Source: SOUTH DAKOTA STATE UNIVERSITY submitted to NRP
REEU-FACT: INTERDISCIPLINARY RESEARCH AND EXTENSION EXPERIENCES FOR UNDERGRADUATES ON PLANT MICROBIOMES - ENGINEERING, IMPACT AND EVOLUTION-FLEXPATH
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1018064
Grant No.
2019-67032-29308
Cumulative Award Amt.
$472,355.00
Proposal No.
2018-05931
Multistate No.
(N/A)
Project Start Date
Apr 1, 2019
Project End Date
Mar 31, 2025
Grant Year
2019
Program Code
[A7401]- Research and Extension Experiences for Undergraduates
Recipient Organization
SOUTH DAKOTA STATE UNIVERSITY
PO BOX 2275A
BROOKINGS,SD 57007
Performing Department
Agronomy, Hort, Plant Science
Non Technical Summary
This project will develop a flexible internship program on agricultural microbiology (microbiomes of plant systems). Each student will participate in the program for a total of 20 weeks during two consecutive summers. In their first year, students will work with on-campus SDSU faculty mentors and develop an independent research project on plant microbiomes for ten weeks and will gain skills in agricultural microbiology, including laboratory, field/greenhouse experiments, data analysis and bioinformatics, and oral and written presentation. At the end of their first program year, the students will choose one of the following options for the second year:1-Research Pathway with faculty mentors on campus. This path will help them to further develop their research skills and put them on track to be a successful graduate student aiming to complete a Ph.D. in the plant sciences.2-Extension Pathway. Students of this path will work with SDSU extension agronomists, while collecting soil samples from collaborating farmers to develop a soil microbiome map of South Dakota. Students will also be integrated into the SDSU plant science extension programs; and3-Industry Pathway. Students in this path will be paired in their second year with collaborating industry partners. Faculty mentors of the program have active ongoing collaborations with industrial partners, including recent start-up companies in the microbial fertilizer and pesticide market, and students will work as interns for the companies.
Animal Health Component
20%
Research Effort Categories
Basic
40%
Applied
20%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90315991060100%
Knowledge Area
903 - Communication, Education, and Information Delivery;

Subject Of Investigation
1599 - Grain crops, general/other;

Field Of Science
1060 - Biology (whole systems);
Goals / Objectives
The overall goals of this project are to attract undergraduate trainees from different disciplines into graduate studies and professional careers in the plant sciences, to help them develop the necessary skills for graduate studies, and to help them explore the career opportunities available in academe, business, government, and other paths. The specific objective of this project is to increase the number of undergraduate trainees in the field of plant microbiomes.The proposed project will enrich undergraduate trainees with interdisciplinary skills in the emerging areas of agricultural microbiology (Microbiomes of Plant Systems) and enable their engagement in a STEM career through flexible professional development pathways (FLEXPATH). Each student will participate in the program for a total of 20 weeks during two consecutive summers (10 weeks per summer). In the first year of the cycle, six trainees will work with on-campus faculty mentors and develop an independent research project on plant microbiomes for ten weeks and will develop important skill sets in agricultural microbiology, including laboratory, field/greenhouse experiments, data analysis and bioinformatics (FACT Initiative), and oral and written expression skills.This project addresses three of the six AFRI Farm Bill priorities (#1-Plant health and production and plant products; #4-Bioenergy, natural resources and environment; #5-Agriculture systems and technology). In addition, this proposal is also aligned with the Food and Agriculture Cyberinformatics and Tools Initiative. The proposal is aligned with two of the three program area priorities: (1) it develops pathways for undergraduates in agriculture to acquire the technical and leadership skills required for employment in the agricultural sector; and (2) it advances science and supports graduate education in agriculture and related disciplines.
Project Methods
Objective 1. To increase the Increase the number of undergraduate trainees in the field of plant microbiomesEach student will participate in the program for a total of 20 weeks during two consecutive summers (10 weeks per summer). In the first year of the cycle, six trainees will work with on-campus faculty mentors and develop an independent research project on plant microbiomes and will develop important skill sets in agricultural microbiology, including laboratory, field/greenhouse experiments, data analysis and bioinformatics (FACT Initiative), and oral and written expression skills. At the end of their first program year, the trainees will choose one of the following options for the second year:1-Research Pathway (R-PATH) with faculty mentors on SDSU campus in Brookings, SD. This path will help them to further develop their research skills and put them on track to be a successful graduate student aiming to complete a Ph.D. in the plant sciences. Trainees in this path will also be able to collaborate with faculty at Dakota Weslyan University (Mitchell, SD) to develop and implement a hands-on undergraduate course in soil microbiomes.2-Extension Pathway (E-PATH). Trainees in this path will work with SDSU extension agronomists in Rapid City, SD and Watertown, SD, while collecting soil samples from collaborating farmers to develop a Soil Microbiome Map of South Dakota. Students will also be integrated into the SDSU plant science extension programs; and3-Industry Pathway (I-PATH). Trainees in this path will be paired in their second year with collaborating industry partners. Faculty mentors of the program have active on-going collaborations with industrial partners, including recent start-up companies in the microbial fertilizer and pesticide market, and trainees will work as interns for the companies. Trainees in I-Path will work with the following industry partners: Indigo (Charlestown, MA), Novozymes (Raleigh, NC), and Bayer CropScience (Lincoln, NE).We propose a 5-year program, in which 6 or 7 new trainees will be recruited per year in year 1 to 4 (6 students in year 2, 7 students in year 1, 3 and 4). In year 2 to 4, the program will have a total of 12-14 trainees (6 or 7 in their first year and 6 or 7 in their second of the program). We will make specific recruitment efforts at SD-Tribal Colleges (through the SDSU Wokini Initiative), Delaware State University, the University of Arkansas at Pine Bluff (both HBCUs), and SDSU.

