Soil Microbial Response to Seven Different Organic Transition Strategies

Final Report for GNC12-154

Project Type: Graduate Student
Funds awarded in 2012: $9,920.00
Projected End Date: 12/31/2015
Grant Recipient: University of Missouri
Region: North Central
State: Missouri
Graduate Student:
Faculty Advisor:
Dr. Randall Miles
University of Missouri
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Project Information


In the three years that is required in the U.S. to transition from conventional to organic practices, producers often experience decreased yields. We compared the effects of seven crop and tillage rotations on soil quality, weeds, and yields. We are reporting here only on soil microbial response to the transition strategies. This research was primarily funded by the Ceres Organic Trust and the full report, including weed response to the treatments, can be found on their website. We found that a three year rotation of winter and summer cover crops was the most effective in decreasing weed pressure but there were no treatment differences in soil quality, including microorganism biomass and community diversity. This was most likely because the study site had 4.3% SOM, indicating that soil quality was already high. We found that using organic no-till during the transition years severely reduced yields and that new methods of mechanical weed control need to be researched to make organic no-till feasible. We recommend that a combination of winter cover crops or wheat for early season weed control, SOC additions, and erosion control; summer cover crops for reducing the soil weed seedbank; and low N-use soybean are important tools for the transition from conventional to organic production methods.



To gain organic certification in the U.S., a three year transitional period is required during which no prohibited materials, such as synthetic chemicals, fertilizers or genetically modified (GM) seeds, may be applied to the land. This transitional period from conventional to organic row cropping can be the most important and the most challenging time for an organic producer because of the need to control weeds, decrease the soil weed seedbank (Riemens et al., 2006) and improve soil quality and fertility (Delate and Cambardella, 2004). Soil quality is a composite view of the soil’s physical, chemical and biological properties and processes that sustain productivity, environmental quality and support healthy organisms (Doran and Zeiss, 2000). Soil organic matter (SOM) and its primary constituent, soil organic carbon (SOC), are closely linked to soil quality and soil fertility, thus maintaining or increasing SOM is an important goal in organic transition (Wander et al., 1994; Clark et al., 1998).

To determine the effect of crop rotation and tillage practices on soil building during the transition into organic row cropping, we examined seven transitional cropping systems listed in table 2.1 These cropping systems utilized a winter cover crop mix (Table 2.2), the cash crops corn, soybean, wheat, and grain sorghum and the summer cover crops sorghum-sudangrass and sunn hemp. All systems utilized fall planted winter cover crops or wheat prior to spring planting. Treatment CCO, cover crop only, utilized three years of winter and summer cover crops with no intervening cash crop. Sorghum-sudangrass was the summer cover crop in year 1-2 and sunn hemp, a tropical legume, was used in year 3. Cover crops provide weed control through resource competition and allelopathic effects (Teasdale, 1996; Creamer at el., 1996). They can also improve soil nutrient cycling efficiency, reduce soil erosion, increase SOC, increase water infiltration and improve soil physical properties (Snapp et al., 2005; Dabney et al., 2001; Lundquist et al., 1999a). We hypothesized that the CCO system would provide the greatest weed control and soil quality building during the transition to organic.

Treatment MCC, modified cover crop, utilized one year of a sorghum-sudangrass summer cover crop followed by grain sorghum in year 2 and corn in year 3. Sorghum species contain sorgoleone, an allelopathic chemical that has been found to reduce growth of weed seedlings (Einhellig and Souza, 1992), so we hypothesized that two consecutive years of sorghum species would lead to lower weed seed growth and seed production. Having grain sorghum in year 2 was expected to be more economically viable than two years of summer cover crop. In treatment MCT, modified conventional tillage, the transition began with one year of sorghum-sudangrass in the summer followed by winter wheat and a soybean double-crop in year 2 and corn in year 3, with tillage as needed to control weeds

CONVCS, conventional tilled corn-soybean-wheat-double crop soybean rotation utilized pre-plant tillage for early weed control and between row cultivation for in-season weed control. NTCS, no-till corn-soybean followed the same rotation as CONVCS but utilized a crimped winter cover crop for weed control and did not use any soil tillage until year 3 when a soybean double-crop was planted following winter wheat. No-till can reduce the carbon footprint of organic farmers by using cover crops flattened and killed by a roller/crimper as a weed blocking mulch instead of relying on multiple tillage for weed control (Carr et al., 2013; Mirsky et al., 2013).

