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Assessment of species richness and diversity of Prunus avium rhizosphere and bulk soil bacterial communities

Qin, S., Zhang, P., Zhou, W., Lyu, D.
Acta horticulturae 2019 no.1235 pp. 327-336
Acidobacteria, Actinobacteria, Proteobacteria, Prunus avium, bacterial communities, bioactive properties, cherries, community structure, edaphic factors, genes, growing season, high-throughput nucleotide sequencing, morphogenesis, orchards, rhizosphere, ribosomal RNA, roots, soil, soil bacteria, species richness, summer, surveys
Microorganisms play an important role in mediating interactions in plant-soil rhizospheres. Cherry roots generally have poor adaptability and are sensitive to soil environment changes; as such, the microbial community structure and soil biological activity largely determine the nature of cherry root physiological functions and morphogenesis. To determine the impact of seasons and the presence of cherry roots on the abundance and structure of bacterial communities in soil, we investigated the bacterial communities colonizing the cherry rhizosphere and non-rhizosphere (bulk soil) during three growing seasons using Illumina high-throughput sequencing of the 16S rRNA gene hypervariable region. In all, 3,627 operational taxonomic units (OTUs) belonging to 58 genera and seven unclassified phyla were identified and assigned to 27 broad taxonomic groups. The bacterial communities were dominated by members of Proteobacteria, followed by those of Acidobacteria and Actinobacteria. The largest number of OTUs was observed in summer. More diverse bacterial communities were observed in the bulk soil than in the rhizosphere; however, the bulk soil generally had a lower abundance of each species. Different functional bacteria could be identified in the rhizosphere and non-rhizosphere, suggesting that cherry roots quantitatively and qualitatively influenced soil bacterial communities of cherry orchards. This study enhances our understanding of the soil niche effect on bacterial diversity in orchards and validates the effectiveness of high-throughput sequencing in surveying soil microbial diversity.