Crop Management Impacts the Soybean (Glycine max) Microbiome

Abstract

Soybean (Glycine max) is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by Sphingomonas and Methylobacterium while belowground samples were dominated by Bradyrhizobium and Sphingomonas. Aboveground fungal communities were dominated by Davidiella across all management systems, while belowground samples were dominated by Fusarium and Mortierella. Specific taxa including potential plant beneficials such as Mortierella were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as Bradyrhizobium and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.

Keywords: agricultural management; amplicon sequencing; plant-microbe interactions; rDNA; soybean.

FIGURE 1

Stacked bar plots showing fungal genera in each management system at each growth stage (V2 – two sets of unfolded trifoliate leaves, R2 – full flower reproductive stage, and R6 – full pod development) with relative abundance ≥4%, (A) present in soil samples throughout the soybean growing season, (B) present in soybean root samples, (C) present in soybean stem samples, and (D) present in soybean leaf samples.

FIGURE 2

Stacked bar plots showing prokaryotic classes or genera in each management system at each growth stage (V2 – two sets of unfolded trifoliate leaves, R2 – full flower reproductive stage, and R6 – full pod development) with relative abundance ≥2%, (A) present in soil samples in soybean fields throughout the growing season, (B) present in soybean root samples, (C) present in soybean stem samples, and (D) present in soybean leaf samples.

FIGURE 3

Alpha diversity boxplots showing OTU richness and Shannon diversity metrics for fungal communities, (A) present in soil samples, (B) present in soybean root samples, (C) present in soybean stem samples, and (D) present in soybean leaf samples. Colors represent the plant growth stage during sampling (V2 – two sets of unfolded trifoliate leaves, R2 – full flower reproductive stage, and R6 – full pod development). Significance groups are represented by letters above the boxes. The letter before the forward slash (/) represents significance groups within a single growth stage by management system. Letters following the forward slash (/) represent significance groups within a single management system by growth stage. Significance groups were calculated using Kruskal Wallis tests followed by Pairwise Wilcox tests with a FDR P-value correction.

FIGURE 4

Alpha diversity boxplots showing OTU richness and Shannon diversity metrics for prokaryotic communities, (A) present in soil samples, (B) present in soybean root samples, (C) present in soybean stem samples, and (D) present in soybean leaf samples. Colors represent the plant growth stage during sampling (V2 – two sets of unfolded trifoliate leaves, R2 – full flower reproductive stage, and R6 – full pod development). Significance groups are represented by letters above the boxes. The letter before the forward slash (/) represents significance groups within a single growth stage by management system. Letters following the forward slash (/) represent significance groups within a single management system by growth stage. Significance groups were calculated using Kruskal Wallis tests followed by Pairwise Wilcox tests with a FDR P-value correction.

FIGURE 5

Principal coordinates analysis plots, based on Bray-Curtis dissimilarity, of fungal communities, (A) associated with soybean soil, root, stem, and leaf samples, (B) associated with soil samples, (C) associated with root samples, (D) associated with stem samples, (E) associated with leaf samples and prokaryotic, (F) associated with soil, root, stem, and leaf samples, (G) associated with soil samples, (H) associated with root samples, (I) associated with stem samples, and (J) associated with leaf samples. The shape represents the management system, while color represents sample origin in (A,F). In all others the color represents the management system.

FIGURE 6

Heatmaps of the relative abundances of the top 30 most abundant indicator taxa of fungal (A) belowground taxa, (B) aboveground taxa and prokaryotic (C) belowground taxa, and (D) aboveground taxa associated with conventional, no-till, organic, conventional and no-till, conventional and organic, or no-till and organic management systems. Samples are clustered by the displayed dendrogram using Bray-Curtis distances. The associated barplots show the relative abundance among indicator species of the taxa. Taxa that were also among the top 30 most important for distinguishing between managements in Random Forest models of above and belowground samples are indicated with an asterisk (*).

FIGURE 7

Summary of hub taxa detected in above and belowground bipartite networks for conventional, no-till, and organic management systems displayed as (A) a table of detected hub genera and (B) stacked barplot showing the distributions of hub taxa across all managements and sample origins.