Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture

Abstract

The production and quality of <i>Rehmannia glutinosa</i> can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of <i>R. glutinosa</i> led to a significant decline in the relative abundance of the phyla <i>Firmicutes</i> and <i>Actinobacteria</i> in the rhizosphere and rhizoplane. Furthermore, the families <i>Flavobacteriaceae</i>, <i>Sphingomonadaceae</i>, and <i>Xanthomonadaceae</i> enriched while <i>Pseudomonadaceae</i>, <i>Bacillaceae</i>, and <i>Micrococcaceae</i> decreased under consecutive monoculture. At the genus level, <i>Pseudomonas</i>, <i>Bacillus</i>, and <i>Arthrobacter</i> were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of <i>Pseudomonas</i> spp. and <i>Bacillus</i> spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, <i>R. glutinosa</i> monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.