We study ecology and evolution of microbes, especially fungi, and plants.
Protocols
QiimeTutorialGrubishaLabMay2017 Here is a tutorial for analyzing Illumina sequence (ITS, 16S), run by the University of Wisconsin Biotechnology Center, using the Qiime pipeline. This tutorial was put together by Samantha Nellis (ES&P graduate Dec 2016) and Josh Moyer (graduated May 2017, Biology).
Invasive Phragmites australis belowground community study
We are investigating how treatment of invasive Phragmites australis affects the soil/sediment microbial community. We are using Illumina sequencing to identify bacteria, archaea, and fungi.
Phragmites australis Exotic vs Native
We are investigating which haplotypes of exotic and native Phragmites australis are present in Northeast Wisconsin.
Agricultural Soil Microbial Community Composition in Wisconsin
We are investigating bacterial and fungal community composition in agricultural soil compared to non-cultivated soil. We are using the Qiime pipeline and associated computer programs to analyze their metagenomic data. Lab alumni Samantha Nellis and Joshua Moyer developing a tutorial for future students to use in analyzing metagenomic data. We are also examining how farming cultivation and conventional vs organic practices affect soil microbial communities associated with corn.
Orchid restoration at the Ridges Sanctuary and Toft Point, WI.
In collaboration with the Ridges Sanctuary, the Smithsonian Environmental Research Center, and the Cofrin Center for Biodiversity, we are investigating mycorrhizal fungal symbionts of orchids at the Ridges Sanctuary and Toft Point, near Bailey’s Harbor, WI. We will isolate pure cultures of the fungal symbionts and use Sanger DNA sequencing to determine genetic identity of the isolated fungal pelotons. As part of his study, we are also conducting soil nutrient analyses of resident “hot spot” populations and potential restoration sites. We are also exploring distribution of genetic diversity of coralroot orchids and fungi.
Northern extent of Aspergillus flavus
Aspergillus flavus is a pathogenic fungus that typically lives in warm, humid environments, typically found in the southern USA. In the USA A. flavus is commonly found in soil and on economically important agricultural crops. We are investigating the potential northern extent of A. flavus. Average annual temperature across the US is expected to increase thus potentially opening up new environmental niches for this fungus.