Seed Starting Medium

A common suggestion in the gardening industry is to use a sterilized, low-nitrogen mix when germinating seeds. Is this recommendation warranted? I wanted to provide an introductory article on this topic. It’s certainly an interesting one. Here goes.

First, it’s important to make sure we’re talking about the same things. When people talk about soil, they’re usually just referring to whatever squishy stuff you grow plants in. A more technical term is substrate, because the term ‘soil’ typically refers to the stuff you find in the ground (which has a high amount of clay, silt and sand, not to mention organic matter and microbes). When you buy a bag of potting mix, for example, it’s likely a mixture of organic matter (like peat moss or coconut fibre), fertilizer, compost and possibly real soil. We would call all of that a ‘substrate’. Alternatively, a substrate could simply be peat moss. In the real world (i.e., outside world), the soil below is a mix of all kinds of wonderful things and resists simplification.

When people talk about sterilized soil, this refers to a substrate that’s been treated in a way where all microbial life forms are killed – including bacteria, fungus, and small insects (and their eggs). The most common way soil is sterilized on a commercial scale is to treat it with high temperature (such as steam). Basically, the organic matter is still present, but there aren’t any microbes. In theory, this is done to prevent fungal diseases down the road (such as damping off). More on this later.

Another term we should define is soil (or any substrate) being referred to as nutritious, which is not very well defined. Plants need certain nutrients in very high quantities but which can vary in quantity depending on the substrate. Nitrogen, phosphorus and potassium (NPK) are the most needed after CO2 and oxygen, and the king of these is Nitrogen. Potassium and phosphorus are rarely deficient in any soil, and which are mostly donated from rock minerals (i.e., sand and rock debris). Almost always, when a growing substrate is called ‘nutritious’ this usually means that it’s particularly high in nitrogen (and its other nutrients are assumed to be relatively sufficient). Nutritious soil is therefore high-nitrogen soil.

Nitrogen is the most special of all plant nutrients because it is cycled through the entire ecosystem. It is floating in the atmosphere as a gas, fixed into the soil by various soil microbes, taken up by plants – eaten by animals – and then returned again to the ground through decomposition and animal droppings. It is also very mobile – and can get washed away with heavy rain. It is a fleeting nutrient.

Forests are high in nitrogen because they cycle so much of it – the large trees overhead collect a lot of nitrogen and then drop it all to the ground in the autumn. Grasslands are also fairly nutritious in nitrogen because they’re constantly letting their above-ground parts die back in autumn, which returns nitrogen back to the soil. Some ecosystems, such as deserts, have much lower nitrogen in the soil. But they all cycle nitrogen.

This might shock you to hear, but soil is a very complex thing. Real soil, that is. The more we uncover, the more complex is our understanding of soil. There are quite possibly more inter-connections and inter-relationships among nutrients and microbes than we will ever fully uncover. Both nitrogen and microbes play a crucial role in both the germination of seeds on soil – and the health of the growing plants.

Nitrogen is, of course, almost always present in the world as as molecular compound – often as some form of nitrate or ammonium/ammonia. Animal urine contains urea, which when soaked into the soil is broken down very quickly into nitrate (called nitrification). This is done in the presence of oxygen by specific soil bacteria. Most plants prefer nitrate as their source of nitrogen. (Ammonia is more of an in-between compound.)

It is often suggested that in order to germinate seeds, the gardener should use a low-nitrogen substrate. These are typically referred to as ‘seed germination mixes’ and are quite expensive to purchase. Especially in the 1980’s onwards, garden centres and gardening experts began promoting such low-nitrogen mixes for germinating seeds because it was thought that they would reduce fungal diseases.

There’s some credibility to this idea, but not much.

First, this idea came from emerging studies in the 1970’s and 1980’s where high nitrogen substrates were shown to have a higher mortality from damping off. (Damping off is a disease where seedlings start to fall over and look like they’ve been choked by a fairy, and it’s caused by various pathogens such as Rhizoctonia or Pythium.) For example, a study by Gladstone and Moorman (1989) found that 7-week-old Pelargonium seedlings were dying a lot more if they were fed a high nitrogen fertilizer (compared to low nitrogen fertilizer). Other studies found similar findings. At the time, even Norman Deno suggested that low-nutrition and sterilized media were important in ensuring the germination of seeds (Deno, 1993). (It’s quite possible he could have achieved higher germination, however, had he tried germinating on real soil.) But, these studies often used very high nitrogen levels – much higher than what you’d find in commercial potting mixes.

Commercial greenhouses are rampant for fungus problems, however, and a lot of commercial nurseries started using biochemical agents to help control the fungus. Also, it was observed that if seeds were started in a soil-less substrate (e.g., peat moss or coconut coir) without any compost or soil – as well as including various biochemical agents – that damping off was very well mitigated. It became the common practice for commercial nurseries, therefore, to use soil-less mixes and spray with fungicides. This became the norm.

