Brian Gallagher

Program: Plant and Microbial Biosciences

Current advisor: Arpita Bose, PhD

Undergraduate university: Hamilton College, 2021

Enrollment year: 2021

Research summary
MO Ozark Fens host diverse microbial communities that drive soil health in these unique wetlands. My goal is to understand these microbiomes in order to develop and test targeted enriched communities to improve soil health in local degraded soils.

Ozark Fens are a unique and often highly productive type of groundwater-fed inland freshwater wetland found in Missouri. These systems boast a wide range of botanical biodiversity and healthy soils. The hydrological mechanism of formation and geographical locations of fens makes them a good example of healthier, “wild” soil counterparts to nearby agricultural land, sharing local climate and soil properties. A scant few characterizations of geomorphology, hydrology, and macroscopic ecology exist for these systems, but as of yet there has been little to no examination of microbiology or microbial ecology in MO Ozark fens.
Soil health is critically important for health and productivity of crops and other plants grown in it. The soil microbiome, the collection of all the microorganisms living in the soil and their metabolic pathways and functional genes, has significant control over the health and properties of a given soil. Mechanized agriculture (chemical fertilizers, tilling, and other practices) improves the food crop yield of a plot of agricultural soil in the short term but can negatively affect the long-term health and productivity of the soil. Harming its native microbiome reduces a soil’s ability to regenerate nutrients naturally and can deteriorate other properties.
Soil microbiomes are difficult to study (compared to, e.g., the human gut), as these are relatively highly complex systems with many close metabolic associations and taxa that have never been successfully characterized or cultured, with local variations in soil conditions at the micrometer scale. This complicates the targeted study of soil microbes’ metabolic capabilities and regulation. One canonical solution is to study a closely related strain as a laboratory proxy, and use genetic and genomic tools to compare it to its wild, uncultured relatives. The model organism Rhodopseudomonas palustris (Rpal), for example, is closely related to both other anoxygenic phototrophs and common soil diazotrophs of the family Nitrobacteraceae.
Three major methods show good promise for capturing the detail and complexity of soil microbiomes and are most useful applied jointly: meta-omics, isolations, and enrichments. Characterizing the community composition, functional gene expression profiles, and anaerobic metabolic regulation of microorganisms in productive fen soil microbiomes may facilitate the creation of targeted microbiota-driven soil restoration solutions for depleted agricultural soils.
Aim 1: Characterize microbiomes and their activities in fen soils with -omics analyses
Meta-omics involves the of bulk extraction and sequencing of identifiable microbial content (e.g., DNA). These reads are then taxonomically identified and/or assembled into contigs of partial or complete microbial genomes, facilitating identification of gene clusters and metabolic pathways.
Aim 2: Confirm and validate anaerobic microbial metabolic activity using isolations, genetic and genomic level analyses, and mutant growth curves under various conditions
To determine how specific abundant community components are interfacing with the broader soil microbiome metabolic activity, single- and multiple-gene knockout mutants of important aerobic-anaerobic global metabolic regulator genes (aadR, fixK, rirA) will be made in Rpal and tested for growth and gene expression on relevant substrates under different metabolic modes.
Aim 3: Test a targeted “Soil Microbiota Transplant” to restore health of MO agricultural soils in mesocosm by characterizing inoculum, soil, and plant health outcomes
Stable and scalable communities enriched from Ozark Fen soils for restorative ecosystem services will be used to inoculate laboratory mesocosms with combinations of soils (depleted and healthy) and corn presence (with and without plants). Inoculum community composition, soil health, and plant growth metrics will be measured before and at time points after inoculation.

Graduate publications