Progress 09/01/23 to 08/31/24
Outputs
Target Audience: Our efforts informed plant microbiome researchers, maize genetics researcher, andcrop scientists. Blog posts, media reports, talks to stakeholder groups, and college news articles amplified the impact to the broader agricultural sciences community (including stakeholders and producers) in Illinois. Changes/Problems: We had a turnover in postdoctoral researchers associated with this project, which slowed progress on Objectives 2 and 3. We now have additional personnel associated with these objectives. What opportunities for training and professional development has the project provided? Training has been provided for two postdoctoral researchers, 3 graduate students, and 3research scientists in these areas: plant breeding, measurement of N cycling processes using isotopic methods, microbiome analyses, and maize genotyping. Fiveundergraduate researchers were trained in field and greenhouse activities, nitrogen cycling activity assays, and DNA extraction. How have the results been disseminated to communities of interest? Research products have been (and will be) communicated to farmers and shareholders through conferencessuch asthe Maize Genetics Conference, and inivited seminars at NC State University and ND State University, and a plenary talk at the University of Nebraska Plant Sciences Retreat. In addition,meetings with the Illinois Nutrient Research and Education Council, and magazine articles, other conferences (ESA, PAG), and websites. What do you plan to do during the next reporting period to accomplish the goals? We experienced a delay in progress for objective 2, but we recruited new personnel for this objective and during this reporting period, wehave finished phenotyping and genotyping the BNIbackcrosses mentioned above. We are creating additional recombinants to further narrow down the genetic regions for BNI, and have submitted samples for transcriptomics analysis to identify differentially expressed genes. We are pursuing a similar process for BDI.From this data, we should be able to determine which genes are directly involved in the suppression of nitrification and denitrification. Based on the literature on BNI and BDI, we anticipate that these genes will be related to the production of some metabolite that directly inhibits the enzymatic machinery of nitrification and denitrification. Once we have this information we will follow up by using metabolomics to determine this compound in the root exudates and determine its inhibitory effects in soil and in microbial cultures. We will also publish results characterizing changes in microbial communities in response to teosinte genes that confer BNI and BDI traits. Based on the one known pathway for BDI (procyanidin), we have initiated a collaboration with a researcher who is an expert in maize secondary metabolites, and another collaborator with expertise in spatial metabolomics.
Impacts
What was accomplished under these goals?
Objective 1: To evaluate ecosystem nutrient retention, we employed isotope pool dilutions to measure N transformation rates, resin lysimeters to evaluate nitrogen leaching, KCl extractions to measure inorganic N pools, and enzyme assays to measurepotential rates of N transformations. While many of these are still ongoing, some preliminary findings from pool dilutions suggest that BNI NILs maintain higher levels of mineralization in their rhizosphere, accompanied by suppressed nitrification. This combination of increased mineralization with nitrification inhibition could explain the higher levels of NH4+ we observe in the maize rhizosphere. Lysimeter data will allow us to determine if this shifting in the N-cycle to ammonium-dominated interactions result in limited leaching of nitrate. The BNI NILs display different patterns of nitrogen accumulation, suggesting there may be multiple mechanisms by which nitrification inhibition might be accomplished. Objective 2: We have genotyped these NILs using KASP-like (competitive allele-specific PCR) to further track genetic changes after recombination events and backcrossing. With this KASP genotyping system, we developed two allele panels (one for BNI and one for BDI). With these panels, we developed BC2 populations, genotyped these lines as seedlings, and selectively propagated lines NILs with small introgressions of our key allelic regions. Around 92 lines new lines were developed for our BNI lines. Seed for these lines was increased for phenotyping, which is under way using greenhouse studies. We are characterizing these lines based on N leaching and nitrification inhibition.A similar process will be followed to map the denitrification inhibition loci. Objective 3: From a metabolomic survey we performed on our BNI NILs, we identified several enriched metabolites shared across both of the BNI NILs. Mechanistically, we anticipated that these metabolites could perhaps be the active molecules in the suppression of nitrification. To test this, we developed a modified nitrification assay where we added potential nitrification- inhibiting metabolites to soils. From the suite of compounds, we found that 3-(Methylthio)Propylamine (enriched in the roots of both BNI NIL lines) has similar BNI capacity to a known BNI molecule (positive control - MHPP). We are still attempting to determine genes involved in the production of (Methylthio)Propylamine in our NIL regions. We are refining the modified nitrification assay for testing of root exudates and other metabolites.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Ghotbi,M., M. Ghotbi, Y. Kuzyakov, W.R. Horwath. (2025) Management and rhizosphere microbial associations modulate genetic-driven nitrogen fate. Agriculture, Ecosystems & Environment 378: 109308. https://doi.org/10.1016/j.agee.2024.109308
