Location: Horticultural Crops Production and Genetic Improvement Research Unit
Project Number: 2072-30500-001-023-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2026
End Date: Jun 30, 2030
Objective:
Research will be conducted to evaluate the long-term effects of crop rotations on soil microbial communities and function.
Specific objectives include:
1. Evaluate the long-term effects of crop rotation on soil microbial community size and diversity.
2. Correlate soil microbial community composition to function and soil health with multi-omics and enzyme activity assays.
Approach:
The Cooperator Agrees To 1. Work closely with ARS in planning and conducting the research outlined below. ARS scientist will provide technical expertise to support activities of post-doctoral scholar.
Objective 1: Soil samples from collected from the oldest continuous agricultural research trial in the United States were collected (0-60 cm), broken up into four depth intervals, and frozen prior to lyophilization for phospholipid fatty acid analysis (PLFA) and DNA extraction for metagenomic analysis. Microbial biomass will be estimated by PLFA analysis. Short and long read metagenomic samples will be assembled and binned using multiple approaches to maximize assembly and metagenome assembled bacterial and archeal genome (MAG) recovery. Special efforts will be made to characterize fungal genomes.
Objective 2: Building on objective 1, protein coding sequences will be predicted using MAGs and long read sequencing. This includes sequences coding carbohydrate active enzymes involved in the decomposition of cellulose, lignin, and chitin. These efforts will inform our understanding of the functional distribution of carbon and nitrogen cycling through the depth profile and point to the potential target compounds for metabolomic, proteomics and lipidomics analysis. Metabolites, proteins, and lipids will be extracted and metagenomic constrained metabolomes, proteomes, and lipidomes will be analyzed. Proteomics results will be connected to function and soil health by enzyme activity assays.