Submitted by Eoin Brodie on
Bacterial traits, encoded by genes determine bacterial fitness and their contributions to biogeochemical cycles in soil. The goal of this project is to identify the functions of select bacterial genes that are hypothesized to confer a fitness advantage on key bacterial members in the rhizosphere of a California annual grass.
To determine the functions of bacterial genes, we will randomly mutagenize bacterial isolates using RB-TnSeq that labels each mutation with a unique genetic identifier. Subsequent competitive fitness assays are used to determine under what conditions specific genes are required for bacterial fitness. Next-generation sequencing will be used to quantify fitness.
Overall, this approach will be tested using approximately 30 well-characterized and genome-sequenced bacterial isolates. The student will induce random mutagenesis in these isolates and contribute to the design and application of the fitness assays, in addition to contributing to data analysis and interpretation. The student will work between the Brodie (ESPM and LBNL), Firestone (ESPM and LBNL) and Deutschbauer (LBNL) labs. Most work will occur in labs in LBNL.
-Maintain bacterial cultures, assistance with creating mutant libraries, assistance with next-generation sequencing library preparation and data analysis for the ongoing project.
-Basic knowledge in genetics and microbiology
-Prior experience with microbial culture is desirable but not required. A desire to learn microbial cultures, sterile techniques, and cutting-edge RB-TnSeq methods helps a lot.
-Close attention to experimental details and careful practice to maintain sterile environment are needed.
-Some experience with statistical analysis is desired but not required.