We have DNA sequences!

It’s been two years since we set out to generate DNA sequence data from the seed samples from the Community Research Network, and we have now acquired DNA sequences for all samples sent to me between spring 2013 and fall of 2015! These sequences are the key to identifying the bacterial and fungal species inherited of the seeds that we save. It is not an easy process. First, it requires sterilizing the surface of the seeds, and then grinding them in a sterile environment, to prevent non-seed-associated microorganisms from contaminating the sample. Then, we extracted the DNA from the ground-up seeds. The most difficult process has been obtaining sufficient microbial DNA product, which is obscured in an ocean of plant DNA. The low-quantity microbial DNA was amplified to sufficient quantities such that we could obtain microbial DNA sequences, rather than those of the plant.

The process took many hours of troubleshooting and moving tiny liquid volumes between many plastic tubes. Now, it will take many more hours on the computer to pour over millions of DNA samples, and begin to disentangle the important factors that determine which microbes become inherited each new generation. If you sent us samples, you may receive call in the coming weeks, asking for some more details of your farming techniques, land history, seed source, etc. You should expect to see more regular updates on this website as the DNA sequence data become more organized and clear.

Meanwhile, we would like to do more sampling! We have streamlined the laboratory process, and are eager to receive more samples for DNA sequencing in the future. The goal is to keep growing the database, in terms of gaining more research participants and more corn varieties, but also getting more years of corn seed harvest from the same community research members. If you are interested in sending seeds, please write an email to lnebert at uoregon.edu for more information.


Each seed sample was reduced to a tiny pool of DNA sitting at the bottom of a 96-well plate.


576 samples containing amplified microbial DNA from six 96-well plates were pooled together.


This tiny volume of liquid contained millions of microbial DNA sequences from 288 samples, with each sample containing its own DNA barcode so it could be linked back to the sample at a later time. The final volume was 40 ul (0.4% of 1 milliliter).

Screenshot from 2016-02-04 15:25:46

Here is an example of a few bacterial sequences that were identified from the seeds. Note the number of nitrogen-fixing bacteria! Corn and other grasses can team with nitrogen fixing bacteria to provide significant amounts of their nitrogen needs, contrary to common knowledge that this process is only found in legumes in agriculture.

Screenshot from 2016-02-04 14:47:09

Here is an example of a Principle Component Analysis (PCoA) plot. Each dot is a seed sample, and the distance between dots is the differences of their entire microbial communities. They are currently colored by ‘type’ such as flint, dent, flour, popcorn and sweet corn. Type does not seem to be a good indicator of seedborne microbes, so we are working to find which factors are most important in determining which microbes are inherited.


Planting Corn with Pitchfork and Crow

The second field trial of the season has been successfully installed at Pitchfork and Crow, an organic farm just outside of Lebanon, Oregon last Thursday! In the pictures below you will see us protecting the seedlings with row cover from these iconic crows, who love to take corn sprouts out of the ground while they are still sweet. Like the trial at Adaptive Seeds, we are using Cascade Ruby-Gold flint corn variety, which I have split into 4 treatments randomly across the field, as follows:

1. Control treatment

2. Seed Disinfection

3. Seed Inoculation

4. Seed Disinfection + Inoculation

The disinfection treatment involves hot-water treatment of the corn seed, while the inoculation treatment includes adding a cocktail of 8 bacteria that are known to protect corn against disease involving Fusarium. While it is generally not advised to hot-water-treat large-seeded crops, I have found a method that appears to work: 5 minutes immersion in 60 degree Celsius water, followed by a quick dunk in ice-water before drying them off. The conventional reason for disinfecting is to protect your plants from seedborne diseases. However, I am also doing it to understand how important these seedborne microbes are in forming healthy microflora early on in the plant’s development. Disinfected seeds might be more susceptible to soilborne pathogens, or make it easier for beneficial microbes to colonize, such as the microbial cocktail that I have added. We always measure the effects of the seed treatments in the lab on the physiology of the germinating seedlings, in addition to sowing it into the field, to get a better idea about what may be going on.

Look forward to more updates, especially when the third and final field experiment is installed in the OSU experimental field, with seeds from both Pithfork and Crow and Adaptive Seeds, together in the same field.

Field Trial Started with Adaptive Seeds!

