Source: UNIVERSITY OF FLORIDA submitted to NRP
HOW LONG-TERM CROP ROTATIONAL MANAGEMENT AND GRAZING AFFECT THE FUNCTIONAL NETWORK OF SOIL BIOTA, SOIL HEALTH, AND CROP PRODUCTIVITY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1032194
Grant No.
2024-67019-42344
Cumulative Award Amt.
$749,785.00
Proposal No.
2023-10226
Multistate No.
(N/A)
Project Start Date
Jul 1, 2024
Project End Date
Jun 30, 2027
Grant Year
2024
Program Code
[A1401]- Foundational Program: Soil Health
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
(N/A)
Non Technical Summary
Crop rotation is a management strategy that can foster sustainable agriculture, although recent evidence suggests that intensive crop rotations could be detrimental to soil health. This issue could be particularly significant in the southeastern US, where coarse-textured soils coupled with a hot and humid climate accelerate soil organic matter decomposition, diminish the soil's nutrient retention capacity, and exacerbate the susceptibility of soil and plants to pests and diseases.Our project aims to enhance the sustainability of farming by integrating perennial grasses and cover crops into traditional crop rotations, along with optimal grazing practices. This approach will be tested at two field sites in North Florida to compare it against the conventional intensive crop rotations. We plan to study how these changes affect various aspects of the farming environment. This includes examining soil biological attributes (soil biodiversity and multi-trophic interactions), soil fertility and biogeochemical cycling (greenhouse gas emissions, nutrient leaching), agroecosystem multifunctionality, and crop yield and quality. By exploring these diverse factors, our project seeks to provide valuable information on how smarter farming practices can improve soil health, make farming more sustainable, and enhance the overall environment.
Animal Health Component
40%
Research Effort Categories
Basic
60%
Applied
40%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110106010%
1021452106010%
1021510106010%
1021560106010%
1021620106010%
1021830106010%
1023130106010%
1024010107010%
1024020107010%
1024099107010%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
1510 - Corn; 1560 - Oats; 4099 - Microorganisms, general/other; 1620 - Warm season perennial grasses; 3130 - Nematodes; 0110 - Soil; 4010 - Bacteria; 4020 - Fungi; 1452 - Carrot; 1830 - Peanut;

Field Of Science
1060 - Biology (whole systems); 1070 - Ecology;
Goals / Objectives
The major goal of this project is to develop a sustainable, resilient, resistant, and economically viable cropping system that can foster healthy soils in the southeastern US. Previous studies suggest that diversifying crop rotations can improve soil health. We hypothesize that increasing the diversity of functional traits found in the crops grown in this rotation, known as functional rotational diversity, would develop healthier soil by fostering soil biodiversity and enhancing agroecosystem multifunctionality, which could potentially alleviate the adverse impacts associated with grazing. To test this hypothesis, we will conduct extensive research at two sites with different soil types but similar climates across North Florida, with the Live Oak and Quincy sites designated as the primary and secondary field trials, respectively. we will achieve the proposal's four specific objectives:(1) Evaluate the impact of increasing functional rotational diversity on biological indicators of soil health, with specific emphasis on spatiotemporal variations in soil biodiversity, functional networks of soil biota, biota-driven C and nutrient cycling, root-biota interactions, and agroecosystem multifunctionality.(2) Assess the variability in the effect of functionally diversified crop rotations on soil health and crop yield and quality under different soil types.(3) Determine the effect of integrating grazing into functionally diversified crop rotations on soil fertility and health, greenhouse gas emissions, nutrient losses, and crop yield and quality.(4) Develop outreach programs to disseminate the findings to stakeholders (producers, extension agents, and 4-H groups).