Also, while I wouldn’t want to imply any evil intentions, it is certainly true that soil-less, sterilized, low-nitrogen bags of substrate can be sold for a lot more money than the natural alternative. (Where there’s smoke, there’s fire?)

Nitrogen isn’t just a building block used for making leaves and stems. Nitrogen is actually a signal molecule controlling various aspects of plant development – including seed dormancy (Duermeyer et al, 2018; Osuna et al, 2015; Alboresi et al, 2005; Liu et al, 2022). Alboresi et al (2005) suggests that nitrogen also plays an important role in the breakdown of a chemical called Abscisic Acid (ABA) which is largely responsible for keeping seed in a dormant state.

One of the most common nitrate salts is, of course, potassium nitrate (KNO3) – and which has been shown in countless studies to increase the germination of seeds. For example, a study by Ali-Rachedi et al (2004) demonstrated this with Arabidopsis seeds. It’s a commonly accepted fact in seed ecology that nitrate promotes germination of most perennial seeds, especially those which are dormant (Liu et al, 2022).

It’s also an interesting observation that if a mother plant has adequate nitrogen in the soil when she’s developing her seeds, that these seeds can exhibit lower levels of dormancy (Alboresi et al, 2005). It’s also been observed that rice seeds that have higher nitrogen content (in the seeds themselves) have a faster and higher germination (Hara and Toriyama, 1998). There are quite literally thousands of published studies showing potassium nitrate having a promotional effect on germination.

If a growing medium has very low (or zero) nitrogen in it, it will almost certainly lower germination. It is thought that nitrogen plays an incredibly important role in destroying dormancy and also promoting germination, likely through increasing biomolecular levels of ABA and GA in the seed itself (Hernández et al, 2021). An easy example to digest is a study published by Pill and Morneau (1991) who found that tomato seeds germinated at a significantly faster rate – and to a higher germination – if potassium nitrate was used. There are hundresd of other studies along these lines.

There’s a catch though. Modest amounts of nitrogen have quite definitively shown to improve germination of plant seeds (especially perennial plant seeds) – but it has to be in reasonable amounts. If an inordinate amount of nitrogen is present, this can definitely have a negative effect on seed germination. For example, Zhang et al (2020) demonstrated that lower nitogen levels – i.e., the amounts typically present in average potting mixes – promote germination of seeds. If the levels are too high, however, this can prevent germination (cf. Liu et al, 2022) – but these are levels not common in the average commercial potting mixes (or soil for that matter). The key is balance. Duermeyer et al (2018) provides some great commentary on this distinction.

I haven’t been able to find any published studies where low-nitrogen soil increased germination of seeds. There certainly might be some species that display this behaviour – perhaps from plants where they naturally have low nitrogen (such as desert plants), in which case it might be better to replicate the soil found around the mother plant. An interesting study by Ugarte et al (2024) came out last year where oak seeds (Quercus ilex) germinated better if they were sown into soil that was gathered from around the mother tree. The authors speculated that the microbes and nutrients had a relationship with the seeds. But I digress.

Low-nitrogen substrates makes no sense from a germination perspective. What about from a soil health perspective? If the seeds germinate but then die because of a disease caused by high nitrogen levels, that’s a problem right?

There is a large (and growing) body of evidence showing that adequate nitrogen in the soil is crucial for early seedling development and health. It isn’t just about germination, it’s about the health of the seedling – from a very young age.

After a seed germinates and throws up its little green seed leaves, it actually feeds off of them. Like a packed lunch. It’s often said that the seed doesn’t really need much more than what’s in the seed leaves. Sounds sweet, but it isn’t really true.

Studies have shown that very young seedlings do need nitrogen (among other nutrients and microbes) in the soil. A study by Monaco et al (2003) found that additional nitrogen promoted the root mass of young annual grass seedlings compared to using a low-nitrogen medium. Their stronger root masses were grown not merely from their cotyledons – but from the enhanced nutrition of the soil. This was just the first 3 weeks of their life, before their first true leaves emerged. At the end of the 3 weeks, the root mass was 2 to 4 times larger than the controls (which had low nitrogen). Also, it’s been found that soils with higher nitrogen can promote better water uptake, so long as the nitrogen levels aren’t off the charts (Hernández et al, 2021).

There are also many published studies that show that young seedlings grown in nutritious soil can better defend against pathogens – especially those that cause damping-off.

