Microbial Processes Underlying the Natural Weed Suppressiveness of Soils

2005 Annual 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

Microbial Processes Underlying the Natural Weed Suppressiveness of Soils


We have analyzed the microbial communities of soils under different weed management systems (Marsden farm, Ames, IA sampled 2001-2005) and measured seed decay in selected soils. Soil microbial communities were different in different stages of the cropping cycle and were more diverse under longer rotations indicating that weed management systems based upon longer, more diverse rotations can contribute to improvements in soil health. Velvetleaf seed decay was highest when seeds were incubated in soils from short-rotation management systems. These findings were presented at the weed science society of America annual meeting and at a field day in Ames, IA.

Objectives/Performance Targets


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.
No visible impact to date.

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.

Conference presentations and field days this year have updated our preliminary findings to farmers and researchers in the field, explaining some of the microbial processes operating in soils under different weed management systems.

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.

Microbial community profiles have been developed for all plots at the Marsden farm for the period Spring 2002 through Spring 2005, and profiles for Spring 2002 through Fall 2003 have been analyzed. When finalized, this will be the largest and most complete analysis to date of the dynamics of microbial communities in soils under different weed management systems.

Seed decay microcosm experiments were performed in the soil samples collected in Fall 2004. Velvetleaf seed decay rates were highest in soils from the 2-year rotation treatments; these were the soil samples with the least diverse soil microbial communities.


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

Soil cores (10 cm depth) were taken from the Marsden farm plots near Ames, IA in Spring and Fall from 2002 through 2005. DNA was extracted from soil samples (FastDNA SPIN kit, QBiogene), and bacterial 16S or fungal ITS DNA amplified using universal bacterial primers and universal fungal primers with a GC-clamp. PCR-products were separated on DGGE gels (Bacteria: 10% T, 19:1 [5%C] acrylamide/bis-acrylamide, 160V, 18 h, 600C, 35-75% denaturant gradient; Fungi: 8% T, 37.5:1 [2.6%C] acrylamide/bis-acrylamide, 120V, 18 h, 600C, 45-70% denaturant gradient). Gels were stained with SYBR Green and photographed over a UV transilluminator. Principal components analysis was performed using the PRINCOMP procedure in SAS and diversity calculated using the Shannon-Weaver diversity index.

Result and Discussion:
We have completed the DNA extractions, PCRs and gels for all samples, and have completed the analyses for samples collected from Spring 2002 through Fall 2003. Analyses for the final samples are currently underway. Our preliminary findings show that soil microbial communities are dynamic through time, with characteristic communities forming in each phase of the rotation (Figure 1). The shifts in microbial community composition between years were dampened in the longer rotations, and microbial community diversity was increased in the longer rotations. These findings show that longer crop rotations, in particular the 4-year corn-soybean-triticale-alfalfa rotations promoted improved soil health over the short corn-soybean rotations. 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. The 2002-2003 samples probably represent a transient stage in the formation of soil microbial communities. The analyses from the 2004-2005 samples will more accurately indicate the composition of more fully formed communities as a result of longer established rotational systems.

II. 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.

Results and Discussion:
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. These seed decay organisms are under investigation by culturing and by PCR-DGGE (see section III).

III. Dynamics of microbial communities in the spermosphere of velvetleaf.

Velvetleaf seeds were incubated in three soil samples collected in Fall 2004; 1) Corn phase of the 2-year rotation, 2) Soybean phase of the 2-year rotation, 3) Corn phase of the 4-year rotation. Twenty five seeds were placed on one side of the dish and the other side of the dish maintained as a seed-free control. Dishes were stored 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. Four replicate dishes of each soil type were removed at each temperature transition, and the microbial communities collected from the spermosphere of the seeds by washing in 10mM phosphate buffer. Soil samples – from outside the spermosphere – were collected from the other side of the Petri dish as controls.

Results and Discussion:
No results this calendar year – currently under analysis.

Impacts and Contributions/Outcomes

We have made considerable progress with this project to date, having refined PCR-DGGE protocols and analyzed the microbial communities from a large number of soil samples. In calendar year 2004, we showed that weeds modify microbial communities in their rhizospheres and that these modified microbial communities can have different impacts upon developing weed seedlings. This year, preliminary analyses of soils from the Marsden farm experiment examining different weed management systems have shown that weed management systems employing longer crop rotations and reduced herbicide inputs improve soil health while delivering effective weed control. Seed decay experiments, however, suggest that soils with increased microbiological diversity in fact decrease the rate of velvetleaf seed decay in the soil. We are currently analyzing the microbial communities associated with velvetleaf seeds in soils from the different management systems in order to identify microbes and microbial communities that contribute to seed decay. In the final phase of the project, we will complete the large-scale analysis of field soils from the weed management experiments managed by Matt Liebman in Iowa, the results of which, to date, support the hypothesis that diverse rotations that exploit multiple stress and mortality factors contribute to weed suppression. Our soil microbial community analysis will be correlated with weed management practices and with weed population demographics to gain an understanding of the role of soil microbial community perturbations on the demographics of weeds in different cropping systems.

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 when all experiments are completed.


Matt Liebman

Iowa State University
Deprtment of Agronomy
3405 Agronomy Hall
Ames, IA 50011-1010
Office Phone: 5152947486