Differential responses of the rhizosphere microbiome structure and soil metabolites in tea (Camellia sinensis) upon application of cow manure

Abstract

Background: The rhizosphere is the narrow zone of soil immediately surrounding the root, and it is a critical hotspot of microbial activity, strongly influencing the physiology and development of plants. For analyzing the relationship between the microbiome and metabolome in the rhizosphere of tea (Camellia sinensis) plants, the bacterial composition and its correlation to soil metabolites were investigated under three different fertilization treatments (unfertilized, urea, cow manure) in different growing seasons (spring, early and late summer).

Results: The bacterial phyla Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria dominated the rhizosphere of tea plants regardless of the sampling time. These indicated that the compositional shift was associated with different fertilizer/manure treatments as well as the sampling time. However, the relative abundance of these enriched bacteria varied under the three different fertilizer regimes. Most of the enriched metabolic pathways stimulated by different fertilizer application were all related to sugars, amino acids fatty acids and alkaloids metabolism. Organic acids and fatty acids were potential metabolites mediating the plant-bacteria interaction in the rhizosphere. Bacteria in the genera Proteiniphilum, Fermentimonas and Pseudomonas in spring, Saccharimonadales and Gaiellales in early summer, Acidobacteriales and Gaiellales in late summer regulated relative contents of organic and fatty acids.

Conclusion: This study documents the profound changes to the rhizosphere microbiome and bacterially derived metabolites under different fertilizer regimes and provides a conceptual framework towards improving the performance of tea plantations.

Keywords: Bacterial microbiome; Fertilizer; Metabolome; Organic; Rhizosphere.

Fig. 1

SPAD values of the young shoot (YS) and mature leaf (ML) under three different treatments in spring, early summer, and late summer

Fig. 2

Differences in microbial community composition in the soil samples using NMDS and PCoA. (1) NMDS using the WUF metric indicates show separations at (a) spring (Sp), (b) early summer (ES), and (c) late summer (LS); (2) PCoA were performed with the Weighted UniFrac (WUF, d) and the Unweighted Unifrac (UUF, e)

Fig. 3

Metabolomics analysis of different fertilizer treatments in spring, early summer and late summer. a1, b1 and c1 (the pie chart) represent the categories and the percentages of soil metabolites based on the number of compounds; a2, b2 and c2 (the heat map) represent the differential relative content of common metabolites under different fertilizer treatments in spring, early summer and late summer, respectively. Six biological replicates for each soil type are displayed in separate stacked bars in each heat map

Fig. 4

The enriched metabolomic pathways in the three rhizosphere soils were analyzed based on the KEGG dataset between T1 and T3, T2 and T3 in spring (a1 and a2, respectively), early summer (b1 and b2, respectively) and late summer (c1 and c2, respectively)

Fig. 5

Correlation analyses of soil microbiome and metabolome. Hierarchical clustering of the soil metabolites based on the microbes of a phylum-level in spring (a), early summer (b), and late summer (c). Positive and negative correlations are represented by red and blue, respectively

Fig. 6

Redundancy analysis (RDA) analysis of MiSeq data and the metabolites of organic acids and fatty acids (arrows) in different growing seasons (a, spring; b, early summer; c, late summer). The values of axes 1 and 2 are the percentages explained by the corresponding axis