Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition

AIMS

In a field study, the effects of treatments of glyphosate-based herbicides (GBHs) in soil, alone and in combination with phosphate fertilizer, were examined on the performance and endophytic microbiota of garden strawberry.

METHODS AND RESULTS

The root and leaf endophytic microbiota of garden strawberries grown in GBH-treated and untreated soil, with and without phosphate fertilizer, were analyzed. Next, bioinformatics analysis on the type of 5-enolpyruvylshikimate-3-phosphate synthase enzyme was conducted to assess the potential sensitivity of strawberry-associated bacteria and fungi to glyphosate, and to compare the results with field observations. GBH treatments altered the abundance and/or frequency of several operational taxonomic units (OTUs), especially those of root-associated fungi and bacteria. These changes were partly related to their sensitivity to glyphosate. Still, GBH treatments did not shape the overall community structure of strawberry microbiota or affect plant performance. Phosphate fertilizer increased the abundance of both glyphosate-resistant and glyphosate-sensitive bacterial OTUs, regardless of the GBH treatments.

CONCLUSIONS

These findings demonstrate that although the overall community structure of strawberry endophytic microbes is not affected by GBH use, some individual taxa are.

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. The target of glyphosate is the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimate pathway, which is virtually universal in plants. The inhibition of the enzyme stops the production of three essential amino acids: phenylalanine, tyrosine, and tryptophan. EPSPS is also present in fungi and prokaryotes, such as archaea and bacteria; thus, the use of GBP may have an impact on the microbiome composition of soils, plants, herbivores, and secondary consumers. This article aims to present general guidelines to assess the effect of GBP on microbiomes from field experiments to bioinformatics analyses and provide a few testable hypotheses. Two field experiments are presented to test the GBP on non-target organisms. First, plant-associated microbes from 10 replicated control and GBP treatment plots simulating no-till cropping are sampled and analyzed. In the second experiment, samples from experimental plots fertilized by either poultry manure containing glyphosate residues or non-treated control manure were obtained. Bioinformatics analysis of EPSPS protein sequences is utilized to determine the potential sensitivity of microbes to glyphosate. The first step in estimating the effect of GBP on microbiomes is to determine their potential sensitivity to the target enzyme (EPSPS). Microbial sequences can be obtained either from public repositories or by means of PCR amplification. However, in the majority of field studies, microbiome composition has been determined based on universal DNA markers such as the 16S rRNA and the internal transcribed spacer (ITS). In these cases, sensitivity to glyphosate can only be estimated through a probabilistic analysis of EPSPS sequences using closely related species. The quantification of the potential sensitivity of organisms to glyphosate, based on the EPSPS enzyme, provides a robust approach for further experiments to study target and non-target resistant mechanisms.