Progress 02/01/15 to 01/31/20
Outputs
Target Audience:The target audience for this work includes researchers working in the areas of soil ecology, microbial ecology, weed science, and agroecology. The target audience also includes Extension specialists, Certified Crop Advisors, and other professionals who work closely with farmers and land managers in an educational or advisory role. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has involved three different graduate students. These students were trained to collect soil samples and conduct seed germination assays. As part of their professional development, these graduate students were also involved in project planning, organization of field trips and lab experiments, and data management. This project also involved ten undergraduates who were trained to collect soil samples, conduct seed germination assays, and extract microbial DNA from soil and seedlings.Undergraduates at the University of Minnesota assisted in greenhouse experiment setup, data collection, plant harvest, pot maintenance, and experiment breakdown. How have the results been disseminated to communities of interest?PD Yannarell and his students have presented research talks and posters of the project results at the Annual Meeting of the Ecological Society of America (2016, 2017, and 2019) and at the 2019 Purdue Microbiome Symposium. PD Yannarell has spoken about the project's results to a number of different groups, including: The Soil and Water Conservation Society, a local foods andsmall farms stakeholders group, Certified Crop Advisors at the Illinois AgMasters Conference, Ontario Certified Crop Advisors, and members of the U.S. Congress at the 2018 Annual Agricultural Research Congressional Exhibition. PD Yannarell has also presented the project's results to participants of two Extension webinar series. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The use of chemical pesticides to control weeds has a number of negative impacts on human and environmental health, and many widely-used chemical pesticides are not viable options for organic farmers. Furthermore, the increasing prevalence of herbicide-resistant weeds suggests that chemical weed control is becoming a less effective strategy for conventional farmers. In this project, we explored alternative weed control strategies centered on a growing understanding of soil ecology and the importance of plant-microbe interactions for plant health. We asked the question: Can interactions between weed plants and soil microbes be the foundation for effective, pesticide-free weed control strategies? Our work sought to provide foundational knowledge of plant-microbe ecology that could be used to develop weed-control strategies. Because of this, the people most like to directly benefit from our research are other scientists working in the fields of soil ecology, microbiology, agronomy, and plant biology. However, we designed our research with the farmer in mind. While managing soils for specific weed-suppressive microbes is a highly technical undertaking, there are a number of farming practices such as cover cropping and tillage that can affect soil microbes. Our research was designed around different cover cropping and tillage practices to understand how a farmers' management decisions can indirectly lead to the formation of soil microbial communities that can help combat weeds. Because of our focus on these management practices that farmers can choose to use, our research should also help farmers, especially those interested in alternatives to chemical weed control. To address the problem of finding microbial weed-control methods, we used two different but complimentary approaches. We took an exploratory approach that aimed to identify weed-suppressive microbial communities in soils. The main thrust of this approach was to determine how different agricultural practices (cover cropping, alternative tillage) changed soil microbial communities to make them more or less able to attack germinating weed seeds and seedlings. We used modern molecular biology tools to look for weed-suppressing microbes in these soils with DNA sequencing. We also took a hypothesis-testing approach to investigate a novel interaction between crops, weeds, and a beneficial group of soil fungi: arbuscular mycorrhizal fungi (AMF). AMF provide benefits to many different kinds of "host" plants that have evolved to cooperate with AMF. Important crops like maize are host plants that can benefit from AMF, but so are some species of weeds that infest maize fields. We hypothesized that AMF encountering two different host plants (e.g. a maize plant and a weed) can be made to favor one plant over the other, which can