Submitted by Jill Banfield on
Microorganisms are the most abundant and diverse cellular life forms on Earth. However, our understanding of the microbial world is largely limited to the tiny set of microbes that can be grown alone (in pure culture). A critical gap in microbiology research is knowledge of how microbes interact within complex communities in the natural environment. Recently, cultivation-independent techniques based upon sequencing of genetic material from natural environments--collectively called metagenomics--has revolutionized our ability to characterize the vast majority of the microbial world which cannot be grown in the laboratory.
In recent years, metagenomics studies carried out by the Banfield lab have led to the discovery of a previously undefined branch in Domain Bacteria called the Candidate Phyla Radiation (CPR). CPR bacteria are found in nearly every known environment, from the human oral cavity to groundwater, but little is known about them because the CPR is composed entirely of groups with no cultivated members (with the exception of a single cultivated representative). There is incredible diversity within the CPR, which may account for up to 25% of all genetic diversity among bacteria. However, despite this genetic diversity, all CPR bacteria share distinct, unusual features: very small cell sizes (can pass through a 0.2 um filter), small genomes (~1 Mbp on average), and a remarkable lack of many integral biosynthetic pathways. These features indicate that CPR bacteria must interact heavily with other microbes (symbiosis) to obtain basic resources, and likely play a unique role in microbial communities.
Almost no experimental characterization of CPR bacteria has been performed, and many unanswered biological questions depend on understanding their symbiotic relationship with a host. The proposed research focuses on developing co-cultures of CPR bacteria and their hosts, with the goal of characterizing the nature of the symbiotic relationship. Co-cultures will be based on groundwater from a local dairy farm, which has been discovered to have a high diversity and abundance of CPR bacteria (estimated >20% of the microbial population). Existing metagenomics analysis of the groundwater will be used to guide and inform enrichment efforts. Some preliminary testing has already identified promising culture conditions and potential hosts for CPR bacteria.
The two undergraduates will take on the role of maintaining, monitoring, and analyzing cultures of CPR bacteria and their hosts. The main goals are to: (1) establish stable cultures of CPR bacteria from groundwater; and (2) develop robust genomics-based tools for monitoring these cultures. Working closely with a postdoctoral fellow, the undergraduates will gain a combination of wet lab and bioinformatics skills. On the wet lab side, the students will learn techniques for anaerobic cultivation, colorimetric monitoring of metabolism in cultures, and DNA extraction. On the bioinformatics side, the students will learn to use nanopore sequencing and metagenomics analysis to monitor cultures.
The undergraduates should have a basic understanding of microbiology, and be comfortable with or willing to learn molecular wet lab techniques. For bioinformatics, any previous experience with sequencing, genomics, and Bash would be helpful (but not necessary).