Today is a clinic episode, a Seedling Troubleshooting Clinic to be exact, because if you’re starting seeds indoors, something is eventually going to look weird. A tray that was perfect yesterday is suddenly leaning. Something looks fuzzy on the soil surface. Or a seedling that seemed fine just flops over.
The good news is most seedling problems come from a small handful of causes, causes that we can actually control - light, temperature, water, airflow, or sanitation. And once you know what you’re looking at, you can usually fix it quickly or at least stop it from spreading to the rest of your tray.
So, I’m going to give you a simple diagnostic checklist and then we’ll walk through the most common seedling symptoms and what to do about each one.
Let's dig in!
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Just Grow Something episodes, videos and blog posts on seed starting: https://justgrowsomethingpodcast.com/search/seed%20starting
References and resources:
University of Illinois Extension: Troubleshooting seed starting problems: https://extension.illinois.edu/blogs/good-growing/2022-02-25-whats-wrong-my-seedlings-troubleshooting-seed-starting-problems
University of Minnesota Extension: How to prevent seedling damping off: https://extension.umn.edu/solve-problem/how-prevent-seedling-damping
Utah State University Extension: Seedling culture, airflow, temps: https://extension.usu.edu/yardandgarden/research/starting-vegetable-seeds-indoors-seeding-culture-and-transplanting.pdf
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00:00:00
Today is a clinic episode. A seedling troubleshooting
00:00:04
clinic, to be exact. Because if you're starting seeds
00:00:07
indoors, something is eventually going to look weird.
00:00:12
A tray that was perfect yesterday may suddenly be
00:00:14
leaning. Something might be looking fuzzy
00:00:17
on the soil surface, or a seedling that seemed just fine
00:00:21
just flops over. Here's the good news.
00:00:24
Most seedling problems come from a small handful of causes.
00:00:29
Causes that we can actually control light, temperature,
00:00:33
water, airflow, or sanitation. And once you know what you're
00:00:38
looking at, you can usually fix it really quickly, or at least
00:00:41
stop it from spreading to the rest of your tray or happening
00:00:45
again if you caught it too late. So I'm going to give you a
00:00:48
simple diagnostic checklist and then we'll walk through the most
00:00:52
common healing symptoms and what to do about each one.
00:00:57
Welcome back to Just Grow Something.
00:00:58
I'm Karen Velez, farmer, horticulturist, plant nerd, and
00:01:02
I am taking the guesswork out of growing your own food with
00:01:04
practical research backed steps that work in real life.
00:01:08
As always with today's episode, I will include resources in the
00:01:12
show notes for diagnosing seedling problems so that you
00:01:15
can go as deep as you want later on.
00:01:18
All right, clinic is open. Let's dig in.
00:01:25
So before we talk fixes to your seedling problems, we need to
00:01:28
diagnose. When you see a problem going on
00:01:32
in your seed starting area, I encourage you to pause and run
00:01:36
these six questions. Question number one, what stage
00:01:40
are we in? Are we pre germination?
00:01:43
Are these newly sprouted plants with just their first cod
00:01:47
leadens their seed leaves or do we have true leaves already on
00:01:51
the plant? This matter because the usual
00:01:54
suspects are going to change depending on the stage of plant
00:01:58
growth. Question 2 would be is it
00:02:00
happening in one cell or one container or is it happening to
00:02:05
the whole tray? One or two cells often points to
00:02:09
either a problem with seed quality or maybe planting depth
00:02:12
or just a localized watering issue.
00:02:15
An entire tray, however, usually points to something in the
00:02:20
environment, so either the light or temperature or watering
00:02:23
patterns are off, or a disease that is favored by those
00:02:27
conditions. Question #3 is it fast or slow?
00:02:32
Is what happens to your seedlings happening very, very
00:02:35
quickly, or is it taking some time?
00:02:36
So if seedlings collapse like in 24 to 48 hours, then we might be
00:02:41
thinking this is a disease or maybe a severe water or oxygen
00:02:46
stress. But if it's slowly getting worse
00:02:49
over a week or two, then we're probably leaning more towards a
00:02:53
light issue or a problem with nutrition or chronic watering
00:02:57
issues. Question 4 is what's the light
00:03:00
setup? Be specific.
00:03:02
Are your plants in a window? Is it supplemented with grow
00:03:06
lights? Is it only grow lights?
00:03:08
How many hours of lights are they getting per day?
00:03:11
How close are the lights to the seedlings?