lead to a situation where AMF simultaneously boost crop growth while suppressing weeds. In pursuit of our project goals, we accomplished the following. Goal 1) Evaluate different cover crops and green manures for their potential to suppress weed germination via pathogenic microbes. We conducted six different field trials over multiple years. In these trials, we evaluated the weed-suppression potential of soils managed under different cover crop regimes, including monocultures of oats, spring wheat, rye, hairy vetch, fava bean, field pea, mustard, and purple-top turnips and multi-species mixtures of these same cover crops. Following termination of these cover crops, we collected soil from the plots and conducted seed germination trials using a wide diversity of weed and crop seeds. We also conducted DNA sequencing of soils from the cover crop plots, germination trials, and emergent seedlings in order to describe the microbial communities associated with weed suppression. We found that seed germination rates, seedling growth rates, and microbial communities varied a great deal between the different cover crop plots, the different weed/crop species, and the amount of time that had passed since cover crop termination. There was no overall "silver bullet" cover crop in terms of weed-suppression, although soils from plots containing mustard or a grass cover crop were suppressive of a wider variety of weed species than other cover crops. Goal 2) Evaluate suppressive effects on weed seedling growth of arbuscular mycorrhizal fungi in conservation tillage/cover-cropping systems. We ran six greenhouse experiments, each five tosevenmonths duration, in order to test whether arbuscular mycorrhizal fungi (AMF) can suppress weed seedlings by "choosing" to cooperate with a more dominant crop plant. All experiments used vetch to create a hyphal network, soils with or without AMF, maize as a dominant host, velvetleaf as a subdominant weed host, and a cache of phosphorus for the AMF to access. Our best experimental design used large box plots with 28-micrometer mesh to allow hyphae, but not roots, to access the supply of P in the cache. Variations in experimental design, including change of pot size, cones and weed selection, were less successful.We have strong evidence for AMF suppression of weed seedlings by "host dominance" when maize is functioning as a dominant host. We hypothesized that dominant hosts would have greater biomass when grown in the presence of nutrient-provisioning AMF than without AMF; however, the biomass of subordinate plant species would not differ between soils with and without AMF because host dominance causes the AMF to preferentially provision the dominant host. This held true for maize but not velvetleaf across all experiments. Staggered maize plantings, when maize is the sub-dominate in this system, found no AMF effect; but velvetleaf greatly benefitted from the presence of AMF. This could indicate that AMF suppressive effect is plant species dependent. We think that these results are promising evidence of this unique microbial weed-suppression mechanism, but differences in the outcomes of different experimental setups suggests that more work is needed to develop this into a reliable weed control practice. Goal 3) Assess the reliability, magnitude, and synergy between microbial and cover-cropping weed-suppression mechanisms. We conducted two field trials that combined different cover cropping treatments (no covers, rye, hairy vetch, and a rye-vetch mixture) with two different tillage regimes (conventional chisel plow and conservation ridge tillage). We ran seed germination experiments (as described for Goal 1) using soils from these field trials. We also followed the growth and root colonization dynamics of five weed species planted into the crop rows (maize) of these field trials. As with the research described for Goal 1, we found varying weed-suppression potential in these trials, leading us to conclude that microbial weed control can be inconsistent and highly context-dependent. We found no evidence for synergies between cover-cropping, tillage, and/or mycorrhizal fungi. However, we found strong differences in root-colonizing microbial communities between weed plants and crop plants, and this selective effect may allow us to explore more effective ways to improve microbial weed control techniques through fine-scale management interventions.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Li, M., A.S. Davis, A.C. Yannarell, N.R. Jordan and R.T. Koide. 2019. Interspecific variation in crop and weed responses to arbuscular mycorrhizal fungal community highlights opportunities for weed biocontrol. Applied Soil Ecology 142: 34-42.
