Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum

Abstract

ABSTRACT Cheatgrass ( Bromus tectorum ) is one of the most problematic invasive plants in the western United States. Invasion by annual grasses disrupts nutrient cycling and negatively affects above- and below-ground biodiversity. Land managers use chemical herbicides, mechanical controls, cultural practices, and bioherbicides to combat this invasive plant. Recently, the biocontrol agent Pseudomonas fluorescens D7 has been touted as a non-chemical herbicide that offers lasting control of cheatgrass. However, experimental results report limited effectiveness under field conditions. To understand the underlying cause of the variable efficacy of this commercially available bioherbicide, soil samples from an active cheatgrass invasion treated with P. fluorescens D7 were collected and screened using high-throughput sequencing. At 18 months post-application, the bioherbicide had limited lasting effects on bacterial community composition, and few reads assigned to P. fluorescens were found in our sequence data. We suggest that the failure to establish sufficiently may partially explain the inability of this biocontrol agent to suppress B. tectorum under field conditions. IMPORTANCE Cheatgrass is one of North America’s most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P . fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.