00:03:14
Natural window light is often not enough for really sturdy
00:03:18
ceilings, and low light is a major driver of stretching, So
00:03:22
if this is what you're seeing, it likely might be part of the
00:03:25
light problem. Question 5.
00:03:27
What's the temperature, Especially after germination?
00:03:30
A lot of gardeners are going to keep their seedlings too warm
00:03:34
after they sprout, so warmer than recommended temperatures
00:03:38
for growing on your plants after they sprout can actually
00:03:40
contribute to spindly growth and some other issues.
00:03:44
And then question 6 would be how wet is the seed starting mix or
00:03:49
your potting mix and how's the air flow?
00:03:52
So moist and wet are not the same thing.
00:03:55
Seedlings need water, yes, but they also need oxygen at the
00:04:00
root zone. So if your seed starting mix or
00:04:02
your potting mix stays saturated, the roots are going
00:04:06
to struggle and that also increases your disease risk.
00:04:10
Also, if a humidity Dome is still on after germination, that
00:04:15
can trap moisture and reduce the airflow.
00:04:18
So we really do recommend removing domes once a
00:04:23
substantial portion of your seeds have germinated and then
00:04:26
using some gentle airflow to deter fungal problems.
00:04:31
So keep those six questions sort of in your back pocket.
00:04:35
And now we're going to tackle the most common problems.
00:04:39
So the first problem we might see in our seed starting area is
00:04:42
seeds that aren't germinating at all or germination is very
00:04:47
uneven. So if the seeds aren't popping
00:04:49
or only a few cells germinate, then I want you to sort of think
00:04:53
in this order. The first thing would be the
00:04:56
temperature. Most garden seeds germinate with
00:04:59
a soil temperature around 65 to 75 Fahrenheit.
00:05:02
Some of them like it warmer. There are some cool season crops
00:05:06
that can start when it's much colder.
00:05:08
But if your seed starting space is chilly, a heat mat can help a
00:05:12
lot with this. It will raise the temperature at
00:05:15
the soil level by anywhere from 5 to 10°F.
00:05:19
You know, if you're worried about this, you can pair it with
00:05:21
a thermostat so that you're not overheating the mix and not like
00:05:24
cooking the seedlings. But This is why we have seedling
00:05:28
seedling heat mats that are specific to starting seeds.
00:05:32
And we're not using something like, you know, a heating pad we
00:05:34
would use for us, right? So temperature could be your #1
00:05:38
hidden issue in terms of it's not germinating or the
00:05:41
germination being uneven. The second might be moisture and
00:05:45
oxygen. Again, seeds do need consistent
00:05:48
moisture, but a waterlogged mix is going to limit the oxygen and
00:05:54
actually encourage rot. We don't want seeds sitting in
00:05:59
water consistently. The goal is evenly moist, not
00:06:03
swampy. Your third concern might be
00:06:05
planting depth. A very simple rule of thumb is
00:06:10
to plant the seeds about twice the width of the seeds.
00:06:15
So if you your seed packet doesn't tell you how deep you
00:06:18
should be planting, that is a really good rule to go by.
00:06:20
If you put the seeds down too deep, that is going to slow the
00:06:24
emergence and it's also going to increase the stress of that
00:06:27
little plant as it's trying to pop out of its seed coating.
00:06:30
If you plant too shallow, then that seedling can dry out or the
00:06:34
seed itself can dry out and it won't end up germinating.
00:06:37
So we really want to go for like a happy medium there.
00:06:40
Twice the width of the seed is the general rule of thumb.
00:06:44
And then the fourth thing would be the seed quality and its
00:06:46
storage. I mean, old seed or seed that
00:06:49
has been stored where it's really warm or really, really
00:06:52
humid sometimes is going to be less reliable.
00:06:56
So if one variety that you planted sort of fails to
00:07:01
germinate or doesn't germinate very well while the others are
00:07:04
thriving under the same condition, then I would suspect
00:07:07
that it's an issue with the seed.
00:07:09
So if you think temperature is the culprit, then adjust the
00:07:12
warmth at the mix level, not just the room.
00:07:15
If you think moisture is the culprit, then we want to do sort
00:07:19
of the same thing that we do with our plants.
00:07:21
We want less frequent, more thorough watering.
00:07:23
So we want to water thoroughly and then allow that surface to
00:07:26
dry out before we water again. Problem #2 would be leggy,
00:07:32
stretched or leaning seedlings. Leggy seedlings.
