Submitted by Jill Banfield on
Microbes seldom live alone, instead, they live in complex ecosystems interacting with tens- to thousands of microbial species around them. Our lab has recently shown that bacteriophage—the viruses that infect bacteria— can be applied to complex communities to selectively deplete an organism of interest. This depletion allows us to infer microbial interactions by identifying which species are most impacted when a specific organism is removed.
In this project, we are looking for a student to carry out bacteriophage isolation against the Rhodanobacter, a key bacterium in our bioreactor-derived microbial communities. This organism is predicted to be a keystone microorganism in these communities. Previous work suggests that Rhodanobacter produces the NAD+ precursor, niacin, which supports the growth of other microbes that are unable to synthesize this essential metabolite themselves. We have established protocols for bacteriophage isolation and their characterization using TEM, genome-sequencing and bioinformatics, and other lab-based phage assays. By isolating phages that specifically infect Rhodanobacter and subsequently applying them to experimental enrichment cultures, we aim to test these predicted interactions and better understand the functional roles of Rhodanobacter within microbial consortia.
Skills and Training
This project offers valuable training in:
Microbiology & Virology: Bacteriophage isolation, microbial culturing,
sterile technique and genome sequencing;
Microscopy & Imaging: Transmission electron microscopy for phage characterization;
Computational Biology: Genome assembly, annotation, and comparative genomics
The selected student will gain hands-on experience in both wet-lab and computational techniques, contributing to a broader understanding of phage-host dynamics in engineered microbial ecosystems.
Specific activities will include:
Bacteriophage enrichment & isolation: Using established protocols, the student will enrich phages from environmental samples, and employ selective techniques to isolate phages against the Rhodanobacter isolate.
Transmission electron microscopy: Isolated phages will be characterized using transmission electron microscopy (TEM) to visualize virion morphology, with the team at the Electron Microscope Laboratory (EML).
Phage genome sequencing, assembly, and annotation: the genomes of isolated phages will be sequenced and assembled using an in-house bioinformatic pipeline. Further bioinformatic analyses will be performed to classify phages and determine their genetic potential.
No prior experience with bacteriophage biology is required. However, candidates with prior coursework and laboratory experience in microbiology or molecular biology are preferred. Proficiency in sterile technique is strongly recommended.