Progress 04/01/23 to 03/31/24

Outputs
Target Audience:We recruited 10 undergraduate students from across the country, including 3 Hispanics; and 5 of them from primary undergraduate institutions with little or no research opportunities. Changes/Problems:The biggest problem was retaining students for the second summer was that students chose not to come back for a second summer because of the low stipends we budgeted. The request to increase the stipend to $6,000 and make it a one-year program was approved to be in effect for the 2023 summer. This resulted in 2 students coming back (we did allow students from the 2022 summer to come back as they originally applied to a 2-year program). What opportunities for training and professional development has the project provided?Each student participated in their research project under each mentor where they learned molecular and field techniques. In addition to the Genomics Jamboree described before we conducted weekly workshops designed to improve diverse skills such as writing, oral presentation, lab note-taking, and experimental design. Students also participated in a panel discussing graduate school applications. How have the results been disseminated to communities of interest?Students presented posters at the South Dakota Undergraduate Summer Research Symposium. This symposium is sponsored every summer by the SD EPSCOR Office. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We did recruit 10 undergraduate students, including two of the students from the 2022 summer; most of the other students cited better stipends in other similar programs. We conducted the proposed Genomics Jamboree; in this activity, students joined 10 students funded by an NSF REU program. In addition to their projects, students worked one day per week (Tuesdays) in genomics analysis projects including bacterial genome assemblies from Nanopore data and 16S RNA metagenomics analysis of soil samples.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Vincent Boothe, Sukhvir Kaur, and Volker Brozel. Diversity of Bradyrhizobium in Symbiotic Nodules with Soy Crops in Eastern South Dakota. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Rachel Burke, Avery Knoll, Melanie Caffe and Patrick Ewing. 2023. Effect of Oat Allelopathy Among Sterile Response Corn. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Elissa Colombo, Vinay Bandarupalli, Emily Fowler, and Benoit St Pierre. 2023. Building the Genome of an Unknown Rumen Bacterial Species from Beef Cattle that Can Digest Starch. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hugo Conde, Tasneem Fathima, Shaukat Ali, Rachel Hall, Jose Gonzalez, Gazala Ameen. 2023. Integrative Genome Analysis of Fusarium graminearum and Associated Toxin Genes. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Claire Galvin, Ahmed Alhusays, Ellen Fitzpatrick, Meenu Sengar, Jose Gonzalez Hernandez, Shyam Solanki and Gazala Ameen. 2023. Learning the Bacterial Leaf Streak Genome. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Isha Hooda, Taufiq Nawaz, Cayden Budd, Matt Lettow, Liping Gu, Ruanbao Zhou. 2023. Identification of Fast-growing Nitrogen-fixing Cyanobacteria from Natural Ecosystems. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hazem Khalaf Mohammed, Athira Madhavan, Lilia Montanez Hernandez, and Senthil Subramanian. 2023. Determining responses to competition between Bradyrhizobium strains. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Athira Sethu Madhavan, Lilia Montanez Hernandez, Hazem Khalaf Mohammed.2023. Understanding Rhizobial competition for nodulation using split root assays. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Brady Steffen, Santosh Thapa, Ruchita Bhattarai, Ram Bhattarai, Bishnu Karki. 2023. Valorization of Thin Stillage into High Value Product Via Microbial Fermentation. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ryan Sullivan, Ashley Frederickson, Madalyn Shires. 2023. Biological control of Bacterial Leaf Streak (BLS) of Barley using Bacillus spp. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Miguel Torres, Ahmed Alhusays, Ellen Fitzpatrick, Meenu Sengar, Jose Gonzalez Hernandez, Shyam Solanki, and Gazala Ameen. 2023. Bacterial Leaf Streak Genome Assembly and Analysis. 10th Annual SD EPCOR Undergraduate Research Symposium . July 25, 2023. Sioux Falls, SD (https://sdepscor.org/wp-content/uploads/2023/07/2023-Symposium-Booklet.pdf)


