Monitoring of Rhizosphere Bacterial Communities in Soil with Sewage Sludge Addition Using Two Molecular Fingerprinting Methods: Do These Methods Give Similar Results?

Abstract

In this study, bacterial genetic diversity from the rhizosphere of barley and wheat were studied. The plants were sown in pots with aliquot amount of 15 t/ha concentration of soil additive derived from sewage sludge and agricultural by-products represented by wastes from grain mill industry and crushed corn cobs. The plants sown in pots without the addition of soil additive represented control samples. The rhizosphere samples were collected on two dates (plant flowering and maturity) and the composition of bacterial communities were detected using two molecular fingerprinting methods – automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (T-RFLP). Microbial biomass expressed as the amount of metagenomics DNA was higher in soils with addition of soil additive, except during maturity stage in barley rhizosphere. Nevertheless, statistically significant differences between control and sludge samples were not detected in any case. Similarly, no changes were detected in the composition of bacterial community between control and sludge samples in barley and wheat rhizosphere by using cluster analysis. Only minor temporal changes in the composition of bacterial community between flowering and maturity periods were observed. These changes were related to the samples collected in the plant maturity stage. In this stage, plants were completely mature and their impact on the rhizosphere bacterial communities in the form of root exudates was limited. Statistically significant differences between ARISA and T-RFLP methods were detected in all measured values of diversity indices. Despite these differences, both methods gave results leading to similar conclusions.

Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress

“…Monte Carlo statistical analysis was conducted to determine if individual treatment combinations had statistically significant effects on community compositions (Van Wijngaarden et al, 1995). Shannon’s diversity index ( H ′) was calculated from binned data to determine differences in biodiversity (relative abundance and evenness) of taxa present within each soil for fungal and bacterial communities upon treatment with melatonin (averaged for four replicates) (Ondreičková et al, 2016). Subsequently, Shannon index values were analyzed by non-parametric Wilcoxon test to determine significant ( p < 0.05) differences upon melatonin treatments under high or low concentration for the stressors (cadmium or Salt).…”

Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress

“…Monte Carlo statistical analysis was conducted to determine if individual treatment combinations had statistically significant effects on community compositions (Van Wijngaarden et al, 1995). Shannon’s diversity index (H’) was calculated from binned data to determine differences in biodiversity (relative abundance and evenness) of taxa present within each soil for fungal and bacterial communities upon treatment with melatonin (averaged for 4 replicates) (Ondreičková et al, 2016). Subsequently, Shannon index values were analysed by non-parametric Wilcoxon test to determine significant (p < 0.05) differences upon melatonin treatments under high or low concentration for the stressors (cadmium or Salt).…”

Unraveling Techniques for Plant Microbiome Structure Analysis

“…Ribosomal intergenic spacer analysis (RISA) is related to the length of the ribosomal intergenic spacer region between the 16S and 23S rRNA genes [71,72]. The method has been applied for characterization of different strains along with to classify groups of complexes popula-tions [73,74].This method also can utilize length variability of rRNA genes to categorize trials into operational taxonomic units (OTUs).…”