First report on the microbial communities of the wild and planted raspberry rhizosphere – A statement on the taxa, processes and a new indicator of functional diversity

Abstract

The considerable worldwide scale of raspberry crops merit thorough research, especially in the context of their root associated microorganisms. The current state of knowledge concerning microbial biodiversity occurring in the rhizosphere of such a desirable plant is rather fragmentary. Nevertheless, a reasonable outlook for growers is anticipated with regard to the threat of disease or the initial exploration of raspberry growing sights for beneficial microbial isolates for the future of probiotechnology applications.Therefore, we combined the Next Generation Sequencing method with the Biolog® technique in order to describe the taxonomic and functional state of microbial communities under both planted and forest raspberries.The main taxa of potentially pathogenic fungi associated with raspberry were revealed to be Fusarium oxysporum, Tremalles and Hymenoscyphus. For prokaryotic pathogenic taxa, these were classified as follows: Nocardioidaceae and Xanthomonadaceae.Also, Ktedonobacteria, Micromonosporaceae and Chitinophagaceae occurring in raspberry rhizosphere were included with taxa from which beneficial isolates might be obtained to serve in the future as the active ingredient of biopreparations or microbial inocula for raspberry plantation naturalization.The most frequent microbial processes that occur in the raspberry rhizosphere were revealed. These were: hydrolase, oxidoreductase or phosphotransferase reactions, isomerization processes and/or the transfer of specific functional groups. The high degree of microbial activity on Putrescine was confirmed thereby indicating that ammonia-forming or deamination processes are more characteristic for raspberries than other plants.The alpha and beta diversity of the microbial communities under raspberry was demonstrated both at the metataxonomic and functional levels. The concept of the Effective Number of Substrates, following the Biolog® MicroPlate method, as a functional biodiversity indicator of the rhizosphere microbial communities was implemented and supported by metataxonomic information. This resulted from our hypothesis that the application of Jost’s ‘true diversity’concept of Effective Number of Species to a functional approach will change the allowance of diversity divergence of microbial communities from tested sites in relation to Richness.