Location: Application Technology Research
Project Number: 5082-30500-001-080-A
Project Type: Cooperative Agreement
Start Date: Apr 1, 2026
End Date: Mar 31, 2029
Objective:
Production of small fruits, vegetables, and ornamentals in container growing media provides numerous advantages in regions of the US with unsuitable field soil or limited available water for crop production. Lack of substrate stability in container growing media is currently limiting the types of crops that can be grown in container growing media, especially those that require multiple years for suitable harvest. Understanding the role of biological communities in substrate decomposition is the first step in developing management strategies to prolong substrate stability. Little is known about the microbial communities and their function in common container growing media. The objective of this research is to document the relative abundance of microbial communities in container growing media and determine which communities play an active role in substrate decomposition.
Approach:
We will characterize the microbial community composition and their function of select growing media across multiple harvest dates. We will determine bacterial and fungal community composition shifts using amplicon sequencing of ribosomal markers, coupled with functional studies based on transcriptomics and whole genome assemblies. For amplicon metabarcoding we will select universal bacterial 16S rRNA primers (515F and 806R) and fungal ITS primers to detect dynamics of individual ribotypes over time and tied to decomposition rates. We will apply standard, phylogenetically informed pipelines for sequence data analysis. A set of selected samples will be used for functional analysis of the eukaryotic community, using an RNAseq approach, to investigate contributions of fungal metabolic pathways for substrate degradation. Shotguns metagenomic will be used to capture (and assemble) the genomes of the most abundant bacteria (and their genes) in substrate samples and make hypothesis about their role in substrate decomposition and. These analyses will be used to determine the relationship between decomposition rates, microbial consortia, including amended bio-stimulants, their genome content and metabolic potential.