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Favela, A., Bohn, M.O. & Kent, A.D. Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems. Plant Soil (2024). https://doi.org/10.1007/s11104-024-06720-9
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Progress 09/01/22 to 08/31/23
Outputs
Target Audience: Our efforts informed plant microbiome researchers and crop scientists. Blog posts, media reports, and college news articles amplified the impact to the broader agricultural sciences community (including stakeholders and producers) in Illinois. Changes/Problems:We had a turnover in postdoctoral researchers associated with this project, which slowed progress on Objectives 2 and 3. We now have additional personnel associated with these objectives. What opportunities for training and professional development has the project provided? Training has been provided for two postdoctoral researchers, 3graduate students, and a research scientist in these areas: plant breeding, measurement of N cycling processes using isotopic methods, microbiome analyses, and maize genotyping. Four undergraduate researchers were trained in field and greenhouse activities, nitrogen cycling activity assays, and DNA extraction. How have the results been disseminated to communities of interest? Research products have been (and will be) communicated to farmers and shareholders through conferences such as Illinois Corn Breeder School, the Maize Genetics Conference, Copenhagen Biosciences Cluster Plant Microbiome Conference, meetings with the Illinois Nutrient Research and Education Council, and magazine articles (i.e. Scientia, College of ACES magazine), invited seminars, and websites. What do you plan to do during the next reporting period to accomplish the goals?We experienced a delay in progress for objective 2, but we have recruited new personnel for this objective and duringthe next reporting period, we expect to have finished phenotyping and genotyping generated backcrosses mentioned above. From this data, we should be able to determine which genes are directly involved in the suppression of nitrification and denitrification. Based on the literature on BNI and BDI, we anticipate that these genes will be related to the production of some metabolite that directly inhibits the enzymatic machinery of nitrification and denitrification. Once we have this information we will follow up by using metabolomics to determine this compound in the root exudates and determine its inhibitory effects in soil and in microbial cultures. We will also publish resultscharacterizingchanges in microbial communities in response to teosinte genes that confer BNI and BDI traits.
Impacts
What was accomplished under these goals?
Objective 1:To evaluate ecosystem nutrient retention, we employed isotope pool dilutions to measure N transformation rates, resin lysimeters to evaluate nitrogen leaching, KCl extractions to measure inorganic N pools, and enzyme assays tomeasure potential rates of N transformations. While many of these are still ongoing, some preliminary findings from pool dilutions suggest that BNI NILs maintain higher levels of mineralization in their rhizosphere, accompanied by suppressed nitrification.This combination of increased mineralization with nitrification inhibition could explain the higher levels of NH4+we observe in the maize rhizosphere. Lysimeter data from 2022/2023 will allow us to determine if this shifting in the N-cycle to ammonium-dominated interactions result in limited leaching of nitrate. The BNI NILs display different patterns of nitrogen accumulation, suggesting there may be multiple mechanisms by which nitrification inhibition might be accomplished. Objective 2:We have genotyped these NILs using KASP-like (competitive allele-specific PCR) to further track genetic changes after recombination events and backcrossing. With this KASP genotyping system, we developed two allele panels (one for BNI and one for BDI). With these panels, we developed BC2 populations, genotyped these lines as seedlings, and selectively propagated lines NILs with small introgressions of our key allelic regions. Around 92 lines new lines were developed for our BNI lines. Seed for theselines was increased for phenotyping, which is under way. A similar process will be followed to map the denitrification inhibition loci. Objective 3:From a metabolomic survey we performed on our BNI NILs, we identified several enriched metabolites shared across both of the BNI NILs. Mechanistically, we anticipated that these metabolites could perhaps be the active molecules in the suppression of nitrification. To test this, we developed a modified nitrification assay where we added potential nitrification-inhibiting metabolites to soils. From the suite of compounds, we found that 3-(Methylthio)Propylamine (enriched in the roots of both BNI NIL lines) has similar BNI capacity to a known BNI molecule (positive control - MHPP). We are still attempting to determine genes involved in the production of (Methylthio)Propylamine in our NIL regions. We are refining the modified nitrification assay for testing of root exudates and other metabolites.?