Project Methods
We will conduct the real farm study to identify the primary soil health indicators influenced by advanced rotation managements (including crop diversity and grazing).We will profile the community composition of soil microbes (including bacteria, fungi, and archaea) and protists using DNA/RNA amplicon sequencing. The absolute abundance of each biological group will be quantified using quantitative PCR. Absolute profiling of soil microbiomes will be determined by integrating data from both amplicon sequencing and qPCR. The extraction of soil nematodes will follow the sucrose-centrifugation method and be identified morphologically to the family level. An integrated estimate of soil biodiversity will be achieved by integrating ASVs from all biological groups and represented by the Shannon index. Changes in soil biodiversity along soil profile and developmental stage will be compared under different rotations. Soil functional diversity will be measured using functional genes from soil metagenomics. Dissimilarities in all soil biological groups among treatments (beta diversity) will be visualized using a PCoA with Bray-Curtis dissimilarity distances, and the effect of studied factors on the community composition of soil biota will be identified by PERMANOVA. The average variation degree method will be utilized to calculate the stability of soil biota, and functional stability will calculated by the ratio of the mean to standard deviation of KEGG pathways across the replicated soil samples. The community assembly of each biological group will be determined by using a neutral community model and normalized stochasticity ratio. Network analysis will be employed to examine multitrophic interactions, and topological properties (e.g., robustness, vulnerability, stability, and complexity) will be determined to assess the impact of functional rotational diversity on the structure of these interactions and soil food webs.Activities of soil extracellular enzymes, key to cycles of C (α-1,4-glucosidase and β-1,4-glucosidase, β-1,4-xylosidase, and β-D-cellobiosidase), N (urease and N-acetyl-glucosaminidase), and P (acid phosphatase) will be measured from the peanut and corn phases using fluorometric techniques. Agroecosystem multifunctionality will be calculated based on soil functions and enzymatic activities. Machine learning models will be used to identify key biological groups/taxa or functional genes that are responsible for agroecosystem multifunctionality.Through our comprehensive multi-omic analyses, we aim to achieve an in-depth mechanistic understanding of how functional rotational diversity influences a range of soil biological attributes (microbial function, community structure, and assembly, soil biodiversity, and multitrophic interactions) across various soil profiles and plant growth stages. Our use of machine learning models seeks to revolutionize soil management by predicting these intricate soil dynamics by linking biological soil properties with agroecosystem multifunctionality, enabling more precise and timely management decisions.To gain a comprehensive understanding of how soil biota drive C and nutrient cycling, we will perform a thorough analysis of C-related (copiotrophs, oligotrophs, saprotrophs) and N-related (nitrifying microbes, denitrifying microbes, and free-living diazotrophs, AMF) microbial groups, and methanogens. Multiple supervised machine-learning approaches will be deployed to identify the key functional microbes driving C and nutrient cycling. Network approaches will be performed to understand how higher trophic biota regulate C and nutrient cycling by modulating soil food webs. The aggregated boosted tree machine learning approach will be used to investigate the relative influences of biotic and abiotic variables in regulating soil C and nutrient pools. Soil health indicators will be measured according to NRCS guidelines and soil health index (SHI) will be calculated using the integrated methods of CASH protocol, and linear and non-linear equations. Finally, structural equation modeling will be employed to assess the cascading effects of biotic and abiotic variables on soil C and nutrient pools and soil health. We anticipate that this study will significantly improve our understanding of soil health by elucidating the complex relationships between soil biota and critical soil processes, namely C and nutrient cycling, under different levels of functional rotational diversity. Leveraging advanced machine-learning approaches will enable us to pinpoint the key microbial players that drive these essential soil functions under different rotation systems.Overall, the findings of this project regarding soil health, climate change mitigation and adaptation, and agricultural resilience and sustainability, will be communicated to vital stakeholders, including extension personnel, livestock producers, other land managers, and 4-H groups. To facilitate this, we plan to host field days, such as perennial grass field days and sod-based rotation field days, and offer professional training programs (e.g., in-service trainings and interactive workshops held at IFAS/UF) annually. Through these activities, we hope to equip our attendees with the knowledge and resources to establish a standard system for measuring soil health and adapting agricultural management to enhance soil health. To broaden our reach, we will record these activities and share them on our YouTube channel (https://www.youtube.com/@Liao_Lab).Additionally, we will create educational materials concerning soil health for 4-H students and distribute them through educational events, such as the Tallahassee Science Festival, the Art, Garden and Farm Family Festival in Quincy, FL, and Gadsden County 4H programs. To cater to a wider audience beyond Florida, these materials will also be made accessible online in video format on our YouTube channel.Lastly, we will publish our key findings in extension publications (http://edis.ifas.ufl.edu) and popular press articles, providing useful management, utilization, and economic information for producers interested in soil health.