In treatments NTSS, no-till sorghum-soybean, and CONVSS, conventional sorghum-soybean both the no-till and conventional rotations were replicated using grain sorghum as the 2nd year cash crop rather than corn. Grain sorghum has a history of success in MO, can get a majority of its fertility needs met through use of a winter legume cover crop (Reinbott et al., 2004), and does not contain any genetically modified (GM) varieties nor can it cross pollinate with GM varieties, which are prohibited by NOP regulations.

Project Objectives:


The overall goal of this research project was to improve the competitiveness of transitional organic grain crop producers by researching cropping systems that can help maintain or increase productivity, suppress weeds and build soil health. The specific goal of the SARE funded project was:

  • Compare seven different rotational and tillage systems for transitioning into organic production and determine which strategies best contribute to microorganism biomass and community diversity as measured by phospholipid fatty acid analysis (PLFA) and response to a β–glucosidase enzyme assay.
  • Create outreach events to reach producers and government personnel interested in organic and sustainable agricultural practices.


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  • Dr. Randall Miles


Materials and methods:

Materials and Methods:

Research Site and Design

This research was conducted from 2012-2014 at the University of Missouri Bradford Research Center (BREC), located 5 miles east of Columbia, MO. Soils at this site are primarily Mexico silt loam (fine, smectitic, mesic Vertic Epiaqualfs) and are on the central glacial till claypan plain. This site has an argillic horizon, or claypan, typically 10 inches below the soil surface. This research site had previously been managed as a fescue meadow until 2010 when the fescue was tilled under and the field was planted with a summer cover crop of buckwheat for two years. These conditions might be similar to land that is put into organic production after being in long-term conservation reserve (CRP). The experiment was conducted as a randomized complete block design with 5 replications of 7 different cropping system treatments. Plots were 30 ft long and 20 ft wide.


Due to the extreme drought in 2012, irrigation was applied at approximately 1 inch of water on each plot and occurred on 6 June, 6 and 20 July, and 3 and 17 August 2012. Although 2013 experienced moderate drought, irrigation was not used. The total rainfall from May through September in 2012-2014 was 6.9 inches, 17.4 inches, and 20.4 inches, respectively. The annual cumulative rainfall for 2012-2014 is shown in Figure 2.1 and is plotted against the 30-year average for Boone County, MO.

Crop Management

A poultry compost product was applied once annually each spring just before tillering in wheat and just after winter cover crop destruction in other treatments. In tilled plots the compost was incorporated into the soil and in no-till plots the compost was left on top of the soil surface. Applied compost amounts were based on the soil-test P recommendation (Buchholz et al., 2004) and the P content of the compost to prevent potential P leaching and pollution. The amount applied annually was approximately 4000 lbs acre-1 compost, 77 lbs acre-1 P, and 113 lbs acre-1 N.

Pre-plant tillage was conducted using a 10 ft wide plot disk and weed control was done in crop plots using a Danish S-tine 4-row cultivator. Cover crops in no-till plots were terminated using a roller-crimper (I&J Mfg, Gap, PA). Cover crops in tilled treatments were first mowed and then disked into the soil. The organic corn (Welter Seed hybrid WS2292), soybean  (Blue River Hybrids 389F.Y) and grain sorghum (VNS, Welter Seed) were planted using a 4-row John Deere planter at 30 inch row spacing at 35,000 seeds acre-1, 156,000 seeds acre-1, and 112,000 seeds acre-1, respectively. Due to the dense mat established by the cover crop in the no-till plots, the no-till coulters were removed and spiked closing wheels were installed on the planter to effectively close the seed-row furrow in 2013 and 2014.

The winter cover crop (Table 2.2) was a mix of hairy vetch, cereal rye, Austrian winter pea, and crimson clover. Shallow tillage before planting of cover crops (-1.

To determine cover crop yields, a 0.25 m2 frame was randomly placed in the plots and above-ground cover crop biomass was removed from each frame area, dried in a forced air dryer, and weights were recorded. Crop treatments were harvested at physiological maturity using plot combines to harvest the middle 2 rows of corn, soybean and grain sorghum and the middle 5 ft of wheat.

Plant Analyses

To determine biomass of winter and summer cover crops, a frame measuring 0.25 m2 was randomly placed at two locations in each plot and within the frame, plants were removed and dried in a forced air dryer and dry weights were recorded.

Soil Analyses

Bulk density was determined gravimetrically. For characterizations of other soil properties, soil was collected using a soil probe with a 0.75 in diameter to a depth of 6 inches. Eight samples were taken in a grid pattern in each plot and were composited and homogenized using a 6.35 mm sieve.

Phospholipid fatty acid analysis was determined using the method of Buyer and Sasser (2012). In brief, samples were placed in test tubes and dried overnight. After a Bligh-Dyer lipid extraction was performed the extract was dried, dissolved in chloroform, and placed into a 96 well extraction plate. Phospholipids were then eluted into vials, dried and transesterfied. The fatty acid methyl esters produced by this process were then analyzed in a GC using MIDI Sherlock software (MIDI Inc., Newark, DE).

β-glucosidase is an enzyme that hydrolyzes degradation products of cellulose. To determine levels of this enzyme in collected soil (Eivazi and Tabatabai, 1988), 1 g of soil was mixed with 4 mL of modified universal buffer at pH 6.0 and 1 mL of p-Nitrophenyl-β-D-glucoside (PNG) solution and incubated at 37 C for 1 hour. To stop the reaction, 1 mL of 0.5 M CaCl2 and 4 mL of 0.1 M THAM buffer (pH 12) were added. The resulting solution was filtered through Q2 filter paper and measured in a spectrophotometer at 410 nm.

Soil was sieved (< 2 mm), air-dried, ground and analyzed on a LECO® combustion analyzer for soil organic carbon (SOC) and total nitrogen (TN) concentration measurements.

The active soil carbon fraction was analyzed colorimetrically using the methods of Weil et al. (2003) and modified by Culman et al. (2012). A 2.5 g soil sample was added to 2.0 ml of potassium permanganate (KMnO4) and 18.0 ml of DI water then shaken for 2 minutes. After settling for 10 minutes, a 0.5 ml sample of the supernatant was extracted, added to 49.5 ml of DI water and read at 550 nm on a spectrophotometer.

Statistical Analysis

Statistical analysis was completed with SAS Enterprise Guide 6.1 (SAS, Cary, North Carolina). Results were analyzed using PROC MIXED at α=0.05. The ANOVA was run as a RCBD design. The fixed effect in the model was crop rotation treatment. All means separation differences were tested using Tukey’s HSD. Analysis was separated by year because the experiment monitored effects of varying crop rotations over time.

Research results and discussion:

[Attachment Exist(s)]

Results and Discussion


Due to very poor stands from low precipitation, biomass production of the cover crop in 2012 ranged from only 36 to 42 % of the 8000 kg ha-1 that has been identified as the threshold for consistent suppression of annual weeds (Mirsky et al., 2013). This led to high levels of summer annual weeds in all treatments and had a strongly adverse effect on NTCS and NTSS soybean yields, which averaged 87% lower than yields in the CONVCS and CONVSS soybean (Table 2.5). Because NTCS and NTSS soybean were reliant on a cover crop mat to block weed growth, the low level of cover crop biomass effectively meant that these treatments had no weed control throughout the growing season. Average yield of soybean in the CONVCS and CONVSS treatments was 86% of the average yield reported in the University of Missouri Variety Testing (UMVT) Columbia 2012 soybean trial (Weibold et al., 2012). This shows that full season soybean can be grown during organic transition without resulting in extreme yield loss. The UMVT tests include many GM varieties that have undergone concentrated breeding and yield testing while many of the organic crop varieties have had less infusion of testing and research due to their not being protected through patents. Therefore reductions in organic crop yield from conventional yields may be due more to varietal differences than production differences.

Drought conditions in 2012 also led to poor stands of sorghum-sudangrass in the CCO, MCC and MCT treatments with an average cover crop biomass yield of 3624 kg ha-1 compared to 40,350 kg ha-1 in the CCO treatment in 2013 (Table 2.4), which had above average rainfall in the spring and early summer (Figure 2.1). Winter cover crop biomass levels were higher in 2013 but were still below the weed suppression threshold in all treatments except NTCS. Grain sorghum yield in the MCT treatment was significantly higher than in CONVSS, although both underwent the same tillage and cultivation (Table 2.5). MCT yield was still 81% lower than the average yield of 112 bushels acre-1 determined by the UMVT state grain sorghum trials for 2007-2009 and 2014, the last 4 years that yield data was compiled (Weibold et al., 2014a). Grain sorghum yield in NTSS was significantly lower than CONVSS. It was observed that grain sorghum seedlings were not competitive against the weeds that were also emerging through the cover crop mat in NTSS treatments. Grain sorghum was also found to have low competitiveness against early season weeds by Burnside and Wicks (1967).

Corn yield in NTCS was half of the CONVCS yield, even though weed biomass in the two treatments was not significantly different. Cover crop biomass in the NTCS was greater than the threshold for weed suppression and was 58% higher than CONVCS biomass, indicating that weed control might not account for the differences in these two treatments. It is possible that the higher cover crop biomass, which had a 59:1 C/N ratio, was tying up nitrogen in the NTCS treatment and leading to inhibited growth of the corn. Several studies have shown that crop residue with a high C/N ratio can lead to immobilization of N in the short term and reduced N uptake by subsequent crops (Kuo et al., 1997; Rannells and Wagger, 1996). Additionally, the compost fertility treatment was applied to the field after cover crops were cut or crimped and before CONVCS was disked, so compost remained on top of the surface in NTCS and was incorporated in CONVCS, which may have led to yield differences from N deficiency in NTCS due to differentials in the compost breakdown and nutrient availability (Eghball and Power, 1999).  Our highest yielding corn in 2013 and 2014 yielded only 62% and 41% of the UMVT average corn yields for the same research farm (Weibold et al., 2013a, 2014b).

Wheat was grown in year 2 in the MCT treatment and yielded 46% of the UMVT average for conventional wheat grown on the same farm (Weibold et al., 2013b). Weed counts were not taken in the wheat but it was observed that curly dock took up between 15 to 20% of the total land area in the CONVCS and CONVSS wheat treatments in both 2013 and 2014. Wheat yields in 2014 were higher in the CONVCS and CONVSS plots than in the NTCS and NTSS plots (Table 2.5) but were only 61% of the UMVT average for conventionally grown wheat on the same farm (Weibold et al., 2014c). In 2014, curly dock and giant ragweed were estimated to cover approximately 30% of the land area in the NTCS and NTSS wheat, which likely accounts for the decreased wheat yield in those treatments.  Winter cover crop residue from previous years in NT plots might also be contributing to N immobilization in the soil, leading to decreased wheat yield. Due to relatively dry conditions in 2012 and 2013, winter cover crop residue did not degrade as rapidly in NT treatments as it did in treatments where it was mowed and tilled into the soil, thus it could be affecting N availability for a longer time period in NT plots. Double-crop soybean was grown after wheat in all treatments but was not harvested for yield due to plants remaining extremely short and non-productive. In 2013, dry summer weather led to very poor double-crop soybean stands and growth and in 2014 higher moisture led to extremely rapid growth of giant foxtail within the rows of double-crop soybean, which shaded out young soybean plants in spite of effective between-row cultivation.

Soil Quality

Although it was hypothesized that growing a three-year rotation of summer and winter cover crops would improve soil quality by increasing microorganism biomass and community diversity, increasing active and total SOC, and improving aggregate stability, this was not found to be the case in this study. PLFA analysis differentiates the microbial biomass extracted into the categories of AM fungi, anaerobic, gram negative and gram positive bacteria, eukaryotes, fungi and actinobacteria, none of which were significantly different between any study treatments (Table 2.9) or between years. Because soil microorganisms are dependent on water for movement and metabolic function (Kieft et al., 1987), it was expected that PLFA numbers would increase after the 2012 drought when soil moisture levels became more conducive to life. That they did not do this either shows that the drought did not have long term effects on microorganisms in this soil, that the small amount of irrigation water placed on the field had a positive effect on soil microorganisms, or that it is taking greater than three years for the PLFA levels to recoup from the drought. We have no pre-drought levels to compare to determine which of these processes is occurring. A limited response of soil microorganisms to water stress may be due to the predominance in soil of inactive or dormant microbes which would not be affected by short term drought (Chen and Alexander, 1973) or due to the adaptive nature of soils and microbial populations in areas where climatic conditions routinely fluctuate (Lundquist et al., 1999b).

Several studies have shown that microbial biomass and community diversity can increase within a short time span when cover crops are utilized (Buyer et al., 2010; Bossio et al., 1998) or when soil is not tilled (Mathew et al., 2012; Helgason et al., 2009) although other studies have shown that seasonal PLFA variation may be greater than variation as an effect of tillage (Zhang et al., 2012; Spedding et al., 2004). Increased microbial biomass or community diversity can occur under conditions where soil C stocks may be increased or retained from production practices. Although the CCO, MCT and MCC treatments in this study added C to the soil in year 1 in the form of sorghum-sudangrass residue, the amount of residue was higher than the weed biomass in only the CCO treatment. It is possible that the high amount of weeds present in the field contributed to the lack of differences in PLFA between treatments as well as lack of significant difference in β-glucosidase activity (Table 2.10), POXC (Table 2.11) and TOC (Table 2.12). However, sorghum-sudangrass had very high biomass levels in 2013 and sunn hemp had greater biomass than the weed cover in 2014, yet there was not a resulting change measured in any of these soil quality indicators. It may be that the period of this study was too short of a time to see changes in soil quality related to the crop rotations and crop species used. Cover crop residue can be slow to break down under certain climatic conditions and may not always result in rapid changes to SOC levels, or residues might contribute to very rapid, temporary increases to microbial activity or active carbon (Hu et al., 1997) that level out again as the season progresses and SOC from the residue breakdown is mineralized.

Many studies that show changes in soil quality indicators from agricultural practices are conducted on soils that have been in very long-term row cropping systems. Because the field used in this study was in long-term (>50 years) tall fescue meadow, it may have shown few treatment effects from cover cropping and no-till because it was not a particularly degraded soil to begin with. The SOM average of 4.3% was very high for agricultural soil in Missouri while the average SOM for cropped ground at the study site is 2%. It could be expected that soils that start with levels of SOM and soil microbial communities conducive to good crop growth would respond slower to management changes than soils that are lacking in these soil system drivers.

Participation Summary

Educational & Outreach Activities

Participation Summary:

Education/outreach description:

Organic Field Days were conducted at the Bradford Research Center in August 2013 and 2014 and were attended by 160 and 120 people, respectively. Topics at field days included organic no-till, cover crops, greenhouse gas emissions from organic production, organic vegetable research, trap cropping, specialty wherat production, organic weed control, beekeeping, vermicomposting, soil health, and how to read a soil test.
We are currently preparing study results for publication.

Project Outcomes

Project outcomes:

Our results indicate that a system transitioning from conventional to organic utilizing three years of continuous cover cropping in a high SOM soil showed little effect on soil quality. We do not recommend the use of organic no-till in a transitioning system as yields were severely reduced by weed pressure and N immobilization. An organic no-till system may require more than the threshold of 8000 kg ha-1 of biomass to suppress weed emergence. Through accidental over application of compost to a winter cover crop growing in a field alley one year, we observed that cover crop growth was improved more through improved fertility than increased planting rate. We observed weed emergence through the cover crop mat even in treatments with high biomass, thus we are currently engaged in a study to determine ways to control weeds that emerge in organic no-till. Conventionally tilled soybean yield was a greater percentage of conventional, non-organic yield than wheat, corn or grain sorghum in this transitional system because soybean did not experience low fertility issues when synthetic fertilizer use ceased and compost had not yet begun to contribute adequate N for crop nutrition and growth. Double crop soybean did not do well in this system due to low mid-summer precipitation and weed competition and in the future we will study the use of a summer cover crop mix planted after wheat. A combination of winter cover crops or wheat for early season weed control, SOC additions, and erosion control; summer cover crops for reducing the soil weed seedbank; and low N-use soybean are important tools for the transition from conventional to organic production methods.

Farmer Adoption

Farmer adoption of organic no-till is slow due to the problems encountered when trying to maintain weed control from a cover crop mulch. After our field days, we have had farmers gain interest in cover crops and transitioning to organic production through repeated use of cover crops. Several farmers in our area have purchased no-till cover crop crimpers.


Areas needing additional study

Areas needing additional study include controlling weeds in organic no-till, fertility needs of cover crops, new methods to plant cover crops into standing crops, improving soil fertility during organic transition, and using continuous cover crops to improve soil quality in degraded soils. Additional research is also needed in non-chemical methods of weed control that do not rely heavily on tillage, which destoys soil structure and burns up soil organic carbon.

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.