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2024
Citation:
Favela, A., M.O. Bohn, and A.D. Kent. 2024. Genetic variation exists within Zea mays to alter unsustainable nitrogen cycling microbiome function. Plant Soil. Manuscript Submitted.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Favela, A., Bohn, M. O., Kent, A. D. (2023). Application of plant extended phenotypes to manage the agricultural microbiome belowground. Front. Microbiomes 2. doi: 10.3389/frmbi.2023.1157681
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Progress 09/01/21 to 08/31/22
Outputs
Target Audience: Our efforts informed plant microbiome researchers and crop scientists. Blog posts, media reports, and college news articles amplified the impact to the broader agricultural sciences community (including stakeholders and producers) in Illinois. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Training has been provided for two postdoctoral researchers, a graduate student,and a research scientistin these areas:plant breeding,measurement of N cycling processes using isotopic methods, microbiome analyses, and maize genotyping. Four undergraduate researchers were trained in field and greenhouse activities, nitrogen cycling activity assays, and DNA extraction. How have the results been disseminated to communities of interest? Research products have been (and will be) communicated to farmers and shareholders through conferences such as Illinois Corn Breeder School, the Maize Genetics Conference, Copenhagen Biosciences Cluster Plant Microbiome Conference,meetings with the Illinois Nutrient Research and Education Council, and magazine articles (i.e. Scientia, College of ACES magazine) and websites. What do you plan to do during the next reporting period to accomplish the goals? During the next reporting period, we expect to have finished phenotyping and genotyping generated backcrosses mentioned above. From this data, we should be able to determine which genes are directly involved in the suppression of nitrification and denitrification. Based on the literature on BNI and BDI, we anticipate that these genes will be related to the production of some metabolite that directly inhibits the enzymatic machinery of nitrification and denitrification. Once we have this information we will follow up by using metabolomics to determine this compound in the root exudates and determine its inhibitory effects in soil and in microbial cultures. We will also characterize changes in microbial communities in response to teosinte genes that confer BNI and BDI traits.
Impacts
What was accomplished under these goals?
