Microbial Processes Underlying the Natural Weed Suppressiveness of Soils

Final Report for LNC03-225

Project Type: Research and Education
Funds awarded in 2003: $103,623.00
Projected End Date: 12/31/2006
Region: North Central
State: Indiana
Project Coordinator:
Steven Hallet
Purdue University
Expand All

Project Information


Soil quality and health can be strongly affected by crop management, with poor management resulting in degraded soils and good management promoting soils with good structure, nutrition and biological health. We investigated the microbial community composition of soils managed with three different weed management systems in a 2-year (corn-soybean), 3-year (corn-soybean-triticale + red clover) and 4-year (corn-soybean-triticale + alfalfa-alfalfa) rotation over a four year period (2002-2005) and found that the longer rotations resulted in gradual increases in the diversity of soil microbial communities. We also investigated the impacts of soils from the different rotations upon the germination of velvetleaf seeds. In this case, we found that velvetleaf germination was similar in all soils, but slightly higher in the soils from the longer rotations. We conclude that weed management systems involving longer crop rotations and reduced herbicide inputs may not result in the direct suppression of weed emergence but improve soil health, as measured by soil microbial diversity.


Weed management in the United States has been dominated by herbicides for the last five decades and while herbicides have made substantial contributions to productivity, particularly of large farm operations, they have also contributed to a farming culture with declining profit margins and compromised environmental impacts. Many farmers rely on alternatives to herbicides and, in their systems; the focus is upon multi-tactic integrated weed management strategies rather than remedial herbicidal control.
Of critical importance is effective management of the soil seed bank and, more fundamentally, effective management of the soil. It is well established that different farming systems can have different impacts upon soil structure, chemistry and biology, and that different soils can have different impacts upon weeds. Microbial processes may be especially important in determining a soil’s ability to suppress weed seed survival and seedling emergence. Alternatively, the promotion of weed seedling emergence could contribute to weed population regulation if germination occurs at the wrong place and wrong time. Weed seeds that germinate too early can be killed by seedbed preparation; weed seeds that germinate too deep in the soil profile may never emerge.

Only a small percentage of soilborne microbes can be readily cultured on standard microbiological media, consequently, the impact of the majority of microbes in the soil is completely unknown. In the last ten years, however, new technology has made it possible to study entire microbial communities, including the large numbers of organisms that can not be easily cultured.
This project was designed to build the link between soil management and weed management by comparing the microbial communities in soils that are conducive towards weeds with those that are suppressive towards weeds. The goals of this research were to: (1) develop a detailed understanding of the soil biological properties that contribute to weed suppression in order to improve our ability to manipulate soils as an important component of integrated weed management systems; and (2) stimulate further research concerning the role of healthy soils in maintaining economically and environmentally sustainable farming systems in the United States.

It has become largely accepted that soil management is a critical to sustainable agriculture. Growers across the world that farm in a sustainable way have developed tried-and-tested techniques to manage soils to their benefit, and sustainable growers know that careful management and manipulation of soils can result in varied crop production, crop protection and environmental benefits.

Microbiology has undergone a revolution in the last 20 years (Woese et al., 1983; Woese, 1987; 1992). In that time, our understanding of the soil as a diverse biological system has developed, and it has become apparent that much of our understanding of soil microbiology has been flawed. For example, only a fraction of the microbial taxa present in the soil can be readily grown on standard laboratory media (Torsvik et al., 1990; Hugenholtz et al., 1998, Buckley et al., 1998). Our understanding of the dynamics of soil microbial communities, and the interaction of those communities with plants is presently undergoing a long-awaited overhaul (Wardle, 1992; Hopkins & Shield, 1996).

The rapid rate of technology adoption in the field of soil microbial ecology in recent years presents a significant opportunity to develop new concepts in the field of biological control. We chose to use PCR-DGGE (denaturing gradient gel electrophoresis of PCR-amplified ribosomal RNA genes) for the analysis of microbial communities since it does not require organisms to be cultured for analysis. This permits the analysis of whole communities, including those species that can not be readily grown on standard laboratory media, and it avoids the bias that normally occurs due to the differential growth of species, thereby permitting the analysis of soil microbial communities with a new degree of accuracy and precision (Atlas et al., 1992; Head et al., 1998).

