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

Abstract

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 PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(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.

Microbiome dysbiosis regulates the level of energy production under anaerobic condition

“…Despite having higher taxonomic resolutions, the microbiomes of the AD remained inconsistent and fluctuates more in Group-II, Group-III and Group-IV than those of Group-I metagenome. The taxonomic annotations of the four groups of AD showed that they were a reservoir of bacteria, followed by archaea and viruses, which corroborated the findings of other studies [49,50]. Among the identified domains, bacteria dominated in abundance, comprising 81.80% of the total microbial populations, followed by archaea (15.43%), while viruses (2.77%) comprised the least abundant population.…”

“…The archaeal species are able to use different methanogenic routes to convert the substrates into methane gas. Nevertheless, the main roles of the identified less abundant bacteriophages were unclear, though the strains could have been active in degrading other microbial cells in the AD systems [49,50].…”

“…In this study, the bacterial phyla Firmicutes (37.0% 42.0%) and Bacteroidetes (22.0% - 38.0%) appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. The initial phase of the AD digestion process involves hydrolytic reactions that convert large macromolecules into smaller substrates [49]. In addition, the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents can affect both the composition and diversity of the methanogenic archaea [49].…”

“…The initial phase of the AD digestion process involves hydrolytic reactions that convert large macromolecules into smaller substrates [49]. In addition, the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents can affect both the composition and diversity of the methanogenic archaea [49]. Only certain methanogenic archaea are able to synthesize CH 4 from the end products of bacterial fermentation.…”

“…During the anaerobic process Clostridiales and Bacteroidales were identified as the top abundant order in all of the four metagenome groups. The syntrophic bacterial genera and strains of Clostridiales order are consumers of 30% of the generated electrons, which bypasses the rate limiting steps of the volatile fatty acids accumulation and contributes to AD stabilities [49,51]. In anaerobic environments, Clostridiales has been reported as the main cellulose degrader [52], and play important role in the hydrolysis step [47].…”