Impact of conservation tillage on wheat performance and its microbiome

Abstract

Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.

Keywords: amplicon sequencing; fertilization; irrigation; soil microbiome; tillage; wheat genotype.

Figure 1

Bar plots showing the relative abundance of (A) bacterial phyla (>2.5%), (B) fungal 1 phyla (>1%), and (C) fungal 2 phyla (>0.05%) in the rhizosphere and root of winter wheat.

Figure 2

Alpha diversity of (A) bacterial,(B) fungal 1, and (C) fungal 2 communities in the rhizosphere (orange) and roots (green) of winter wheat. Means ±standard error of three replicates are shown.

Figure 3

Beta diversity assessed with Bray–Curtis distance of (A) bacterial, (B) fungal 1, and (C) fungal 2 communities in the rhizosphere (orange) and roots (green) of winter wheat.

Figure 4

Constrained distance-based redundancy analysis (db-RDA) of bacterial (A, B), fungal 1 (C, D) and fungal 2 (E) community composition in the rhizosphere (A, C, E) and roots (B, D) of winter wheat based on significant factors identified in PERMANOVA.

Figure 5

Heat plot showing the most abundant rhizosphere- and root-associated bacterial genera of winter wheat evaluated on combination of false discovery rate (FDR) and log fold change (logFC) using two sets of thresholds (FRD < 0.001 and logFC > 2).

Figure 6

Heat plot showing the most abundant rhizosphere- and root-associated fungal 1 genera of winter wheat evaluated on combination of false discovery rate (FDR) and log fold change (logFC) using two sets of thresholds (FRD < 0.001 and logFC > 2).

Figure 7

Heat plot showing the most abundant rhizosphere- and root-associated fungal 2 genera of winter wheat evaluated on combination of false discovery rate (FDR) and log fold change (logFC) using two sets of thresholds (FRD < 0.001 and logFC > 2).