macpat

I'm growng cyanobacteria on agar plates using BG110 media. Does anyone know of a specific protocol for DNA extraction when using agar? Will contamination by agar inhibit or affect the PCR or DNA extraction at all? References?

I'm currently working on a research project which aims to identify cyanbacterial species present on moss leaves through morphological and molecular methods (polyphasic approach to cyanobacterial identification). The genera in question are Nostoc, Stigonema, Cylindrospermum, and Calothrix. My question is, is anyone aware of a technique which can be used to separate bacteria based on size, charge, or other morphological characteristics? We have been attempting to culture the various cyanobacteria on agar, which has its drawbacks. I'd like to find way to identify the actual cyanobacterial species/strains growing epiphytically on the moss, as opposed to working with the isolated species/strains on the agar. The difficulty I'm having in the experimental design is that if I were to use a denaturing gradient gel electrophoresis (DGGE) or other molecular method for microbial community analysis, I would not be able to connect the genetic identity to a morphological one (as far as I know). My thought has been that if I can find a way to physically separate the various cyanobacterial morphologies in large enough amounts, then I can run PCR on each of the morphological groups. Is there a method of using gel electrophoresis or other filter? Any information on the topic will be greatly appreciated! I should have included that I plan to detach the cyanobacteria from the moss leaves into sterile water by vortexing in a plastic tube.