Microbial Processes Underlying the Natural Weed Suppressiveness of Soils

Project Overview

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

Annual Reports


  • Agronomic: corn, soybeans, wheat, hay


  • Animal Production: feed/forage
  • Crop Production: conservation tillage
  • Education and Training: demonstration, extension, focus group
  • Natural Resources/Environment: biodiversity, habitat enhancement
  • Pest Management: biological control, cultural control, integrated pest management, physical control, weed ecology
  • Production Systems: agroecosystems
  • Soil Management: organic matter, soil analysis, soil quality/health
  • Sustainable Communities: sustainability measures


    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.
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    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.
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    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.
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    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.
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    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.
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    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.

    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.