Source: PENNSYLVANIA STATE UNIVERSITY submitted to NRP
USING COVER CROP MIXTURES TO SHAPE THE SOIL MICROBIOME FOR TARGETED NITROGEN CYCLING SERVICES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1019203
Grant No.
2019-67011-29621
Cumulative Award Amt.
$119,976.00
Proposal No.
2018-07871
Multistate No.
(N/A)
Project Start Date
May 1, 2019
Project End Date
Nov 30, 2021
Grant Year
2019
Program Code
[A7101]- AFRI Predoctoral Fellowships
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
408 Old Main
UNIVERSITY PARK,PA 16802-1505
Performing Department
Ecosystem Science and Manageme
Non Technical Summary
The goal of this research is to understand how cover crop mixtures engineer the soil microbiome and the resulting impacts on nitrogen (N) cycling. N management is a critical agronomic challenge with environmental and economic implications across scales. Both plant and soil microbial communities are key drivers of N-cycling functions in terrestrial ecosystems. This project will build knowledge for how farmers might use cover crops to manage belowground communities for reduced N losses and greater N retention. I will establish a full factorial pot experiment with three cover crops species grown in monoculture and in mixtures with two levels of N fertilization. Response variables include microbial community structure, N-cycling functions, microbial biomass, and soil and plant nutrient dynamics. Results will provide a foundation for further research into manageable regulators of soil microbiomes across landscapes, with potential for agronomic, economic, and environmental consequences. This project addresses the AFRI Farm Bill priority areas of Plant health and production and plant products and Bioenergy, natural resources, and environment.This project includes academic training experiences including advanced coursework and microbial ecology research methods training, an interactive mentoring plan, and career development activities including teaching, undergraduate mentoring, and professional networking. There is also a formal evaluation plan for both research and teaching goals. This proposal addresses the AFRI EWD goal of advancing science through cultivating future leaders, and focuses on the agricultural challenges of nitrogen management and soil microbial management.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
10240991070100%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
4099 - Microorganisms, general/other;

Field Of Science
1070 - Ecology;
Goals / Objectives
This project has three major goals in research and professional development.1. Research: To understand how cover crop mixtures engineer the soil microbiome and the resulting impacts on N cycling.This will build knowledge for how farmers might use cover crops to manage belowground communities for reduced N losses and greater N retention.Objectives:i) To evaluate the relative influence of each cover crop species in a mixture on structuring the soil microbiome.ii) To assess the potential for soil N retention and loss in the soil microbiomes generated by cover crop monocultures and mixtures.iii) To assess the impact of soil N availability on the structure and function of the soil microbiome as driven by different cover crops.2. Professional Development, Research Training: To gain experience and knowledge in microbial ecology techniques and theory.Objectives:i) To progress from an intermediate to advanced level in analyzing and interpreting microbial population and community dataii) To progress from an intermediate to advanced level in microbial ecology methods, experimental design, and techniques.iii) To engage with other agricultural microbial ecology researchers both nationally and internationally.3. Professional Development, Teaching: To gain experience and develop skills as a teacher and mentor.Objectives:i) To progress from advanced to professional in classroom teaching at the college level.ii) To build skills and gain experience in mentoring undergraduate students in research.
Project Methods
TRAINING METHODS:Research:1) Enroll in the Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) advanced training course through the Marine Biological Laboratory in Woods Hole, MA. This course is designed for investigators and advanced graduate students from diverse biological fields, and offers interdisciplinary bioinformatic and statistical training along with an opportunity to learn from the experts who have designed the tools used in molecular microbial ecology;2) Complete research exchange in the microbial ecology lab of Dr. Etienne Yergeau, Assistant professor at the Institut Armand-Frappier ResearchCentre in Quebec, Canada. This laboratory's research program aims to sustainably enhance the beneficial rhizosphere microbiome of important crops, and includes opportunities for me to learn from multiple projects exploring the relationship between crops and the microbiome, to work with metatranscriptomics and metagenomics, as well as to network with an international research group;3) Attend and present my research at both a national conference (American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America annual meeting) and international conference (International Society for Microbial Ecology's biannual symposium).Teaching: 1) Teach Environmental Sustainability for undergraduates at Penn State (Spring 2020, SOILS 071);2) Complete the Penn State Graduate School Teaching Certificate, which includes completing theSchreyer Institute Penn State Course in College Teaching, and developing a website that includes a statement of teaching philosophy;3) Participate as a mentor in the WISER (Women in Science and Engineering Research) program at Penn State.RESEARCH METHODS:Experimental design: I will establish a full factorial pot experiment in a Penn State greenhouse with two factors: cover crop type and N level. Cover crop type will include eight treatments: three monocultures (a grass, a legume, a brassica), three bicultures (all combinations of the monocultures), a mixture of all three species, and a fallow. I will also include a zero, standard and a high N fertilization treatment. This will result in 8 plant communities× 3fertilization levels×4 replicates= 96pots, which will be arranged in a randomized block design in a greenhouse. Pots will be at least 30 cm deep and 30 cm wide. Soil for the pots will be collected from the Russell E. Larson Agricultural Research Center in central Pennsylvania from surface soils (0-20 cm). Soil will be sieved to 8 mm to eliminate rocks but keep soil aggregates intact, uniformly mixed, combined with sand and transferred into pots. Initial soil samples will be collected for analysis before treatments are applied. Cover crops will be germinated and transplanted into pots to be grown for at least 10 weeks in natural light at 20±5°C. N fertilization will occur before seeding. Pots will be watered consistently and uniformly. After 10 weeks, aboveground biomass will be harvested and soils will be collected from each pot.Measuring response variables:Microbial community structure: Molecular methods will be used (16S rRNA gene and ITS amplicon sequencing) to provide data for taxonomic classification of both bacterial and fungal communities. DNA will be extracted from frozen soils to be prepared for amplicon sequencing.Microbial community N-cycling functions: I will use the PICRUSt(phylogenetic investigation of communities by reconstruction of unobserved states) tool to assign function to microbial communities generated from each treatment.Microbial biomass: Total microbial biomass, an important component of N retention, will be estimated from soil samples using a phospholipid fatty acid (PLFA) analysis. PLFAs have been used in many agricultural experiments to identify and quantify coarse microbial groups in agricultural soils. It will also be used to approximate total microbial N.Soil and plant nutrient dynamics: I will track the concentration of inorganic N in soils every two weeks throughout the experiment to document when N becomes available for nitrification or nitrate leaching. Briefly, soil cores will be composited from each pot, homogenized, and subsampled for 2M KCl extraction. Extracts will be analyzed colorimetrically for ammonium and nitrate concentrations. Additionally, I will measure cover crop N uptake by analyzing the N content in biomass samples of the cover crop. All aboveground biomass will be dried, weighed, and ground, and a subsample will be analyzed for N concentration by combustion analysis. A soil fertility analysis (pH, phosphorus, potassium, magnesium, calcium, and total carbon) will also be conducted to determine if the treatments are driving other nutrient or soil property differences that may be important in our analyses and interpretation.Data analysis: Statistical analysis will be carried out using the R software. Amplicon sequencing data will be processed and analyzed using the established pipeline from the Bell Lab at Penn State, which I will modify based on new knowledge and skills gained from the proposed bioinformatics and statistical training. PLFA data will be analyzed with multivariate analyses. Additional analyses will use a mixed model approach, as well as repeated measures analysis for time series inorganic N data (data will be checked for normality and transformed as needed to meet this assumption).

