Page Title

Research Questions


How can we maximize the efficiency  of plant-microbe symbiosis?

We believe harnessing beneficial microbiome for agriculture relies on a mechanistic understanding of how plants select their microbiota. Beneficial microbes must not only be able to promote plant growth, but also thrive in the microbiome of the plant, where they must compete with well-adapted natural microbiota for colonization of this niche.

Because of their intimate relationship with the plant, rhizobia that are applied as inoculants in agriculture must also compete for occupation of root nodules against natural rhizobia that may be inferior partners for the plant. To make an efficient symbiont, rhizobia must not only be competitive, but also a compatible partner for the legume, and effective at fixing nitrogen and providing it to its host.

Figure describing how plants select their microbiota, competition for nodule occupancy, compatibility with host legume, and effectiveness of symbiotic partnership
Photo Credit:
Barney Geddes


Synthetic Biology

Advances in synthetic biology this decade have opened the door to engineering symbiotic relationships in agriculture to improve crop yield. To support these efforts we are developing foundational knowledge about natural symbioses to guide engineering and building platforms to improve our ability to reliably and predictably engineer microbes in the context of the microbiome.

Functional Genomics

Ascribing function to genes has perhaps never been more important in an era of big data. Using functional genomics approaches we seek to identify and characterize the genes that underly beneficial plant-microbe interactions. We are utilizing synthetic genomics and high-throughput molecular screening to identify important genes, and interdisciplinary approaches to understand the mechanisms through which they act.

Microbiome Analysis

Understanding how plants recruit and assemble their microbiota may be the key to unlocking the plant microbiome for sustainable agriculture. By blending next-generation sequencing and high-throughput culturing with synthetic biology and functional genomics we hope to gain foundational insights into this question.

Evaluating rhizobium populations in field soil


Successful nodulation of soybean plants by rhizobia from the soil is important to maximize yield and alleviate the requirement for nitrogen fertilizer. It is important to introduce rhizobia into fields by inoculation during planting when legumes are grown for the first time. Inoculation in subsequent years (at least 5 after initial inoculation) is generally not required for soybeans in eastern North Dakota. However challenging soil conditions (acidic pH, salinity) or weather conditions (drought, flooding) may affect inoculant survival in the soil and benefits in subsequent years. We are developing tools for quantification of rhizobia populations in farmer’s fields that could help inform farmers whether or not inoculation could be beneficial.


Interested in Getting Involved? 


We are looking for farmers interested in having their fields tested for rhizobia abundance in Fall 2022. Currently we are focused on soybean, pea and chickpea. fields should be planned for soybean or pulse production in 2023 and have a known production and inoculation history (last 5 years). Participation by growers from Western North Dakota where inoculant persistence in soils is less well understood is especially desired.


Participating farmers will receive a report indicating the results of the assay as well as a chemical analysis of their field soil. Select fields will also be scouted in Summer 2023 to assess soybean nodulation. There are also opportunities for longer term engagement in the project to investigate effects that agronomic practices such as crop rotation have on the beneficial microbes in their soils.


Interested farmers should reach out to Geddes by email, barney.geddes@ndsu


The Geddes lab thanks the North Dakota Soybean Council for funding this work.