039-How-to Start Seeds Indoors: Digging Deeper, Pt. 3

| Plant, Podcast

Welcome to Part Three of Starting Seeds Indoors: The Non-Negotiables for Success series. Hopefully, you have already enjoyed Part One and Part Two , during which we spoke with Craig LeHoullier to learn the seed-starting techniques he has developed during the past 20-plus years. Parts One and Two provided lots of basic (and in-depth) information on seed starting, transplanting, hardening off, etc. So if you haven’t already checked those out, I highly recommend them.

In this podcast, we dive deeper, with questions for John Porter. As a 3-plus year member, John is still the newest of the esteemed Garden Professors group, and he provides great insight into the academic perspective on all the seed-starting steps we’ve covered in this series.


John Porter

Garden Professor and Nebraska Extension Educator, John Porter shares his seed starting expertise in this Part 3 of our podcast series.


Know What You’re Buying

In Part One, we covered how to determine which plants are best suited to starting as seeds indoors. Once you’ve decided which seed type and variety you wish to start, how do choose from among the different labels? Do you purchase organic seeds? Certified organic? Non-GMO?


assorted seed packets

Seed packets will provide descriptive information such as Heirloom, Certified Organic (USDA or otherwise), or Hybrid.

The terms often used when describing types of seed choices can be a bit confusing. While some terms have a solid meaning, others are subject to interpretation. And others are just marketing magnets. Here are some of the most common terms and what they mean:

Organic – Generated through organic practices, but the producer is not certified. It’s a common misperception that organic equals “no pesticides.” There are some pesticides approved as “organic.” These are typically produced from an animal extract, bacteria extract, or a naturally-occurring element. Lime sulfur is an example of an organic pesticide ingredient.

Certified Organic – Also generated from plants grown organically, but the producer is certified. Certification may be through a state’s Department of Agriculture or through a separate third party. The certification process can be expensive and varies from state to state. Interestingly, there is no watchdog group or overarching certification guidelines.

USDA Certified Organic – Generated under the most stringent and highest certification standard. You can learn more on the USDA website.

Non-GMO – Indicates the seeds are grown from non-genetically-modified plants. This label is a bit misleading. All home garden seeds and plants are, in fact, non-GMO (not genetically-modified).
Typically, the only genetically-modified crops are the big commodity crops – soybeans, cotton, corn, etc. Each type of GMO seed falls under a patent, and producers of them require growers to follow strict guidelines. So if you were growing a GMO seed, you would be well aware that they fall into that category.

Non-organic – Actually, seeds that are not certified as organic, simply omit any labeling as such. The packets are descriptive but absent of any labeling as “non-organic.” Such seeds may have been generated in an environment where synthetic fertilizers, pesticides or other non-organic methods were used.

Now that you understand those different labels, you can make an educated choice. John confirms that seeds aren’t impacted by whether or not their production environment was organic.

I do prefer any of the organic labels when purchasing seeds for my garden. As an organic gardener myself, I like knowing that my seeds are coming from plants grown using organic methods. I also like supporting other efforts to garden organically.

Heirloom vs. Hybrid Seeds

So, what are the differences between hybrid and heirloom variety seeds and plants? The distinctions are pretty simple:

Hybrid plants have been cross-pollinated to try to control and produce specific plant or fruit properties — such as disease resistance or higher sugar content.

Heirloom plants are open-pollinated, where pollination occurs by insect, bird, wind, humans or other natural mechanisms. If properly isolated from other varieties of the same plant species, heirlooms provide seed that is genetically “true to type. They have been grown with the same properties for 50 years or more. Therefore, they have stable genetic traits.

Why does hybrid versus heirloom matter when choosing seeds? Which you choose matters only if you like to save seeds at the end of your growing season.

If you save seeds from the fruit of an heirloom plant, you will grow an heirloom seedling. The heirloom seedling will grow and bear fruit with the same qualities of its parent.

If you save seeds from the fruit of a hybrid plant, those seeds will produce differently than the parent plant. Since hybrid plants don’t have stable genetics, some unexpected or even undesirable traits may reside in the seeds. Perhaps, the fruit won’t be as sweet, or the plant won’t have the disease resistance of the parent plant.

Best Seed-Starting Practices

Using sterile mix is still the best practice for seed starting. Research confirms that sterile mix won’t carry any of the pathogens or diseases which so commonly damage or kill seedling crops.


sterile seed starting mix

Most sterile soilless seed starting mixes are peat based, such as the sample on the right. But in recent years, coconut fiber has become a popular alternative (shown on the left.)


A sterile, soilless seed starting mix is also sterile in terms of nutrients. John confirms that the seeds, themselves, typically contain enough nutrition to carry them through their growth up to the first set of “true leaves” which come after the cotyledon leaves. Not only are supplemental nutrients not necessary during germination, they can make plants more vulnerable to disease.

Roots require oxygen at every phase of their life cycle. If your planting medium is heavy or remains too wet, it creates hypoxia and suffocates – kills – the roots. So, your seed starting mix should be light and fluffy to ensure new roots will have access to the oxygen they need. Soilless mixes are ideal for this.

In the world of soilless sterile mixes – such as peat-based, vermiculite, and perlite – coir-based mix has become increasingly popular. It’s made of coconut hull and is considered more sustainable than other materials. However, there are also drawbacks to coir:

Coir is slower to absorb water.

Coir sometimes contains a high salt content, which can harm your plants.

While coconut hull is sustainable, that benefit is lessened when you consider the distance it must be shipped for processing.

John recommends blending soilless mix types (like peat-based and coir-based) to take advantage of their strengths.

In spite of all the arguments for using a sterile mix when starting seeds, you may be experiencing good results using potting soil, compost or soil blocks. Just remember those mediums do carry more risk to your seedling crop. If you experience problems down the road, a switch to a sterile mix may solve your issues.

Defending Against Plant Disease

When starting seeds inside, we’re keeping their environment humid and, ideally, warm. That’s the best practice for success, but unfortunately humidity + heat = Pathogen spa day.


damping off

These young tomato seedlings are showing early signs of damping off disease. (photo: Stephen Garrett)


Even when you use a sterile mix to avoid soil-borne disease, there are still seed-borne diseases to contend with. Fungi thrive in those warm, moist spots too. Despite our best efforts, disease can still hit your seedling crop.

As an additional precaution against disease, I’ve had a lot of success using a small fan to increase air flow around my seed starts. Think gentle breeze – not gale force. If there is any disease in the air, the air movement will reduce the likelihood of that disease landing or staying on your plants long enough to establish.

Best Practices When Transplanting Seedlings

When seedlings reach transplanting size (approximately 2” high), research confirms that the best transplanting medium is potting soil with some form of supplemental nutrients. Commercial garden soil and potting soil are very different – so watch those bag labels. Never use garden soil for plants in containers at any stage.


potting soil

There are many options for potting soil, also labeled as container mix. The benefit of using this option when seedlings are first transplanted is the supplemental nutrients found in most potting mixes.


For the remainder of the plant’s lifespan, the nutrients provided in most potting soil products and compost will promote healthier growth and reduce the risk of leggy growth.

Consider, too, your container size. Using small containers may require more frequent feeding. Since they hold less soil, small containers hold fewer nutrients. Each time you fertilize, you introduce that disease risk again. Larger containers hold more soil and, thus, fertility; so you don’t have to supplement as much.

Using a commercial soil product with a slow-release fertilizer is always a low-risk option. Adding vermiculite to your compost or potting soil can also reduce risk. Vermiculite is sterile and plays a role in releasing nutrients to the seedling more efficiently.

When transplanting, never pull a seedling up by the stem – be sure to hold and pull only from the true leaves. A plant can grow new leaves, but it only has one stem. Pulling by the stem can break or crush that stem and kill the plant.

To Transplant or Not

Would it be simpler to germinate the seed in a larger pot to hold growth all the way through planting in the garden? That approach has some drawbacks to consider:

How many seeds are you starting? Consider your available space and quantity of materials used. If you’re starting just a small crop, planting seeds directly into larger pots may be feasible for you.
Not every seed you plant will germinate. Your peat pot or other planting material will be wasted on a seed that didn’t survive.
Not germinating in sterile mix puts your crop at risk of disease and suffocation.

Transplanting with Compost

Whether you use potting soil or more sterile mix (or a blend of both), you can add compost to your transplanting medium, but John recommends against planting directly into compost only.


homemade compost

While homemade compost offers valuable nutrients, think twice before adding it to your potting mix for seedlings. Pathogens may still be present which you don’t want to introduce to a sterile soil environment.


If you use home compost during transplanting, be sure your compost pile reached a temperature of around 160 degrees F to kill pathogens which may have existed in your raw compost materials. (130 degrees F is typically recommended when composting, but sustaining 160 degrees F is the safest approach for tender, susceptible seedlings.) If you aren’t sure of your compost source, it’s best to use a commercial product, which will have been processed at that high temperature needed to try to eliminate disease.

I’m a big fan of composting, but I know it can be challenging to keep your home compost pile at that right temperature for the time necessary to kill off all those pathogens. You don’t want the tomato blight that hit a few of your tomatoes last season to make its way into your transplant mix and infect your whole seedling crop. Check out my Compost Guide for some great tips on this and all the information you need to begin or improve your home compost.

Hold on to Your Wallet

Container options are virtually limitless, and you don’t need to spend a lot here. There are great recycled options, and even a cut-off milk carton can be a great, low-cost option.


seedling containers made from newspaper

Options abound for containers for starting seeds. From purchased seed packs to homemade newspaper pots, good drainage is the most important requirement.


The key feature of any container is bottom drainage – make sure that excess water has somewhere to go, so it doesn’t drown your plant. (Poke some holes in the bottom of that milk carton.)

If you are re-using containers season after season, John stresses the importance of sterilizing them before each use.

Wash the container with warm, soapy water to remove as much dirt and residue as you can.

Sterilizing agents won’t sterilize dirty surfaces in the container, so a thorough cleaning is important.

Prepare or purchase a sterilizing agent.

Household bleach is a great sterilizer. Use a 10 percent solution – 1 part bleach to 9 parts water. The chlorine will dissipate during drying and won’t harm your plants.

Household vinegar (5-7% acetic acid), using the same dilution or even a bit stronger, can work but is not as effective.

Horticultural-grade vinegar (20% acetic acid) is not recommended, as it can burn you and leave a residue that may harm seedlings.

Organic options are available and work well, but they can be expensive.

Dip the container into the sterilizing agent, and let it air dry.

Let the planting begin!

What’s Hiding in Your Water

Many gardeners ask me if they should be concerned about additives in their water. Will a fluoride additive harm their plants? Can trace elements in their water negatively affect the soil’s pH balance?

Plants have a remarkable ability to adapt to less-than-perfect environments. John confirms that common additives, such as fluoride and chloride, dissipate so quickly once they hit light and air that they will have virtually no impact on tender seedlings.

If your water has a higher or lower pH level than would be considered optimal, that isn’t much cause for concern either. Plants have natural systems in place which buffer them from pH variation.

Seeing New Light

Grow light technology is exploding, and I hear from many people, asking my advice on the latest trends and developments.


LED Grow Lights over seedlings

New technology using LED grow lights has become a popular way in recent years to replace fluorescent shop lights for home seed starting.


LED lighting is the biggest movement in urban agriculture — primarily due to its energy efficiency. Hydroponic and vertical farming operations are almost exclusively using LED lighting. There are lots of LED options (and price points) for the home gardener too.

I recently ordered a variety of new lighting types — LED, different outputs, etc. — and I’ve begun to put them through their paces to explore differences in performance and growth results. Watch for my frequent updates on Instagram, as I’m sharing my experiences and results throughout the coming weeks.

According to John, grow light research throughout the past several years has proven that plants don’t use all the light in their environment equally. Different compounds within the plants use different wavelengths of light.

White light – what we see with the naked eye — contains every color. Remember ROY G BIV from your school days? White or full-spectrum light contains the wavelengths of all those rainbow colors.

Plants make the most use of the red and blue wavelengths present in white light. Blue light most influences a plant’s vegetative growth. Red light promotes flowering. More recent research indicates that green light enhances seedling growth, and far-red (which we humans can’t see at all) is also useful.


Red and Blue LED Grow Lights

Since plants mostly utilize red and blue light for growth processes, many LED grow lights used commercially and even in home operations are designed this way too. These lights are 45W and cost about $26 each online (photo: Paula Thomas).


Is there a benefit to using exclusively red and blue light, instead of providing plants the full spectrum of white light? Research finds that the differences in growth rate are minimal. The primary benefit is in energy efficiency.

Most large, commercial growers use exclusively red LED, and blue LED for their plants. When growing a large volume of plants, restricting energy use to a system producing just two color wavelengths can add up to cost savings.

For the home gardener, it comes down to the value of energy saved versus the cost of the grow light system.

I found lighting systems that output 600 watts versus the standard 300 watts, but they were also twice the cost. As important, is a real concern of providing too much light. Increased light intensity also means increased heat output, so bigger doesn’t mean better. Plants can overheat, and excess warmth will also dry out your potting medium more quickly.

So far, my lighting research and experience clearly shows that LED lights require a different approach than fluorescents. As mentioned in Part One of this series, fluorescent lights should be placed about an inch above seedlings.


light bleached leaves

A common problem with using LED grow lights is that they are deceptively strong. Placing them too close to tender leaves can quickly cause leaves to fade in a condition known as “light-bleach.” A few of the plants in this photo are exhibiting signs of this.


Before spending time under LED lights, my tomato seedlings quickly became tall and leggy. I placed the 300 watt LED lights approximately six inches from the seedling tops, and after just two days, some seed leaves were already showing signs of over-exposure, also known as light bleaching.

To help mitigate the problem, I raised the lights to eight inches, but within 24 hours, it was obvious that distance was still not enough. Through additional observation and research, I then raised the lights to 25” above the plants. However, light-bleaching was still an issue. I’ve continued to monitor plants and make adjustments.

At the time of this posting (day six under lights), I’ve disconnected one of the two lights, which is currently 20″ above the plants. I’m sure I’ll be going higher still as plants continue to get taller.

If you don’t have the budget for or interest in setting up a more advanced grow light system, remember that you can find success in the simplicity of a basic, 40-watt shop light. Rest assured that you won’t lose much regarding growth by using shop lights or any other full-spectrum light.

Revisit Part One of this series for all the details on lighting basics and Craig LeHoullier’s frugal — and successful — approach.

If you have tried some of these newer grow light options, share your experiences and comments below. I would love to hear what is working for you and may include your comments in my future posts on this topic.

Some Like it Hot

It’s a common misperception that seedlings require lots of light to germinate. What they need is moisture and sterile mix at an ideal temperature.

What is the ideal mix temperature for germination? Seedling germination and the survival rate is highest when grown at around the 75-degree F mark. Even those cool weather crops like kale and cabbage require planting medium at this same temperature for optimal germination.

If the temperature of your sterile mix is much too cool, the seedlings develop more slowly and inefficiently, meaning:

  • They are at greater risk of disease.
  • They may expend the seed’s food stores before producing the cotyledon leaves and first true leaves.
  • Your crop’s survival rate drops.

Keeping your room at 75 degrees F isn’t feasible or efficient. Remember, the planting medium temperature – not the air temperature – is the focus here. So, a heat mat is a great tool to have.


heat mat under seedlings

A basic heat mat can hasten the germination rate of seeds, which leads to less risk of future problems. (photo: Craig LeHoullier)


It isn’t necessary to spend a lot of money on a thermostatically-controlled heat mat. Most basic, inexpensive heat mats generate enough heat for the target soil temperature in the 75-degree F range, and they can perform for years.

Once you transplant your seedlings, remove the additional heat provided by the mat. This stage of growth is best suited to a cooler (55-65 degrees F) environment.

Why do transplants need to be kept cooler? Surprisingly, research shows that temperature has as much impact on the legginess of your plants as does light. The cooler temperature, along with the proper amount of light, sustains a slower growth rate – which means your plants are less likely to become leggy. If your plants do become leggy, be sure to revisit Part Two of this series for easy corrective steps.

Now, I teach a lot more about all of these seed-starting and seedling care topics in my online gardening course, Master Seed Starting. I grew thousands of seedlings over about two years to experiment with various types of soil, fertilizers, grow light options – all kinds of topics that I get questions on all the time. I put it all together in my online course, along with demonstration videos and bonus materials, so you can see for yourself what works, what doesn’t and how you can do all of this. It doesn’t need to cost a lot of money either. In the course, I cover what’s worth the money, and what you can do for less or even free.

When you’re ready to prevent the pitfalls that many seed starters struggle with, I hope you’ll join me in my Master Seed Starting course.

If you haven’t done so already, I really recommend that you listen to my interview with John Porter. John shares some of his gardening experiences, and our discussion will help to drive home the information provided, here, in the show notes. The podcast is linked at the top of this page.

And before I close, a special thanks to Paula Thomas. She’s been my virtual mentor through much of this. So many questions – so little time. Thank you, Paula, for being patient and generous with your LED grow light wisdom and knowledge. If you want to see what Paula is up to, like I do, then be sure to check out her Instagram page. She really is worth following!


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Links & Resources

Episode 037: Starting Seeds Indoors: The non-negotiables for success, Pt.1

Episode 038: How to Start Seeds Indoors: The non-negotiables for success, Pt.2

joegardener Online Academy™  Three popular online courses on gardening fundamentals; managing pests, diseases & weeds; and seed starting!

joegardener Online Gardening Academy Master Seed Starting: Everything you need to know to start your own plants from seed — indoors and out. Relaunching Thursday, January 28, 2021.

The Complete Guide to Home Composting

GGW Episode 402: Seed Starting 101

joegardenerTV YouTube Video: Starting Seeds Indoors

Milorganite® – Our podcast episode sponsor and Brand Partner of

About Joe Lamp'l

Joe Lamp’l is the creator and “joe” behind joe gardener®. His lifetime passion and devotion to all things horticulture has led him to a long-time career as one of the country’s most recognized and trusted personalities in organic gardening and sustainability. That is most evident in his role as host and creator of Emmy Award-winning Growing a Greener World®, a national green-living lifestyle series on PBS currently broadcasting in its tenth season. When he’s not working in his large, raised bed vegetable garden, he’s likely planting or digging something up, or spending time with his family on their organic farm just north of Atlanta, GA.

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