Progress 05/01/19 to 11/30/21

Outputs
Target Audience:Agricultural professionals, scientists, and farmers reached through outreach articles scientific publication, and scientific presentations. Changes/Problems:As previously reported,due to Covid-19 restrictionsall of my international travel was unable to be rescheduled. I was not able to find another lab to do a reserach exchange. What opportunities for training and professional development has the project provided?Attended and present at both the Ecological Society of American conference (virtual posted and ligtning talk) and the ASA, CSSA, SSSA conference in Saly Lake City, Utah (15 minute talk). How have the results been disseminated to communities of interest?Presentations at scientific conferences, as well as through my dissertation defense presenttation which was virtually attended by both scientists and farmers throughout the northeast. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. Research: All data processing, analysis, and interpretation is completed. Manuscript draft is completed. This work contributed to a chapter of my doctoral dissertation which has been completed and successfully defended in December 2021. 2. Professional Development, Research Training: Poster presented at the Ecological Society of American conference (virtual) and presentation givn at the ASA, CSSA, SSSA conference in Saly Lake City, Utah. 3. Professional Development, Teaching: All goals completed previously. Continued to work with student mentee to refine, sumbit, ad revise publication.

Publications

  • Type: Theses/Dissertations Status: Submitted Year Published: 2022 Citation: Sarah A. Isbell. Ecological management for enhancing nitrogen ecosystem services on agricultural land through crop, soil, and microbiome interactions. Doctoral dissertation in Ecology, Penn State University.
  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Isbell, S. A., Alonso-Ayosu, M., Bell, T.H., Bradley, B. A., Rowles, T. and Kaye, J. P. (2022) Nitrogen Services Provided by Interseeded Cover Crops in Organic Corn Systems. Agronomy Journal.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Sarah Isbell, Terrence Bell, Jason Kaye. Using Cover Crop Mixtures To Shape The Soil Microbiome For Targeted Nitrogen Cycling Services. ASA, CSSA, SSSA ANNUAL MEETING, Salt Lake City, UT, 2021.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Sarah Isbell, Terrence Bell, Jason Kaye. Using interseeded cover crops to enhance nitrogen ecosystem services driven by plant-soil microbial relationships in agroecosystems. Ecology Society of America Annual Meeting 2021 (Virtual).


