A Beginner’s Guide To Saving Tomato Seeds Using Fermentation

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Seed fermentation 'Fig 1. Simple Tools'.
Seed fermentation 'Fig 2. Cut them open'.
Seed fermentation 'Fig 3. Squeeze out'.
Seed fermentation 'Fig 4. Knife point'.
Seed fermentation 'Fig 5. Gel colors'.
Seed fermentation 'Fig 6. Gentle scrub'.
Seed fermentation 'Fig 7. Clumps broken up'.
Seed fermentation 'Fig 8. Pour into jar'.
Seed fermentation 'Fig 9. Mark the jar'.
Seed fermentation 'Fig 10. Dehydrator'.
Seed fermentation 'Fig 11. Fungus mat'.
Seed fermentation 'Fig 12. White fungi'.
Seed fermentation 'Fig 13. Mix it up'.
Seed fermentation 'Fig 14. Stir too hard'.
Seed fermentation 'Fig 15. Juice only'.
Seed fermentation 'Fig 16. New mat'.
Seed fermentation 'Fig 17. Water added jar'.
Seed fermentation 'Fig 18. Cloudy soup'.
Seed fermentation 'Fig 19. Gel debris'.
Seed fermentation 'Fig 20. Less debris'.
Seed fermentation 'Fig 21. Almost clean'.
Seed fermentation 'Fig 22. Clean seeds'.
Seed fermentation 'Fig 23. Bleach'.
Seed fermentation 'Fig 24. Last rinse'.
Seed fermentation 'Fig 25. Blot the water'.
Seed fermentation 'Fig 26. Dump onto paper plate'.
Seed fermentation 'Fig 27. Separate seeds'.
Seed fermentation 'Fig 28. Small rejected seed'.
Seed fermentation 'Fig 29. Evenly sized'.
Seed fermentation 'Fig 30. Ready to dry'.
Seed fermentation 'Fig 31. Lots of seeds'.


Ted Maiden, TN (a.k.a ContainerTed)


January 2009

There are a lot of methods of saving these precious tomato seeds – some elaborate and some almost overly simplistic. This document defines a method that uses simple tools, and will be easy to follow, especially for the beginner. Some descriptions of seed saving found out on the forums and on other websites can be, to say the least, intimidating. When you read about “phosphates”, dish detergents, “Oxiclean”, and scouring cleansers, you may have toxicity or environmental concerns. Most of the chemicals suggested are actually very safe to use. However, the dish detergent must have bleach in it, the TriSodium Phosphate is expensive and banned in some states, and Oxiclean can be hard to find.

This method uses only one chemical that is found in the laundry supplies at most homes – standard chlorite based bleach. Any brand name is okay as long as it is chlorite based. There is nothing extra to buy and we all know how to handle this product confidently.

Selecting Tomatoes: Select a tomato that is very well formed. It should be of a good size for that particular variety. You can choose a tomato that is fully ripe or even over-ripe, but as a minimum, one with a good blush of color, especially on the blossom end. It is generally accepted that when the ripening tomato begins turning from green to its harvest color, the seeds are adequately mature and will germinate and produce a new plant. To boost your confidence on this first run-thru, choose a tomato that is free of major blemishes and other serious physical defects. This will give you a good start. With confidence and practice, you will know that those “less than perfect” tomatoes we all get are also good candidates for seed saving.

Seed Size: Let’s get one thing straight.about the size of tomato seeds. In general, there is no hard and fast rule that says small tomatoes must have small seeds and large tomatoes must have large seeds. This is NOT the way to judge your seeds. Sub-Arctic Plenty tomatoes are generally about 2-4 ounces each, yet they have fairly large seeds. Giant Tree (aka Italian Tree) will grow some tomatoes in the 1 to 2 pound range, and the seeds from this one are quite small. What we are going to be looking for are seeds from a variety to tell us what is normal for THAT variety. In other words, we want the tomato to tell us what is the average size for its seeds.

Okay, let’s dispatch all the mystery and uncomplicate the words with some pictures. Step by step, you’re easily going to be very successful in completing this process and, when your first batch of seeds is ready to put away to wait for the next planting season, you’re going to ask yourself why it had always seemed such a mystery before. Now, without further ado, get out your best set of “close-in” glasses and let’s get started.

Gather some tools As you can see in the picture (Figure 1), there aren’t many things needed. A strainer and something to catch the seeds and juice. The bamboo skewers are handy to both stir the fermentation mixtures and to help remove unwanted things (pulp chunks, bad seeds, etc) from the jars before, during, and after the fermentation.