PCR-DGGE has been used to describe changes in microbial communities occurring as a result of changes in various soil factors (Atlas et al., 1991; Ovreas & Torsvik, 1998), in response to the influence of plants and different land use and cropping practices (Buckley & Schmidt, 2001; Davis et al., 2006), and in response to bioaugmentation with disease-suppressive bacteria (Yang et al., 2001). Several teams of researchers have established a link between weed seed bank decline and the activity of soil microbial communities (Davis et al., 2006; Kennedy et al., 1991; Kennedy & Kremer, 1996; Skipper et al., 1996; Kennedy & Gewin, 1997) and, in a number of cases, have attempted to employ soilborne microbes as biological herbicides for the control of weeds (Tranel et al., 1993; Mazzola et al., 1995; Boyetchko, 1996; Héraux et al., 2005a,b; Kremer, 2000).

References Cited

Atlas, RM, G Sayler, RS Burlage & AK Bej. 1992. Molecular approaches for environmental monitoring of microorganisms. Biotechniques. 12:706.
Boyetchko, SM. 1996. Impact of soil microorganisms on weed biology and ecology. Phytoprotection. 77:41-56.
Buckley, DH, JR Graber & TM Schmidt. 1998. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Applied and Environmental Microbiology. 64:4333-4339.
Buckley, DH & TM Schmidt. 2001. The structure of microbial communities in soil and the lasting impact of cultivation. Microbial Ecology. 42:11-21.
Callaway, R.M. and W.M. Ridenour. 2004. Novel weapons: invasive success and the evolution of increased competitive ability. Frontiers in Ecology and Environment 2:436-443.
Davis, AS, KI Anderson, SG Hallett & KA Renner. 2006. Weed seed mortality in soils with contrasting agricultural management histories. Weed Science 54:291-297.
Don, R.H., P.T. Cox, B.J. Wainwright, K. Baker & J.S. Mattick. 1991. Touchdown PCR to circumvent spurious priming during gene amplification. Nucleic Acids Research 19:4008.
Gomez, K.A. and A.A. Gomez. 1984. Statistical procedures for agricultural research. 2nd Edition. Wiley, NY.
Head, IM, JR Saunders & RW Pickup. 1998. Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated organisms. Microbial Ecology. 35:1-21.
Héraux, FMD, SG Hallett & SC Weller. 2005. Combining Trichoderma virens-inoculated compost and a Rye Cover Crop for Weed Control in Transplanted Vegetables. Biological Control 34:21-26.
Héraux, FMD, SG Hallett & SC Weller. 2005. Composted Chicken Manure as a Medium for the Production and Delivery of Trichoderma virens for Weed Control. Hortscience 40:1394-1397.
Hoitink, HAJ & MJ Boehm. 1999. Biocontrol within the context of soil microbial communities: A substrate-dependent phenomenon. Annual Review of Phytopathology. 37:427-446.
Hoitink, HAJ & PC Fahy. 1986. Basis for the control of soilborne plant pathogens with composts. Annual Review of Phytopathology. 24:93-114.
Hopkins, DW & RS Shield. 1996. Size and activity of soil microbial communities in long-term experimental grassland plots treated with manure and inorganic fertilizers. Biology and Fertility of Soils. 22:66-70.
Hugenholtz, P, BM Goebel & NR Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology. 180:4765-4774.
Kennedy, AC, LF Elliot, FL Young & CL Douglas. 1991. Rhizobacteria suppressive to the weed downy brome. Soil Science Society of America Journal. 55:722-727.
Kennedy, AC & VL Gewin. 1997. Soil microbial diversity: present and future considerations. Soil Science. 607-617.
Kennedy, AC & RJ Kremer. 1996. Microorganisms in weed control strategies. Journal of Production Agriculture. 9:480-485.
Kremer, RJ. 2000. Growth suppression of annual weeds by deleterious rhizobacteria integrated with cover crops. In: NR Spencer (ed.) Proceedings of the X International Symposium on Biological Control of Weeds. 4-14 July, 1999. Montana State Univ., Bozeman, MT. pp. 931-940.
Mazzola, M, PW Stahlman & JE Leach. 1995. Application method affects the distribution and efficacy of rhizobacteria suppressive of downy brome (Bromus tectorum). Soil Biology and Biochemistry. 27:1271-1278.
Muyzer, G., S. Hottentrager, A. Teske and C. Wawer 1996. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA-A new molecular approach to analyse the genetic diversity of mixed microbial communities. In A. Akkermans, van Elsas, J.D. and F. J. de Bruijn. Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Nowell, MA. pp.1-23.
Skipper, HD, AG Ogg & AC Kennedy. 1996. Root biology of grasses and ecology of phizobacteria for biological control. Weed Technology. 10:610-620.
Stinson, KA, S Campbell, JR Powell, BE Wolfe, RM Callaway, GC Thelen, SG Hallett, D Prati & JN Klironomos. 2006. Invasive plant suppresses the establishment and growth of native trees by allelochemical disruption of belowground mutualists. PLoS Biology 4:727-731.
Torsvik, V, J Goksoyr & FL Daae. 1990. High diversity in DNA of soil bacteria. Applied and Environmental Microbiology. 56:782-787.
Tranel, PJ, DR Gealy & AC Kennedy. 1993. Inhibition of downy brome (Bromus tectorum) root growth by a phytotoxin from Pseudomonas fluorescens strain D7. Weed Technology. 7:134-139.
Wardle, D.A. 1992. A comparative assessment of factors which influence microbial biomass carbon and nitrogen levels in soil. Biological Reviews. 67:321-358.
Woese, C. 1992. Prokaryote systematics: the evolution of the science. In: Truper, HG et al (eds): The Prokaryotes. Springer Verlag, NY, NY.
Woese, CR. 1987. Bacterial evolution. Microbiological Reviews. 51:221-271.
Woese, CR, R Gutell, R Gupta & HR Noller. 1983. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews. 47:621-669.

