Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil

Abstract

Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.

Keywords: Microbiome; Rhizosphere; Root endosphere; Root-rot diseases; Zanthoxylum bungeanum.

Figure 1. Comparative analysis of (bio-) physicochemical factors rhizosphere and bulk soils.

HE, healthy root endosphere; DE, diseased root endosphere; HR, healthy rhizosphere soil; DR, diseased rhizosphere soil; HB, healthy bulk soil; DB, diseased bulk soil; TC, total carbon; TN, total nitrogen; NH${}_4^{+}$-N, ammonium nitrogen; NO${}_3^{-}$-N, nitrate nitrogen; AP, available phosphorus; AK, available potassium; EC, electrical conductivity; SIR, substrate-induced respiration; MBC, microbial biomass carbon; MBN, microbial biomass nitrogen; ns, not significant. An asterisk (*) indicates P < 0.05.

Figure 2. The comparison of the bacterial phyla (A) and the genera (B) with significant differences healthy tree and diseased tree in roots, rhizosphere, and bulk soils.

Data are visualized using STAMP analysis with error bars representing Welch’s t-interval.

Figure 3. Effects of root-rot on the taxonomic ((A) the genus level) and functional ((B) KEGG pathway level and (C) CAZy level) composition of microbiomes.

HR, healthy rhizosphere soil; DR, diseased rhizosphere soil; HB, healthy bulk soil; DB, diseased bulk soil.

Figure 4. The relative abundances of functional genes responsible for the nitrogen cycle and carbon cycle in the KEGG database.

HE, healthy root endosphere; DE, diseased root endosphere; HR, healthy rhizosphere soil; DR, diseased rhizosphere soil; HB, healthy bulk soil; DB, diseased bulk soil.

Figure 5. The heatmaps show the distribution of gene classes in the CAZy database (A) and the 50 most abundant CAZy gene families (B).

HE, healthy root endosphere; DE, diseased root endosphere; HR, healthy rhizosphere soil; DR, diseased rhizosphere soil; HB, healthy bulk soil; DB, diseased bulk soil.

Figure 6. Correlations between significantly changed microbial taxa and environmental factors using the Spearman correlation coefficient (red, positive; blue, negative).

An asterisk (*) indicates P < 0.05, two asterisks (**) indicate P < 0.01.

Figure 7. Redundancy analysis (RDA) was used to investigate the relationships between healthy trees and diseased trees with soil properties for the taxonomic ((A) the genus level) and functional ((B) KEGG pathway level and (C) CAZy level) composition of microbiomes.

HR, healthy rhizosphere soil; DR, diseased rhizosphere soil; HB, healthy bulk soil; DB, diseased bulk soil. TC, total carbon; TN, total nitrogen, NH${}_4^{+}$-N, ammonium nitrogen; NO${}_3^{-}$-N, nitrate nitrogen; AK, available potassium; AP, available phosphorus, EC, electrical conductivity; SIR, substrate-induced respiration; MBC, microbial biomass carbon MBN, microbial biomass nitrogen.