Jill Banfield

Closed (1) Construction and characterization of model benthic Cyanobacteria communities

Applications for fall 2021 are now closed for this project.

Cyanobacteria are a group of microorganisms that play critical roles in mediating global carbon and nitrogen cycling. Cyanobacteria are also well known for producing potent toxins that have important impacts on human and animal health, but generally have no understood functions in their natural environmental contexts. However, these amazing organisms do not act alone. Being photosynthetic primary producers Cyanobacteria form the foundation of many microbial communities globally and are often found living in biofilms that contain a wide variety of other bacteria that exchange nutrients and interact with the cyanobacterial members. Unfortunately, due to the complexity of natural bacterial communities, and the difficulty in isolating and dissecting individual microbial interactions within communities, most interactions that occur between cyanobacteria and other bacterial partners are not well characterized. In this project we are attempting to collect cyanobacterial samples from mat biofilms that grow in the wild and use these samples to construct reduced lab-based communities that contain a single cyanobacterial species and several associated heterotrophic bacterial partners. To do so we are using classic microbiology techniques to build the communities (microscopy, single filament isolation, and culturing) as well as -omic’s based methods for characterization of the resulting communities (16s rRNA and genome resolved metagenomic sequencing). In the end we hope to obtain stable, reduced, and genomically characterized communities that can be used to dissect and understand core principals governing microbial community assembly, nutrient exchange, and the impact of cyanobacterial toxin production on community dynamics.

The student selected for this project will take on their own sub-project where we will attempt to obtain and characterize a reduced cyanobacterial mat community from a natural sample. This will include the following tasks and learning outcomes:

- Learning the basics of microbial (and cyanobacterial) community cultivation: Preparing media and growth chambers, picking microbial colonies, weekly and bi-weekly passaging of strains

- Learning cyanobacterial specific microbiology: Isolating single filaments of cyanobacteria under the microscope, performing epi-fluorescence microscopy on cyanobacterial communities for cell counting and community phenotype analysis.

- Learning -omic’s and bioinformatics techniques for community characterization: Extraction of DNA from community samples, analysis of 16s rRNA amplicon data, assembly and analysis of microbial genomes from genome resolved shotgun metagenomics data.

Day-to-day supervisor for this project: Spencer Diamond, Staff Researcher

Qualifications: Required: - Should be highly motivated with excellent written and oral communication skills - Strong command of the English language - Willing to keep an organized lab notebook with details of experimental procedures that will be regularly reviewed - Majoring in a science, math, computational, or related technical field Desired: - In Sophomore (2nd) or Junior (3rd) year of undergraduate studies - Completed course work covering microbiology, computational biology, or cyanobacteria specifically - Previous lab experience with microbiology, molecular biology, or computational biology

Weekly Hours: to be negotiated

Related website: https://nanogeoscience.berkeley.edu/