Tomato seeds are surrounded by a jelly-like coat that contains a germination inhibiting substance. The coat prevents the seeds from germinating too early so that tender seedlings do not emerge in the fall or winter. A simple way to clean and store tomato seeds is to squeeze out the contents of the tomato and soak it in water, washing away any of this coating that surrounds the seed. You then dry the seeds on a paper towel and store.
But aficionados have a more elaborate method of cleaning tomato seeds that involves fermentation. Fermentation protects the seeds against bacterial canker and is a good way of ensuring that your seeds are disease free.
The process for fermenting tomato seeds is not difficult. Scoop out the seeds and all the pulp and juice into a glass jar. Cover the seeds with water and set the seeds aside, storing at room temperature. Check daily and stir the mixture. After 3 to 4 days, the viable seeds will have sunk to the bottom and the pulp and any poor quality seeds will have floated to the top (they are lighter). Pour off the gunk from the top; strain out the seeds and rinse in a sieve.
Dry on a paper towel and store in a Ziploc bag or plastic container in a cool, dark place. The seeds will stay viable for up to 4 years.
Fermentation is not the only way to control seed-borne diseases. Washing seeds in plain water, in salt water or in hot water (around 122°F) for 15 minutes are all methods for controlling seed-borne diseases.
Remember not to store your F1 hybrids as they will not come true to seed. Your heirlooms are ideal for storing. Most tomatoes are self-pollinating but you do get cross-pollination from time to time. If you want to make sure that your tomatoes don’t cross-pollinate you can create a barrier by covering them with a pollination cage (use a fine mesh screen so that bees will not be able to access your plant) or you can space different varieties at a good distance from each other. There is a difference in opinion on spacing: some say 10 feet is sufficient, others 25 feet and some say for truly pure seeds you need up to 100 feet. For the homeowner, crossing of heirloom seeds should not be a major issue; leave that concern for the grower.