Microbial ecology seeks to understand and characterize microbial community structure. Around 99% of microbes have yet to be cultured in the lab, as they require conditions we are unable to imitate. To circumvent this problem, researchers have developed a method to sequence all the genetic material of an environmental sample. This method, called metagenomic sequencing, allows for identification of novel microbial species by comparing their DNA to known sequences. Metagenomic analysis has become the modern methodology for identifying microorganisms and assigning metabolic function. One program, the online knowledgebase KBase Narrative Interface by the Department of Energy (Arkin et al. 2018), allows non-bioinformatic specialized scientists to conduct a variety of analyses on genomic and metagenomic data. We were able to use the program to identify heterotrophic bacteria in co-culture with ammonia oxidizing archaea (AOA). This in itself is valuable information; AOA convert ammonia (NH4+) to nitrite (NO2-), a vital role in the nitrogen biogeochemical cycle. It is hypothesized the two groups of microbes have a mutually beneficial relationship, trading organic carbon and other nutrients. By using KBase, we were able to perform quality control, metagenome assembly, annotation, and species tree creation. This work is the foundation of further more in-depth community analysis, and allows building of metabolic models and expression studies. It is also the first step towards identification and characterization of the complex interactions in microbial communities. By discussing the process of this analysis, we hope to increase the accessibility of metagenomic analysis for the average microbiology student. This work is relevant to our careers as it has trained us in common bioinformatic techniques that are widespread in environmental work. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
Authors: Avery Imes, Maddy Spencer, Annette Bollman, Ph.D.
Faculty Advisor: Annette Bollmann, Microbiology
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