I normally use two glass canning jars – one is a wide mouth pint size and the other ½ pint size. The ½ pint size is used for the actual fermentation. The pint size is used to initially catch the seeds, juice, and gel. The wide-mouth jar was chosen mostly because the strainer fits it. Cherry tomatoes generally will need some additional juice. We’ll discuss later how to get that extra juice. For the larger tomatoes, a small bowl like the one below makes it easy to catch the seeds and juice. Those bamboo skewers you see are very inexpensive - about a dollar for a package of 100 at Wal-Mart.

A couple of rules At this point, a couple of rules are suggested to go by when collecting the seeds into the fermentation jars and when rinsing and finishing the seeds into storage after fermentation.

1. Process only one variety at a time. Trying to do two or more at the same time in the same work area invites stray seeds to find their way into other containers. You can have any number of containers with seeds at various stages in the process, but you should work on only one at a time and carefully clean up the processing area and all tools before starting on the next variety.

2. Any seed that accidentally finds its way into any area you have not cleaned up is not to be returned to the fermentation process. A good rule here is “if it ain’t exactly where it’s supposed to be, then you don’t know for sure what it is and therefore, you don’t want it.” (Someone could have made a BLT and a seed hit fell out and nobody saw it. Then you’re collecting seeds and one slips out of the jar. And the two are side by side. Which is which????)

Cut up some tomatoes and Squeeze out the seeds To be able to get the seeds out easily, cut the tomato around its middle circumference. In Figure #2, my thumb is on the stem end of the little tomato and my index finger is on the blossom end.

The next thing to do is squeeze out the seeds. Hold the tomato halves over the strainer, which is now on top of the larger jar, and squeeze until the seeds bulge out. Then get the seeds into the strainer. Many times, I’ll use the tomato half from one side to “scrape” the seeds loose from the other side and vice-versa.

Another method to get seeds out of the tomato is shown below in Figure 4. Slice the tomato into ½” or ¾” thick slices. Using the point of the knife, break the seeds and their gel casing away from the inside of the locule and let it fall into a small bowl. When done, the contents of the bowl are put into the strainer, which is positioned above the pint jar as shown before. Both of these methods get the seeds and their gel coatings into the strainer, while preserving as much juice as possible.

When you’re done with whatever number of tomatoes you choose to use, you should have something that looks like Figure 5. Note that the “gel” that normally surrounds the seeds comes in different colors. The next picture shows that the gel colors can vary from green to red to yellow to deep reddish-purple. The color is not what's important here. What’s most important is to see that the gel “surrounds” the seeds, encapsulating them. That gel is the primary focus of the whole process. We need to remove that gel as completely as possible without harming the seeds.

Use a gentle mechanical scrub to start breaking up the gel. Keeping the strainer over the large jar or other container, stick one or two fingers into the seed/gel mass and, using firm but gentle pressure, scrub the seeds against the strainer’s screen and break up the larger gel clumps. With a little practice, you'll find that you can “feel” the larger clumps, making it easier to work on them.

While you are scrubbing, more juice will be released from the gel mass and fall through the strainer into the jar. When the scrub is done, your strainer should look something like Figure 7 below. Note that the gel clumps are broken up and the seeds are no longer in clusters. Also, note that there is still a thin layer of gel remaining around each seed. The scrub has made the fermentation job easier by breaking up the thick gel clumps. Also, at this point, you have an opportunity to pick out any undesirable seeds you happen to see.

Pour the strainer contents into the fermentation jar (Figure 8). Make sure you get all the seeds out of the strainer and into the jar. You can use one of those bamboo skewers to help.

Now, pour the juice into the jar and then mark the jar as to what variety is inside and what day you started this batch. Here, in Figure 9, a small “post-it” was used with some scotch tape reinforcement. As a minimum, the info should include the variety name and the date fermentation is started.

Now is a good time to use the strainer to get additional juice from another tomato. This “other” tomato can be of the same or a different variety. Simply squeeze some juice through the strainer and add it to your jar. If you don’t want to use another tomato for extra juice, a very small amount of water can be added, but should not be more than 15% of the total volume. Tap water usually contains chlorine and/or softeners that can retard the growth of the fungi we’re hoping to get started. These fungi will dissolve the remaining gel. Note that the majority of the seeds are starting off at the bottom.

The actual fermentation Okay, it’s time to clean up the mess you created in the kitchen (or where ever) and let the real work begin. Set the jar in a safe place where it won’t be knocked over or upset. Some folks leave off any kind of lid, while some put a loose cover over it. Just don’t tighten anything down. It IS very important to set it into a warm place. A good mean temp would be 75-80 degrees Fahrenheit. During the next couple of days, the fermentation process will be breaking down the gel. You’ll want to stir and/or swirl the contents frequently to insure the mixture is evenly distributed. This also allows you to observe how the gel is slowly but surely dissolving away from the seeds.