00:07:36
These are the seedlings that are really tall and really thin and
00:07:40
sort of leaning over. These are one of the most common
00:07:44
seed starting frustrations and the most common cause of this is
00:07:49
insufficient light. So low light is the driver of
00:07:54
seedlings just sort of trying to stretch towards the light and
00:07:57
that causes the stems to weaken and then of course the plant is
00:08:00
going to struggle to support itself.
00:08:02
So in order to have enough light, oftentimes we are going
00:08:07
to need some supplemental lighting.
00:08:09
Windows are going to rarely provide enough intensity or
00:08:13
light duration to really get nice stocky ceilings.
00:08:18
If you're going to use supplemental light, then you
00:08:21
want the seedlings about a couple of inches beneath those
00:08:25
fixtures, so 2 inches difference between the top of the plant and
00:08:30
the light. So you're going to have to
00:08:32
continue to raise the light up as those seeds or those
00:08:35
seedlings get taller. And we want to provide sometimes
00:08:39
as much as 12 hours of daylight on up to even 16 hours per day.
00:08:45
And then after your seedlings germinate, we want to avoid
00:08:49
keeping them very warm because those higher temperatures can
00:08:52
actually contribute to that spindly growth.
00:08:54
So once everything in your tray has started to sprout or the
00:08:57
majority of them have sprouted, then make sure that you are
00:09:00
removing them off of any heat mat and that will help prevent
00:09:04
them from getting too hot. But you also have to look too at
00:09:07
your your air temperatures. Also, a lot of times they like
00:09:10
to grow in cooler temperatures than what they sprouted in.
00:09:14
So if your seedlings are leggy, you want to move the lights
00:09:17
closer. We don't want them to scorch the
00:09:19
foliage, so don't make them touching, but a couple of inches
00:09:21
off of the foliage is good. We want to increase the duration
00:09:25
of the light so it's a consistent more day length, so
00:09:29
12 hours or so on up to 16. We want to drop the post
00:09:33
germination temperature just a little bit.
00:09:35
A lot of these veggies are going to do better with cooler nights
00:09:37
and more moderate days after sprouting.
00:09:40
And then add some gentle airflow.
00:09:43
A little fan is perfect for in your seat starting area.
00:09:46
We're not trying to create like a wind tunnel or anything, but
00:09:49
we want some intermittent airflow.
00:09:50
So I will generally use an oscillating fan just to kind of
00:09:55
simulate what they would experience if they were outside.
00:09:58
And that's going to help those seedlings grow more sturdy.
00:10:00
Problem #3 seedlings collapsing at the soil line.
00:10:05
So if your seedling looks fine and then suddenly the next day
00:10:09
it has completely fallen over, especially if you see a very
00:10:12
thin, pinched or rotted looking stem right at the soil surface,
00:10:17
this is damping off disease. This is caused by a fungus or a
00:10:22
fungus like Organism that thrives in cool wet conditions
00:10:28
and it is most common in very young seedlings.
00:10:31
So the risk of damping off happens when the surface is very
00:10:38
damp and there is low light. You might have high salt content
00:10:43
for if you've been fertilizing your seedlings, which you
00:10:45
probably don't need to be doing yet at this stage.
00:10:48
And very cool soil temperatures all associated with increased
00:10:52
problem from damping off disease.
00:10:54
And with with damping off, really it is all about
00:10:57
prevention because once seedlings collapse, that's it,
00:11:01
they're done, they are not going to recover.
00:11:03
So your goal is to prevent this from happening.
00:11:06
And if you see this happening, your goal is to prevent it from
00:11:09
spreading and you want to sort of reset those conditions.
00:11:12
So the number one thing here is if you have had damping off in
00:11:18
seasons before and you reuse your trays, you likely are going
00:11:23
to want to sort of clean and disinfect those trays or
00:11:26
whatever your seed starting materials are.
00:11:29
So you're going to wash off all of your soil and stuff and then
00:11:32
sanitize the containers in a 10% bleach solution and then just
00:11:36
let them air dry? I am not a huge stickler for
00:11:39
this type of sanitation. Just as a matter of routine.
00:11:43
If you haven't seen problems, then I'm not so worried about
00:11:46
it, right? If you really want to be sure
00:11:49
that you're preventing problems, then yes, absolutely you would
00:11:51
do this every single year. But if you have seen damping off
00:11:54
or anything else, then this is the first.
00:11:57
Your first line of defense is to sanitize those trays at the end
00:11:59
of the season before using them again next year.
00:12:02
Your second thing would be to make sure that you are using a
00:12:05
clean, fast draining seed starting medium.
00:12:08
We never want to use garden soil indoors.