Progress 07/01/24 to 06/30/25

Outputs
Target Audience:A. Train the graduate students, postdocs, and other scientists to conduct the research proposed in this study, including: Kaile Zhang (postdoc, supervisor: Liao) Valkiria Borsa Piroli (PhD student, supervisors: Sidhu and Maltais-Landry) Haihua Wang (postdoc, supervisor: Liao) Benjamin Reimer (PhD student, supervisor: Liao) Hee-Sung Bae (Biologist, supervisor: Liao) Allison Schmidt (OPS, supervisors: Maltais-Landry) B. The project also involves the dissemination of research outcomes of this project through Extension/outreach training programs 1. 2024: One-on-one communication with stakeholders on the topic of soil health management A case example: We analyzed samples provided by stakeholders and generated scientific reports detailing microbial activities related to carbon dynamics in their compost products. These findings are shared during scientist-stakeholder meetings, which aim to help stakeholders apply the results to inform management practices and better support their clientele. Led by: Liao and Zhang Target audience: stakeholders (e.g., Florida Proven Organic) 2. Summer 2024: Led an Extension lecture on soil biological indicators Scope: Delivered an Extension lecture covering three key topics: (1) beneficial biological indicators in soil, (2) microbially mediated biodegradation, and (3) the biodegradability of biodegradable plastics. The session received highly positive feedback from attendees, and I subsequently provided one-on-one consultations with Master Gardeners who sought additional guidance. Speaker: Liao Target audiences: Polk County Master Gardeners and Extension agents, 3. Jan. 2025: Present at the AFGC Conference Scope of AFGC: Provided an updated overview of current research on how microbial endophytes influence sod systems (e.g., bahiagrass), and discussed how management practices can be optimized to enhance sod health and productivity (Several poster presentations) Speakers: Liao, Zhang, Wang, Reimer Target audiences: Extension agents, industry personnel, and producers 4. Feb. 2025: Led an Extension lecture at the 2025 Soil Health & Cover Crop Field Day (UF/IFAS North Florida Research and Education Center-Suwannee Valley, Live Oak, FL) Scope: Delivered an Extension lecture demonstrating how diversifying cover crops can enhance soil health. The field day drew over 85 stakeholders from across Florida. Speaker: Jay Capasso Changes/Problems:Since grazing is no longer implemented during the cover crop phase at the Live Oak site, we have incorporated a new rotation system located in Marianna, FL, to investigate the effects of grazing and cover cropping treatments under different rotation systems on soil health. Detailed descriptions of the field treatments are provided in the previous section. What opportunities for training and professional development has the project provided?As indicated in the "target audience" section, the project has provided opportunities to train postdocs, graduate students, and biological scientists. Through the supervision and training activities, graduate trainees are expected to receive professional skills on molecular/biogeochemical technologies, bioinformatics, and soil health assessment. The professorial training for graduate students and postdoctoral scientists includes research proposal development, experimental designs, sample collection/processing, data collection/analysis, data integration, scientific presentations, coordination for team meetings, and leading the manuscript preparation for his/her projects. All the trainees have been actively involved in scientific presentations and extension activities, with the evidence shown in the sections of "Product" and "Other products". 1) Kaile Zhang (co-PI; supervisor: Liao): Kaile's research focuses on understanding how diversified crop rotations and grazing impact biological indicators of soil health. He is leading the implementation of this project, including coordinating PI meetings, developing the sampling plan, and overseeing field sampling activities. 2) Valkiria Borsa Piroli (PhD student, supervisors: Sidhu and Maltais-Landry): Valkiria's doctoral research focuses on assessing how diversified crop rotations and grazing influence soil fertility, soil health, nutrient losses, greenhouse gas emissions, and crop productivity. She is leading soil sampling efforts at the Live Oak and Quincy sites. 