Project Objectives:

Long term:
• Systemic changes in the way farmers manage soils through a clear understanding of the ways in which microbial communities and key soil microbe species can be manipulated.
• Systemic changes in the purposes for which farmers manage soil, including weed management.

Intermediate term:
• Deepening of the understanding farmers and extension officers have of the complexity, composition and dynamics of soil microbial communities.
• Provide needed information to farmers and extension personnel regarding the impact of management regimes upon soil microbial communities.

Short term:
• Develop microbial community profiles from soils under different management.
• Quantify the relationship between microbial community structure and key microbial species with soil management regimes.
• Correlate key microbial taxa with weed management outcomes.


Click linked name(s) to expand
  • Matt Liebman


Materials and methods:

I. Preliminary validations of PCR-DGGE for analysis of soilborne microbial communities.

Soil cores (10 cm depth) were taken from the plots at Iowa State University’s Marsden Farm, near Ames, IA, in Fall 2002. DNA was extracted using the FastDNA® SPIN kit (for soil) and instrument (Q-Biogene Inc., Carlsbad, CA). Fragments from bacterial 16S ribosomal DNA were amplified by a modification of the protocol of Muyzer et al. (1996) with the universal bacterial primers PRBA338F (CAC GGG GGG ACT CCT ACG GGA GGC AGC AG) with a GC clamp (CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G) and PRUN518R (AAT ACC GCG GCT CGT GG) for amplification of 196 bp products from the V3 region. Our PCR protocol employed a touchdown cycle with a high initial annealing temperature in order to maximize reaction specificity (Don et al. 1991): 5 min @ 94 oC then 10 cycles of 30 s @ 94 oC, 30 s @ 65 oC [touchdown – decrease by 1 oC each cycle], 30 s @ 72 oC then 19 cycles of 30 s @ 94 oC, 30 s @ 55 oC, 30 s @ 72 oC with a final extension of 15 min @ 72 oC. PCR-products were separated on DGGE gels (10% T, 19:1 [5%C] acrylamide/bis-acrylamide, 35-65% formamide/urea gradient, 160V, 18 h, 60 oC) with an agitated CBS gradient former and CBS-2201 DGGE apparatus (CBS Scientific, Del Mar, CA), stained with SYBR Green (Applied Biosystems, Foster City, CA), and photographed with a Polaroid camera over a UV transilluminator. Amplicons previously shown to run different distances were used as “ladder” standards (Nakatsu et al. 2000). Photographs were analyzed with a band recognition program (Quantity One; BioRad, Hercules, CA), and a composite profile for each experiment representing the bands found in any lane. Band intensity was then scored with the aid of line plot profiles (Quantity One) on a 0-4 scale, where a score of zero represented a band that was absent from the sample and a score of 4 represented the brightest band on the gel. Scores for each sample were then analyzed by principal components analysis using the PRINCOMP procedure in SAS (SAS Inst., Cary, NJ) and diversity calculated using the Shannon-Weaver diversity index. Samples were analyzed from replicated PCR reactions from the same DNA extraction, replicated DNA extractions from the same sub-sample, replicated sub-samples of the same soil aliquot, replicated plots under the same management regime and from different treatment plots to test the repeatability and reliability of our sampling and analyses and the efficacy of our techniques in detecting differences among different samples.

II. Effects of Selected Weed Species on Soil Microbial Community Composition and Impact.

Soil Conditioning
Seedlings of six common weeds in agricultural and horticultural production systems in the midwestern USA were selected for this study: shattercane (Sorghum bicolor [L.] Moench), common lambsquarters (Chenopodium album L.), redroot pigweed (Amaranthus retroflexus L.), jimsonweed (Datura stramonium L.), barnyard grass (Echinocloa crus-galli [L.] Beauv.) and ivyleaf morningglory (Ipomoea hederacea [L.] Jacq.). Seeds of each species were surface disinfested (6% hypochlorite for 2 min then 3 washes in sterile water) and then sown into field soil collected from a nearby field with a history of corn and soybean production and a weed community including all of the weeds listed above. Plants were grown in the greenhouse in plastic “Conetainers” (37 mm diam x 105 mm depth) for 21 d then removed, and their rhizosphere microbial communities sampled and analyzed. New individuals of the same plant species were re-planted into the same pots and plants were maintained at the seedling stage for a further 79 d (100 d total soil conditioning period) by repeatedly removing the plant, including the roots, after 21-28 d and re-planting new individuals. Pots were fertilized once, after 35 d, with ¼ strength 15-30-15 (N-P-K) soluble fertilizer. Twenty-four pots of the same soil were conditioned by each weed species this way. As controls, twenty-four pots with unconditioned soil (unplanted, unfertilized) and twenty-four pots with sterilized soil conditioned by each weed species were maintained unplanted in the greenhouse with the same management. Soil was sterilized by autoclaving at 121oC for 30 min on two occasions 48 h apart. At the end of this 100 d soil conditioning period, the rhizosphere microbial communities of shattercane and velvetleaf were sampled and analyzed again.

Plant Growth Effects
The conditioned and unconditioned soils prepared above were used in a factorial experiment in which each soil was planted with each weed species. Plants were grown for 28 d and aboveground dry biomass was measured after cutting plants at the soil surface and drying at 60o C for 72 h. The growth of each weed species in self-conditioned soil was compared with its growth in soil conditioned by each other species, and its growth in unconditioned soil and conditioned, sterilized soil. The experiment had four replicates per treatment, was repeated once, and plant growth data from the two trials was pooled following a test for homogeneity of variances (Gomez and Gomez, 1984). Pairwise comparisons were made using Student’s t-test.

Rhizosphere Microbial Communities
Pots were left unwatered for the last 24 h of the experiment to ensure that the soil was not too wet to be sampled. Plant roots were teased apart from the soil and then the soil that remained attached to the roots was collected by washing with 0.1 M sodium phosphate buffer (pH 8) followed by centrifugation. DNA extraction, PCR amplification, separation by DGGE, staining and analyses were performed as described above.

III. Soil Microbial Community Dynamics Under Different Weed Management Systems.

Soil samples were collected in fall 2002-2005 and spring 2003 and 2005 from the long term trial at Marsden Farm, Ames, IA. The trial, directed by M. Liebman, imposed a range of weed management treatments based upon four replicated crop rotations; a 2-year rotation (corn-soybean), a 3-year rotation (corn-soybean-triticale) and a 4-year rotation (corn-soybean-triticale-alfalfa).
Pulses of seed of velvetleaf (Abutilon theophrasti) and giant foxtail (Setaria faberi) (sub-plot treatments) were introduced into plots (rotations) in 2001, and their demographic parameters measured each year by Dr. Liebman’s team.

Soil samples for microbial analysis were taken from each subplot in order to correlate soil microbial communities with both the treatments imposed and the weed demographic data gathered. DNA extraction, PCR amplification, separation by DGGE, staining and analyses were performed as described above.

IV. Decay of seeds in soils under different weed management systems.

Velvetleaf seeds were incubated in the soil samples taken from the Marsden Farm field experiment in Fall 2004. Fifty seeds were embedded in soil samples maintained in Petri dishes in a dark incubator programmed to change temperature as follows: 14 d @ 4oC then 3 d @ -2oC then 14 d @ 4oC then 7 d @ 10oC then 14 d @ 25oC. The number of seedlings was recorded at the end of the incubation. Four replicates were used per treatment, and the experiment was arranged in randomized complete blocks, repeated, and the data from the two trials combined.

Research results and discussion:

I. Preliminary validations of PCR-DGGE for analysis of soilborne microbial communities.

There was a high level of similarity in the DGGE profiles from all our validation tests. Replicated PCRs and DNA extractions gave identical profiles. Replicated subsamples gave near-identical profiles, and profiles from same-treatment plots gave profiles that were significantly more similar than different-treatment plots. Thus, we demonstrated that PCR-DGGE is a reliable and repeatable technique for the analyses undertaken. Where microbial communities were identical, the repeated PCR-DGGE analyses showed identical profiles. Where microbial communities were expected to be different, PCR-DGGE demonstrated significant differences and treatment differences were detected despite the inevitable microbial community variability among different plots of the same treatment (data not shown).

II. Effects of Selected Weed Species on Soil Microbial Community Composition and Impact.

Plant Growth Effects
The growth of weeds was generally better in conditioned soils than unconditioned soils with the exception of common lambsquarters (Figure 1). Jimsonweed growth was significantly greater than in jimsonweed-conditioned, sterilized soil than unconditioned soil. Common lambsquarters growth was less in common lambsquarters-conditioned, sterilized soil than in unconditioned soil. The growth of the other weeds was not significantly different in self-conditioned sterilized soils than unconditioned soil (Figure 2).

The conditioning of soil for 100 d by weed seedlings had significant effects upon the growth of subsequent plantings of those weeds. The most striking effects were observed when velvetleaf and shattercane were continuously grown in their own soil. Velvetleaf failed to grow in a soil in which velvetleaf had grown previously. Although velvetleaf germinated in its own soil, only 12.5% of emerged plants survived for 28 d. Surviving plants had a mean dry weight of only 11% that of velvetleaf plants grown in soil conditioned by the other five weed species (Figures 3, 4). All the other plant species grew well in soil conditioned by velvetleaf (Figure 1). In contrast, shattercane grew better in its own soil and produced 35% more aboveground biomass compared with soils conditioned by the other five weed species (Figures 3, 4). The other weed species grew similarly well in soil conditioned by shattercane (Figure 1). Although less dramatic than the effects with velvetleaf, the growth of jimsonweed was also suppressed in self-conditioned soil, and the growth of redroot pigweed was enhanced by growth in self-conditioned soil (Figures 3, 4).

Rhizosphere Microbial Communities
The conditioning of soil with different weed species had striking effects upon the composition of rhizosphere microbial communities after only 28 d. The largest perturbations to rhizosphere microbial communities were caused by conditioning with common lambsquarters and shattercane (Figure 5). Prolonged soil conditioning (100 d) by velvetleaf and shattercane resulted in further changes to rhizosphere microbial communities beyond those observed after 28 d (Figure 6).

III. Soil Microbial Community Dynamics Under Different Weed Management Systems.

PCR-DGGE analysis demonstrated that soil microbial community composition is strongly dependent upon the identity of the growing crop. Microbial communities clustered strongly in a crop-specific way, with the microbial communities following each crop showing a “signature” composition each year. These communities, however, were significantly altered by the following spring, and spring microbial communities were significantly different from the fall microbial communities in the same plot in all cases. These fall microbial community “signatures”, however, were less clear in the longer rotations, indicating that the growth of different crops may have supported different microbes, thus diluting the crop-specific impact upon microbial community composition. In the longer rotations, this loss of microbial community identity was gradually lost through the four years of sampling, although this effect was subtle (Figures 9, 10, 11).

The effects of crop rotation upon microbial community diversity were much more clear. In the 2-year (corn-soybean) rotation, soil microbial community diversity remained constant across the four years of sampling (Figures 7, 8). In contrast, microbial community diversity in the 3-year (corn-soybean-triticale + red clover) and 4-year (corn-soybean-triticale + alfalfa-alfalfa) rotations increased through time. Microbial community diversity was significantly higher in 2004 and 2005 than in 2002, soon after the plots had been initiated. The changes over time are particularly interesting and suggest that the systems needed to become established during the early years of the experiment.

These findings show that longer crop rotations, both the 3-year corn-soybean-triticale + red clover and the 4-year corn-soybean-triticale + alfalfa-alfalfa rotations promoted improved soil health over the 2-year corn-soybean rotation. This is important since the efficacy of weed control was similar in all management systems despite the fact that herbicide inputs were significantly lower in the longer rotations. Our experiments support the contention that diversified weed management systems can deliver effective weed control while improving the biology of soils in the medium- and long-term.