00:12:10
It is too dense. It can carry pathogens, not to
00:12:13
mention weed seeds. If you use a regular potting
00:12:17
soil soil, that's fine so long as it is fine enough to be able
00:12:21
to drain really, really well. And there aren't that many
00:12:24
potting soils out there, regular potting soils that I would ever
00:12:27
recommend for seed starting. The pro mix that I use is one
00:12:31
that I would absolutely recommend.
00:12:32
Other than that, you might be better off using a soil less
00:12:35
medium that just drains very, very well.
00:12:38
We're trying to avoid that excess moisture, and these
00:12:42
pathogens thrive when it is cool and wet.
00:12:46
So we want to keep that mix moist, but we don't want it
00:12:49
saturated all the time. And so we want to make sure that
00:12:52
if we're using humidity domes to help sprout things, that we want
00:12:56
to remove those domes after a substantial portion of those
00:12:59
seeds have germinated. And then again, use some gentle
00:13:02
airflow because not only is that good for the seedlings, but it
00:13:05
also helps to dry that soil surface and that is going to
00:13:08
deter that fungal growth. The other thing too with air
00:13:13
movement is we want to sort of avoid overcrowding the
00:13:17
seedlings, right? So not only are they not going
00:13:20
to get as good of air movement if they're too close together,
00:13:23
but that also is going to reduce the light exposure when they are
00:13:27
crowded. So, you know, you're reducing
00:13:29
airflow, you're increasing those favorable conditions for
00:13:33
dampening off, not dampening, damping, damping off.
00:13:37
And so, you know, if you've got some really dense plantings, you
00:13:40
might need to thin those out just to prevent damping off from
00:13:43
happening. So stop if you see it happen,
00:13:46
right? If you suspect that damping off
00:13:48
is starting, stop over watering immediately.
00:13:50
Let everything dry out really, really well.
00:13:52
Increase your spacing in your airflow.
00:13:55
Remove and get rid of any of the plants that were affected in the
00:13:59
cells that they were in. And if it's widespread, then
00:14:03
make sure that you sort of, you know, make sure that you are
00:14:06
sanitizing your equipment and you might have to actually
00:14:08
restart if you starting to lose all your seedlings, start over
00:14:11
again, sanitize that equipment, get some fresh medium and plant
00:14:15
again. Problem #4 would be yellowing,
00:14:19
pale, scorched or spotted leaves.
00:14:23
This category can be really tricky because multiple
00:14:28
stressors can look very similar to each other.
00:14:31
But we can still troubleshoot this logically and we want to
00:14:33
start with the basics and that is water and roots, uneven
00:14:38
watering or over watering or extreme drying out, right?
00:14:42
These are very common sealing problems.
00:14:44
And so the goal is to supply the plant roots with water and
00:14:51
oxygen. So we don't want overly
00:14:54
saturated containers because that can actually stop root
00:14:56
growth and favor pathogens. And any one of those things can
00:15:00
cause a description that I just talked about yellowing leaves or
00:15:03
pale or scorched or spotted leaves, right?
00:15:05
So you know the same thing with our seedlings, the less
00:15:08
frequent, more thorough waterings.
00:15:09
If you are somebody who prefers to bottom water your seedlings
00:15:13
because it seems like the plants will just take up what they
00:15:16
need, that's fine. But that water should not be
00:15:20
sitting in that bottom container at all times.
00:15:24
That is too much water. So as soon as the soil surface
00:15:28
is damp, you can see that it's taken up enough water.
00:15:31
You need to be dumping those trays and not let that water sit
00:15:33
there and not add any more water back into those trays until
00:15:37
again, the soil surface is dry. So it doesn't matter if you're
00:15:40
watering from the top or you're watering from the bottom, the
00:15:42
condition should be the same. The next thing is to carefully
00:15:47
consider your nutrition. Many potting mixes contain
00:15:52
enough fertility to carry seedlings for about 5 to 6
00:15:56
weeks. This depends on what it is that
00:15:58
you're using. If you're growing seedlings for
00:16:02
longer than that, or if you are using a soilless medium that
00:16:08
does not contain any fertilizers, then you may need
00:16:11
to use a soilable fertilizer of some sort to feed your
00:16:16
seedlings. But young seedlings are very
00:16:18
easily damaged by too much fertilizer.
