User:David Johnston Monje/Notebook/Maize Endophyte Biofertilizers/2013/10/07

Applied Soil Microbial Ecology

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Remains of the Day Figuring out clade specific TRFLP for the strawberries - Alpha proteobacteria (Methylobacteria), Beta proteobacteria (Burkholderia), Gamma proteobacteria (Pseudomonas) and Bacillus (Firmicutes) Looking at several papers to research this TRFLP (http://aem.asm.org/content/71/7/4117/T1.expansion.html) - (http://www.ncbi.nlm.nih.gov/pubmed/17635538?dopt=Abstract&holding=npg) - (http://www.ncbi.nlm.nih.gov/pubmed/19554039) Thinking on it more, it seems likely that real time PCR would be better. Want to try using Sbyr Green method for all, and compare to a general bacterial RT PCR. For P. fluorescencs this may be a start (http://aem.asm.org/content/72/4/2421.full), for B. subtilis (http://www.ncbi.nlm.nih.gov/pubmed/21356471) or (http://pubs.rsc.org.proxy1.lib.uwo.ca/en/content/articlehtml/2008/em/b806603e) and Burkholderia phytofirmans (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069435) -- this is not straightforward, gonna have to talk with Keri to see what we can do. Strawberry microbial community profiling by DGGE - http://www.ncbi.nlm.nih.gov/pubmed/16629753?dopt=Abstract&holding=npg Write up tree stuff to include in Kristin report Successful Fungal TRFLP from my small root rot symptoms the other day: Beneficial PGPR - http://www.ncbi.nlm.nih.gov/pubmed/20635120