Loss in the rare bacterial diversity drives the monocropping obstacle of cut chrysanthemum

Uncovering the diversity of abundant and rare bacterial subcommunities in different years of continuous monocropping are essential to predict microbial community changes and understand soil functions in the cut chrysanthemum cropping system.

The Illumina MiSeq high-throughput sequencing platform was employed to analyze the composition, structure, and diversity of rare and abundant bacterial subcommunities in three different continuous monocropping years of cut chrysanthemum, namely, 1 year (Y1), 6 years (Y6), and 12 years (Y12)

The short- (Y6) and long-term (Y12) monocropping significantly enhanced the alpha diversity (e.g., Shannon index) of the abundant bacterial subcommunity (P < 0.05), but Y6 and Y12 treatments had a completely opposite impact on the rare bacterial subcommunity, with a remarkable decline in the Y12 and an increase in the Y6. Both Y6 and Y12 significantly reshaped the subcommunity structure of rare and abundant bacteria; Y12 significantly enriched the Acidobacteria in both rare and abundant taxa and decreased the abundant taxa Proteobacteria, while Y6 mainly increased the relative abundance of Gemmatimonadetes in the abundant phylum. The imbalance of soil nutrients including carbon, nitrogen, and phosphorus drove alterations of abundant and rare subcommunities.

The monocropping obstacle of cut chrysanthemum may be attributed to the decrease in the rare bacterial diversity.