Yesterday was a beautiful day to put seeds in the ground at Adaptive Seeds’ farm! The freshly tilled soil was warmed from the sun, and rain was brewing in the western horizon. This marks the first big field trial of the season. Funded by the Organic Farming Research Foundation, I am exploring the microbial ecology of seeds, in this case, seeds from Cascade Ruby-Gold flint corn that was saved by Adaptive Seeds. To explore the importance of seedborne microbes, I am disinfecting some seeds, and inoculating others with beneficial microbes. Some research questions from this project are:

-If you disinfect the seeds, are you leaving the seedlings more vulnerable to colonization by microbes in the environment? (for better or for worse)

-Does the bacterial inoculation of seeds protect plants from fungal diseases?

Randomized plot design will statistically account for all of the variation in the field

Randomized plot design will statistically account for all of the variation in the field

Looking West from Adaptive Seeds farm. Red flags mark the plots where I planted Cascade Ruby-Gold.

Looking West from Adaptive Seeds farm. Red flags mark the plots where I planted Cascade Ruby-Gold.

Cascade Gold

Cascade Gold

Cascade Ruby

Cascade Ruby

It’s corn planting season!

It’s corn planting season the the Pacific Northwest! We’ve had a mild spring, so the Cascade Ruby-Gold got an early start in my garden. Here it is about 10 days old. I’m trying a no-till leaf mulch method.  I did a heavy leaf mulch over an unruly patch of grass during the winter, so the corn can now feed off of the nutrients of the rotting grass. I planted the seeds with some composted horse manure to give them a lively start. We’ll see how it goes!

I saved some of the batch of seed I planted so I will be able to do a before/after comparison of the microbial communities. I imagine this unconventional method will yield some interesting changes in the microbiome of the course of a growing season.

It’s not too late to register to participate in the research project this year! Register today, and you get your seeds analyzed to determine their microbial communities.



Open Source Seeds Have Arrived!

NPR has covered an exciting new development in the seed world: Open Source Seeds.

Click here for the NPR story

Why is this a big deal?

Most of the seeds in modern agriculture are controlled by large, multinational corporations such as Monsanto and Syngenta. They are claiming proprietary ownership of the seeds, which prevents farmers and public plant breeders from saving or modifying them. What used to be part of a common, human heritage for over 10,000 years is now locked up in patent castles, whose lords demand that seed growers pay them rent.

Open Source Seeds come with a seed pledge, that your seeds are allowed to be replanted or modified in the future, much like Open Source Software says about code. Seeds are encoding our heritage and the future of our food supply. Just like patenting software, patenting seeds stifles innovation, because they are only innovated in one, hegemonic way, by the profit-driven motives of large industrial agricultural interests – the Microsoft’s of the seed world. And we all know that in this increasingly networked world, the real innovation for the future rests in the hands of open, passionate and motivated communities, not secretly and in the dark.

Check out the Open Source Seed Initiative website, and even buy some to support their cause: http://www.opensourceseedinitiative.org/

Planting seeds at the 2014 Organic Seed Growers Conference

A few days ago I had the pleasure of attending the 2014 Organic Seed Grower’s Conference, arranged by the Organic Seed Alliance, in Corvallis, OR. Despite the intense, whirlwind of workshops, lectures, and conversation, I have left the conference feeling energized! I am thrilled to be doing work among such a solid group of people: passionate, intelligent, fun-loving, kind, warm, wholesome, dedicated, persistent are just a few words to describe the organic seed community.

In case you missed it, eOrganic has posted many of the talks on YouTube. Also, the conference proceedings are freely available for download from the Organic Seed Alliance.


1. The community research network received 24 new members, which triples the membership of our first year!

2. Matthew Dillon’s keynote address on Friday night. He stressed that seeds are about relationships, that biology is about networking and nourishing connections, that organic seed breeders are drawing from the 10,000 years of human ingenuity. I am told his address will be available on the web in the coming weeks.

3. The Open Source Seed Initiative seeks to create a protective umbrella for seeds against the bane of intellectual property rights, much like the Open Source Software license does for software. How it will actually look is still unclear, but here is a great article written on the subject by Jack Kloppenburg.