Progress 04/01/22 to 03/31/23

Outputs
Target Audience:We recruited 10 undergraduate students from across the country, including 3 Hispanic and 1 African American; 7 of them from primarily undergraduate institutions. Changes/Problems:The biggest problem is retaining students for the second summer was that students choose not to come back for a second summer because of the low stipends we budgeted. Therefore, we requested to change to a single summer format and an increase of the stipends. This request has been approved by the NIFA program manager. What opportunities for training and professional development has the project provided?Each student participated in their research project under each mentor where they learned molecular and field techniques. In addition to the Genomics Jamboree described before we conducted weekly workshops designed to improve diverse skills such as writing, oral presentation, lab note-taking, and experimental design. Students also participated in a panel discussing graduate school applications. How have the results been disseminated to communities of interest?Students presented posters at the South Dakota Undergraduate Summer Research Symposium. This symposium is sponsored every summer by the SD EPSCOR Office. What do you plan to do during the next reporting period to accomplish the goals?We request a change in the format given that students are not returning to the second year. We request a change to a one-year format and an increase in the stipend to match NSF REU programs up to $6,000/10 weeks.

Impacts
What was accomplished under these goals? We did recruit 8 undergraduate students. Unfortunately, none of the students from the 2021 summer returned; most of them cited better stipends in other similar programs. We conducted the proposed Genomics Jamboree; in this activity, students joined 10 students funded by an NSF REU program. In addition to their individual projects, students worked one day per week in genomics analysis projects including bacterial genome assemblies from Nanopore data and 16S RNA metagenomics analysis of soil samples.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hugo Conde, Sunish K. Seghal, Harshimardeep S Gill, Dinesh K. Saini, Emmily Moses, Sierra Wynn, Connor Thaler, Michael Eddy Harvey, and Sunish Sehgal.2022. Microbiome diversity in the soil surrounding root zone of winter wheat under different levels of nitrogen fertilization. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Evan Zhou, Jaswinder Kaur, Tasneem Fathima, Hannah Voirin, Gazala Ameen, Jose Gonzalez, Shaukat Ali, and Shyam Solanki. 2022. Towards Constructing a Pangenome of Diverse Pyrenophora tritici-repentis Isolates and Evaluating Their Host Specificity. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hannah Voirin, Tasneem Fathima, Jaswinder Kaur, Evan Zhou, Sunish K. Sehgal, Christopher Graham, Jose Gonzalez, Shaukat Ali, Gazala Ameen, Shyam Solanki. 2022. Integrative Genome Analysis of Fusarium graminearum Associated with the Small Grains in South Dakota. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Conner Thaler, Hasimardep Gill, Swas Kaushal, Emmily Moses, Hugo Conde, Michael Eddy Harvey, Sierra Wynn, and Sunish Sehgal.2022. Rhizosphere Diversity Among Old and New Wheat Cultivars. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Austin Taylor, Cheyenne Hron, and St. Pierre Benoit.2022. Predicting the metabolic potential of an uncharacterized bacterial species from the rumen of beef cattle. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Wyatt Seagren, Jose Gonzalez, Sen Subramanian and Sanjeev Anand. 2022. Comparing Genetic Determinants for Virulence and Determinacies Within Different Strains of Listeria Previously Isolated from Dairy Processing Facilities. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Natalie Claire Sansom Botstein, Brian Kontz, Ruchika Kashyap, Karthika Mohan, Bijula Mankara Sureshbabu, and Febina Mathew. 2022. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Emmily Moses, Harsimar Gill, Sierra Wynn, Connor Thaler, Michael Eddy Harvey, Hugo Conde, Shyam Solanki, and Sunish Sehgal. 2022. 9th Annual SD EPCOR Undergraduate Research Symposium. July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hazem Khalaf Mohammed, Athira Sethumadhavan, Lilia Montanez Hernandez, and Senthil Subramanian. 2022. Rhizobial Root Nodule Count. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Brandon Jatico, Kathryn Kass, Maxwell Jakubiak, and Ruanbao Zhou. 2022. Testing Guanidines toxicity and its Potential as a Nitrogen-Fertilizer Using Non-N2-fixing Cyanobacteria. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Isha Hooda, Emily Fowler, Anlly Fresno Rueda, and Benoit St. Pierre. 2022. Effect of Excell All Natural on Characterization of Bacteria in Rumen Fluid of Beef Cattle. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Michael Eddy Harvey, Dinesh K. Saini. Harsimardeep S Gill, Sierra Wynn, Hugo Conde, Connor Thaler, Emmily Moses, and Sunish K. Sehgal. 2022. Rhizosphere microbiome analysis in winter wheat reveals the presence of different types of nitrogen-fixing diazotrophic bacteria. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Nikita Dougan, Prashant Dahal, Said Badshah, Ali M. Nafchi, and Srinivas Janaswamy. 2022. Biodegradable polysaccharide seed coating as a method for delayed seed germination. 9th Annual SD EPCOR Undergraduate Research Symposium . July 28, 2022. Brookings, SD (https://sdepscor.org/wp-content/uploads/2022/07/2022-Symposium-Booklet-Final.pdf)


