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Why and How to Repot Seedlings

If you start your own seedlings from seed, it’s really important that you understand why and how to repot seedlings.

Imagine…you’ve started your seeds and watched them come up. They’re doing so good! But suddenly, you notice they seemed to have stopped growing. Why? Well, in a healthy seedling, just about as much effort is spent toward developing strong roots as stems and leaves.

One of the problems with starting seeds indoors is that the seedling’s root system sometimes ends up outgrowing the small cell it was started in. This can lead to all kinds of problems, like stunted growth and later issues with fruit production. All because the roots didn’t have enough room to grow early in development! So that’s your “why.”

Let’s cover the “when” of repotting or “potting up” seedlings.

When to Repot Seedlings

You can’t just pot up seedlings any old time. They need to meet a few conditions first.

1. When you start to see trailing roots

If you’re starting your seedlings in a cell tray with a reservoir, eventually when you lift up the cell tray to refill the reservoir, you’ll find that the roots have made their way out the drainage hole at the bottom of the cell and into the reservoir itself.

Once you find this happening, you’ll need to repot them. Why is this time so critical? Because it hints at two bad things that are about to happen:

  1. The seedling’s taproot will get bound up and tangled in the reservoir, making removal difficult and damage much more likely.
  2. The roots that don’t make their way down into the watering hole will wind themselves around and around the cells, resulting in the seedling being “rootbound.”

Now, trailing roots often appear days or even weeks before the plant stops growing. And that’s a good thing! You want to repot before the plant stops actively growing, or it may have trouble recovering.

Real quick though, let’s talk about the terms “taproot” and “rootbound.”

What’s a taproot?

The taproot is the longest, strongest root of a plant. It helps anchor the the seedling. Until a more extensive root system develops, the taproot is the main source of water and nutrients for the seedling. Plants with a long taproot are drought tolerant and often more easy to care for. (Here’s more about the purpose and benefits of a taproot.)

Not all plants rely significantly on a taproot to establish themselves. These plants can withstand damage to the taproot and come out the other side perfectly healthy. But they must be repotted or transplanted before the taproot begins to mature.

If a seedling’s taproot is damaged once it’s begun to mature, the seedling will have to put effort into repairing it, rather than growing taller and stronger. For some plants, if the taproot is too badly damaged, and not enough other roots have developed, the seedling may die.

What’s it mean to be rootbound?

You know how kids outgrow their shoes SO FAST? Secondary seedling roots—the roots that are additional to the taproot—act the same way. They grow really fast, and if they don’t have room to spread out or down, they’ll start circling around and around the inside of the pot.

Eventually, with nowhere for the roots to go, the seedlings will stop growing. This keeps them from getting as big and strong as they can before transplanting them.

2. After the seedling has at least one set of true leaves

Even if you do see trailing roots, it’s best to wait until the seedling has at least one set of true leaves. These aren’t the first leaves that came up when the seedling sprouted—also known as the “cotelydons.” Many cotelydons actually naturally die as the plant matures.

True leaves are leaves that will photosynthesize (not all cotelydons have this ability) and will grow and mature with the plant.

This is an important part of learning how to repot seedlings—you want to make sure your little seedling is up and running in terms of photosynthesis with a set of true leaves before you move it to a bigger pot.

How to Repot Seedlings

On to the process itself!

It can feel a little scary to uproot a seedling from its cozy little cell it was started in. So here are my tips for how to repot seedlings in a way that helps make sure they stay healthy.

