Placing Student Feet (Framework for Engaging, Educating, Training) on Soil to Learn about Microbes in the Rhizosphere.

The rhizosphere contains an abundant and largely understudied community of diverse soil bacteria poised for discovery-based investigations that are ideally suited for undergraduates interested in science.  Many of these microorganisms interact with the plants in various ways, promoting their growth and contributing to overall soil health.  In our classes at UCLA, we encourage undergraduate students to focus on real world problems such as global climate change, soil degradation, and the increasing presence of antibiotic-resistant microbes in the environment (1).  The soil, which students collect from the rhizospheres of plants growing in the UCLA Botanical Garden or from other locations, provides a medium by which instructors may introduce these important and highly relevant concepts. Working in teams of three or four, the students utilize either cultivation-based or molecular–based methods to look for novel plant growth promoting bacteria, cellulase producers, or antibiotic resistant bacteria, or to perform metagenomics analyses, respectively.  Some teams learn not only classic microbiology techniques, but also how to test plants for bacteria that fix nitrogen symbiotically or that promote plant growth.  A collaborating team takes the same soil and directly isolates DNA, creating a 16S rDNA library, which is pyrosequenced and organized into operational taxonomic units (OTU) by an outside service. All students learn how to work with large data sets and use statistical methods to analyze them.  They present scientific papers on topics related to their studies, prepare posters for public symposia, and culminate their research experience by writing a scientific paper on their results.  Several students have been involved as co-authors on publications based on these studies (2).

 

1. Sanders, E.R., and Hirsch, A.M. 2014. Immersing undergraduate students into research on the metagenomics of the plant rhizosphere: a pedagogical strategy to engage civic-mindedness and retain undergraduates in STEM.  Front. Plant Sci. Apr 30;5:157. doi: 10.3389/fpls.2014.00157.
2. Schwartz, A.R., Ortiz, I., Maymon, M., Fujishige, N.A. Hanamoto K., Diener, A., Sanders, E.R., DeMason, D.A., and Hirsch, A.M.  2013. Bacillus simplex alters legume root architecture and nodule morphology when co-inoculated with Rhizobium. Agronomy. 3:595-620; doi:10.3390/agronomy3040595.