Profiling 16S bacterial DNA and RNA: Difference between community structure and transcriptional activity in phenanthrene polluted sand in the vicinity of plant roots

Biodegradation of polycyclic aromatic hydrocarbons (PAH) in soil is mainly performed by endogenous bacteria. The density and activity of soil bacteria are usually increased in the rhizosphere. A compartmentalized device was used to follow biodegradation of phenanthrene and bacterial community structure as a function of distance from roots. Isolation of total DNA and RNA, followed by PCR-TTGE and RT-PCR-TTGE on a 16S rDNA partial sequence, was performed to describe the structure of bacterial community and of active species, respectively. After 4 weeks, active species profiles in the immediate vicinity of roots were the same as in non-planted treatment, with similar biodegradation efficiency (approx. 60%) whereas community structure clearly indicated that bacterial populations were different. On the opposite, at a furthest distance (6–9 mm) from the roots where biodegradation was lower, bacterial community structure was similar to the non-planted treatment whereas active species differed. A specie activity factor (Saf) was calculated for five relevant species to follow their transcriptional state in the rhizosphere and showed spatial variations as a function of species and distance from roots. We conclude that depending on distance from roots, the rhizosphere selected different bacterial communities, and different active species within these communities, resulting in different degradation values. Potential biases of molecular protocols used in this study are discussed as well as their relevance to describe the bacterial component of the rhizosphere involved in PAH biodegradation.