Underground Defenses

Investigating how 1,3-D fumigation affects the soil microbial community

Published online: Feb 20, 2020 Articles, Fungicide, Insecticide
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This article appears in the February 2020 issue of Potato Grower.

Insecticides, fungicides, nematicides and herbicides are increasingly used to improve crop yield and quality, but sometimes the widespread adoption and use of pesticides has unanticipated negative impacts on non-target organisms in the surrounding ecosystems. Often, effects of pesticides on non-target organisms are understudied. Since soil microbial communities support a wide range of ecosystem services required for maintaining soil structure and fertility; supporting carbon, nitrogen and phosphorus cycling; and removing soil contaminants, we were interested to learn how a fumigant, commonly used for nematode management in the potato cropping system, influences soil microbial communities.

Nematicides are widely used in vegetable production to control nematodes that reduce plant yields. 1,3-Dichloropropene (1,3-D) is a well-known nematicidal soil fumigant used on many crop species, including potato. Despite the widespread use of 1,3-D as a soil fumigant to manage nematodes, there are relatively few studies that have analyzed its effect on non-target organisms compared to the number of studies reporting effects on its specific target pests. In the fall of 2016, we conducted a study to examine the short-term soil microbial response to 1,3-D application, using high-throughput sequencing techniques to examine soil microbial structure prior to and one month after application.

In a field experiment at the Hermiston Agricultural Research and Extension Center south of Hermiston, Ore., the soil was a fine sandy loam with approximately 65 percent sand, 25 percent silt, 10 percent clay, and less than 1 percent organic matter. The previous crop was winter wheat, and fall tillage practices prior to experiment establishment included ripping to a depth of 18 inches, discing twice, and roller-harrowing. The field was watered prior to 1,3-D application to obtain proper soil moisture to a depth of 12 inches.

The four treatments included different rates of 1,3-D (11, 13, 15 and 20 gallons per acre), which were broadcast-applied (i.e., shank-injected) at a depth of 18 inches by a commercial applicator. Soil was sampled prior to fumigation and approximately one month after application. The post-treatment sample was taken following several common farming practices, such as irrigating and cover crop planting.

Using high-throughput sequencing techniques, we investigated changes in soil bacterial and fungal community structure in response to application of 1,3-D. Three bacterial phyla—Proteobacteria, Firmicutes and Actinobacteria—and one fungal phylum—Ascomycota—were dominant in soils, and the effects of the fumigant was minor on soil microbial communities. The abundance of 45 bacterial and 24 fungal families was affected by sample depth, 1,3-D rate, or the interaction of sample depth and 1,3-D. However, most families did not show consistent patterns of increasing or decreasing abundances that correlated with fumigation, suggesting that soil can be a robust ecosystem and fumigants may not have a long-term impact on the overall microbial community.

Maybe most interesting, we found that 1,3-D appeared to have two non-target effects on soil microbes. One effect was a reduction in fungi known to be nematode pathogens, and the second effect was an increase in bacteria known to be able to decay complex carbohydrates, including carbohydrates of nematode corpses.

In terms of nematodes in this experiment, we found that 1,3-D killed 98 percent of the nematodes present in pre-treatment measurements across all nematode species assessed, primarily root lesion and stubby root nematodes. Although we did not observe statistically significant differences in potato yield in 2017, we did observe an average 3.4 ton-per-acre (14.5 percent) increase in yield in treatments fumigated with 1,3-D over the non-fumigated control. There also appeared to be a rate response, with 11, 13, 15 and 20 gallons per acre yielding 11, 15, 15 and 18 percent more than the non-fumigated control, respectively.

Investigating soil microbial community structure in response to different crop management strategies, including pesticide application, may eventually help growers manage their soil microbial communities in ways that will enhance crop health and productivity. In potato cropping systems in the short-term, there may be a greater impact on the soil microbial community from agricultural practices such as tillage, use of cover crops and irrigation than from fumigant application.


Ken Frost is a plant pathologist at Oregon State University’s Hermiston Agricultural Research and Extension Center. He can be contacted at kenneth.frost@oregonstate.edu.

Yuan Zeng is a post-doctoral researcher in Colorado State University’s Department of Bioagricultural Sciences and Pest Management.

Jane Stewart is a professor of plant pathology at Colorado State University, and can be reached at jane.stewart@colostate.edu.

Zaid Abdo is a computational biologist specializing in metagenomics and microbiome research at Colorado State University. He can be contacted at zaid.abdo@colostate.edu .

Amy Charkowski is a plant pathologist and head of Colorado State University’s Department of Bioagricultural Sciences & Pest Management. She can be reached at amy.charkowski@colostate.edu. ?