Center for Metagenomic Microbial Community Analysis
September-November 2015
Dev and Samik have begun their training seminars. Groups of students, post-docs, and professors are meeting every Friday morning to learn about experimental design, sample preparation, protein extraction, library prep, and sequencing runs. Dev has given these first seminars. Samik is giving subsequent seminars on data analysis.
September 2015
Dev has successfully extracted DNA from soils obtained at the Calhoun Critical Zone Observatory - not an easy feat - and has completed library prep. These samples represent soils underlying replicated, forested stands that have experienced distinct land use histories.
Dr. Sikes' CMMCA-supported paper, "Plant and root-endophyte assembly history: interactive of native and exotic plants" is published in Ecology (doi:10.1890/15-0635.1).
July 2015
Dr. Kate Buckeridge, post-doctoral scholar in Dr. Billings' lab, has left for a post-doc position at the University of Lancaster, UK. Her Canadian soil samples continue to be pushed through the CMMCA pipeline: she has successfully extracted and quantified microbial DNA from them, and has generated 9 samples for RNAseq analysis on the hiseq. The run was a success and she is now in the midst of working on the data via the CMMCA network drive.
May 2015
Dev and students in the CMMCA lab have generated DNA samples from mock microbial communities, which can help inform us about the extent to which our extraction techniques and subsequent analyses represent the "real" microbial communities in our samples.
April 2015
Dr. Sikes' lab members have successfully generated amplicon sequencing data describing the fungal communities residing in the rhizospheres of multiple plant communities. Ph.D. candidate Az Klymiuk will use these data as part of her dissertation, exploring how inundation gradients in wetlands alters root endophytic fungi in aquatic plants.
March 2015
Dr. Samik Bagchi joins the CMMCA as a Research Associate. His background is in microbiology, and he brings the expertise needed to round out our team of environmental scientists.
The Sikes lab is analyzing CMMCA-derived data describing the effects of fire on rhizosphere fungal communities.
The Billings lab publishes a CMMCA-supported paper, "Investigating microbial transformations of soil organic
matter: synthesizing knowledge from disparate fields to guide new experimentation" in Soil, a publication of the European Geophysical Union (doi:10.5194/soil-1-313-2015).
June 2014
Dev Hiripitiyage has joined the CMMCA as a research technician. He brings expertise in extracting proteins from diverse environmental samples, as well as significant background in soil microbe exo-enzyme analyses and elemental fluxes through soils.
February 2014
The KU Provost Office has funded our proposal to establish a Center for Metagenomic Microbial Community Analysis! The proposal is a collaborative effort between Belinda Sturm, Sharon Billings, Stuart Macdonald, Jennifer Roberts and Ben Sikes, combining expertise across four KU departments and the Kansas Biological Survey. The CMMCA seeks to describe microbial community structure using next generation sequencing technologies coupled with rigorous computational analyses.
