formate, CO 2(g) , acetate and methylated substrates into CH 4(g) .  Thermococci ,  Thermoplasmata  and  Thermoprotei  were among the sulfur and other metal reducing  Archaea  that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely  Ascomycota  and  Basidiomycota  species.  Chytridiomycetes ,  Blastocladiomycetes  and  Mortierellomycetes  were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities’ abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its’ productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya