The Root Microbiome

The Schachtman Lab at the University of Nebraska Lincoln started in February 2014.  The focus of our research is on soil microbe interactions with plant roots.  Our long term goal is to optimize root microbes for agriculture.
Being in Nebraska where agriculture is one the state’s major industry we focus on crop plants such as soybeans, corn and sorghum.  Our aims are to understand how crops shape their root microbiome and to identify microbes that will be useful in agriculture.  We use both culture-dependent and culture-independent methods.  Currently the culture-independent methods use 16s, nif amplicons and next generation sequencing to determine changes in microbial populations and to generate hypotheses.  To test hypotheses regarding specific microbes we intend to use our developing culture collect of bacteria and fungi.

The lab is currently focusing on several topics mainly related to plant abiotic stress tolerance and the root/soil microbiome. Several projects have been funded including:

Project 1 – Funded by DOE-BER (click here for project pictures)
Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome.
Personnel – Allyn Pella, project coordinator, Ellen Marsh, Research Associate, Stephanie Futrell, Technical Assistant + 3 – 5 undergraduates in the summer
Collaborators – Cody Creech, UNL Assistant Professor, John Rajewski, Technical Associate, Ismail Dweikat, UNL Professor
This is a large multi-institutional project that involves 7 universities and a DOE user facility. The URL describing this grant is: The main objective of the grant is to provide basic information that will be used to develop sustainable systems for biofuel feedstocks. We are approaching this projects from two angles. First, we are working to understand and improve the root microbiome under drought and low nitrogen conditions and second, we are identifying the most productive germplasm for growth of sorghum on marginal land.

Project 2 – Funded by USDA –NIFA (click here for project pictures)
Genomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop.
We are working with groups at the Danforth Center and at the USDA in Maricopa, Arizona to identify drought tolerant lines of the oil seed crop Camelina.

Project 3 – Funded by NSF – EPSCOR (click here for project pictures)
Center for Root and Rhizobiome Innovation (CRRI)
Personnel – Peng Wang (postdoc)
The aim of this project is to develop a systems level understanding of root metabolism and its influence on interactions with soil microbes, determine how these interactions are affected by genetic variation and environmental perturbations, and use this information for iterative, synthetic re-design of root metabolism to promote plant health and beneficial root-soil microbe interactions. Our part of the project is to: quantify the chemical diversity of root exudates across maize genotypes and the impact of this diversity on rhizobiomes. Currently we are screening 400 maize lines to identify diversity in root exudates.  See for more information about the project.

Project 4 – Funded by UNL – ARD Internal Funding (click here for project pictures)
Microbial contributions to nitrogen nutrition in cereal crops
Nitrogen fixation and stable colonizationYen Ning Chai (PhD student)
This project currently has two aims which are to identify nitrogen use efficient and inefficient sorghum lines and to identify microbes that fix nitrogen and may function as nitrogen fixing endophytes for sorghum.

Project 5 – Funded by startup funding (click here for project pictures)
Microbial Communities of Plant Roots Growing on Alkaline Soils – Soybeans and Native GrassesMorgan McPherson (PhD student)
This project is focused on prospecting for novel microbes that may enhance plant tolerance to alkaline soils and to understand the basis of the changes of the microbiome in soybean lines that are tolerant or sensitive to alkaline soils.