IV. Decay of seeds in soils under different weed management systems.

Emergence of velvetleaf from soil microcosms was greatest from soil samples taken from the 4-year rotation plots and least from soil samples taken from the 2-year rotation plots (Figure 2). These results show that weed seed decay is inhibited rather than accelerated in soils with more diverse microbial communities, and suggest that pathogens of weeds may be suppressed by diverse microbial communities. A large number of the seeds that did not germinate were visibly decayed and colonized by a number of fungal and bacterial species.

Research conclusions:

This research represents one of the few extensive studies of the link between soil health and weed demography, delivering a broad analysis of the dynamics of soil microbial communities and weed management inputs and outcomes following multiple weed management systems over multiple years.

Our findings demonstrate that soil microbial communities become increasingly diverse through time [over four years, in this study] when longer rotations are used, adding triticale and forage legume phases into a corn-soybean rotation. In contrast, short rotations of only corn and soybean did not contribute to increases in soil microbial diversity. Soil microbial communities were highly crop specific with different “signature” communities found following each crop. These signatures, however, were less well defined after three or four years of the long rotations, indicating that the growth of different crops supported the survival of larger numbers of microbial taxa in soils through time. We hypothesize that more diverse microbial communities contribute to overall plant health, such as disease suppressiveness as has been suggested by a number of researchers (e.g. Hoitink & Fahy, 1989; Hoitink & Boehm, 1999).

On the other hand, in experiments where we incubated velvetleaf seed in soils from different treatments at the Marsden Farm we did not find a correlation between increased microbial community diversity and weed suppressiveness. Differences were subtle, but velvetleaf germination was generally higher in soils from the longer rotations (more diverse microbial community) than soil from the shorter rotations (less diverse microbial community). We acknowledge that this finding is restricted to the analysis of a single weed species from single field experiment, but it indicates that soil health may be linked with weed health as well as crop health. Further research would be needed to see if this effect is more general. If it is, it would suggest that improved weed management via seed decay in the soil may not be possible by soil management from improved microbial diversity.

This hypothesis is supported by our findings from a sequence of pot experiments in which we grew a range of weed species in the same soil as repeating planting of seedlings. In this case we found that the growth of velvetleaf in the same soil five times eventually resulted in its own suppression. In the fifth planting event, velvetleaf seedlings were killed by a vascular wilt disease (we were unable to isolate a single organism into pure culture, but rather found a mixture of organisms; Fusarium sp. was found in nearly all isolations and Verticillium sp. was found in many). This indicates that velvetleaf may have gradually accumulated inoculum of a pathogen in its rhizosphere, eventually succumbing to the disease when it reached lethal inoculum levels. We hypothesize that velvetleaf may be protected from disease in soils with a more diverse microbial community that inhibit such diseases from reaching such high inoculum levels. Thus, we conclude – unfortunately – that healthy soils may promote healthy weeds as well as healthy crops.

On a more positive note, our experiments have shown that effective weed management can be achieved in a range of different management systems, and that some of those management systems contribute to the building, rather than the destruction, of soil biological health. Weed management in the 3-year and 4-year rotations, using reduced amounts of chemical herbicide delivered weed control and crop yields that were just as good as those in the 2-year, herbicide-intensive system (data not shown). The longer rotations, however, at the same time as delivering equal short-term gains in weed control and crop productivity also delivered long term gains in soil health. We hypothesize, therefore, that 3-year and 4-year rotations will be more economical and sustainable for midwestern farmers in the long term.

Economic Analysis

No formal economic analysis was undertaken within this project, and it is not possible to define a specific economic outcome for this type of research. In terms of economics, our research is aimed at the long term sustainability and economic health of the midwestern region and so short term economic indicators are of limited value. What our research does is contribute to our understanding of the long term implications of different crop production systems. We have shown that longer rotations can be designed that provide effective weed management with reduced chemical inputs, that short- and long-rotations deliver equivalent crop yields and that longer rotations support the development of more diverse microbial communities. These findings indicate that longer rotations provide ecological benefits over the long term. Furthermore, if midwestern agriculture becomes impacted by increasing fuel prices and fuel availability, improved knowledge of the impacts of different weed management practices on soil health with be increasingly important as farmers modify their practices to remain economically viable.

