Soil microbial communities in diverse agroecosystems exposed to glyphosate

Authors: KEPLER, RYAN - Oak Ridge Institute For Science And Education (ORISE); EPP SCHMIDT, DIETRICH - University Of Maryland; YARWOOD, STEPHANIE - University Of Maryland; Cavigelli, Michel; BUYER, JEFFREY - Former ARS Employee; Duke, Stephen; Reddy, Krishna; Williams, Martin; BRADLEY, CARL - University Of Kentucky; Maul, Jude

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2019
Publication Date: 2/18/2020
Citation: Kepler, R., Epp Schmidt, D.J., Yarwood, S.A., Cavigelli, M.A., Buyer, J.S., Duke, S.O., Reddy, K.N., Williams, M., Bradley, C.A., Maul, J.E. 2020. Soil microbial communities in diverse agroecosystems exposed to glyphosate. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.01744-19.
DOI: https://doi.org/10.1128/AEM.01744-19

Interpretive Summary: Modern farming systems often lead the the way for adoption of new technologies. No-till farming has been an extremely successful implementation of soil conservation technology, but it has been predicated on the use of selective herbicides and in some cases herbicides have been paired with genetic modifications (GM) to facilitate the use of non-selective herbicides. As with many GM crops, there has been concern with potential unintended effects of the transgenic crop on the ecosystem and in particular, in systems in which a non-selective herbicide is paired with a herbicide resistant GMO crop. In the case of the Glyphosate/Roundup-ready® system, there have been mixed results in regards to diserning the impact of glyphosate application and the GM transgene on plant disease potential of the system over time. Some researchers have reported stark increases in Fusarium root rot on corn and soybean whereas other researchers have reported no effect. As with many new technologies, questions and concerns exist within the public sector about the potentially unintended effects of the technology. There have been conflicting scientific reports regarding whether the use of the herbicide glyphosate causes an increase in some fungal plant pathogens. In this report, we designed a series of experiments that aimed to specifically answer questions that have been raised by the public, especially whether the use of glyphosate in corn and soybean crop rotations causes an increase of plant fungal diseases. We were able to determine that year to year weather variation, soil type and farming system history (crop rotation legacy) had more impact than the GM transgene or application of glyphosate. These results will give farmers and land managers confidence that continued use of glyphosate/glyphosate resistant system will not result in shifting the soil microbial community towards a community with more pathogenic potential. This report clarifies and corrects previously published information that may mislead farmers and land managers into believing that adoption of technologies such as GMO/herbicide systems are detrimental to their farm and local ecosystem.

Technical Abstract: We designed a multi-area study in Long Term Agricultural Research sites to thoroughly assess the impact of the glyphosate/Roundup-ready® system on root associated bacteria, and fungi of corn and soybean specifically testing: 1) the impact of the GM transgene without application of glyphosate, 2) the impact of transient glyphosate application, and 3) the legacy of repeated glyphosate application (>15 yrs). We used a combination of classic microbiological and next generation sequencing techniques to determine if the root associated microbial populations of Fusarium are impacted by the legacy of glyphosate application or the transient application of glyphosate. We screened over 6100 root segments to assess the root endophyte community. Over the two years of the study significantly more colony forming units (CFU)s were observed in 2013 than in 2014 at the Beltsville site (p<0.0003), but no differences in CFUs were observed between years at the Stoneville site. A total of 384 of the typical morphotypes were ITS amplicon sequenced, resulting in 11 identified dominent taxa: Fusarium sp., Macrophomina sp., Alternaria sp., Cladosporium sp., Penicillium sp., Zygomycota sp., Trichoderma sp., and Epicoccum sp. There was no significant difference in abundance of Fusarium sp. among the glyphosate sprayed and unsprayed plots, regardless of location, crop, or year (p>0.07). Using next generation sequencing, we assessed the fungal and bacterial communities associated with both corn and soybean roots. A total of 68,964 unique fungal and 72,454 unique prokaryotic sequence variants were identified across all samples. Permanova analysis of relative abundance transformed fungal counts and rarified bacterial counts revealed that site was the most significant factor accounting for Bray-Curtis dissimilarity distances in fungi (p = 0.001). Fungi communities in Beltsville clearly differed by farming system management history across both crops when Bray-Curtis dissimilarity values were subjected to principal component analysis (corn: p = 0.001; soy; p = 0.001). Likelihood ratio tests of taxon abundance also confirmed a lack of effect from treatment with glyphosate, finding no differentially abundant fungi or prokaryotes in any of the treatments for either Beltsville or Stoneville sites.