Experiences, learning and different species of Metarhizium fungi
As of this month (February), I’ve completed half of the time allotted towards my PhD project. Over this year and a half, I’ve attended courses, made friends, lived in two new countries, contributed to conferences, worked in different labs, learned new languages, carried out experiments, and collaborated with my peers, among other things. The constant bombardment of novel experiences makes one wonder how plastic a brain can be. If there’s one thing I’ve learned since starting this program, it’s that humans are remarkably adaptable to changing situations!
Of course, I’ve also learned plenty of other things relevant to my project. Among the courses, I found the “omics” courses to be the most thought-provoking and informative: hologenomics and our INSECT DOCTORS course on metagenomics. I am happy to have developed a solid understanding of the basic principles and development of nucleotide sequencing technologies, from Sanger sequencing to the third-generation approach using nanopore technology, and to have glimpsed the potential implications of the emerging hologenome theory of evolution, which recasts the collective host-symbiont genome as an evolutionary unit. In October, our PhD cohort spent two weeks in Paris attending delayed INSECT DOCTORS courses. As part of our metagenomics training, I was thrilled to sequence a metagenome on a nanopore sequencer and learn how genomes are computationally constructed. This involved the DNA extraction from a “sample” (a diseased caterpillar) comprised of multiple organisms. We ran the prepared DNA through a tabletop USB device - the MinION sequencer, and constructed a reference library with which to compare the sequenced DNA reads. This allowed us to determine the amount of DNA accounted for by different organisms present in the samples: the caterpillar, its symbionts, and pathogens potentially responsible for its untimely demise, like pathogenic bacteria and viruses. This exercise also demonstrated the application potential of metagenomics in disease identification and management.
Regarding my own work, accomplished at the University of Copenhagen, I was able to develop and optimize a novel method for measuring fungal growth using spectrophotometry, which allows for rapid and high-throughput generation of data. This experience with raw trial and error was frustrating at times but turned out to be a lot of fun. Coming up with a new technique is sort of like doing a puzzle. I intend to use this new method for measuring fungal growth to perform my next phase of experiments, which will investigate the nutritional niches of different species of Metarhizium fungi, my entomopathogenic fungus of choice. I’m hoping to complete these experiments in the coming months here at the UK Centre for Ecology and Hydrology, where I’m working under Helen Hesketh in the Terrestrial Organisms Lab as part of the Biodiversity department before I will move to work with Steve Sait at Leeds University. I look forward to the work ahead and all the knowledge to be gained from it.