Written by Mark Schonbeck and OFRF staff

We recently launched a new newsletter section, “Ask OFRF,” a place where our community can submit questions for our staff to answer. Our first question came from Brian Caldwell of Hemlock Grove Farm, a certified organic farm in NY.

The life within our soils provides the foundation for successful farming and all terrestrial ecosystems. The diverse community of soil organisms—bacteria, fungi, protozoa, worms, and more—forms what we now call the soil food web. This web of life converts fresh residues into soil organic matter (SOM) and supports essential soil functions critical for agricultural production. Ever since the early 20th century, pioneers of organic agriculture like Sir Albert Howard and Ehrenfried Pfeiffer understood that “if you feed the soil, the soil will feed the plant.” Yet, despite their insights, mainstream agricultural science of the time often overlooked the vital role of soil life in plant nutrition.

In recent decades, extensive research has begun to illuminate how an optimally functioning soil biota feeds crops, enhances resilience, protects water quality, and contributes to long-term farm viability. However, concerns about the impact of agrochemicals, including herbicides and synthetic fertilizers, on soil health and soil life remain pressing.

Recently an important question was raised:

“Do you know if there is much research on the impacts of herbicides and synthetic fertilizer on SOM or soil health? Organic pioneers reported that soil health declined under chemical fertility management. For reasons that are not clear to me, some scientists discount the Morrow plot findings of Khan et al (2007), which support that. Do you have other research reports on that topic?”

To address this, we turned to OFRF’s Senior Research Associate, Mark Schonbeck. A respected researcher and long-time advocate for organic farming systems, Mark has dedicated his career to exploring the complex interactions between soil management, crop resilience, and farm sustainability. With his extensive knowledge, Mark offers valuable insights into the impacts of herbicides and synthetic fertilizers on SOM and overall soil health. Here’s what he has to say (all resources can be found at the end of this post):

Expert Insights from Mark Schonbeck on Soil Health

There is a growing body of research showing that all classes of crop protection chemicals (insecticides, fungicides, herbicides, nematicides, etc.) adversely affect all major taxa of soil organisms. From prokaryotes (bacteria and archaea) and fungi through nematodes, micro-arthropods (mites, springtails, etc), earthworms, and more, the soil biotic community is harmed by chemical applications. In fact, routine use of conventional agricultural chemicals have shown greater negative impacts on soil microbiomes than routine tillage in several recent meta analyses.

As for synthetic fertilizers and the Khan and Mulvaney analyses out of the University of Illinois, those papers (this one and this one) included not only the results from the Morrow plots themselves but also a review of a large number of other medium to long-term (5-100+ year) farming systems trials around the world. I used to emphasize those findings, which show that adding synthetic Nitrogen (N) undermines soil carbon sequestration as clear evidence that synthetic Nitrogen, Potassium, Phosphorous (NPK) fail to build Soil Organic Matter (SOM) despite higher crop biomass, and even sometimes burns up SOM.   

In a 2023 personal conversation, Dr. Ray Weil of University of Maryland (whom I respect highly as a world-class soil scientist) raised concerns about the reliability of the Khan and Mulvaney papers during a National Institute of Food and Agriculture (NIFA) project meeting (for OREI and ORG) in Washington, DC in 2023. He shared that the studies are being questioned because those showing negative impacts of soluble NPK on SOM may have been selectively chosen in the literature review while those showing positive or neutral effects were de-emphasized. Recent research suggests that soluble fertilizer used along with organic inputs can build SOM and I believe that it is more a matter of what soluble fertilizer by itself lacks and not what it contains that can harm soil life. Recent research suggests that it’s not the presence of soluble nitrogen itself that harms soil health, but rather the imbalance between N and organic carbon inputs.

If a farmer is providing lots of organic inputs (high biomass cover crops, compost, etc.) and then uses some synthetic N or NPK, the yield increase elicited by the synthetic fertilizer can indeed improve SOM accrual. There was at least one meta-analysis comparing organic, organic + synthetic, and synthetic-only fertilization on microbial (fungal and bacterial) biomass. The result was: organic ~ organic + synthetic >> synthetic only (with a highly significant two-fold difference). 

When it comes to fertility and nutrient sources and soil life or SOM, it is a matter of balance between organic carbon inputs and nitrogen inputs (whether organic and/or synthetic). When there is sufficient organic carbon (C) and the C:N ratio is balanced (~15-25:1), the soil life thrives and microbial biomass and respiration increase, as does the formation of stable mineral-associated organic matter (MAOM) and more labile or active particulate organic matter (POM)—both important to the functions of healthy soil.

If the C:N ratio is too narrow (for example poultry litter is 7:1), less SOM accrues and the soil microbiome is less capable of cycling N to ensure crop nutrition while minimizing leaching and denitrification losses. In an organic systems study, researchers at Washington State University found that vegetable rotations fertilized with compost (C:N ~20) accrued much more SOM (active and total) and sustained higher microbial activity and function than vegetable rotations fertilized with poultry litter (7:1) at the same total N rate. Crop yields were similar in the two systems. (More on that here).

In conclusion, the intricate relationship between chemical inputs, soil health, and agricultural productivity is a complex one. As research continues to illuminate the complexities of soil ecology, the importance of organic practices in preserving this vital resource becomes increasingly apparent. To foster sustainable agricultural practices, a holistic approach is essential. A transition to more organic and regenerative agricultural systems is essential for ensuring the health of our planet and future generations. Prioritizing soil health through practices like cover cropping and organic matter incorporation is crucial for long-term agricultural success. By understanding the complex interactions between soil organisms, nutrients, and crop production, we can develop strategies to enhance both yield and environmental sustainability.

A Deeper Dive: Key Studies and Findings

The following is a series of excerpts from a webinar Mark gave on Soil Disturbance, where he dives more into each of these topics, including specific studies that are relevant to this question.

The Case of Glyphosate: making sense of conflicting results

While the overall impact of pesticides on soil health is clear, the specific effects of individual chemicals can be more nuanced. Glyphosate, the most widely used herbicide in conventional agriculture across the world, is a prime example of this complexity.

There are plenty of studies showing everything from no harmful effect to subtle yet alarming disruptions to plant physiology, soil microbiology, or ecosystem functions due to glyphosate applications. Here are a sample of findings:

  • Experiments were conducted within long-term farming systems trials at Beltsville, MD and Stoneville, MS to determine whether foliar applications of glyphosate at normal rates (two applications at 0.75 lb active ingredient per acre) would affect rhizosphere microbiomes (Kepler et al., 2020). Glyphosate-resistant (GR) corn and soybean cultivars were planted in plots with (conventional) or without (organic at Beltsville, unsprayed perennial grass at Stoneville) a history of glyphosate use, and either foliar-sprayed with the herbicide or left untreated. Root and root zone soil samples collected 20 days after treatment showed no differential effect of glyphosate sprays on endophytic, rhizosphere, or bulk soil microbiomes (Kepler et al. 2020). 
  • Field applications of glyphosate at 1⁄4 and 1X recommend rates sharply (>80%) reduced the spore viability of arbuscular mycorrhizal fungi (AMF) in soil samples collected 10 or 30 days after field application and reduced the ability of AMF to form functional arbuscules in ryegrass (Lolium multiflorum) roots (Druille et al., 2013).
  • Application of glyphosate at roughly half-label rates to orchard grass, dandelion, or white clover growing in greenhouse mesocosm trials (large pots, 12-gallon capacity) significantly reduced the activity and reproductive success of two earthworm species (Lumbricus terrestris and Apporectodea caligenosa) that were introduced into the pots five weeks before treatment (Gaupp-Berghausen et al., 2015). Herbicide treatment also caused a sharp increase in soluble soil N and a slight increase in soluble P. Field studies would be needed to clarify the practical implications of these greenhouse observations for earthworms, soil health, and water quality in agricultural production.
  • A study of the prevalence of wheat head blight caused by two species of Fusarium in wheat production in Saskatchewan showed an apparent positive association between the disease and a history of glyphosate use (Fernandez et al., 2009).
  • Ten years of field trials in Missouri showed significantly increased root colonization by Fusarium fungi of glyphosate-resistant corn and soybean treated with the herbicide compared to the same crop cultivars without herbicide treatment. Glyphosate treatment also appeared to affect soil microbes involved in manganese (Mn) availability, N fixation, and disease suppression (Kremer and Means, 2009). It is notable and surprising that this trial gave such different results from Kepler et al. (2020). One possible factor is different regions and soil types. In a review of 67 published studies of the impacts of herbicides on soil invertebrates (arthropods, earthworms, pot worms, and nematodes), 77% of “tested parameters” studied in lab experiments and 32% of parameters in field conditions showed negative impacts (Gunstone et al., 2021).

Glyphosate showed adverse effects in some studies, and no effect in others, and appeared less damaging to soil life than amide/anilide herbicides and most insecticides and fungicides. Possible mechanisms of glyphosate effects on soil life include direct exposure via spray reaching the soil surface or translocation of the chemical from sprayed foliage to the root system, changes in the physiological condition of treated plants that curtail or alter the composition of root exudates including chemical signals, and long-term effects of low-level herbicide exposure year after year. One concern is that, given its frequent and widespread use and sometimes overuse, glyphosate may exert significant agroecosystem impacts despite its relatively low toxicity compared to other crop protection chemicals.

Pesticide Impacts on Soil Organisms: A Quantitative Perspective

To gain a clearer picture of the extent to which pesticides affect soil organisms, it is essential to examine quantitative data from multiple studies. A recent meta-analysis provides valuable insights into this complex issue. The following is another excerpt from the Soil Disturbance webinar:

  • In an extensive review of 398 studies that included a total of 2,842 tested parameters, Gunstone et al. (2021) evaluated the impacts of five classes of crop protection chemicals—insecticides, herbicides, fungicides, bactericides, and mixtures of two or more chemicals—on a wide range of soil invertebrates including nematodes, annelids (earthworms and pot worms), and arthropods (mites, springtails, insects, centipedes, etc). The authors defined a “tested parameter” as the chemical’s effect on one aspect of the health of one species or larger taxonomic group of soil organisms—the survival, growth, reproduction, or a behavioral or physiological function of the organism studied. Most studies addressed multiple organisms and/or multiple indicators of pesticide impacts on a single organism. All classes of pesticides affected all groups of organisms with negative impacts found in 70% of tested parameters. Lab studies found negative impacts more often (81%) than field trials (53%), and the field studies found more negative impacts of insecticides (61%) than fungicides (38%) or herbicides (32%). Earthworms were the most widely studied organisms (1,321 tested parameters) and showed sensitivity to all classes of agrochemicals including insecticides (82%), fungicides (78%), and herbicides (72%).
  • Researchers have documented significant impacts of corn and soybean seed treatments (fungicides and neonicotinoid pesticides) on the crop rhizosphere microbiomes (bacteria and fungi) and on several trophic levels of the soil fauna (Atwood et al., 2018; Nettles et al., 2016). Neonic seed treatment had a greater impact on non-target soil organisms, especially predatory and mixed-feeding guilds, while having relatively little impact on the target herbivore (pest) species.
  • In laboratory studies, mixtures of Mesotrione and S-metolachlor herbicides degraded more slowly and exerted a tenfold greater impact on soil microbial biomass and activity than either herbicide alone (Joly et al., 2012). A similar synergism related to enhanced persistence was documented for diflufenican and glyphosate (Tejada, 2009).

Balancing C:N for optimal soil health

To optimize soil health and crop productivity, it is essential to consider the balance of nutrients provided to the soil. The following research explores how different nutrient management strategies impact soil microbial communities and overall ecosystem function.

  • Based on five meta-analyses, Young et al. (2022) found that fertilizer regimens that combined organic and soluble N sources supported at least as much SOC accrual (1.3% per year) as all-organic N fertilization. The combination reduced leaching and NH3 volatilization by 28% (intermediate values between all organic and all soluble N treatments), but eliminated the increase in N2O emissions seen with all-organic sources.
  • In a long-term (10-year) greenhouse vegetable production trial, substituting half of the soluble NPK inputs with organic nutrient sources (manure, straw, manure + straw) enhanced soil taxonomic and functional microbial diversity, and specifically promoted the diversity and function of soil microbes involved in P cycling, resulting in greater P mineralization for crop uptake and at the same time holding excess P against leaching or runoff losses (Zhang et al., 2022b).

These findings suggest that soluble N sources disturb the soil microbiome not because of what they contain (nitrate, ammonium, urea) but because of what they lack—organic carbon. Soil microbes thrive on a balanced mixture of organic carbon and nitrogen, and soil health can suffer under organic management if C and N inputs are not balanced. This was clearly illustrated in an 11-year organic vegetable farming systems trial conducted in Washington State comparing plots fertilized with poultry litter (C:N ~7) versus finished compost (C:N ~ 20) at equivalent total N rates. While the two treatments gave similar crop yields, the compost-amended soil had 43% higher total SOC, 65% higher active SOC, and 35% higher microbial activity than the poultry litter-amended soil (Bhowmik et al., 2016, 2017).

The evidence presented underscores the critical role of organic agriculture in safeguarding soil health. By eschewing synthetic pesticides and fertilizers, organic systems inherently protect soil biota from harmful chemicals, fostering a thriving ecosystem beneath the surface. The emphasis on organic matter inputs in organic farming is crucial for building soil structure, enhancing water retention, and providing a steady supply of nutrients.

Mark Schonbeck has worked for 37 years as a researcher, consultant, and educator in sustainable and organic agriculture. He has participated in on-farm research into mulching, cover crops, minimum tillage, and nutrient management for organic vegetables. For many years, he has written for the Virginia Association for Biological Farming newsletter and served as their policy liaison to the National Sustainable Agriculture Coalition. He has also participated in different research projects to analyze, evaluate, and improve federally funded organic and sustainable agriculture programs. In addition, Mark offers individual consulting in soil test interpretation, soil quality and nutrient management, crop rotation, cover cropping, and weed management. He has worked with OFRF as a research, education, and policy consultant for many years. 

For more from Mark on this topic, you may be interested in checking out the Conservation Agriculture Webinar Series he presented, which we hosted in partnership with the NRCS: https://ofrf.org/news/conservation-ag-webinars/

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