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  • Author: Igor Goryanin x
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The modelling of biological intra-cellular pathways requires the systematic capture and representation of interactions between components that are biologically correct and computationally rigorous. The challenge is two fold, to verify and extend our understanding of such pathways by comparing in silico models to experiments; and to ensure that such models are understandable by biologists and for checking biological validity. In this report we present a graphical notation, the Edinburgh Pathway Notation (EPN), which satisfies the central biologically driven requirements while providing a strict formal framework for analysis. The EPN emphasises the use of a logical representation of pathways, which is particularly suited to pathways were some mechanisms are not known in detail.


The combined processes of microbial biodegradation accompanied by extracellular electron transfer make microbial fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although a number of microbial species that build biofilms on the anode surfaces of operating MFCs have been identified, studies on the metagenomics of entire electrogenic communities are limited. Here we present the results of wholegenome metagenomic analysis of electrochemically active robust anodic microbial communities, and their anaerobic digester (AD) sludge inocula, from two pilot-scale MFC bioreactors fed with different distillery wastewaters operated under ambient conditions in distinct climatic zones. Taxonomic analysis showed that Proteobacteria, Bacteroidetes and Firmicutes were abundant in AD sludge from distinct climatic zones, and constituted the dominant core of the MFC microbiomes. Functional analysis revealed species involved in degradation of organic compounds commonly present in food industry wastewaters. Also, accumulation of methanogenic Archaea was observed in the electrogenic biofilms, suggesting a possibility for simultaneous electricity and biogas recovery from one integrated wastewater treatment system. Finally, we found a range of species within the anode communities possessing the capacity for extracellular electron transfer, both via direct contact and electron shuttles, and show differential distribution of bacterial groups on the carbon cloth and activated carbon granules of the anode surface. Overall, this study provides insights into structural shifts that occur in the transition from an AD sludge to an MFC microbial community and the metabolic potential of electrochemically active microbial populations with wastewater-treating MFCs.