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Secrets of the Soil: Part 1

This post was getting way too long, so I decided to cut it in half. Part 1 introduces general soil chemistry and biology and then describes some of the specific practices we use to build our soil. Part 2 will take a more detailed look at the soil at Lilliputopia by using different tools and resources.


Fungus and other microbes are the foundation for healthy living soils.

You are what you eat, and everything you eat was produced by the living soil. One cup of healthy soil contains billions of microbes, not to mention a myriad of other creatures, such as earthworms, arthropods, nematodes and mollusks. Soil may look like a small and insignificant fraction of the farm, but it comprises an immense and foundational ecosystem that we actually know very little about; we are often completely unaware of the complex and alien biology that ultimately sustains us. Luckily, even without a complete understanding, we can learn from nature to implement nourishing and restorative practices to grow our soil.

A history of destruction and imbalance

Conventional agriculture has attributed very little value to the soil due to the predominant belief that plants only require predefined chemistry, primarily in the form of NPK (nitrogen, phosphorus, and potassium), called macronutrients. In my opinion, this reductionist (and naive) perspective has been very detrimental to the overall state of the world's farmland. Not only has the rich topsoil, which was once ubiquitous and fertile, been almost completely decimated, but the pervasive application of chemicals to the soil has destroyed and polluted land, water, and air.

Chemicals create widespread imbalances in the soil biology, destroying beneficial creatures such as these worms. Worms aerate and fertilize soil.

Consider nitrogen (N), the single most important fertilizer for growing plants (or so they say). Nitrogen is an essential component in amino acids, which chain together to make proteins and are required in all cells. Since Fritz Haber won the Nobel Prize in 1918 for inventing artificial nitrogen fixation (which was first used for explosives in WWI and which we have become entirely dependent on for agriculture), the world's population has skyrocketed. Nitrogen fixation is the process by which atmospheric nitrogen gas, which is practically inert, is converted to ammonia, a biologically usable form. It has been estimated that the majority of the nitrogen within our tissues is derived from this process; whereas little over a hundred years ago, all of the fixed nitrogen in the world came from natural sources such as nitrogen-fixing plants and, to a lesser extent, lightning strikes. Sadly, approximately 50% of nitrogen (and most soluble fertilizers) that is applied to soils is simply washed away, polluting the waterways and creating ideal conditions for harmful and pathogenic algal blooms.

Nitrogen fixing plants such as these lupine seedlings as well as peas and beans form symbiotic relationships with microbes to naturally fertilize the soil.

Phosphorous (P) is an essential component to nucleic acids, that is, DNA and RNA, which are essential in all cells. Generally, phosphorous is considered to be required for healthy root development and seed production. Unfortunately, phosphorous is not a renewable resource and is mined as rock phosphate, which is converted into the more soluble form ubiquitously used as fertilizer. Not only does most of it get washed away as pollutants, it is being depleted at an alarming rate. Learn more about peak phosphorous here.

Potassium (K) is required for many cellular processes, including photosynthesis, osmosis (water regulation), stress tolerance, and enzyme activation. Potassium is also mined from deposits around the world, and thus, is not a renewable resource. Fortunately, microbes have been shown to increase the solubility of potassium, enhancing its uptake in plants. These microbes essentially mine tiny rocks and minerals, allowing them to become soluble nutrients for other organisms. A detailed review of the role of potassium in sustainable agriculture can be found here.

Do your own experiments! Observe and record your data. Take careful notes, and then you can share your results with others!

NPK are only three of many components required for healthy soil biology. As my PhD advisor would say, they are necessary, but not sufficient. Soil is a complex and a thriving ecosystem requiring both major elements and trace elements. Thus, you should avoid buying chemical fertilizers and make your own compost, as it is chemically balanced and full of beneficial microbes. If you do wish to use fertilizer, look for something that is natural and slow release; it won't be as soluble and will take longer to incorporate into the soil. Seaweed, fish emulsion, and seed meals (such as alfalfa) are good choices if you don't have compost. Rock dust and greensand contain micronutrients and are purportedly safe and natural amendments. However, I conducted an experiment in 2016 with rock dust and found, surprisingly, that it was detrimental to radish growth. Further research indicated that rockdust does not provide soluble nutrients unless your soil is extremely acidic (pH<5.5). This interesting website also claims that using rock dust is extraneous. Thus, it is necessary that you conduct your own experiments, as every site is different and there are many variables that can influence results.


