CULTIVATING RESILIENCE: EVALUATING ORGANIC AMENDMENTS FOR OPTIMIZING SOIL MICROBIOME FUNCTIONS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: ACTIVE
• Funding Source: AFRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 1032222
• Grant No.: 2024-67019-42337
• Cumulative Award Amt.: $299,213.00
• Proposal No.: 2023-10244
• Project Start Date: Aug 1, 2024
• Project End Date: Jul 31, 2026
• Grant Year: 2024
• Program Code: [A1401]- Foundational Program: Soil Health

Recipient Organization
NORTH CAROLINA STATE UNIV
(N/A)
RALEIGH,NC 27695

Performing Department
(N/A)

Non Technical Summary
Soil microbiomes play vital roles in agroecosystems, mediating processes like decomposition and carbon sequestration. Given their intrinsic connections to soil health, integrating new microbial perspectives offers transformative approaches for sustainable soil management. However, we currently lack a robust framework for understanding how different agronomic practices can effectively recruit and optimize soil microbiomes that enhance ecosystem functions and climate change resilience. Organic farming practices such as the use of cover crops or carbon-rich soil amendments can increase soil carbon. For farmers in the Coastal Plains, these benefits can be highly variable across systems. The goal of this project is to measure how soil microbiomes respond to organic transition and to quantify microbial functions related to carbon dynamics and community resilience. We will study soils from a three-year organic transition field experiment at two locations in North Carolina testing how different amendments (compost, 50/50 compost and biochar, biochar) and application rates can accelerate soil health benefits. To accomplish this, we will perform amplicon and metagenome sequencing to determine how different organic treatments shape microbiome composition and genetic functional potential (Objective 1). Molecular data will leverage measurements of microbial biomass, respiration, carbon utilization, and enzyme functional potential (Objective 2). Finally, we will assess how organic amendments impact community resilience by measuring CO2 and N2O flux using soil incubations with simulated extreme precipitation events (Objective 3). We aim to build a predictive framework for using agronomic practices and organic amendments to optimize soil microbiomes and beneficial ecosystem functions that support climate change resilience.

Animal Health Component

75%

Research Effort Categories

Basic

25%

Applied

75%

Developmental

0%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
102	0110	1070	50%
102	4099	1040	50%

Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
4099 - Microorganisms, general/other; 0110 - Soil;

Field Of Science
1040 - Molecular biology; 1070 - Ecology;

Keywords

ghg emissions

climate resilience

metagenomes

microbial activity

microbiome

organic amendments

Goals / Objectives
The goal of this project is to measure how soil microbiomes respond to organic management transition and quantify microbial dynamics related to soil carbon transformations and greenhouse gas emissions. Our long-term aim is to build a predictive framework of how organic amendment regimes can optimize soil microbiomes and beneficial ecosystem functions that support climate change resilience. We will leverage microbiome sequencingwith community functional analyses focusing on microbial processes related to nutrient cycling and carbon substrate utilization. We will also assess microbial community resilience, decomposition, and greenhouse gas emissions with soil mesocosms and simulated extreme precipitation events.Objective 1. Soil microbiome taxonomic diversity and genetic functional potential. Measure how transition to organic production and organic amendment regimes shape soil microbiome taxonomic diversity, community composition, and genetic functional potential.Objective 2. Soil microbiome community function. Assess microbial indicators of soil health, including functional group biomass and short-term C mineralization, and quantify potential activity of enzymes related to plant matter decomposition and carbon substrate usage from soil communities across organic amendment regimes at two field locations and two time points.Objective 3.Soil microbiome resilience.Assess resilience of microbial communities across soil incubation experiments with simulated extreme climate evetns (i.e., repeated flooding). Quantify greenhosue gas emissions, crop residue decomposition, and community stability and recovery between organic amendemtn regimes.

