Tonight I watched the London Calling 2023 session entitled “Fantastic methanotrophs and where to find them” by Kalinka Sand Knudsen from Aaborg University in Denmark. Knudsen spoke about how methane retains heat and reducing emissions is critical. Knudsen is interested in methane-consuming bacteria that can survive on elevated concentrations of methane and some can oxidize atmospheric methane. These organisms are very difficult to isolate yet also hold promising capabilities for the production of useful substances. Knudsen and team are searching for methanotrophs across Denmark. They are using a tool called GraftM to translate sequences to proteins and find specific proteins. The team has processed 10,000 sediment samples, extracted DNA, and sequenced with Illumina. Using long-read sequencing, the researchers are using raw reads to find sequences of interest. Knudsen noted that the raw long-reads are being used to find proteins from low-abundance methanotrophic groups. The research team is “populating the methanotroph tree of life with HQ genomes” and finding completely new genomes. Knudsen noted that from fourteen samples using PromethION sequencing they obtained a wealth of information and helped find unique sequences of methane eaters. The team can then go back to the 10,000 samples and search for sequences of interest. Knudsen explained how they are using predictive metabolic models to learn how these organisms can handle methane and other metabolic properties. I thought the approach was really interesting, as it leverages deep short-read sequencing of metagenomes with long-reads for raw sequence analysis and metagenome and metabolic reconstructions.
