Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya
Authors: Muturi S.M. , Muthui L.W. , Njogu P.M. , Onguso J.M. , Wachira F.N. , Opiyo S.O. , Pelle R. 
Published: April 2020

The obstacle to optimal utilization of biogas technology is poor understanding of biogas’ microbiome diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. A randomized complete block design was utilized to assign the twelve biogas reactor 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-diversities studies. We identified 37 phyla, 65 classes and 132 orders of micro-organisms.Bacteriadominated the microbiome and comprised of 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though,fungiandArchaeacomprised of only 5 phyla, thefungiwere richer; suggesting the importance of hydrolysis and fermentation in biogas production systems. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities.ClostridialesandBacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified affiliates ofCytophagales,Alteromonadales,Flavobacteriales, Fusobacteriales,Deferribacterales,Elusimicrobiales,Chlamydiales,Synergistalesto mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore,δ-Proteobacteria,GloeobacteriaandClostridiaaffiliates syntrophically regulatePH2and reduce metal to provide reducing equivalents.Methanomicrobialesand otherMethanomicrobiaspecies were the most prevalenceArchaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g).Thermococci,ThermoplasmataandThermoproteiwere among the sulfur and other metal reducingArchaeathat contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprised largelyAscomycotaandBasidiomycotaspecies.Chytridiomycetes,BlastocladiomycetesandMortierellomyceteswere 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. The study of the diversity of the biogas’ microbiomes over wide environmental variables and the productivity of biogas reactor systems has provided insights into better management strategies that may ameliorate biochemical limitations to effective biogas production.

Author Summary

The failure of biochemical reactions in biogas producing systems is a common problem and results from poor functioning of the inhabiting micro-organisms. A poor understanding of the global diversities of these micro-organisms and lack of information on the link between environmental variables, biogas production, and community composition, contrains the development of strategies that can ameliorate these biochemical issues. We have integrated sequencing-by-synthesis technology and intensive computational approaches to reveal metacommunities in the studied reactor treatments. The identified communities were compared with the treatment’s phenotypic and environmental data in an attempt to fill the existing knowledge gaps on biogas microbiomes and their production capacities. We present 132 biogas taxonomic profiles systematically and comparatively, linking the abundance with the identified environmental variables. The local composition of microbiome and variations in abundance were also linked to the observed differences in biogas productivity, suggesting the possible cause of the observed variations. The detailed information presented in this study can aid in the genetic manipulation or formulation of optimal microbial ratios to improve their effectiveness in biogas production.