Objective 1: To evaluate ecosystem nutrient retention, we employed isotope pool dilutions to measure N transformation rates, resin lysimeters to evaluate nitrogen leaching, KCl extractions to measure inorganic N pools, and enzyme assays to measure potential rates of N transformations. While many of these are still ongoing, some preliminary findings from pool dilutions suggest that BNI NILs maintain higher levels of mineralization in their rhizosphere, accompanied by suppressed nitrification. This combination of increased mineralization with nitrification inhibition could explain the higher levels of NH4+we are finding in the maize rhizosphere. Lysimeter data from 2022/2023 will allow us to determine if this shifting in the N-cycle to ammonium-dominated interactions result in limited leaching of nitrate. Objective 2: We have genotyped these NILs using KASP-like (competitive allele-specific PCR) to further track genetic changes after recombination events and backcrossing. With this KASP genotyping system, we developed two allele panels (one for BNI and one for BDI). With these panels, we developed BC2 populations, genotyped these lines as seedlings, and selectively propagated lines NILs with small introgressions of our key allelic regions. Around 35 lines new lines were developed for our BNI lines. These lines are currently in a winter nursery for seed production. Objective 3: From a previous metabolomic survey we performed on our BNI NILs, we identified several enriched metabolites shared across both of the BNI NILs. Mechanistically, we anticipated that these metabolites could perhaps be the active molecules in the suppression of nitrification. To test this, we developed a modified nitrification assay where we added potential nitrification-inhibiting metabolites to soils. From the suite of compounds, we found that 3-(Methylthio)Propylamine (enriched in the roots of both BNI NIL lines) has similar BNI capacity to a known BNI molecule (positive control - MHPP). We are still attempting to determine genes involved in the production of (Methylthio)Propylamine in our NIL regions.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Favela, A., M.O. Bohn, and A.D. Kent. 2022. N-Cycling Microbiome Recruitment Differences Between Modern and Wild Zea mays. Phytobiomes Journal. 6(2): 2471-2906. https://doi.org/10.1094/PBIOMES-08-21-0049-R.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2023
Citation:
Favela, A., M.O. Bohn, and A.D. Kent. 2023. Genetic variation exists within Zea mays to alter unsustainable nitrogen cycling microbiome function. Soil Biology and Biochemistry, Manuscript Submitted.
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Progress 09/01/20 to 08/31/21
Outputs
Target Audience:Our efforts informed plant microbiome researchers andcrop scientists. Blog posts, media reports, andcollege news articles amplified the impact to the broader agricultural sciences community (inclduing stakeholders andproducers) in Illinois. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training has been provided for a postdoctoral reseacher and a research scientist in plant breeding and measurement of N cycling processes using isotopic methods.Three undergraduate researchers were trained in field and greenhouse activities, nitrogen cycling activity assays, and DNA extraction. How have the results been disseminated to communities of interest?Research products have/will be communicated to farmers and shareholders through conferences such as Illinois Corn Breeder School, Meetings with the Illinois Nutrient Research and Education Council, and magazine articles (i.e. Scientia, College of ACES magazine). What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we expect to have finished phenotyping and genotyping generated backcrosses mentioned above. From this data we should be able to determine which genes are directly involved in the suppression of nitrification and denitrification. Based on the literature on BNI and BDI, we anticipate that these genes will be related to the production of some metabolite that directly inhibits the enzymatic machinery of these nitrification and denitrification. Once we have this information we will follow up by using metabolomics to determine this compound in the root exudates and determine its inhibitory effects in soil and in microbial cultures.
Impacts
What was accomplished under these goals?
A number of goals were achieved that will enable us to determine the genetic and biochemical basis of our microbiome sustainability traits. First, we carried out additional backcrosses of our biological nitrification inhibition (BNI) and biological denitrification inhibition (BDI) locus. These backcrosses ( BNI-BC2 F3, BDI-BC1 F2) will allow us to create segregating populations within our loci of interest with/without our sustainability phenotypes. Currently, we are phenotyping and genotyping these crosses (generated in the summer of 2021) in the greenhouse to further narrow down our genetic region of interest to identify potential genetic mechanisms. Furthermore, to accomplish this we have begun to develop high throughput 96-well plate potential nitrification inhibition assay and potential denitrification assay. This will allow us to phenotype larger numbers of plant genotypes generated from crosses. These activities are synergistically to develop novel methods that will allow for practical ways of breeding for plant microbiome function.
Publications
- Type:
Theses/Dissertations
Status:
Accepted
Year Published:
2021
Citation:
Favela, A. 2021. Understanding Zea Mays genetic influence on the structure and function of the rhizosphere microbiome. (Accepted).
- Type:
Websites
Status:
Published
Year Published:
2021
Citation:
Favela, A. 2021. Have we unknowingly altered the maize microbiome interaction? https://microbiologycommunity.nature.com/posts/have-we-unknowingly-altered-the-maize-microbiome-interaction.
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