Now, most of us don’t believe in wasting anything, and there’s no waste going on here. As toms were cut and seeds were squeezed out, the dehydrator shown in Figure 10 was being loaded with the leftover halves. When this day was done, there were 5 of these trays fully loaded. After drying, you can use a food processor to grind them for soups. Yum!!!

Aromas The fermentation process will produce some odor. But it’s not going to stink up the whole house. The odor comes from the fungi doing the “gel eating”. It also means everything is going just fine. In summer, set it outside. A lid or other cover placed loosely on the top of the container can greatly reduce or eliminate the odor problem in the house.

The speed of fermentation is very dependent on the ambient temperature where the jar is set. In cooler temps, it could take 4 or 5 days, but in warm temps, 2 days will usually be sufficient. Howver, if you suspect canker disease, then make sure the temperature is at or slightly below 70 degrees Fahrenheit to extend the fermentation process to at least 3 days. So, after about 24 hours, the mixture should look something like Figure 11.

If you had to add water to the mix, then it might look closer to Figure 12. Note that some white-ish looking slime has formed at the top of the water level.

Even after stirring, the white slime still shows in the jar. It has been widely dispersed and will return in larger quantities and once again begin forming a “mat” (Figure 13).

I either swirl or stir them in a manner that will break up the mat and/or the slime, and remix the contents of the jar as in the following two pictures. Sometimes I use that bamboo skewer to do the stirring. In the “water added” jar (Figure 14), note the small air bubbles attached to some seeds. This was caused by stirring too vigorously. These bubbles need to be “popped” to allow any viable seeds to drop to the bottom. The bubbles act like “water-wings”, keeping seeds at the top.

And here, the “juice only” jar (Figure 15) also has some bubbles, but they don’t seem to adhere to the seeds. The liquid is noticeably thicker and the seeds seem somewhat uniformly dispersed throughout the liquid.

Give it one more day and you should see something like the Figures 16 and 17. Even with additional stirring every few hours, the contents are quickly forming another “mat” on top of the liquid and some of the seeds seem embedded, while others are at the bottom. Quickly reforming the "mat" is a good sign that the much-wanted fungi is present in strong quantities.

Are we done yet? And, now it’s decision time. Look closely at the seeds on the bottom. If they appear to be reasonably free of the gel, then you are ready to go to the next phase. If not, stir again and wait another 12 to 24 hours and repeat the observation. Don’t worry about some exact time schedule. We’re not counting hours or days. We’re dissolving and removing the gel.

What if? And if you decide to go to the next phase and find out the gel is still not completely gone, all is not lost. The next phase begins with rinses to clear away all the solids that have come loose from the seeds. You can complete the rinses – getting rid of the heavy debris - and then put the seeds into the strainer and gently scrub again to remove more of the remaining gel. Then do more rinses to get rid of debris.

Now, we’re going to assume that everything is okay and the fermentation has done its job. The next phase has more to do with the quality of the seeds you get from your efforts than anything else in this procedure. Keep your patience and don’t get in a hurry. This is your best chance to cull out the bad, non-viable seeds that may be in your jar. This is Quality Control.

The final rinsing and bleach soak to kill any remaining pathogens Besides removing gel, the fermentation process can kill pathogens that may be on your seeds. Bring your stinky jar to the sink and begin with the first of several rinses. As we start, the liquid in the jar is very cloudy as shown in Figure 18 and we really need to see what we’re doing. So, we need a few cycles of “fill and pour” to thin out and clarify the contents of our jar. Fill the jar with cool or cold tap water and WAIT A MOMENT while the seeds sink back to the bottom. Then slowly pour off the liquid while watching the lip edge of the jar to make sure you don’t pour away your seeds. After you’ve poured off about ¾ of the liquid. Stop and refill again with tap water, wait for the seeds to settle back to the bottom and then pour off.

After a few of these cycles, the thick pink liquid will clear up. As the liquid gets less cloudy, you’ll be able to pour off more and more (not the seeds) and, thus, more of the pulp fragments. Seeds are slightly heavier the than pulp and gel and will remain at or near the bottom. Swirling, stirring, or just refilling the jar with water creates turbulence. This stratifies the seeds and the debris into two levels with the undesirable debris on top. Note in Figure 19 that the pulp and gel is now detached from the seeds and can be poured out without those precious seeds following. It might take a few rinses to get the rest of this out.

Now with a few more rinses where you pour off the pulp but not the seeds, you will find less and less pulp and other debris left. You can see this in Figures 20 and 21. Patience is a big winner here. Don't get in a hurry.

During these last rinses, you will also see immature seeds, seeds with blackened areas on them, large pieces of pulp, and other debris that you don’t want. Pour them away, or, if you need to, use something like that bamboo skewer to reach into the jar and simply pull the unwanted item out of the jar. When all this is done, you should see clean, gel-free seeds and nothing else in your jar as in Figure 22.

