Ecological inference on bacterial succession using curve-based community fingerprint data analysis, demonstrated with rhizoremediation experiment

Nucleic acid-based community fingerprintingmethods are valuable tools in microbial ecology, as they offer rapid and robust means to compare large series of replicates and references. To avoid the time-consuming and potentially subjective procedures of peak-based examination, we assessed the possibility to apply direct curve-based data analysis on community fingerprintsproduced with bacterial length heterogeneity PCR (LH-PCR). The dataset comprised 180 profiles from a 21-week rhizoremediation greenhouse experiment with three treatments and 10 sampling times. Curve-based analysis quantified the progressive effect of the plant ( Galega orientalis) and the reversible effect of the contaminant ( fuel oil) on bacterial succession. The major observed community shifts were assigned to changes in plant biomass and contamination level by canonical correlationanalysis. A novel method to extract relative abundance data from the fingerprint curves for Shannon diversity indexrevealed contamination to reversibly decrease community complexity. By cloning and sequencing the fragment lengths, recognized to change in time in the averaged LH-PCR profiles, we identified Aquabacterium( Betaproteobacteria) as the putative r-strategic fuel oildegrader, and K-strategic Alphaproteobacteriagrowing in abundance later in succession. Curve-based community fingerprintanalysis can be used for rapid data prescreening or as a robust alternative for the more heavily parameterized peak-based analysis.