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  • Writer's pictureWes Hepker

Seed Starts: Indoor Germination - Part One

Updated: Mar 29

Welcome to part 1 of 2 covering our seedling chamber. Let's dive in.


We use Bootstrap Farmer’s 1020 Heavy Duty Trays. They are durable and reusable. The best feature is their rigidity. They can be picked up and moved with one hand without the tray bending or cracking.

Tray Insert

Depending on the seedling, we plant directly into a seed starting tray insert or might use the insert as support for mini pots. Onion seeds can go into 200 cell inserts and tomatoes start out in 2.5 inch pots with corresponding support inserts.

The most important aspect of the inserts is uniformity. Any insert must fit into a 1020 tray to maximize efficiency. Speed was not important when we were starting out with our hobby garden, but as we ramp up to caring for hundreds or thousands of seedlings compatibility is important.


We moved away from the typical 6 pack seedling plug trays in recent years. They just produced too much trash and often started to crack before the plants were big enough to be transplanted. We have used and reused a lot of 2.5 inch pots over the years and like the vigor of the seedlings we transplant from the bigger pot. Recently, reusable 6 pack plug inserts have become available and we’re giving them another shot this year.

In our example from above, the tomato seedlings will be up-potted from their 2.5 inch pots into 5 inch pots before being hardened off and transplanted. The same protocol is used for other larger, full season plants like peppers and eggplant. Smaller, cool weather starts like lettuce and cabbage skip up-potting and head to the greenhouse or low tunnel for hardening off when they are ready.


The use of a well-timed humidity dome is an important accessory for maximizing seed starting. Seeds must maintain consistent moisture levels to germinate. We use clear humidity domes with adjustable vents for most of our trays. The dome remains closed until we see the first sprouts at which time the small vents are opened. When the trays reach close to full germination, the dome is removed. While seeds want to be wet, sprouts do not. Restricting air movement over young sprouts is asking for mold and fungus trouble.

We also use blackout humidity domes for a few plants that like to germinate in the darkness. One of our favorite examples is the flower Calendula. The blackout dome allows us to leave the grow lights on while keeping select trays in the dark.

Grow Media

On the advice of other growers, we started using Pro-mix BX Mycorrhizae Plus Biofungicide this year. Using a clean, soilless grow media with plant starts is very important. The environment inside the seedling chamber is ideal for growth of young plants, but also mold. We’re careful not to introduce contamination whenever possible.

We also started using perlite as a seed cover this year. The theory being perlite allows the grow media to maintain proper moisture levels under the seeds, but lower moisture levels and light at the top of the grow media where fungus can take hold. Additionally, and perhaps more importantly, sprinkling perlite on the seeds is just faster than using the grow media.


We are careful not to allow the seedlings to dry out or become saturated with water. Plants need moisture and air infiltration at their roots to maintain health and vigor. Fresh clean water at proper intervals is critical and one of the processes in the seedling chamber that is less automated. Light and temperature is mostly set it and forget it. Watering timing is more random and requires daily attention.

We use reverse osmosis (RO) in our seedling chamber as it is the cleanest water readily available. The initial cost for an RO system is fairly high, but this ensures we’re using pure water and not introducing mineral or pH imbalances into our seed starting system.


Seeds have everything they need to get started as soon as the conditions for germination are met. The seedling chamber provides the proper light, temperature, and humidity balance for germination. Nothing else is needed. In a few days, you see cotyledons which are also known as ‘seed leaves’. It’s a little different in a plant like onions, but most vegetable seedlings have two seed leaves.

The next set is known as ‘true leaves’. These leaves can perform photosynthesis and require a growth media with nutrients to function properly and produce more plant material.

We use Bonide’s Root & Grow root stimulator and plant starter in our seedling chamber as soon as we see true leaves. One dose does the trick during the seedling stage. We’ll add in additional nutrients as we up-pot and transplant.

Stop back soon...

That concludes part 1 of 2 of our seed starting set up. We’ll be back next time to cover the stand, reflective cover, heatmats, lights, and ventilation.

Note: As an affiliate of Boostrap Farmer, we earn a small commission from qualifying purchases through our affiliate links. Thanks for your support!

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