00:16:21
So my recommendation is whatever your normal consistency is or
00:16:27
your normal ratio is that you use for your fertilizer, do half
00:16:32
that with your seedlings. So 50% of what you would
00:16:35
normally use if you were using it for a regular plant outdoors
00:16:40
just to get them through until they're getting ready to be
00:16:42
transplanted outside. So if your leaves are pale and
00:16:46
your growth is sort of stalled and the seedlings are older than
00:16:50
a month, then consider a a light feeding of some sort.
00:16:56
And then problem #5 would be moldy surfaces or fungus gnats
00:17:03
or seedlings that don't survive when you finally put them
00:17:08
outside. This is sort of a rapid fire
00:17:10
little thing here. So if you're seeing like white
00:17:13
or silvery growth on the soil surface of your plants, this is
00:17:18
commonly an indicator of overly wet growth medium.
00:17:21
Same thing goes if you're seeing sort of a green fungus that's
00:17:24
growing across. This may not be instantly
00:17:27
harmful, but it does signal that conditions may be right for
00:17:32
damping off risk. So you likely want to adjust
00:17:35
your watering at that point and increase the air movement a
00:17:38
little bit if you're getting fungus gnats.
00:17:41
These guys thrive in constantly moist media.
00:17:46
Again, we want to let the surface dry more between the
00:17:49
waterings. You can also with fungus gnats
00:17:52
use yellow sticky traps so that you can monitor and capture the
00:17:55
adults. There are some extension
00:17:58
resources that talk about using BTI as an option for like larvae
00:18:02
management when you use it according to the directions.
00:18:04
I prefer just to water with a solution of hydrogen peroxide
00:18:10
and water to kind of get take care of the egg situation in the
00:18:14
soil if I ever have them. But ever since I really started
00:18:17
paying attention to my watering practices and making sure that
00:18:21
that moist that that that media was not moist all the time, I
00:18:24
have not had a fungus gnat problem.
00:18:26
And my seed starting area, I mean, I grow thousands of plants
00:18:31
every year and I don't have a problem with fungus gnats
00:18:33
anymore. So that would be my
00:18:35
recommendation. Really start with letting the
00:18:38
surface dry out and then go on from there.
00:18:41
And then if your seedlings are having problems when you get
00:18:43
them outside, that is 100% a hardening off problem.
00:18:47
If you managed to get your seedlings growing and they
00:18:50
looked nice and healthy when they were inside, and then you
00:18:53
got them out into the garden and all of a sudden they died, that
00:18:57
means they got too much sun or too much wind or a temperature
00:19:00
swing way too fast. The hardening off process should
00:19:04
take you about 7 days, sometimes as long as 10 days, starting
00:19:08
with short periods outdoors, like in the shade and then
00:19:11
gradually increasing the time and the sun exposure while still
00:19:16
being protected from major wind gusts until they finally sort of
00:19:20
are acclimated to being outdoors before you put them out in their
00:19:24
final place. Another thing that I recommend
00:19:26
with this is also backing off of the amount of water that they
00:19:29
get during that seven day period.
00:19:31
So they've gotten used to being sort of pampered in their little
00:19:35
seed starting area, right? And now you got to put them out
00:19:38
into the harsh world of the actual garden.
00:19:41
And they need to be prepared for that.
00:19:43
And you're not going to be hovering over them every single
00:19:45
day, giving them water as soon as the soil surface dries out.
00:19:49
I mean, if you are, then we have to have another conversation,
00:19:52
OK. But you know, that should be
00:19:55
part of your hardening off process is backing off how
00:19:57
frequently you're giving them water to get them used to those
00:20:00
conditions out in the garden. So if you take nothing else from
00:20:07
today's seedling troubleshooting clinic, then take this.
00:20:12
Most seedling problems are not true mysteries.
00:20:16
They are predictable outcomes of light, temperature, moisture,
00:20:22
airflow or sanitation. And once you adjust those
00:20:26
things, then your seedlings are usually turn around really
00:20:29
quickly. And if you didn't get to them in
00:20:31
time, at least you can know how to prevent it from happening
00:20:35
again next time. If you want a step by step
00:20:38
system for indoor seed starting from choosing a setup to timing
00:20:43
to lighting to keeping seedlings healthy all the way to
00:20:46
transplant day, my Seed to Sprout course is built exactly
00:20:50
for that. It is quick, it is practical,
00:20:52
and it is designed to prevent the problems that we talked
00:20:56
about today before they even start.
00:20:58
You can find it at justgrowsomething.com/courses or
00:21:03
I will also leave a link to that in the show notes.
00:21:06
Until next time, my gardening friends, keep on cultivating
00:21:08
that dream garden, and we'll talk again soon.