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Progress 02/01/18 to 01/31/19
Outputs
Target Audience:The target audience for this work includes researchers working in the areas of soil ecology, microbial ecology, weed science, and agroecology. The target audience also includes Extension specialists, Certified Crop Advisors, and other professions who work closely with farmers and land managers in an educational or advisory role. Changes/Problems:We have discovered some flaws in thenovel protocol that we developed to explore "host-dominance" effects of crop/weed interactions with arbuscular mycorrhizal fungi. These flaws greatly limit the inferences that we can draw from these experiments, which are crucial for the successful completion of project aim #2 (Evaluate the suppressive effects on weed seedling growth of arbuscular mycorrhizal fungi in conservation tillage/cover-cropping systems). We therefore are hoping that a no-cost extension (1 year) can be approved, which would allow us to address this aim in two trials using an older experimental protocol that we developed in succesfulpilot experiments. What opportunities for training and professional development has the project provided?This project has involved three different graduate students. These students were trained to collect soil samples and conduct seed germination assays. As part of their professional development, these graduate students were also involved in project planning, organization of field trips and lab experiments, and data management. This project also involved ten undergraduates who were trained to collect soil samples, conduct seed germination assays, and extract microbial DNA from soil and seedlings.Undergraduates at the University of Minnesota assisted in greenhouse experiment setup, data collection, plant harvest, pot maintenance, and experiment breakdown. How have the results been disseminated to communities of interest?A manuscript is currently in review at Applied Soil Ecology. What do you plan to do during the next reporting period to accomplish the goals?We are seeking a one-year no-cost extension to further advance the project goals. We have amassed a large dataset on microbial community composition in field soils from a variety of settings and from weed and crop seedlings that we used in lab-based growth trials. We will use multivariate models and partial least squares analysis to identify specific microbial taxa with the strongest negative (and positive) potential interactions with weed and crop species; we will then use classification and regression trees to understand how these candidate microbial taxa respond to cover crop mixtures and conservation tillage. We will also conduct a much-refined greenhouse experiment to evaluate the weed suppressive capacity of arbuscular mycorrhizal fungi, as outlined in our "host-dominance" hypothesis (Project Goal #2): Arbuscular mycorrhizal fungi will preferentially provision the largest host with phosphorus when exposed to different plant hosts.The new experiment tests four host weeds and four non-host weeds in a common mycorrhizal network (CMN) system with corn to investigate host dominance and the ability of the CMN to modify growth dynamics with and without the presence of mycorrhizal fungi.
Impacts
What was accomplished under these goals?
1) Evaluate different cover crops and green manures for their potential to suppress weed germination via pathogenic microbes. This project goal has largely been completed (please refer to our 2017 Annual report for details). We are currently using multivariate data analyses and machine learning techniques (e.g. partial least squares regression,multivariate classification and regression trees) to compare microbial communities (characterized by high-throughput DNA sequencing) from field settings, growth experiments, and seedling roots. These analyses will help us identify key microbial taxa that play outsized roles in weed suppression and help us understand how cover-cropping and conservation tillage influence these key taxa. 2) Evaluate suppressive effects on weed seedling growth of arbuscular mycorrhizal fungi in conservation tillage/cover-cropping systems. We have made further refinements to the complex experimental system/protocol we are using to explore specific mechanistic hypotheses about weed-suppressive effects of arbuscular mycorrhizal fungi. In particular, we have determined that an initially-promising protocol that we had developed will not be sufficient for our purposes. We ran two experimental trials using this protocol, but our results have identified some flaws in this approach. Instead, we will apply a slightly modified version of the protocol we used in pilot experiments related to this aim. 3) Assess the reliability, magnitude, and synergy between microbial and cover-cropping weed-suppression mechanisms. This project goal has largely been completed (please refer to our 2017 Annual report for details). During this project year we have completed some fine-scale microbial community analyses of a field trial investigating the impact of mycorrhizal colonization on the competition between five different weed species and a live corn crop. Based on these analyses, we have determined that the species of arbuscular mycorrhizal fungi colonizing corn roots are substantial different than those that colonize the roots of weeds, demonstrating a strong plant species selection effect on their mycorrhizal communities. These results are the basis of a manuscript currently in review.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Li, M., N.R. Jordan, R.T. Koide, A.C. Yannarell and A.S. Davis. 2019. Interspecific variation in crop and weed responses to the arbuscular mycorrhizal fungal community highlights opportunities for weed biocontrol. In Review at Applied Soil Ecology.