Into those clean, gel-free seeds (Figure 23), add a mixture of 4 parts water and 1 part standard bleach (with chlorite) to the jar and stir for 2 to 5 minutes. If you add the bleach and water separately directly to the jar, ADD THE WATER TO THE JAR FIRST – THEN THE BLEACH.

Now comes the final rinsing Pour off the bleach solution and rinse the seeds with tap water. Then pour the seeds from the jar into the strainer and begin rinsing with running water (Figure 24). Continue rinsing until the bleach aroma is gone or is only barely perceptible. This should take less than a minute.

Allow the strainer to drip and then use a fresh paper towel to remove any remaining water droplets. It's very important here to NOT use the paper towel INSIDE the strainer in direct contact with the seeds. They have a tendency to stick to things at this point. Touching the outside of the strainer, as in Figure 25, will sufficiently wick away excess water.

Write the variety name and the date on a “cheap” un-coated paper plate and then gently tap the seeds out on to it. Use a corner of that paper towel to carefully blot any larger water droplets from the plate.

At this point, many folks just use their fingers or whatever to spread the wet seeds out, trying to get them to a sinle layer. Then, as the seeds dry, they return and try to break up the clumps. My experience with this method meant a lot of time gently squeezing them between fingers and the plate and whatever. Many time, two or more seeds were stuck together and nearly impossible to separate without damaging one or the other of them. I prefer not to have to make contact between the seeds and bare skin at this wet stage.

Instead, grab that bamboo skewer or other pointed instrument of your choice and start placing the seeds so that they don’t touch one another (Figure 27). BTW, those skewers are great when used as “mini stakes” for young seedling plants.

While separating the seeds, you have an excellent opportunity to cull out any remaining undesirable seeds. You may still see some immature seeds, seeds with black spots or edges, and extremely small seeds for the variety you are working with. Figure 28 shows how the still wet "too-small" seed lightly sticks to the bamboo skewer and allows for easy removal without getting big fingers in there.

The next picture shows a plate with seeds placed. Note that as promised in the text above, Figure 29 displays how the tomato has told us what is a normal sized seed for this variety. Larger seeds are always okay, but seeds that are tiny when compared to the normal size have less chance of producing mature plants.

When they’re all placed, set the paper plate in a location with low-humidity where it will not be disturbed. They will need to remain there for a few days. After two or three days, you can take a credit card or some other plastic straight edge and gently loosen the seeds from the plate. The motion would be similar to scraping soft ice off your vehicle’s windshield. They should come loose easily with only gentle nudging, but cover with your hand, as they may want to fly as they unstick themselves. They should be dry enough now to not stick to each other. Continue spreading them about periodically as they finish drying for a few more days. Figure 30 shows the yield from one "smallish" Cherokee Purple tomato that weighed about 7 ounces.

If you are doing a lot of seeds in the one batch, you will need to place them closer together on the paper plate. I’ve done as many as 1000-1200 on one plate. That many seeds will tend to cover even the ruffled areas of that “cheap” paper plate. The final picture (Figure 31) shows more than 500 Siberian tomato seeds.

Summary Hey, you’ve done it. And, it wasn’t really all that hard to do, was it? Your effort has given you a great bunch of fresh seeds to plant, trade, or give to family or friends. And look at the money you’ve saved on not having to buy additional seeds of the same variety. (What did that retail packet of 30 seeds plus shipping cost?????)

Storing your Seeds All you need to do now is package them for storage. I put mine into small clear ziplock bags, put the ziplock bag into a small coin envelope for more physical protection against bumps and such, and then store in a cool dark place. Many folks store theirs in airtight containers and put them in the fridge or even the freezer. The only problem I see with cold storage is that you must allow the seed container and the seeds to slowly warm up to room temperature before you can open them up. This is to prevent condensation of moisture on the cold seeds. Additional or fluctuating internal moisture content of the seeds themselves will result in greatly shortening the storage life. How and where you store your seeds is up to you. Most properly handled seeds will be viable for 5 to 7 years or more. However, germination rates tend to go down with time.

Testing Germination Most seed savers will want to do a germination test. You can choose seeds now that have been dried or you could take seeds from the final rinse that are still wet. Whatever you decide, take a few seeds chosen at random from your new treasure and place them on a paper towel that has been dampened to almost wet. Put the paper towel with the seeds spread out into a clear plastic bag (perhaps a ziplock) and place in a warm location. After a few days, you’ll be able to see how many have sprouted. And don’t be too quick to judge your germination rate. Many seeds will take an extra day or two or three to germinate. Be patient now and you’ll have a better idea of what to expect at spring planting time.

I hope you have found this document helpful. Good luck and good gardening.

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