Progress 04/01/21 to 03/31/22

Outputs
Target Audience:The primary audience of this program are the undergraduate students participating in the program. A secondary audience includes agricultural producers and industry partners who will interact with the students and faculty Changes/Problems:The biggest challenge was the effects of the Covid 19 pandemic. What opportunities for training and professional development has the project provided?We recruited 6 students nationally and 2 from SDSU. Each of them worked with a faculty mentor to conduct different research projects. In addition, we conducted a 'Genomics Jambouree' where the students learned amplicon based (16S RNA) metagenomics bioinformatics analysis and plant transcriptome assembly and RNAseq analysis. How have the results been disseminated to communities of interest?The students presented their research results at the Annual Undergraduate Research Symposium sponsored by the SD EPSCOR program. Due to the COVID 19 pandemic this symposium was conducted virtually. During the symposium they also had the opportunity to network with other students and researchers. What do you plan to do during the next reporting period to accomplish the goals?We plan to conduct the program as planned. Depending on the how many students decide to come back for their second year in 2022 we may reconsider the 2-year model. The COVID 19 pandemic has put us behind in the number of students we should have in the program.

Impacts
What was accomplished under these goals? Objective 1: To increase the number of undergraduate trainees in the field of plant microbiomes. (100% for the students attending in year 3) After not being able to conduct our 2020 program due to COVID 19, we were able to resume in 2021. Our original plan called for the students in the first year to be able to come back for a second year. However, 4 of the 5 students graduated in May 2021 making then not eligible for the program. Only Monica Alba from Texas AM was able to return. In addition to Monica, we recruited 7 other students. The program in 2021 was marked by two other developments: 1) three of our faculty mentors left SDSU forcing us to expand our range of mentors, and 2) we started an NSF funded REU program in Plant Genomes and Phenomes that provided opportunities for synergies. The 8 students that participated in year 3 were: Monica Alba from Texas AM University worked under Dr. Subramanian's supervision in legumes rhizophore microbiomes, specifically nitrogen fixing bacteria. She learned general molecular biology and fluorescence microscopy. Dallas Kreisa from Marian University, a small (<2,000 students) undergraduate institution in Wisconsin. Dallas worked with Dr. Xu, a recent addition to SDSU located in Pierre, SD. Dallas expended part of the time working with Dr. Xu in Pierre and part working with Drs. Subramanian, Perkins, and Gonzalez Hernandez on campus. Dallas learned soil field techniques, DNA extractions from soils, and sequencing library construction. Jacob Ingram from Colorado College a small (~2,000 students) undergraduate institution in CO. Jacob worked with Dr. Matthews on pathogenic microbiomes in sunflowers and soybeans. He learned general plant pathology field and lab techniques, DNA extractions, general molecular biology, and PCR. Tatum Okamoto from Hawaii Community College in Hilo, Hawai. Tatum worked with Dr. Subramanian and Dr. Gonzalez on the development and use of QPCR assays to quantify specific functional components of the soil microbiome. Tatum learned soil sampling techniques, molecular biology techniques including QPCR assays. Ian Hastings from South Dakota State University worked under Dr. Subramanian and Dr. Gonzalez on the development and use of QPCR assys to quantify specific functional components of the soil microbiome. Ian learned soil sampling techniques, molecular biology techniques including QPCR assays. Austin Taylor from Jackson State University and HBCU in MS with ~7,000 students. He worked with Dr. St Pierre on ruminant gut microbiomes and how they change with different diets. He learned general animal management, sampling from canulated animals, sequencing library preparation, and bioinformatic analysis. Conner Thaler from South Dakota State University worked with Dr. Seghal investigating bacterial nitrogen fixation in a diversity wheat panel. In addition to field and greenhouse inoculation techniques, he learned wheat breeding, note taking, and selection principles. Kyle Pfaffenberger from Hanover College a small (~1,000 students) undergraduate college in Indiana. Kyle worked with Dr. Srinivas on the development and assay of degradable biopolymers to be used to inoculate plant rhizopheres with desirable microbial strains. In addition, all 8 students learned characterization of microbial communities using 16S RNA sequencing and plant transcriptome analysis in synergy with the REU Plant Genomes and Phenomes funded by NSF.