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Progress 02/01/17 to 01/31/18
Outputs
Target Audience:The target audience for this work includes researchers working in the areas of soil ecology, microbial ecology, weed science, and agroecology. The target audience also includes Extension specialists, Certified Crop Advisors, and other professions who work closely with farmers and land managers in an educational or advisory role. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has involved three different graduate students. These students were trained to collect soil samples and conduct seed germination assays. As part of their professional development, these graduate students were also involved in project planning, organization of field trips and lab experiments, and data management. This project also involved eight undergraduates who were trained to collect soil samples, conduct seed germination assays, and extract microbial DNA from soil and seedlings. Undergraduates at the University of Minnesota assisted in greenhouse experiment setup, data collection, plant harvest, plot maintenance, and experiment breakdown. How have the results been disseminated to communities of interest?PD Yannarell has spoken about the project's results to a number of different groups, including the Soil and Water Conservation Society, a local foods andsmall farms stakeholders group, Certified Crop Advisors at the Illinois AgMasters Conference, and Ontario Certified Crop Advisors. PD Yannarell has also presented the project's results to participants of two Extension webinar series. What do you plan to do during the next reporting period to accomplish the goals?In order to identify species-specific interactions between soil microbes and various weed species, and in order to understand how these relationships are affected by field management techniques that are readily available to farmers, we are in the midst of a massive (over 1,400 seedling rhizosphere and bulk soil samples collected in Project Years Oneand Two) DNA sequencing effort. We will use multivariate models and partial least squares analysis to identify specific microbial taxa with the strongest negative (and positive) potential interactions with weed and crop species. We will then use classification and regression trees to understand how these candidate microbial taxa respond to a variety of management techniques, including cover crop mixtures and conservation tillage. We will also conduct a much-refined greenhouse experiment to evaluate the weed suppressive capacity of arbuscular mycorrhizal fungi, as outlined in our "host-dominance" hypothesis (Project Goal Two). Arbuscular mycorrhizal fungi will preferentially provision the largest host with phosphorus when exposed to different plant hosts. The new experiment tests fourhost weeds and fournon-host weeds in a common mycorrhizal network (CMN) system with corn to investigate host dominance and the ability of the CMN to modify growth dynamics with and without the presence of mycorrhizal fungi.
Impacts
What was accomplished under these goals?
Goal 1. Evaluate different cover crops and green manures for their potential to suppress weed germination via pathogenic microbes. We have evaluated 376 different combinations of cover crops and soil management for their capacity to suppress germination and seedling growth against 16 different weed and crop species. We also tested for weed suppression by the soil microbial community by comparing the germination rate of sevendifferent weed and crop species in live vs. sterilized soil obtained from four different cover crop and soil management combinations. We found that fourof the surveyed plant species had significantly different germination rates in the presence of live microbial communities than in sterilized soils. Two other weed species had marginally significant responses to these same treatments. This suggests that there is latent weed suppression potential in the microbial community. We also found that microbial communities differed in their weed suppression potential if they came from conventionally tilled soil vs. soils under conservation tillage. We have also used classification and regression trees to characterize how different establishment rates of cover crops affect weed suppressiveness when used as green manures. Goal 2. Evaluate suppressive effects on weed seedling growth of arbuscular mycorrhizal fungi in conservation tillage/cover-cropping systems. We have conducted a greenhouse experiment to test the "host-dominance" hypothesis described in our research grant. We have found mixed support for this hypothesis, but we have also identified weaknesses in our experimental approach that we will address in a revised version of this experiment. Goal 3. We detected negative effects of mycorrhizal colonization on the growth rates of fivedifferent weed species when grown in competition with a live corn crop. However, the growth rate reduction was small and may not be biologically significant with regard to weed control. In addition, we found that root colonization of mycorrhizal fungi was different in our experiment in Rosemont, Minnesota vs. our experiment in Urbana, Illinois(it was overall lower at the latter site). We also did not find strong effects of the various management techniques (conventional/conservation tillage and presence/absence of cover crops) on mycorrhizal colonization. Thus, at present, these soil microbe-based biocontrol techniques appear to vary from place to place and are not amenable to management tools that are readily available to growers. We have planned some finer-scale analyses, including microbial community characterization, to identify potential ways to improve the synergy between microbial and cover-cropping weed suppression techniques (for example, which microbial species appear to be most suppressive of different weeds, and which of these microbial species respond most readily to cover crop usage?).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Li, M., N.R. Jordan, R.T. Koide, A.C. Yannarell and A.S. Davis. 2016. Meta-analysis of crop and weed growth responses to arbuscular mycorrhizal fungi: Implications for integrated weed management. Weed Science. 64(4): 642-652.