3) Other students and scientists assisted with field sampling and laboratory analyses, include: Haihua Wang (postdoc, supervisor: Liao), Benjamin Reimer (PhD student, supervisor: Liao), Hee-Sung Bae (Biologist, supervisor: Liao), and Allison Schmidt (OPS, supervisor: Maltais-Landry). How have the results been disseminated to communities of interest?We have been using a combination of publications, in-person meetings, and social media as our methods for disseminating information (See "Target Audience" section and "Products" section). What do you plan to do during the next reporting period to accomplish the goals?To further address Objectives 1-3, we will continue collecting surface soil samples (0-15 cm) during the flowering and maturity stages of peanuts under different rotation systems at both the Live Oak and Quincy sites. In addition, rhizosphere soil and peanut root samples will be collected at these two growth stages to investigate how various rotation systems influence root-microbiome interactions and the contributions of microbiomes in different soil/root compartments to crop productivity and quality. For all collected soil and root samples, we will conduct a comprehensive suite of analyses, including multi-omics approaches (amplicon sequencing, metabolomics, and metatranscriptomics), soil nematode profiling, and standard soil fertility and health assessments. Deep soil samples will also be collected bi-weekly from each rotation system at the Live Oak site to monitor nutrient losses. Furthermore, to evaluate the impact of rotation systems on greenhouse gas emissions, we will conduct monthly in situ gas flux measurements during the cover crop phase at the Live Oak site. Additionally, we will collect surface soil samples (0-20 cm) at the cotton maturity stage from a rotation field trial at the Marianna site, which incorporates three crop-livestock integration systems: Traditional rotation systems: peanut-cotton-cotton rotation without grazing during the cover crop phase, with three treatments, including • No cover crop without grazing • Oat cover crop without grazing • Fertilized oat cover crop (30 lbs N/acre) without grazing Integrated crop-livestock system: Peanut-cotton-cotton rotation with grazing during the cover crop phase, with three treatments, including • Oat-crimson clover mix with grazing every two weeks • Fertilized oat-crimson mix (30 lbs N/acre) with grazing every two weeks • Fertilized oat-crimson mix (80 lbs N/acre) with grazing every two weeks Sod-based rotation: Bahiagrass-bahiagrass-cotton-peanut rotation with grazing during the cover crop phase, with three treatments, including • Oat-crimson mix with grazing every two weeks • Fertilized oat-crimson mix (30 lbs N/acre) with grazing every two weeks • Fertilized oat-crimson mix (80 lbs N/acre) with grazing every two weeks For the collected soil samples, we will conduct amplicon sequencing to characterize soil microbial communities, perform soil nematode profiling, and carry out comprehensive soil health assessments.

Impacts
What was accomplished under these goals? The major goal of this project is to develop a sustainable, resilient, resistant, and economically viable cropping system that can foster healthy soils in the southeastern US. Previous studies suggest that diversifying crop rotations can improve soil health. We hypothesize that increasing the diversity of functional traits found in the crops grown in this rotation, known as functional rotational diversity, would develop healthier soil by fostering soil biodiversity and enhancing agroecosystem multifunctionality, which could potentially alleviate the adverse impacts associated with grazing. To test this hypothesis, we are conducting extensive research at three sites (Live Oak, Quincy, and Marianna) with different soil types but similar climates across North Florida. We are studying the proposal's four specific objectives: (1) Evaluate the impact of increasing functional rotational diversity on biological indicators of soil health, with specific emphasis on spatiotemporal variations in soil biodiversity, functional networks of soil biota, biota-driven C and nutrient cycling, root-biota interactions, and agroecosystem multifunctionality. (2) Assess the variability in the effect of functionally diversified crop rotations on soil health and crop yield and quality under different soil types. (3) Determine the effect of integrating grazing into functionally