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Microbial Inheritance in Seeds

Main Project Information
Presented By A PhD project of Lucas Nebert
Goal Uncovering the hidden world of seedborne microbes in agriculture
Task Grow corn, send in samples and metadata, on-farm experiments
Where Global, anywhere on the planet

Plants are not just plants - rather, a plant is a host to thousands of species of symbiotic bacteria and fungi that reside on its surface and inside its roots, stems and leaves, greatly impacting its overall health and functioning. The plant microbiome plays a fundamental role in a plant's ability to acquire nutrients, resist diseases, and tolerate drought, herbivores and other environmental stresses. Plants are experts at regulating their microbiome, as part of its adaptive responses to environmental conditions. They can pick up new microbes from the environment or break ties with microbial symbionts to increase their chances of survival. For example, associating with a particular species of endophytic fungi can mean the difference between life and death during drought conditions.

Similarly, seeds are not simply packets of plant genes, but also propagules of the plant-symbiotic microorganisms, passing along diverse bacteria and fungi to their offspring. Seedborne "microbial inheritance" allows plant species to maintain beneficial relationships with microbes across plant generations, which is particularly important in agriculture, where the vast majority of our crops are annuals or biennials, dying back every year or so. We can consider the plant microbiome as a more fluid, adaptable form of plant inheritance than plant genetics. The acquired microbial associations that increase the fitness of the plant are the most likely to be passed along in seeds. Thus, seeds are a good place to look for beneficial plant microbes. To make things more complicated, pathogens can 'hitch-hike' across plant generations via the seed. Seed companies often treat their seeds against pathogens as a precaution of spreading disease. But at what cost? What benficial microbes are are we losing by disinfecting seeds against pathogens?

This research project seeks to uncover the hidden world of seedborne microbial inheritance, focusing on open-pollinated corn. How efficient is this form of transmission? How are we affecting microbial inheritance through our farming practices? Can we link desired plant traits (e.g. drought tolerance or disease resistance) to the presence of particular seedborne microbes?

How to participate

The simplest way to participate in this project is to grow and send in open-pollinated corn seeds! We are building a database of seedborne microbes from a growing diversity of corn seed samples - dent, flour, flint, sweet, and popcorn (over 80 samples so far!). We are using cutting-edge DNA sequencing technology to identify the entire population of seedborne bacteria and fungi in each sample. The goal is to look for overall trends between seedborne microbes and corn variety type, traits, and growing practices. If you are looking for a source of seeds, I would recommend growing the Cascade Ruby-Gold flint corn variety from Carol Deppe's Fertile Valley Seeds - Carol is the original breeder. You can also order it from Adaptive Seeds, who is also participating in the project. This particular variety has been most characterized in the project so far, so it will be informative to see how it grows in more locations and farming systems. If you have your own variety that you have been stewarding, that's great too!

Another way to participate is to conduct your own experiments, and send in seed samples from different treatments or selections. For example, perhaps you have been saving seeds of a particular corn variety from plants that do well in low irrigation conditions. You can send in seeds from the better-performing plants, and also seeds from the worse-performing plants, and see how their seedborne microbes are different, to identify candidate beneficial microbes. Another example might be a controlled field experiment where you use a special amendment (say, a microbial inoculant) and are testing how well it performs against a control treatment. You can send in seeds from the control and the treatment, and see how that affected the seedborne microbes. If you decide to go this route, please contact me ( to plan out experiment details.

Sending in your seed samples

A seed sample should represent a particular harvest or selection of seeds from a corn variety that you grew in a single season. Because we are interested in how we affect microbial inheritance through time, we encourage you to also send in samples from any previous years you grew them, and also samples from original seed sources - unless you sourced seeds directly from me or participating seed companies Adaptive Seeds ( or Carol Deppeā€™s Fertile Valley Seeds ( because we already have seed microbial data from those sources. Each sample should contain a representative 20-50 seeds. Visit the website for more details ( To receive microbial community data from your seed samples, please fill out the online Seed Sample Submission Form for each seed sample. After filling out the each form, you will receive an email with ID number to include along with your seed sample, in addition to the mailing address where to send the sample.

How to Join

Register at

To participate, you need enough space to grow at least 20 corn plants. Acquire corn seeds, flint, dent, flour, sweet or popcorn. Send in a subsample of your acquisition, plant the rest, and send a subsample of your harvest.

Social Media
Required Gear

Enough space and resources to grow 20+ corn plants.

Special Skills Participants need enough of a green thumb to successfully grow corn plants and yield a harvest.
Ideal Age Group Elementary school (6 - 10 years), Middle school (11 - 13 years), High school (14 - 17 years), College, Graduate students, Adults, Families
Spend the Time outdoors
Type of Activity At home
Tags adaptation, agroecology, bacteria, breeding, climate change, fungi, maize, microbiology, microbiome, plants, seeds, soil
Project Updated 04/21/2017