  1. Find a dabbler or a spoon to remove seedlings. Many seed starting kits come with dabblers and little shovel-like tools to remove the seedlings from the cells. If yours didn’t come with one, you can totally use a small spoon. You’ll just need to dig carefully, and make sure you do it around the edges. Why not use your fingers? Sometimes cells are too small to really get in there without squeezing the living daylights out of the roots!
  2. Fill the larger pot about halfway with growing medium—I like to stick with seed starting mix just to be safe.
  3. Create a hole for the transplant by digging a few inches into the soil. If you want to plant two seedlings to a pot, you totally can! Just create two holes in the pot, as far away from each other as possible, against the sides.
  4. Use the dabbler or the spoon to remove the seedling from its cell as gently as possible, disturbing the root ball as little as possible. (Turning the cell over often really isn’t an option, since seed starting trays have multiple cells.)
  5. Don’t remove, shake or brush the soil from the roots—the less they’re bothered, the better.
  6. Gently tease seedling roots apart from one another if there’s more than one and they’re a little tangled up. Use the same pressure you’d use to untangle a knot in a necklace. If your seedling is extremely root bound, loosen some of the smaller roots on the outside of the rootball. This will encourage them to spread out in their new home.
  7. Gently set the rootball of the seedling down into the new pot. These 4″ pots are usually big enough for the seedling to live in until transplant.
  8. Lightly pack soil around the stem, making sure the roots are completely covered. Packing soil against the roots signals to them that they’re safe to start growing again.
  9. Water the seedlings in their new, larger pot to help them re-establish their root systems.

Here’s an Instagram video of the process (sorry, it won’t embed in the post for some annoying reason)!

Waiting for roots to re-establish

After you repot your seedling, you’ll probably notice a significant slow down in growth. Don’t worry—this is totally normal!

Whenever you transplant a seedling, even if you’re reeeeeeeally careful, the microscopic root hairs that grow out from each root are damaged. As young as the plant is, it takes a fair amount of energy to regrow them.

Check out these tiny little root hairs on this newly germinated spinach seed!

So you will likely see little to no growth happening in that first week or so after repotting. Just make sure the soil stays moist (but not completely saturated) to encourage rooting. I put my 4″ pots on old cookie sheets and fill the cookie sheet with water so they can continue to be watered from below.

As long as the seedling doesn’t appear to be dying or wilting, it will eventually start growing again.

Need more seed starting help? Check out my online course, hosted by Udemy! You can preview it for free right here.

Handling seedlings can be scary, but these tips for how to repot seedlings can help make sure they stay healthy! Let me know if you find them helpful.

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Wednesday – March 31, 2010

From: Port Lavaca, TX
Region: Southwest
Topic: Butterfly Gardens, Compost and Mulch, Propagation, Transplants, Herbs/Forbs
Title: How to grow milkweeds (Asclepias spp.) for monarch butterflies
Answered by: Nan Hampton and Sean Watson


Mr. Smarty Plants consulted our Nursery Manager, Sean Watson, to answer this question. Here is what he said:

“I start them in the Spring or Summer (they like heat to germinate well). The fresher the seed the better. I just sow them and cover with maybe 1/8 inch of sterile seed starting media (peat based) and keep the propagation tray in part shade. They have long tap roots, so it is better to start them in a deep propagation tray (bulb trays work great, or 5” (or deeper) cell seed starting trays). Keep the media moist until it looks like all have germinated that are going to germinate (they tend to germinate very fast/easily). It is best to not transplant them until the taproot begins to thicken (root swells and begins to harden, starts to become a true taproot). This alleviates a lot of the shock they go through when transplanting. After transplanting (we use a container mix–compost–cut with 25% sand, but can just use straight compost), I water them in immediately, and water them everyday for the next week while they are becoming established into the pot. After 1 week, allow the top 1/2 inch of soil to dry before giving them a little drink, do this for one more weeks (try to avoid flooding them at this stage–except Asclepias incarnata which is a water species and loves water, keep this species wet). Allow them to dry out 1 inch before watering during the third week. After the third week, you can start giving them a little more sun to harden them off. After a week of hardening off, place the plant in full sun and water only once the top inch of soil dries. You want to avoid watering them when they are dormant (just let the rain water them).

Another trick is to bury the seedling up to the cotyledons when you transplant. The cotyledons should rest just above the soil level, not on the soil. This will allow everything below the cotyledon to root out, thus giving your transplant an instantly longer taproot. I have had success transplanting seedlings of different Asclepias species once I see the first set of true leaves (many books suggest this). I usually transplant our seedlings directly into gallon pots to allow room for the taproot. I have had great success with Asclepias tuberosa in this way, and moderate success with Asclepias asperula. We are trying bulb trays this year and I have a feeling if we leave them in these trays longer so they can fully develop a taproot before transplanting, we may have Asclepias coming out of our ears!”

Here are a few photos from our Image Gallery of the milkweeds mentioned above: