The Effect of Best Management Practices on Soil Health in Wisconsin: A Comparison of Soil Biological Measurements Using Long-Term Trials

Final report for GNC17-249

Project Type: Graduate Student
Funds awarded in 2017: $11,906.00
Projected End Date: 09/01/2019
Grant Recipient: University of Wisconsin-Madison
Region: North Central
State: Wisconsin
Graduate Student:
Faculty Advisor:
Dr. Matthew Ruark
University of Wisconsin- Madison
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Project Information


Amid farmers’ ever-increasing enthusiasm for soil health there remains considerable uncertainty about how best to measure it, to interpret the results, and to adapt agricultural land management accordingly. To address this, research on over 250 farm fields across Wisconsin is being conducted to document how the adoption of cover crops, more diverse cash crop rotations, and no-till influences soil health. Due to the participating farms’ disparate field histories, annual weather, and soils, preliminary results show inconclusive results. The demand for information connecting farm management and soil health remains, however, as does the potential to capitalize on the multiple agronomic and environmental benefits that enhanced soil health brings.

This SARE-funded project will result in complementary research that leverages five existing, long-term research station trials in Wisconsin, collectively representing variations in crop rotations and management that represent the majority of cropland in the region. In addition to routine soil analyses, soils will be tested for potentially mineralizable carbon (PMC), potentially mineralizable nitrogen (PMN), and permanganate oxidizeable carbon (POxC).  These are three leading soil health measurements that are quick and affordable for farmers, have been adopted by several soil testing laboratories, and focus on biological nutrient cycling. Biological nutrient cycling is essential to soil fertility and its significance is reinforced by numerous studies that have found that crops take up more nitrogen from soils (due to mineralization of soil organic matter by soil microbes) than from applied fertilizers.

By identifying which management practices have the greatest effect on biological nutrient cycling, farmers will be able to make more informed decisions about how to build the natural fertility of their soil and reduce their dependency on synthetic inputs. Adoption of such practices (e.g. cover crops, or no-till) will have the added benefit of reducing nutrient and sediment loading in waterways, thus conserving vital topsoil and protecting surface and groundwater water quality.

Results from this research will be communicated to farmers, crop consultants and other agricultural stakeholders through on-farm and research station field days, conferences, Discovery Farms newsletters, and a peer-reviewed publication. Evaluation of farmer knowledge will be conducted at the start and finish of field day and Extension events, and through the monitoring of changes in behavior of Discovery Farms participants.

Project Objectives:

Learning Outcomes:

This research will identify the degree that long-term implementation of best management practices (BMPs) influences soil health in Wisconsin and the Upper Midwest, with a focus on biological nutrient cycling. Results will be shared with farmers, crop consultants, fertilizer and seed dealers, and conservation professionals via the UW- Discovery Farms newsletter, presentations at a minimum of three field days and three conferences, and a peer-reviewed journal publication. Added clarity about the connection of farm management to biological nutrient cycling will increase the agricultural community’s familiarity with soil health tests and their value.

Action Outcomes:

The results from this research will offer additional justification for farmer adoption of BMPs that reduce (1) soil erosion, (2) nutrient runoff from fields, and (3) farmers’ dependency on off-farm inputs. Such adoption will be monitored through direct farmer contact via the Discovery Farms program. Heightened awareness and action will lead to greater availability and use of soil health tests at soil testing laboratories.


Click linked name(s) to expand
  • Amber Radatz (Educator)
  • Eric Cooley (Educator)


Materials and methods:

Trial descriptions

This research utilized long-term research trials located at the University of Wisconsin’s Lancaster Agricultural Research Station (42o 50‘ – 90o 47‘; Fayette silt loam) and Arlington Agricultural Research Station (43o 18’ – 89o 21’; Plano silt loam). Each study is described in detail below, in the trial’s corresponding segment of the Results section. The utilization of long-term trials allows recently collected soil samples to reflect historic management effects.

Corn-Soybean-Wheat-Alfalfa Response to Rotation Trial (CSWAt)

Background: The CSWAt began in 1955 and is the only trial in our study that is located at the Lancaster Agricultural Research Station. Soil samples were collected from both the 0-N and 100-N plots of the continuous corn (CC), corn soy (CS), corn-corn-oat-alfalfa-alfalfa (CCOAAA) and corn-soy-wheat (CSW) rotations. Soil was only collected from the 100-N plots for the soy and wheat phases of the CSW rotation, however. Each plot is 20’ by 50’ and each treatment contains two field replicates. Two sets of composite samples were collected from each replicate by dividing them in half. Each year, corn is planted on 30 in. rows with a target density of 35,000 plants ac-1. All treatments receive 195 lbs. of 5-23-30 starter fertilizer and 34-0-0 (urea) at the given N rate for each treatment. Rates were 50% higher between 1967 and 1976. Alfalfa is planted on 6 in. rows, also at a target density of 35,000 plants ac-1. Tillage is conducted in all treatments and includes use of a chisel, disc, and mulcher. Weeds are managed with conventional herbicide treatments but no fungicides are used in these fields.

Corn-Soybean-Wheat Response to Rotation Trial (CSWt)

Background: This study began in 1984 and contains three field replicates of five treatments: continuous corn (CC), corn-soy (CS), and each phase of a corn-soy-wheat rotation (Csw, cSw, and csW). Corn is planted on 30 in. rows at 35,000 plants ac.-1 and soybean is planted on 15 in. rows at 180,000 plants ac.-1. Wheat is seeded every 0.5 in. at a target density of 1.7 million plants ac.-1. About 200 lbs. ac.-1 of 28-0-0 fertilizer is applied to the corn, no fertilizer is applied to the soybeans and 80 lbs. ac.-1 is applied to the wheat. This study is managed with conventional herbicide, fungicide and seed treatments. All corn is harvested as grain (in the fields from which samples were collected), and residue is left on the fields. All fields are managed as no-till.

Corn – Soybean Response to Tillage and Rotation Trial (CSt)

Background: This trial began in 1983 and includes two rotation treatments (CC, CS) and two tillage treatments, which are no-till (NT) and conventional till (CT). Each plot is 10’ by 35’ with four field replicates for each treatment. Each phase of the CS rotation is represented such that soil samples were collected from both the corn and soybean phases of this rotation. Corn was planted on 30 in. rows with a target density of 32,500 plants ac.-1, and soybean was planted on 30 in. rows with a target density of 150,000 plants ac.-1. Fertilizer applications are made in late-May to mid-June using 28-0-0 at 190 lbs. ac.-1 for CC or 160 lbs. ac.-1 for corn after soybeans. Fields are managed with conventional herbicide treatments in May and late-June, and insecticide seed treatments. Conventionally tilled fields received a fall pass with a chisel, followed by a field cultivator and soil finisher in the spring.

Alfalfa – Corn Response to Rotation Trial (ACt)

Background: This study began in spring 2010 and includes three treatments: Alfalfa-alfalfa-corn-corn (AACCg) where corn is harvested as grain; alfalfa-alfalfa-corn-corn (AACCs) where corn is harvested as silage; and continuous corn (CC) harvested as grain. The trial contains 10’ by 30’ plot sizes with three in-field replicates. Three cuttings are taken each year off of the alfalfa fields, which are planted on 6 in. rows at a target plant density of 35,000 plants ac-1. Corn is planted on 30 in. rows at the same density. All fields receive 70 lbs. ac.-1 of 28-0-0 starter fertilizer. Continuous corn and fields in their second phase of corn receive 130 lbs. ac.-1 of 28-0-0, whereas fields in their first year of corn after alfalfa receive only 90 lbs. ac.-1 of the same fertilizer. Fields are tilled (chisel in fall; cultivator and cultipacker in spring) only to establish alfalfa after two years of corn.

One-Year Effect of Manure and Cover Crops Trial (MCt)

Background: This 1-year trial includes four replicates of three treatments: (1) fields that were planted into cover crops and received manure; (2) those that received manure but did not get planted into cover crops; (3) and fields receiving no manure nor cover crops. The field was harvested as silage corn the previous season and the cover crop was winter rye. This trial is managed using conventional herbicide treatments.

Soil Sampling

Composite soil samples were taken to a depth of 15 cm from 128 unique treatments representing a mix of crop rotations, nitrogen application rates, tillage intensities and the use of cover crops. None of the studies receive irrigation. Soil samples were collected in late-spring of 2017 prior to crop planting and fertilizer application, to mimic when most farmers get their soils tested and when the results would be most actionable.  Within 24-hours soils were air-dried at 90˚F for a week, after which they were ground and stored in Whirl-Pak ® plastic bags.


Soil Analysis

In addition to running routine soil analyses (pH, SOM, P, K) and total C and N tests, we measured labile soil C and N. Potentially Mineralizable Carbon (PMC) is a 24-hour incubation of rewetted soil that measures CO2 released from microbial respiration (Franzluebbers et al.,2000; Haney et al., 2001). Similar versions of this test are included as part of the Cornell Soil Health Test and the Haney Test. Resulting levels of CO2 reflect soil microbial activity and the release of nutrients via organic matter mineralization. Potentially Mineralizable Nitrogen (PMN) was conducting using a seven-day anaerobic incubation to determine ammonium (NH4) released from soil organic matter by microbes during this time (Drinkwater et al., 1996). This same procedure is included as part of Cornell’s Comprehensive Assessment of Soil Health program. Permanganate Oxidizable Carbon (POXC) is a chemical extraction measuring the fraction of soil carbon that is most easily oxidized and is sensitive to changes in management (Culman et al., 2012; Weil et al., 2003). It is also a component of Cornell’s Comprehensive Assessment of Soil Health program.



Data analysis was performed using R Studio, version 3.4.2.  Analysis of variance (ANOVA) and Tukey’s Honest Significant Difference (HSD) test were run using the “agricolae” package to determine statistically significant differences between treatments within each study. Results were considered statistically significant at a p-value < 0.05. Only the graphs for statistically significant results are shown below. Linear regression was used to compare soil carbon and nitrogen tests to one another.



Research results and discussion:

All tables and figures can be found in attached document: Tables-and-Figures_Richardson

Corn-Soybean-Wheat-Alfalfa Response to Rotation Trial (CSWAt)

Results and Discussion: In order to make fair comparisons, we first focused on the fields that received 100 lbs. N ac-1 and whose soils were sampled after the corn phase of each rotation (Figure 1). The levels of TC and PMN were highest in the CSW and CCOAA rotations – those with the greatest crop diversity. Additionally, the CSW rotation also had the highest SOM values whereas CCOAA had the highest PMC values. Continuous corn had among the lowest values in all categories. While other studies have found that the high biomass inputs of corn crops leads to higher organic matter values (Geisseler and Scow, 2014; Collier et al., 2017; Poffenbarger et al., 2017 ), it is also known that not using a crop rotation can augment pest and disease pressures and reduce yields. After five decades, the CC rotation has had much lower corn yields over the past 5 years than the other rotations. The CS rotation also had the lowest SOM, perhaps due to soy containing lower biomass and the simplicity of this crop rotation.

Interesting results also arose when comparing soils sampled from different phases within the same rotation. For example, the CCOAA rotation had higher PMN values in the first and second years after alfalfa, and lower values after the second year of corn (Figure 2). This may be a result of corn’s high nitrogen demand reducing the quantity of readily available nitrogen in the soil. On the other hand, living oat crops sown in the fall were growing in this field when it was sampled in the spring. They may have taken up the excess N that remained in the soil in the fall. The same effect was seen for PMC when comparing the CSW rotations of this trial. Values declined significantly when sampling from the wheat phase when a living crop was present (Figure 3). This was the opposite of what we expected, as plant roots are thought to stimulate greater microbial activity in the rhizosphere – which would lead to greater PMC and PMN values. Soil samples were collected in mid-May when soils would have likely warmed up across all plots and soil moisture was not an issue at the time, so these factors cannot easily explain the differences. In this same trail, the application of 100 lbs. N ac-1 or no nitrogen inputs did not have a noticeable effect on soil C and N levels.

Corn-Soybean-Wheat Response to Rotation Trial (CSWt)

Results and Discussion: Similar to CSWAt above, the soil measurements that were statistically significant (POXC and TN) were lowest in the wheat phase of the CSW rotation (Figure 4).  Interestingly, TN would not be expected to change on a yearly basis since these values change slowly over time. Therefore, a single planting of a small grain in the fall should not change the TN values within a CSW rotation. As such, this finding is likely due to spatial variability in the field, versus management. While the same may be true for POXC, it’s possible that POXC values dip during the wheat phase of a rotation due to reduced plant biomass levels.


The CC rotation contains a larger quantity of most soil C and N values than the other rotations. This is in contrast with the CSWAt study previously mentioned. When conditions are optimal, corn produces more biomass than almost all other crops, leading to greater plant-based residue (i.e. organic matter) that can be incorporated into the soils. Where CC production does not result in declines of yield over time, values of soil C and N content can increase more in field growing CC than other conventional rotations. This particular trial takes place on rich, prairie soils that tend to produce better corn yields than the Fayette silt loams of the Lancaster Research Station – which is likely why this opposite effect is taking place.

Corn – Soybean Response to Tillage and Rotation Trial (CSt)

Results and Discussion: The CSt provides insights into the two-way effects of tillage and basic rotation on soil C and N measures.  In this case, changes in tillage practices led to statistically significant differences whereas there was no clear distinction between the CC and CS rotations (Table 4). The lack of a rotation effect may result from the limited diversity found in the rotations studied in this trial. No-till treatments generally had higher soil C values (e.g. Figure 5), especially for the labile pools. This latter point infers that no-till practices increase microbial processing (i.e. activity) and storage of carbon in the soils. Interestingly, neither total nor potentially mineralizable N levels were statistically greater in the no-till plots.

Alfalfa – Corn Response to Rotation Trial (ACt)

Results and Discussion:  Across all soil C and N measurements, no statistical differences were identified across the three rotations (Table 5). This study has only been established for seven years, meaning that two out of the three rotations have not completed two full cycles. As such, it may take more time before statistically significant differences become noticeable between treatments.

One-Year Effect of Manure and Cover Crops Trial (MCt)

Results and Discussion: This was the only short-term trial included in this body of research and evaluates the potential for single-season manure applications and cover crop usage to stimulate microbial activity and nutrient cycling. It is not surprising that single-season practices had no noticeable effect on larger pools of SOM, TC or TN, given that these are slow to change. One of the labile pool measures did pick up on differences, however, and that was PMC (Table 6). Plots that both received manure and had grown rye cover crops in them had the highest PMC values, whereas plots with neither manure nor cover crops had the lowest (Figure 6). Therefore, the combination of these practices can stimulate an increase in microbial activity in the soil. It was surprising to see that both PMN and POXC values did not noticeably increase with addition of either cover crop or manure, particularly as there would be more nitrogen and organic matter. If the rye covers were taking up excess nitrogen from the soil left over from the prior growing season, this might reduce the potentially mineralizable nitrogen in the soil.

Summary of Findings:

The different labile C and N test varied in their sensitivity to treatment effects across the five trials. For example, in the one-year manure and cover crop trial, only the ANOVA for PMC was statistically significant. The 33 year-old rotation trial for corn, soy and wheat, POXC and TN contained statistically significant differences across treatments whereas the other measurements did not. PMN and SOM values were only statistically different across treatments in the 51-year corn-soy-wheat-alfalfa rotation study. None of the measurements had statistically significant results in the seven-year-old alfalfa and corn trial, though this could be due in part to the shorter duration that this study has been in effect.

While the relationship between the measurements was lower than expected (Table 7), steps were taken to ensure the accuracy of results. All samples were run in duplicate for POXC and PMN and soils were rerun for all tests when coefficient of variation values were above ten across replicates. Additionally, soil standards were included in each batch of soil testing to ensure consistency.

It has been reported that POXC is an early indicator of changes to bulk C whereas PMC more closely reflects short-term C mineralization (sources).  In our study, the coefficient of determination (R2) indicates that POXC is more related to SOM, TC and TN (R2 between 0.44 and 0.52) than PMC (R2 = 0.118) or PMN (R2=0.080). The relationship between PMN and PMC and the bulk soil C and N measurements were either not statistically significant or explained only between 3 and 12 percent of the variability (i.e. R2 between 0.03 and 0.12).

Generally, the crop rotations that were able to produce the most biomass contained higher labile and bulk soil C and N. In some cases this was continuous corn (where soils and management were able to sustain production) whereas in other cases the rotations with the greatest diversity prevailed. A single season of manure additions and use of cover crops were able to stimulate soil microbial activity, but did not have a meaningful effect on soil C and N levels. In the long-term trial comparing tillage, no-till fields had consistently higher soil C levels but tillage did not have a sizable effect on soil N.



Collier, S., et al. 2017. Apparent Stability and Subtle Change in Surface and Subsurface Soil Carbon and Nitrogen under a Long-Term Fertilizer Gradient. Soil Sci. Soc. Am.  J. 81:310-321. doi: 10.2136/sssaj2016.09.0299

Culman, S.W., et al. 2012. Permanganate Oxidizable Carbon Reflects a Processed Soil Fraction that is Sensitive to Management. Soil Sci. Soc. Am. J. 76:494-504.

Culman, S.W., et al. 2013. Short- and Long-Term Labile Soil Carbon and Nitrogen Dynamics Reflect Management and Predict Corn Agronomic Performance. Agron. J. 105:493-502.

Drinkwater, L.E., et al. 1996. Potentially mineralizable nitrogen as an indicator of biologically active soil nitrogen. In: J.W. Doran, A.J. Jones, editors, Methods for assessing soil quality. SSSA Spec. Publ. 49. SSSA, Madison, WI. p. 217–219.

Franco, H.C.J., et al. 2011. Nitrogen in sugarcane derived from fertilizer under Brazilian field conditions. Field Crops Research, Volume 121, Issue 1, Pages 29-41, ISSN 0378-4290.

Franzluebbers, A.J., et al. 2000. Flush of carbon dioxide following rewetting of dried soil relates to active organic pools. Soil Sci. Soc. Am. J. 64:613–623.

Geisseler, D., and K. Scow. 2014. Long-term effects of mineral fertilizers on soil microorganisms: A Review. Soil Biology and Biochemistry. 75:54-63,  doi: 10.1016/j.soilbio.2014.03.023.

Haney, R., et al. 2001. A rapid procedure for estimating nitrogen mineralization in manured soil. Biol. Fertil. Soils 33:100–104.

Hurisso, T. T., et al. 2016. Comparison of Permanganate-Oxidizable Carbon and Mineralizable Carbon for Assessment of Organic Matter Stabilization and Mineralization. Soil Sci. Soc. Am. J. 80:1352-1364.

Kramer, A.W., et al. 2002. Short-term nitrogen-15 recovery vs. long-term total soil N gains in conventional and alternative cropping systems. Soil Biology and Biochemistry, Volume 34, Issue 1, Pages 43-50, ISSN 0038-0717.

Morrow, J.G., et al. 2016. Evaluating Measures to Assess Soil Health in Long-Term Agroecosystem Trials. Soil Sci. Soc. Am. J. 80:450-462.

Mulvaney, R.L., et al. 2006. Need for a Soil-Based Approach in Managing Nitrogen Fertilizers for Profitable Corn Production. Soil Sci. Soc. Am. J. 70:172-182.

Osterholtz, W.R., et al. 2016. Can mineralization of organic nitrogen meet maize nitrogen demand? Plant and Soil, 415:73–84, doi:10.1007/s11104-016-3137-1.

Poffenbarger, H., et al. 2017. Maximum soil organic carbon storage in Midwest U.S. cropping systems when crops are optimally nitrogen-fertilized. PLOS ONE. 12(3):e0172293. doi: 10.1371/journal.pone.0172293.

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Participation Summary
50 Farmers participating in research

Educational & Outreach Activities

3 Curricula, factsheets or educational tools
4 Published press articles, newsletters
5 Webinars / talks / presentations
2 Workshop field days

Participation Summary

197 Farmers
52 Ag professionals participated
Education/outreach description:

This project was the cornerstone for soil health extension programming in Wisconsin. Through Discovery Farms and the Water Way Network we hosted several field days, held farmer-centric workshops, and developed research updates for our website ( A webinar was hosted that highlighted the research results and educated farmers, consultants, and those in the agricultural world about important measures of soil health and management practices that can be used to improve soil health ( Two journal publications will be submitted over the next 12 months. 

Project Outcomes

197 Farmers reporting change in knowledge, attitudes, skills and/or awareness
10 Farmers changed or adopted a practice
1 Grant received that built upon this project
26 New working collaborations
Project outcomes:

The outcomes of this project are that we have a better understanding how differences in cropping systems lead to changes in soil health. This information will allow producers to understand what changes to expect upon adoption new management practices (e.g. reduction in tillage, extending of the crop rotation, or manure and cover crop use). This data also provides farmers benchmarks for soil health values in Wisconsin.

Knowledge Gained:

The knowledge gained in this project connected management practices with biological measurements of soil health. Crop rotations that were able to produce the most biomass contained higher labile and bulk soil C and N. In some cases this was continuous corn (where soils and management were able to sustain production) whereas in other cases the rotations with the greatest diversity prevailed. A single season of manure additions and use of cover crops were able to stimulate soil microbial activity, but did not have a meaningful effect on soil C and N levels. In the long-term trial comparing tillage, no-till fields had consistently higher soil C levels but tillage did not have a sizable effect on soil N. 

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.