Gordon F. Custer

Chemical herbicides, including glyphosate, atrazine, and many others, are commonly used to control unwanted vegetation in agroecosystems and protect crop yield potential. While the effects of herbicides on aboveground weedy vegetation are well documented, by comparison, the influence of herbicides on below-ground processes is poorly understood. Given the importance of the soil microbiome for providing ecosystem services, understanding microbial responses to herbicide application is of pressing interest. In this study, we examined the non-target effects of herbicide application by comparing three commonly used chemical herbicides — glyphosate, dicamba, and a tank mixture of atrazine plus mesotrione — to handweeded and non-treated controls. We assessed changes in soil microbial function, nutrient pools, and microbiome composition in Zea mays over 20 days post-treatment. The examined herbicides were shown to have limited and transient effects on soil edaphic properties and microbial function. Changes in enzymatic activities, nutrient concentrations, and fungal community structure were predicted primarily by weedy vegetation cover, suggesting that the observed responses are indirectly mediated by herbicide application. Conversely, we show that weed removal treatment was a significant predictor of bacterial community composition and that chemical herbicide application resulted in homogenization of the bacterial community, a trend not observed in the non-treated and handweeded controls. Together, our results suggest that chemical herbicide application has a limited effect on microbial diversity and function in heavily managed agroecosystems. However, the trend of biotic homogenization following pesticide application warrants further examination.

Coral holobionts acquire energy and nutrients from heterotrophic feeding, Symbiodiniaceae symbiosis, and additional metabolic functions (e.g. nitrogen (N) fixation) from associated bacterial communities. Since symbioses often require stable environmental conditions, corals in environments with seasonal variability have likely evolved adaptation strategies by either maintaining (i.e. regulating) or shifting (i.e. conforming) key functional traits, but empirical data is needed. We investigated carbon (C) and N elemental and stable isotope ratios alongside bacterial community composition in the hydrocoral Millepora dichotoma and the scleractinian coral Stylophora pistillata every two months over one year. These data were integrated with environmental parameters to investigate potential adaptation strategies of the coral holobionts over a seasonal cycle. S. pistillata showed temporal changes in δ13C, δ15N and C:N ratios in both host and Symbiodiniaceae tissues (indicating stable host-Symbiodiniaceae C/N cycling), in combination with stable bacterial communities. M. dichotoma, did not exhibit temporal changes in elemental and stable isotope ratios, but higher δ15N and C:N variability, and 61% higher C:N ratios in Symbiodiniaceae compared to host tissue. Temporal shifts in bacterial communities resulted in significantly enriched predicted metabolic functions for C, N, and sulfur cycling in winter. Stable C/N cycling and bacterial community composition suggest a regulator-like life history strategy of S. pistillata, whereas variable C/N cycling and flexible bacterial communities indicate a conformer-like life history strategy for M. dichotoma. Both contrasting adaptation strategies enable these organisms to succeed amid current environmental change, yet to what extent this can be maintained under future climate scenarios remains to be investigated.

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.