Overview

A microbiome refers to the collection of all microbes, including bacteria, archaea, fungi, protists, and their genetic material within a specific habitat. While some microbiomes are associated with a host (e.g. the human gut or a plant root), there are environmental microbiomes (e.g. air, soil water). Microbiomes differ in the types of microbes present, their abundance, and their ecological diversity. In agroecosystems, these dynamic and interacting environmental and plant-associated microbiomes carry out important beneficial functions including decomposition of organic matter, soil nutrient cycling, and plant growth promotion. Optimizing these beneficial microbiome functions is a promising and sustainable solution for addressing future agronomic challenges related to food insecurity and climate change. In order to harness beneficial microbes, we need to better understand the complex ecological interactions occurring in the field and feedback mechanisms between microbes, plants, and soil.

G. Murali, G. Alka, Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies, Front. Microbiol., Sec. Microbial Symbioses, Volume 7 (2016)

Project Goals

The goal of the Choudoir Lab’s applied soil microbiome extension research program is to translate microbiome science to sustainable agriculture. Climate change, continued intensive agriculture practices, and the increasing demands of food systems threaten soil microbiome biodiversity and their important ecosystem functions. At the same time, microbial solutions to agronomic challenges can support sustainability goals! Our research philosophy aligns with environmental, social, and climate justice goals.

Project Design

We study soil microbiomes  at CEFS’ Cherry Research Farm in Goldsboro, NC. Here at the Farming Systems Research Unit, since 1999 five distinct land management practices have been consistently implemented for over 24 years. This long-term study allows us to measure and quantify  changes in soil microbial communities across time scales that are relevant to changes in  ecosystem function.

By sampling soil and rhizosphere microbiomes, we  aim to understand how these microbial communities  contribute to soil and plant health and other agroecosystem functions. This large-scale system-level experiment provides a unique opportunity for exploring the complex relationships between long-term land management practices and soil microbial biodiversity and function. We are using DNA sequencing methods to ask two distinct, but related questions.

1. How does long-term agronomic management impact soil microbiome composition, structure, and diversity? To address this question, we are using microbiome sequencing to explore presence/absence patterns and the relative abundances of microbial species in soil collected in 1999, 2015, and 2023. This allows us to explore how these communities may be changing over time. We are looking at bacteria, fungal, and protist communities.
2. How does annual variation and environmental disturbance influence microbial functional potential and greenhouse gas emissions? To address this question, we are using metagenomic sequencing to quantify the diversity and abundances of functional genes in soils from different treatment plots. The objective is to link these functional gene patterns to greenhouse gas emissions, and to further observe these relationships between gene content and function in soils following environmental disturbance (i.e. extreme climate event or flooding). This project is supported by the DOE JGI’s New Investigator Community Sequence Project (CSP).