High-throughput full-genome characterisation of the microbes responsible for efficient biogas production in anaerobic digesters

In recent years, biogas technology has been increasingly prioritised as countries, including Denmark, transition from fossil fuels to sustainable energy production. Municipalities, farms and industry have embraced anaerobic digestion (AD) as a method of harnessing microbes to process waste and to generate biogas used to power their own operations and provide energy to the national grid. Optimisation to improve efficiency and economy is needed to comply with sustainability targets and move towards a circular economy. In order to improve the AD process, we need to have a good understanding of the thousands of microbial species underpinning it. Studies based on DNA fragments have shown that the majority of AD microbes are undescribed yet integral to AD stability and efficiency. Currently, our understanding of these microbes is limited to these fragments and a few species culturable under lab conditions. Recently we developed a high-throughput approach using long-read sequencing and big data from the activated sludge system and, for the first time, recovered hundreds of high-quality full genomes, raising the bar in the field of genome-centric metagenomics. I plan to apply the method to Danish AD samples to create a comprehensive database of high-quality genomes for the important microbes. The microbes of different AD feedstocks will be compared to determine how the microbial community reflects input and treatment conditions. Additionally, I will link this database to previous gene surveys to test hypotheses regarding the drivers responsible for AD process stability and efficiency. Genomic functional potential does not necessarily represent function in the environment. Consequently, I will confirm functions of populations identified with central roles in resource recovery with experiments and phylogenetic analysis. Ultimately, this knowledge can be used for the surveillance and control of AD, and discovery of novel processes relevant to biotechnology.

Anaerobic digesters are used all over Denmark to create biogas (a mix of methane and CO2) from various waste inputs such as crop residues, manure, household or industrial waste and will be even more important in the future to ensure sustainable development. However, we know little about the team of thousands of microbe species responsible for waste treatment and biogas production, except for fragments of their DNA and few lab-grown isolates. New sequencing and bioinformatic approaches will change this. I aim to recover the entire genomes of hundreds of these microbial populations, which will allow us to investigate what they are doing in the system. By linking their functional potential to previous work, and to the microbes from various digester types, we will be able to determine the microbes with integral roles in our efforts to recover nutrients and produce biogas in a more economic and sustainable way.