Publications


    Progress 04/01/20 to 03/31/21

    Outputs
    Target Audience:The primary audience of this program are the undergraduate students participating in the program. A secondary audience includes agricultural producers and industry partners who will interact with the students and faculty Changes/Problems:The Covid-19 pandemic shut down the SDSU campus for the summer and thus we were not able to continue the program in year 2. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?In year 3 we plan to conduct the program as planned. The 5 students who attended the 2019 session will be offered a second year as described in the original proposal. We plan to recruit a new cohort of 6-7 students.

    Impacts
    What was accomplished under these goals? Objective 1: To increase the number of undergraduate trainees in the field of plant microbiomes. (no additional accomplishment in year 2 due to Covid 19) In the summer of 2020, South Dakota State University campus was closed due to the COVID19 epidemic, so we were not able to conduct this program.

    Publications


      Progress 04/01/19 to 03/31/20

      Outputs
      Target Audience:The primary audience of this program are the undergraduate students participating in the program. A secondary audience includes agricultural producers and industry partners who will interact with the students and faculty Changes/Problems:The biggest challenge was recruitment given the short time from the award notice to the start of the program. What opportunities for training and professional development has the project provided?We recruited 5 students nationally. Each of them worked with a faculty mentor to conduct different research projects. In addition, we conducted a 'Genomics Jambouree' where the students extracted DNA and RNA from soil samples, constructed sequencing libraries, sequenced the libraries, and analyzed the resulting data. The students acquired molecular biology laboratory skills, DNA and RNA extractions, sequencing library preparation and bioinformatics analysis for amplicon based microbiomes, and metatranscriptomes. How have the results been disseminated to communities of interest?The students presented their research results at the Annual Undergraduate Research Symposium sponsored by the SD EPSCOR program. During the symposium they also had the opportunity to network with other students and researchers, and visit several research institutions and private companies engaged in research. What do you plan to do during the next reporting period to accomplish the goals?We plan to conduct the program as planned. The 5 students who attended the 2019 session will be offered a second year as described in the original proposal. We plan to recruit a new cohort of 6-7 students.

      Impacts
      What was accomplished under these goals? Objective 1: To increase the number of undergraduate trainees in the field of plant microbiomes. (100% for the students attending this year) We were able to initiate the project, although when the award was finalized, we did not have enough time to maximize student recruitment. We were able to recruit 5 students. Two others declined the offer just weeks from the starting date and we were not able to refill those 2 spots. The 5 students that attended were: Hunter Quinn, from Skidmore College, a small (<3,000 students) undergraduate institution in NY. Hunter worked under Dr. Subramanian's supervision in legumes rhizophore microbiomes, specifically nitrogen fixing bacteria. He learned general molecular biology and fluorescence microscopy. Clairion DuBose from Cornell University. Clairion also worked under Dr. Subramanian's supervision in legumes rhizophore microbiomes, specifically nitrogen fixing bacteria. He learned general molecular biology and fluorescence microscopy. Cora Hirst from Emory University in GA worked with Dr. H. Bucking on mycorrhizal-plant interactions. She learned general molecular laboratory skills, growing plants in artificial substrate, and nutrient analysis. Tanya Li from Emory College in GA worked with Dr. H. Bucking on plant endophytes interactions. She learned general molecular laboratory skills, growing plants in artificial substrate, and nutrient analysis. Monica Alba from Texas AM University worked with Dr. S. Kumar in soil fertility as affected by microbial processes. She learned general soil laboratory and field skills, and enzymatic assays for microbial processes. In addition all 5 students learned characterization of microbial communities using 16S RNA sequencing and metatranscriptomics.

      Publications