Microbial Community Investigation of Wild Brambles with Root Nodulation from a Calcareous Nitrogen-Deficient Soil

This study examines culturable diazotrophs and non-culturable bacteria found in the rhizospheres and root pseudonodules of wild blackberry plants (Rubus ulmifolius) that dwell on an unmanaged calcareous nitrogen-deficient soil. The DNA was extracted from the nodules and rhizospheres, and 16S rRNA gene metabarcoding was carried out. The metagenome functions were predicted with bioinformatic approaches. The soil samples were analyzed for the physico-chemical properties. The culturable diazotrophs were isolated and evaluated for the biochemical and plant growth-promoting properties. The soil was classified as nutrient-depleted calcareous soil. The microbial communities of the nodules and rhizospheres showed marked differences. The Pseudomonadota was the nodules’ dominant phyla (90%), while the Actinobacteriota was the most abundant (63%) in the rhizospheres. Stenotrophomonas was the dominant genus (55%) in the nodules, while the Streptomyces genus was widely present (39%) in the rhizospheres. The differences among the nodule and rhizosphere microbial communities were also highlighted by the metagenome function predictions. The gene copies (KOs) revealed the most interesting findings. Similar KOs involved in the nitrogen fixation were found to be similar in terms of the nodules and rhizospheres. However, the nitrate reduction was higher in the rhizosphere, while the denitrification was more prominent in the nodules. Nine diazotrophs were isolated from the nodules and rhizospheres. The plant growth promoting traits’ characterization has shown the interesting potential of the isolates in improving the acquisition of nutrients in plants, promoting their growth, and tolerating stress. Based on interesting biochemical and plant growth-promoting traits, the isolate N2A was further characterized and identified as Pantoea agglomerans.