Composting is probably the most safe, natural and effective soil amendment, and anyone can make it. Although many books and sources will profess that composting is a complex subject requiring diligent watering, mixing, and input ratios, it can be as simple as throwing organic matter into a pile. Admittedly, this is the slowest way to compost, but it is also the simplest, because compost is just decomposed organic matter. To speed up the decomposition process, you can water, cover, and aerate the pile. Additionally, you can add material in predetermined ratios, which most sources say is 30 parts carbon (brown, i.e., paper, dry leaves, sticks): 1 part nitrogen (green, i.e., vegetables, grass clippings, manure). These conditions allow the complex microbial community to thrive, accelerating their metabolism and heating your pile. Finished compost contains all of the required nutrients that plants need, which is much more than just N, P, and K. You'll know when your compost is finished when it's black and crumbly. We won't get into humanure here, but I assure you, it is one of the most direct (and safe when done properly) ways to returning nutrients back into depleted soils.

Our indoor worm bin: made out of a plastic recycling container placed into a wooden box with lid. Make sure there are holes for adequate ventilation.

In addition to having a regular compost pile, we have an indoor worm bin, which is another fun way to make compost (often called worm castings). Red wigglers (Eisenia fetida) are specialized worms distinct from typical earthworms and don't normally survive outside. They thrive on vegetable scraps and bedding material (again carbon; we use shredded paper but you can also use sawdust or shavings). They are super easy to manage, are not messy and don't smell. You can make a worm bin out of any large plastic container and lid. There are many plans online, but ours is a simple wooden box with a plastic container inside, drilled with holes for ventilation. You can often buy red worms online, at your local farmers market, or here if you live nearby!

Yammy is not impressed with the worms.


One of the easiest rules to making healthy soil is to make sure it is always covered and never exposed. This can mean covering it by growing plants or using mulch.

Much is super useful! It's also steamy on a cold winter day and smells good.

Mulch is the first step in nature's fertilization program. Leaves fall to the ground and then decompose (compost) slowly, making the forest soil richer every year. By mimicking this process, we can prevent weeds, conserve soil moisture, insulate our plants, and fertilize the soil all at once. Any carbon source is usually a good mulch and includes paper, sawdust, bark, wood chips, and cardboard. Carbon is probably the least appreciated and most underestimated ingredient to healthy soil. Ignore the myth claiming that too much carbon promotes the microbial depletion of nitrogen; I've found no evidence of this. In contrast, these large carbon deposits are favorite homes for symbiotic fungi, which can be found as great masses of stringy white mycelium.

Mulching the trees with straw.

Green mulch (aka living plants)

We use a scythe to cut the grass, then use it for mulch.

Our ideal system has our useful plants such as edibles, medicinals, and flowers growing happily together and completely filling all of the spaces. We should aspire to this by planting as many things as we can; but we should not despair when we see armies of weeds filling in the gaps. Weeds are pioneer plants taking advantage of the local conditions and building the soil. They are indicators of the soil conditions and are nature's quick fix to repairing exposed soil. Many common weeds are edible and medicinal, so it's also wise to learn about your local weeds because they can be a great resource. The next time you get upset about weeds, remember they are nature's response to bare earth.

Cover cropping is another form of green mulch, but I won't talk about them here in detail. They are just another way of using plants to cover bare earth when you aren't growing your normal crops.

I also highly suggest growing many nitrogen fixing crops. These plants (and their microbial symbionts) are responsible for making natural fertilizer. Their tissues are high in nitrogen (proteins) and are thus released when you eat them or they break down into the soil. Common N-fixing plants include clover, peas, beans, vetch, and lupine. There are also more interesting N-fixing shrubs and trees you can try planting. We have planted autumn olive (Elaeagnus umbellata), siberian pea shrub (Caragana arborescens), and seabuckthorn (Hippophae spp.) in our field.


Solarizing and mulching the beds. Make sure that your tarps are weighed down correctly, or the wind will rip them up and blow them away. We use T posts or bury the edges.

Another easy rule of healthy soil is to minimize soil perturbation, which can cause compaction as well as destroy the beneficial organisms such as earthworms and fungal mycelium. Instead of using tillage or have heavy equipment, we prefer the simple process of solarization to help prepare beds for the spring. Solarization entails covering the mulched beds with plastic, tarps, or other suitable covers (we use lumber wrap, a common waste product in the PNW). This process utilizes solar energy to warm the soil, which smothers weeds, destroys pathogens, and hastens microbial decomposition. We are still experimenting with this method and shall report back our findings soon.

Although we often try to avoid plastic on the farm, solarization is a simple and effective method that can be repeated annually with the same materials. We just make sure that we remove and store the plastic after the spring and it will last for many years. Note: exposed plastic becomes brittle and breaks down into microplastics, which are harmful to ecosystems.


This concludes Part 1 of the Secrets of the Soil. Continue reading Part 2 to learn about the status of our soils at Lilliputopia, including soil tests and soil moisture data, and how you can analyze your own site.

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