Progress 05/01/20 to 04/30/21

Outputs
Target Audience:Agricultural professionals, scientists, and farmers reached through eOrganic outreach articles and one scientific publication. Changes/Problems:Due to cancellation of travel and in-person activities over the last year and a half, all of my international travel was unable to be rescheduled. I was not able to find another lab to do a reserach exchange. What opportunities for training and professional development has the project provided?Attended Ecological Society of America Conference (virtual), Northeast Cover Crops council conference (virtual), and ASA, CSSA, SSSA conference (virtual). Abstracts submitted to attend and present atboth the Ecological Society of American conference (virtual posted and ligtning talk) and the ASA, CSSA, SSSA conference in Saly Lake City, Utah (15 minute talk). 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?Complete all data analysis, interpretation, and sumbit manuscript for publication. Attend and present results at the ASA, CSSA, SSSA annual conference in November. Sumbit maniscript co-written with undergraduate mentee in August.

Impacts
What was accomplished under these goals? 1. Research:All sample analyeses have been completed, incuding soil DNA amplicon sequencing, dissolved organic carbon analysis from soil samples, PLFA analysis from soil samples, and inorganic nitrogen extractions. Data processing and analysis is underway. Manuscript draft is underway. 2. Professional Development, Research Training:Attended multiple annual meetings and conferences virtually, including Ecological Society of America Conference and the Northeast Cover Crops council conference. Abstracts submitted to attend and present atboth the Ecological Society of American conference (virtual) and the ASA, CSSA, SSSA conference in Saly Lake City, Utah. 3. Professional Development, Teaching:Penn State Teaching Certificate completed. Co-wrote manuscript with undergraduate mentee as co-author (to be sumbitted to the Agronomy Journal).

Publications


    Progress 05/01/19 to 04/30/20

    Outputs
    Target Audience: Nothing Reported Changes/Problems:There have been siginficant issues with delays related to travel restrictions, lab and facility closures, and conference cancellations: 1. My experimental setup took several trys to perfect, so my experimental data collection was delayed until the winter of 2020. Now, sample processing is on pause until repoening of facilities. 2. The ISME conference (previosly Aug. 2020, South AFrica) has been postposed until 2021, which is after the end of my grant period. I would need either an extension to use these travel and conference funds, or to explore other options for conference. 3. The national conference I proposed attending is not yet decided on if it will be virtual or in-person. 4. The proposed training via an international exchange has been cancelled due to travel restrictions. What opportunities for training and professional development has the project provided?2. Professional Development, Research Training: i) To progress from an intermediate to advanced level in analyzing and interpreting microbial population and community data: Completed advance training course in August 2019 -Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) through the Marine Biological Laboratory at Woods Hole. ii) To progress from an intermediate to advanced level in microbial ecology methods, experimental design, and techniques: The reserach exchange I had proposed is no longer able to occur becuase of travel restrictions. iii) To engage with other agricultural microbial ecology researchers both nationally and internationally: Conferences I had proposed to attend in summer 2020 have been cancelled. Currently exploring other options for viritual conferences in 2020. 3. Professional Development, Teaching:To gain experience and develop skills as a teacher and mentor. Objectives: i) To progress from advanced to professional in classroom teaching at the college level: I successfully co-taught for 1 semester, andwas the sole instructor of record for 1 semester, the course SOILS 071 Environmental Sustainability. Student feedback was collected via survey through the semester, and final feedback is forthcoming. ii) To build skills and gain experience in mentoring undergraduate students in research: I participated in a 1 year undergraduate mentoring program. Taran Rowles completed a reserach project under my metorship, culminating in a poster presentation at a univeristy symposium. 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?1. Research goals: Complete sample processing and analysis, complete data analaysis, and produce manuscript for publication. 2. Reserach training: Find alternate conferences to attend, or (if funding can be extended) attend these conferences in 2021;Seek out alternative mentorship virtually to replace proposed "lab exchange" experience. 3. Teaching training: Complete manuscript with undergraduate mentee; Complete the Penn State teaching certificate.

    Impacts
    What was accomplished under these goals? 1. Research: I have made progress towards these goals - experimental design finalization, execution of experiment, and sample collection have all been completed. Due to the current shut-down of the University, soil samples are frozen and waiting to be processed (DNA extraction, amplicon sequencing). Plant samples are oven dried and stored for further analysis. 2. Professional Development, Research Training: i) To progress from an intermediate to advanced level in analyzing and interpreting microbial population and community data: Completed advance training course in August 2019 - Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) through the Marine Biological Laboratory at Woods Hole. ii) To progress from an intermediate to advanced level in microbial ecology methods, experimental design, and techniques: The reserach exchange I had proposed is no longer able to occur becuase of travel restrictions. iii) To engage with other agricultural microbial ecology researchers both nationally and internationally: Conferences I had proposed to attend in summer 2020 have been cancelled. Currently exploring other options for viritual conferences in 2020. 3. Professional Development, Teaching:To gain experience and develop skills as a teacher and mentor. Objectives: i) To progress from advanced to professional in classroom teaching at the college level: I successfully co-taught for 1 semester, and was the sole instructor of record for 1 semester, the course SOILS 071 Environmental Sustainability. Student feedback was collected via survey through the semester, and final feedback is forthcoming. ii) To build skills and gain experience in mentoring undergraduate students in research: I participated in a 1 year undergraduate mentoring program. Taran Rowles completed a reserach project under my metorship, culminating in a poster presentation at a univeristy symposium.

    Publications