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Citizen Science Project on the Tomato Seed Microbiome

(cross posted to the UCD Microbiome SRP blog)

Tomato seedling grown in a peat pellet

What do you get when you combine UC Davis alumni, tomato seeds, and citizen science?   That would be Project GASP (“Germ”-ination Alumni Science Project).  I didn’t come up with the name, I swear.   This project, sponsored and paid for by the College of Biological Sciences at UC Davis, is interested in looking at the heritability of the tomato seed microbiome.  There is a large body of research on the importance of the microbiome for the health and productivity of plants in agriculture.   There are whole companies dedicated to assessing the microbiome health of soil and to offering probiotic solutions.  But less is understood about the heritability of the microbiome.  Are beneficial microbes recruited from the soil or are any passed down through the seeds?  Maybe not directly, but maybe analogous to humans where the first bacteria you get from your mother help to structure the subsequent microbial community.

Samantha working on test germinations

To begin to examine this question more closely we wanted to germinate a bunch of similar seeds (grown under identical conditions, harvested at the same time, treated the same way) under a few different conditions.  We then wanted to look at the microbiome of the plants, their roots, and their seeds.  So with the help of two undergraduates in the lab, Paige Derryman and Samantha Levy, we have spent some of the last few months testing things and designing a (hopefully) robust protocol for people to follow.  The basics are as follows:

Each participant will receive a packet of M82 tomato seeds (a strain for which we have extensive genetic tools), some peat pellets, and a variety of odds and ends to conduct the experiment.  They will be asked to germinate 10 seeds in each of three conditions; water, soil, and peat pellets.   The water condition is simply water-soaked paper towels in a plastic bag, the soil is “soil of your choice”, and the peat pellets are commercially available and are a very convenient way to germinate seeds under similar conditions across participants.   Once the seedlings are a couple of inches tall the participants will trim off the top of the plant and place that into a buffer that prevents growth of microbes and preserves nucleic acids.   Then they will wash the dirt from the roots and place the roots into some more buffer.   All of this will get sent back to UC Davis for a 16S rRNA analysis of the tomato seedling microbiome.  Some subset of the participants will (hopefully!) plant the seedling in their gardens, and then send us seeds… both for microbiome analysis and for the next generation of the experiment.

Right now it’s just a pilot with 45 participants, all UCD alumni.   After we work out the kinks we hope to scale this up, open it to the public, and run the experiment over multiple seasons.  Stay tuned!

Status:  As of 3/17/20 I have set up a small lab in my living room in order to make the kits and prepare everything while working from home.  My kids helped count out the tomato seeds and peat pellets which I counted as “science homeschooling”.  Hoping to send out the kits soon!

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