diversified crop rotations on soil fertility and health, greenhouse gas emissions, nutrient losses, and crop yield and quality. (4) Develop outreach programs to disseminate the findings to stakeholders (producers, extension agents, and 4-H groups). Key accomplishments aligned with each objective Objectives 1 and 2: We collected deep soil samples at three depths (0-15 cm, 15-30 cm, and 30-60 cm) before peanut planting from each rotation system at the Live Oak site. These systems included: peanut-corn, peanut-oat-corn-oat, peanut-oat-corn-carrot, peanut-oat-corn-oat-bahiagrass-bahiagrass, and peanut-oat-corn-carrot-bahiagrass-bahiagrass rotations. At the Quincy site, we conducted similar deep soil sampling (0-15 cm, 15-30 cm, and 30-60 cm) before peanut planting under two rotation systems: conventional peanut-cotton-cotton, and peanut-cotton-bahiagrass-bahiagrass. Objective 3: To evaluate the legacy effects of grazing and diversified crop rotations on soil fertility, soil health, and nutrient losses, we collected soil samples at three depths (0-15 cm, 15-30 cm, and 30-60 cm) from both inside and outside of cage areas that had been previously installed during the bahiagrass phase at the Live Oak site. Sampling was conducted under two sod-based rotation systems (peanut-oat-corn-oat-bahiagrass-bahiagrass and peanut-oat-corn-carrot-bahiagrass-bahiagrass) following the termination of an oat cover crop. Additionally, deep soil samples were collected bi-weekly from each rotation system to assess nutrient losses.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Wang H, Wu S, Zhang K, Chen K-H, Vilgalys R, Liao H-L. MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using hypervariable markers. 2025 MSA Annual Meeting, Madison WI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Benjamin Reimer, Wang H, Zhang K, Verma V, Mendez V, Blount A. Justesen B, Walter J, Mackowiak C, Jones R, Tomlinson AP, DeValerio JT, Mayo D, Liao H-L. 2025. Ergot-Infested Seedheads in Florida Bahiagrass Pastures. American Forage and Grassland Council (AFGC), Kissimmee, FL (Poster presentation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Wang H, Benjamin Reimer, Zhang K, Verma V, Mendez V, Justesen B, Walter J, Blount A, Mackowiak C, Jones R, Tomlinson AP, Liao H-L. 2025. Mycotoxin detection using HPLC and real-time qPCR at molecular levels, American Forage and Grassland Council (AFGC), Kissimmee, FL (Poster presentation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Zhang K, Liao H-L, Wang H, Reimer B, Verma V, Justesen B, Walter J, Tomlinson P, Jones R, Mendez V, Blount A, Mackowiak C, Wallau M, Chen, K-H, Buringer J, Love J, Yarborough JK, Mayo D. 2024. Endophyte and Mycotoxin Advancement Laboratory: Research and Service Updates. American Forage and Grassland Council (AFGC), Kissimmee, FL (Poster presentation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Erhunmwunse AS, Reimer B, Verma VC, Mackowiak C, Blount A, Liao H-L. 2025. Investing soil microbes mediating nutrient cycling in grass-legume pastures. American Forage and Grassland Council (AFGC), Kissimmee, FL (Poster presentation)
  • Type: Book Chapters Status: Under Review Year Published: 2025 Citation: Lira Junior MA, Zhang K, Erhunmwunse A, Liao H-L, de Freitas ADS, Jaramillo DM. 2025. Biological nitrogen fixation in dry regions. In Book Forage Systems on Drylands.
  • Type: Other Journal Articles Status: Published Year Published: 2025 Citation: Liao HL, Zhang K, Verma V, Wang H, Justesen B, Walter J, Mendez V, Blount A, Mackowiak C, Wallau M, Jones R. Survey of Mycotoxins Present in Florida Pastures Across Time, Locations, and Grass Species: SL529/SS744, 3/2025. EDIS, 2025(2).
  • Type: Other Journal Articles Status: Published Year Published: 2025 Citation: Andres H, Liao HL, Zhang K. Biology, Ecology, and Benefits of Arbuscular Mycorrhizal Fungi in Agricultural Ecosystems: PP383, 3/2025. EDIS,2025(2).
  • Type: Other Journal Articles Status: Accepted Year Published: 2025 Citation: Andres H, Zhang K, Liao H-L. 2025. Biology, Ecology, and Benefits of Ectomycorrhizal Fungi in Natural and Managed Forest Ecosystems. (Peer-Reviewed) (Accepted, archive ID: 137789)
  • Type: Other Journal Articles Status: Published Year Published: 2024 Citation: Liao HL, Erhunmwunse A. Integrating Rhizoma Perennial Peanut into Bahiagrass Pastures Enhances Beneficial Soil Microbes in Florida: SS-AGR-482/AG478, 7/2024. EDIS, 2024(4).