4. There was a workshop for making open-pollinated varieties out of F1 hybrids. While hybrids are great for particular suites of traits, and uniformity in growth and timing, ecologically speaking I feel that they are not very adaptable in the long-term. Novel hybrids often require specialized expertise, space, and 7+ years to produce, and their breeding trials are usually not  situated within the particular ecosystems (microclimates, soils, pest pressures) where they end up being grown for food. This makes them less adaptable to changing climate, insect, weed, and pathogen pressures. On the other hand open-pollinated has been a tried-and-true method for thousands of years, are relatively easy to manage, and can more easily be situated within the ecosystems in which they are grown for food. It was nice to see techniques for taking the offspring of proprietary F1 hybrids and letting them grow wild and differentiate for a couple years before selecting for desired traits.

I am excited to move this project forward, as I get a bigger picture of the current state of open-pollinated seeds, interact with the individuals and communities dedicated to their perseverance, and reflect their utmost importance of an adaptive seed supply for the future of our food.

New Year, New Opportunities for Seed Research!

The Microbial Inheritance in Seeds Project was recently awarded a grant of $13,000 from the Organic Farming Research Foundation! This grant will cover another year of field research and all of the lab supplies essential for exploring microbial communities in seeds, plants and soils. I am extremely grateful for this financial boost, and also see it as a vote of confidence for this research project by a very reputable ally in the organic food movement. I am looking forward to contributing cutting-edge scientific research for a more informed, innovative model for alternative food production.

Perhaps most importantly, this grant allows me to cultivate relationships with two Oregon Tilth organic certified farms in the Willamette Valley: Adaptive Seeds and Pitchfork and Crow. I have been working with Adaptive Seeds, and conducted a preliminary field trial with them this past year, with their Cascade Ruby-Gold corn variety. We were looking at the effect of organic seed disinfection techniques on the overall seed-to-seed transmission of microbes. Now we can expand this research, including exploring the effects of microbial inoculation of seeds on plant health. Pitchfork and Crow, who already collaborate with Adaptive Seeds in growing corn, graciously agreed to participate with field research. I am humbled to have the support of both of these stellar farms, and excited to embark on the next phase of research with them.

Expect more exciting details to come, as we get nearer to planting time!


Microbial Inheritance from the womb

In a brief departure from microbial inheritance in plants, I would like to highlight a New York Times article reporting on new scientific observations about microbial inheritance in people. The article, entitled Human Microbiome May Be Seeded Before Birth discusses the mounting evidence that babies are not born sterile – rather they receive their first, diverse, microbial inoculum in the womb, from their mother. This comes at a time when we are beginning to appreciate the importance of mother-infant microbial transmission in determining the child’s health, discussed here, in a recent NY Times article from Michael Pollan.

Fusarium: not your friendliest seedborne microbe

Hi all,

It’s been one hot summer in the Pacific NW! I hope your corn is doing okay!

I’ve been plowing through a bunch of lab and field work, with plenty of pictures to share.

Let’s start with one of the more infamous, but beautiful, seed-associated microbes of them all, Fusarium. This fungus is highly prevalent in seeds. If the conditions favor it, some pathogenic strains of this fungus can attack your corn. Cold, wet springs give it the pathogen an advantage over seedlings. Hot, dry summers will cause a late-season rot, as Fusarium takes over stressed plants. Although Fusarium can also confer benefits to the plant under other circumstances, we generally would prefer it NOT to be inherited in our seeds. Some of you may see the effects of Fusarium this summer, especially if your corn was water-stressed.

Here are some pictures I’ve taken from the lab as I have been working with Fusarium.

Has your corn been struggling with the sumer heat? Think you might have a Fusarium infection?  Add a comment below or email me. lnebert <at> uoregon <dot> edu

Moving right along!

Hi all,

The last few weeks I’ve been working hard on the official proposal for this dissertation research. Just yesterday I defended it with an 40-minute  public seminar, in front of a committee comprised of faculty from the U of Oregon and Oregon State University. After meeting the requirements set by the department of Biology, I’m officially a PhD candidate for the U of Oregon Environmental Science, Studies and Policy (ESSP) program!

This means we have the green light to move forward with this research! For those people planting seeds this year as part of the community research network, I will send you detailed information about what samples I need so we can make sense of the data. The big question now is: how many seeds from each grower do we need, to make sure we have a clear picture of the microbes they have in their seeds? 5 seeds? 10 seeds? 20 seeds? It all depends on the variation from seed-to-seed, which I am working to find out. Hopefully you have about 20 seeds to spare this spring, and then 20 more in the fall.

In one week, I’ll be meeting about the research plan for the next few months. So keep posted for a clearer picture of what’s ahead!

Best wishes,