Project Methods
Objective 1 methods: Soil samples will be collected for microbiome sequencing at Upper Coastal Plain Research Station and Cunningham Research Station in April 2024 at corn planting. This sample point will capture the legacy impacts of organic input regimes after 3 years. At both locations, we will collect soils from all experimental plots and extract DNA for molecular sequening.We will use amplicon community sequencing to assess microbiome diversity and community compositionusing primers targeting bacterial/archaeal 16S rRNA genes, fungal ITS genes, and microbial eukaryotic 18S rRNA genes.We will use shotgun metagenomic sequencing to measure the microbiome functional genetic potential across organic treatments. Objective 2 methods:Soils will be sampled throughout the 2024 grow season to measure soil microbial functions at important crop production and ecosystem stages such as early crop development and harvest/residue decomposition. We wll measure microbial functionsrelated to carbon transformations including potential activity of hydrolytic enzymes, carbon substrate utilization, and carbon mineralization.Objective 3 methods:Soils for laboratory incubations will be collected from treatment plots at corn harvest in October 2024. We will carry out soil incubations by simulating differnent conditions ranging in environmental stress (i.e., repeated flooding). We will incubate soils for at approximately 2-3 months and measure CO2 and N2O gas fluxes, relative decomposition rates (inferred from differences in total carbon and nitrogen before and after incubation), and microbiome community resilience (inferred from differences in community composition).The automated gas analyzer in co-PD Woodley's lab enables automaticand continuoussampling of greenhouse gas fluxes from soil incubations.

Progress 08/01/24 to 07/31/25

Outputs
Target Audience:Target audiences reached during the reporting period include Southeastern organic producers; producers, farmers, and non-profit agencies; and Extension Specialists and agents. Secondary target audiences include academics communities interested in applied soil microbiologyand agroecosystem ecology. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has supportedtrainingand mentoring for oneMicrobiology PhD student and two undergradute student researchers. Professional development activities for the graduate student include presenting their preliminary finding at an internal seminar (i.e., NC State Microbiomes and Complex Communities Monthly Meetup) and a poster at the American Society for Microbiology Annual Microbe Meeting (June 20-22, 2025 in Los Angeles, CA). How have the results been disseminated to communities of interest?Preliminary results were shared to target audiences at regional conferences incluing: Optimizing Soil Health Outcomes in Southeastern Organic Farming Systems, Climate Resiliency: Land and Technology track (Choudoir M & Woodley A) SOWTH Georgia Organics Conference, Atlanta, GA, 2/4/2025-2/6/2025 Soil health and what it means for North Carolina (Choudoir M, Ozlu E, Biswanath D); 2025 North Carolina State Extension Conference, 1/6/2025-1/8/2025 Cover Crops and Soil Microbes; Part 1: Roots to Rhizosphere Overview; Part 2:Demonstration of the Cover Crop Selector Tool (Choudoir M and Menker A); Carolina Farm Stewardship Association's 2024 Sustainable Agriculture Conference, Durham NC, 11/2/2024-11/3/2024 Preliminary results were also shared to academic research audiences including: Microbial community ecology dynamics of agroecosystems, 2025; Earth Sciences Department Seminar Series, Southern Methodist University, 10/10/2025 Microbial community ecology insights for sustainable agroecosystems, 2024; EBIO Colloquium Seminar, University of Colorado Boulder, 10/4/2024 What do you plan to do during the next reporting period to accomplish the goals?Reserach activities for the upcoming period include collecting additional soil samples for laboratory incubaction experiments (e.g., measuring community resilience and greenhouse gas emmissions following a simulated flooding event or similar disturbance) (Objective 3). Activies also include synthesizing current sequencing and functional data,manuscript preparation, and submission of raw data to public repositories.

Impacts
What was accomplished under these goals? Research accomplishments include collecting soil samples from two field locations,two sampling times (at planting/May 2024 and at harvest/October 2024), and from plots with different histories of organic amendments applications. From these samples, we generated sequencing dataprofilingmicrobial taxonomy withamplicon surveys targeting bacterial (16S), fungal (ITS), and micro-eukaryotic (18S) taxa andshotgun metagenomic data from a subset of these samples to investigate potential different in functional gene content (Objective 1). We also performed functional assays including quantification of enzyme activity, short-term carbon mineralization, and carbon substrate utilization profiling (Objective 2).

Publications