Farmer Adoption

The level of adoption of long rotations is low, with most farmers continuing to pursue corn-soybean rotations. Furthermore, with the increasing dedication of acreage to glyphosate resistant corn, the corn-soybean rotation is rapidly becoming a much less valuable rotation with respect to weed communities and soil microbial communities. Another concern is the rush towards ethanol production that is likely to put increasing pressure upon farmers to grow more corn, further decreasing the likelihood that long rotations will be considered.

Farmers should strongly consider reducing herbicide inputs and relying upon short corn-soybean rotations and consider longer rotations. As the combined impacts of the declining availability of cheap gasoline and diesel and the increasing demand for bioethanol continue to pressure midwestern farmers, they need to continue to be aware that the maintenance of soil health is an important medium- and long-term need. The use of long rotations will help to maintain soil health and economically viable crop production into the future.

Participation Summary

Educational & Outreach Activities

Participation Summary

Education/outreach description:

Extension and outreach for this project have been active, with the presentation of our findings at farmer field days, and with the following conference presentations to date:

Anderson, KI & SG Hallett. 2005. Investigating the dynamics of microbial communities in the rhizosphere of weeds by PCR-DGGE. Weed Science Society of America annual meeting, Waikiki, HI, 2/04.

Anderson, KI & SG Hallett. 2004. Development of PCR-DGGE for the investigation of soilborne natural enemies of weeds. 4th International Weed Science Congress, Durban, Republic of South Africa, 6/04.

Anderson, KI & SG Hallett. 2004. Application of denaturing gradient gel electrophoresis of PCR-amplified ribosomal RNA genes (PCR-DGGE) for the analysis of soil microbial communities found in different crop and weed management systems. Weed Science Society of America annual meeting, Kansas City, MO, 2/04.

Anderson, KI, M. Liebman & SG Hallett. 2003. Analysis of soil microbial communities associated with weeds using denaturing gradient gel electrophoresis of PCR-amplified ribosomal RNA genes (PCR-DGGE). North Central Weed Science Society annual meeting, Louisville, KY, 12/03.

Our research was recently reported in The Furrow (Vol. 23) in an article by Dean Houghton entitled CSI for soils, and our findings will be published as refereed journal articles in the near future.

Project Outcomes


Areas needing additional study

Our understanding of the biological parameters of soil health remains poor although there is now a balance of knowledge that suggests that increased microbial community diversity may contribute to plant health by suppressing soil borne pathogens. Our findings contribute to this knowledge base, but suggest that the maintenance of soil health may not have direct impacts upon weed seed decline in the soil seed bank. Nonetheless, many microbes that are antagonistic to weed species are resident in midwestern soils and crop management techniques that exploit these organisms may yet be found. We hypothesize that the maintenance of healthy soils, which delivers benefits such as improved soil building, soil structure and nutrient cycling, and improved protection from soil borne plant pathogens to the crop, may also deliver these benefits to weeds. Thus, the maintenance of soil health remains an important goal for farmers, but improved weed control is unlikely to be a major benefit.

This research was undertaken before concerns about the lifetime of cheap oil were commonplace and before the push for corn ethanol gathered steam. Further research is now needed to understand the likely impacts of the changing face of midwestern agriculture in the biofuels era. Increased planting of corn for ethanol is likely, and this may have detrimental impacts upon the short-term economic viability of long rotations. A decline in soil health is likely if farmers rely entirely upon corn-soybean rotations and even more so if they shift to increasing acreages dedicated to monoculture corn.

An additional research need is emerging in the area of cellulosic ethanol. If the processing of cellulose becomes viable, we can expect to see extensive plantings of new crops such as switchgrass, Miscanthus and Arundo. In some ways, this new cultivation will diversify the region’s acreage. On the other hand, there will be an enormous temptation to grow Miscanthus, in particular. Miscanthus is a risky proposition since it is a noxious invasive weed. The impacts of Miscanthus may be numerous on the midwestern region. In terms of soil biology, we know that invasive plants such as knapweeds (Centaurea spp.) and garlic mustard (Alliaria petiolata) owe part of their invasiveness to impacts upon the naïve soil biota of North America (Callaway & Ridenour, 2004; Stinson et al., 2006). Alliaria, for example, releases glucosynolates and flavonoids that are lethal to mycorrhizal fungi. There should be significant concern that extensive plantings of Miscanthus might cause significant damage to soil microbial communities.

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.