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Progress 02/01/16 to 01/31/17
Outputs
Target Audience:The target audience for this work includes researchers working in the areas of soil ecology, microbial ecology, weed science, and agroecology. The target audience also includes Extension specialists, Certified Crop Advisors, and other professions who work closely with farmers and land managers in an educational or advisory role. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has involved three different graduate students. These students were trained to collect soil samples and conduct seed germination assays. As part of their professional development, these graduate students were also involved in project planning, organization of field trips and lab experiments, and data management. This project also involved eight undergraduates who were trained to collect soil samples, conduct seed germination assays, and extract microbial DNA from soil and seedlings. Undergraduates at the University of Minnesota assisted in greenhouse experiment setup, data collection, plant harvest, pot maintenance, and experiment breakdown. How have the results been disseminated to communities of interest?PD Yannarell has spoken about the project's results to a number of different groups, including the Soil and Water Conservation Society, a local foods and small farms stakeholders group, Certified Crop Advisors at the Illinois AgMasters Conference, and Ontario Certified Crop Advisors. PD Yannarell has also presented the project's results to participants of two Extension webinar series. What do you plan to do during the next reporting period to accomplish the goals?We will initiate a massive (over 1,400 seedling rhizosphere and bulk soil samples collected in project years one and two) DNA sequencing effort this project year to identify soil bacteria and fungi associated with weed-suppressive soils and also to identify bacteria and fungi that colonize germinating seedlings in weed-suppressive and non-suppressive soils. We will also conduct a greenhouse experiment to evaluate the weed suppressive capacity of arbuscular mycorrhizal fungi. This experiment expands on the initial design to test the "host-dominance" hypothesis (Project Goal #2): that arbuscular mycorrhizal fungi will preferentially provision the largest host with phosphorus when exposed to different plant hosts. The new experiment tests four host weeds and four non-host weeds in a common mycorrhizal network (CMN) system with corn to investigate host dominance and the ability of the CMN to modify growth dynamics with and without the presence of mycorrhizal fungi. We will conduct a field experiment where we investigate the impacts of intact arbuscular mycorrhizal mycelia vs disrupted mycelia, along with the impacts of high or low cover crop residues, on weed seedling development. This field experiment will take place in long-term experimental plots that have been under conventional or conservation tillage regimes for more thansix years, so that we will be able to understand how cover crop management and robust microbial communities interact with long-term tillage legacies to shape the weed suppressive capabilities of soils.
Impacts
What was accomplished under these goals?
Under Goal 1.Evaluate different cover crops and green manures for their potential to suppress weed germination via pathogenic microbes - We have evaluated 376 different combinations of cover crops and soil management for their capacity to suppress germination and seedling growth against 16 different weed and crop species. We also tested for weed suppression by the soil microbial community by comparing the germination rate of 7 different weed and crop species in live vs. sterilized soil obtained from 4 different cover crop and soil management combinations. We found that 4 of the surveyed plant species had significantly different germination rates in the presence of live microbial communities than in sterilized soils. Two other weed species had marginally significant responses to these same treatments. This suggests that there is latent weed suppression potential in the microbial community. We also found that microbial communities differed in their weed suppression potential if they came from conventionally tilled soil vs. soils under conservation tillage. We have also used classification and regression trees to characterize how different establishment rates of cover crops affect weed suppressiveness when used as green manures. Under Goal 2.Evaluate suppressive effects on weed seedling growth of arbuscular mycorrhizal fungi in conservation tillage/cover-cropping systems - We have conducted a greenhouse experiment to test the "host-dominance" hypothesis described in our research grant. We have found mixed support for this hypothesis, but we have also identified weaknesses in our experimental approach that we will address in a revised version of this experiment.
Publications
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