Dunlap (1936) was an early study which found that seedlings raised in sand could withstand damping off caused by Pythium inoculation – but only if the seedlings were fed adequate nitrogen and potassium. In other words, seedlings grown in pure sand didn’t stand a chance against the damping off disease unless they had enough nitrogen. Hofer et al (2016) found similar preventative effects against damping off in barley seedlings.

Cucumber seedlings raised in a higher nitrogen medium from birth had better defences against Fusarium-related infections (McClure and Roberts, 1942). It’s even been found that if sterilized soil has higher nitrogen content, that it can help prevent damping off caused by Pythium (Al-Azizi et al, 2013) in radish seedlings. In other words, even if you kill all living things in the soil – and inoculate it with a pathogen that causes disease – the mere act of adding nitrogen to the soil can help young radish seedling defend themselves better. Who knew.

Adding composted manure or garden waste is a tremendously wonderful source of nutrition for any growing medium. Ringer et al (1997) found that adding composted manure can suppress damping off disease – and the authors specifically noted that the modest nitrate/nitrogen boost is a factor in preventing and fighting the disease. A related study by Das and Western (1959) found that if sterilized soil was infected with R. solani (a pathogen causing damping off disease) – and then supplemented with nitrogen, that the presence of nitrogen significantly inhibited the development of damping off disease. Not only this, but these researchers also tested the beneficial effects of supplemental nitrogen in unsterilized soil – and even the modest amounts of the disease that were observed (modest because unsterilized soil is healthier and lower pathogens) were attenuated due to the supplemented nitrogen.

For young seedlings (even very young seedlings), nitrogen seems to play an important role in enabling the young plants to fight off diseases.

Germinating seeds should be done on a substrate that has a modest amount of nitrogen – such as a potting mix with added compost or soil – and which will also set up the seedlings for success. Not only down the road, but also for in the short term.

But ‘seed germination mixes’ are also touted to improve resistance or prevention of disease because they’re sterilized. This is untrue.

A wonderful study was published by Scheuerell et al (2005) where the researchers added locally manufactured compost to sterile potting mixes, and then they purposely injected these with pathogens that cause damping off. They found that mixing even a small amount of non-sterilized compost into the sterilized potting mix significantly reduced damping off. The researchers noted that improved microbes were the likely reason. The good microbes. Ringer et al (1997) had similar findings.

A ’healthy gut’ is the talk around the human health watercooler these days, including a healthy ‘biome’. It’s no different with soil. Even baby seedlings need a healthy biome of bacteria, fungus and other microbes to help it fight for its life.

Microbes can come from many sources, including composted fish parts. Fish emulsion is a commonly added ingredient to potting mixes and compost, and for good reason: it increases the microbiome complexity of the substrate. More bacteria, more fungus, more microbes. Abbasi et al (2004) added fish emulsion to a sterile seed-starting mix – and they purposely injected it with Rhizoctonia solani (which can cause damping off). The inclusion of fish emulsion had a dramatic effect in preventing damping off disease – and the researchers suggested that it was both the nitrogen content and the microbial environment from the fish emulsion that led to this increase protection of the seedlings. Apparently microbes aren’t all bad.

But it actually isn’t just about plant health. Sterilized soil can prevent germination of seeds. Ugarte et al (2024) found that Quercus ilex seeds germinated higher if the seeds themselves were not sterilised (i.e., the seeds were not cleaned with bleach etc). Not only this, but if seeds were incubated with non-sterilized soil collected from around the mother tree, that germination was improved. Also, Kapilan and Thavaranjit (2015) found that various vegetable seeds inoculated with soil bacteria had improved germination – and Barney (2010) found that if seeds were treated with fungicides, that they had a lower germination overall.

Turns out the bugs are pretty important. If you kill ALL the bugs and microbes in a substrate, you lose the benefits – and leave yourself open to disease.

There is a tremendous amount of research on soil health, but not nearly enough. Prior to twenty years ago most of the research was on which chemical should be used to kill which bugs. Agricultural fields have been treated like wastelands – stuffing them with synthetic fertilizers, removing the organic matter, and spraying with insecticides and fungicides. Commercial nurseries have been following the same path. Perhaps enough is enough.

But for the seed gardener at home, we can do better. Maybe it just starts with wanting healthier seedlings and plants – or higher germination! All of these are great reasons to stay away from sterilized soil or low-nitrogen soil. Commercial nurseries still often use low-nitrogen substrate for seed starting, but they’re quick to add nitrogen after they germinate – because it’s important for seedlings, even before their true leaves unfurl.

Personally, I don’t endorse any specific brand of substrate, but I use a locally made organic potting mix that has both compost and slow-release fertilizer in it. I also like to mix in some locally made compost (with fish emulsion) when I can. For me, it’s always been great. To reduce damping off, I find it works well to clean my starter trays every year with some soap and water, and provide modest air circulation (little fans). It’s more than enough.

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