Reduce the impact of plastid DNA in root bacterial community analyses
One other thought. The paper below suggests that the impact of plastid DNA in bacterial analyses can be mitigated by employing RNA extraction-reverse transcription-PCR analyses. Since plastids are not particularly active in root cells, the relative contribution of plastids to total RNA in a root extract will be reduced. This probably won't work in leaf extracts!
Nikolausz, M., K. Marialigeti, and G. Kovacs. 2004. Comparison of RNA-and DNA-based species diversity investigations in rhizoplane bacteriology with respect to chloroplast sequence exclusion. J. Microbiol. Methods 56:365–373.