A significant number of studies exist on the metagenomics of anaerobic digestion, with over 80 papers published in the past 10 years that have used
advanced gene sequencing techniques to identify methanogenic archaeal and bacterial populations. (It should be noted that this is only a small fraction of the
attention given to aerobic systems). Despite this effort, however, there are still only a few examples where population structure has been linked to more than
broad functionality, although changes in community structure can in some cases be directly linked to process failure. Mapping the relationship between the
gene sequences that determine the phylogenetic characteristics of a group and its metabolic functionality is proving to be an elusive goal.
Metatranscriptomes, when directly associated with metagenomic data, identify those genes that are actively transcribed by a community, and therefore
potentially allow prediction of active metabolism in response to spatial or temporal environmental gradients.
Metaproteomics, however, allows us to identify the actual microbial proteins that are post-transcriptionally regulated and translated under particular
environment conditions, and thus provides a tool allowing us to explore new biochemical pathways as well as monitoring metabolic activities within the
community. Despite the attraction of metabolomics in potentially providing a metabolic profile that gives an instantaneous snapshot of the physiology of cells,
the literature suggests that the techniques employed have yet to be used to study anaerobic digesters. Identified research needs therefore include a
requirement for the creation of links between the use of advanced biomolecular tools and mapping of functionality within anaerobic processes. These
techniques can be further enhanced by metabolic modelling which allows an in-depth insight into the molecular mechanisms of a particular organism; and
community structure modelling, which can be used to predict the structure and diversity of key members of the community.
There is also a need to develop bio-molecular markers for targeting specific microbes in particular transformations. These will provide a route to
establishment of accurate diagnostics based on the population functionality. These techniques will also play a key role in the mapping of pathways which
could lead to selection of intermediate products for extraction or in-situ conversion to more complex value added materials in a biorefinery.
Biomolecular Tools Working Group
Anaerobic digestion by its very nature is carried out by a community of micro-organisms, allowing
complex conversions to occur despite the unfavourable thermodynamics of some of the individual
reactions when carried out independently rather than syntrophically. As such, the concerted activities of
many microbial species are harnessed, making these systems much more difficult to optimise. Current
industrial practice is to treat the underlying microbial system as a ‘black box’.
One of the goals of the Network is to open this black box and identify key principles that will better enable
the rational design and manipulation of microbial communities through synthetic biology, on the basis of
hypothesis-driven research. By considering the physiology, metabolic pathways and thermodynamics of
the reactions, the anaerobic system can be directed towards desired outputs (e.g. maximum CH4
production, hydrogen production and capture for selective hydrogenation, inhibition of syntrophically-
mediated pathways for VFA accumulation, selective product extraction to regulate reversible reactions
e.g. acetate cleavage or oxidation).
Understanding these factors is the first step in learning how to engineer microbial communities from the
bottom up, i.e. to make targeted ‘synthetic’ microbial communities for specific purposes which can be self-
regulating. These activities will move us a step closer to creating biorefineries that would not depend on
aseptic conditions, with the high capital expenditure and size restrictions that these entail.