The Soil Microbiome

We are well on our way to a unified theory of biology that will merge body and environment, brain and mind, genome and microbiome.” – Deepak Chopra

Without healthy soil, there can be no health. Thanks to new technology, scientists are catching up to this view. The revelation underfoot involves “microbiomes,” now possible to explore thanks to gene sequencing.

Human Microbiome

The human genome is a map of an organism’s complete set of DNA, including all its genes. Though barely a decade has passed since this remarkable discovery, the cost of sequencing genes has lowered so dramatically as to make the exploration of other microscopic communities possible.

The human microbiome is one such community, comprised of microorganisms that live in, on and around your body. These are the “healthy” bacteria you may have heard about in yogurt or pro-biotics, some 100 trillion microorganisms that live in your gut, mouth, skin and elsewhere in your body. The number of genes associated with the human microbiome exceeds the number of human genes by a factor of 100 to one. Just as we’ve come to understand more about human health by understanding the genome, this map of bacteria, fungi, one-celled archaea, and viruses has shown scientists a microbial world of organisms with whom we have co-evolved, organisms that perform vital functions and services, and outnumber our own human cells by about ten to one. This has everything to do with the ground beneath your feet.

Soil is a Microbiome

Whereas we have long seen this connection, this new technology is making it possible for scientists to begin to quantify the link between soil microorganisms and plant nutrition. In the same way the microbes in the human body aid in digestion and help maintain our immune system, the microbial community in the soil offers symbiotic benefits to plants. Like fascia in the human body, roots and fungi (mycorrhizae) beneath the earth’s surface form a vast network that connects plants. A recent experiment in the U.K. showed how mycorrhizae actually enable plants to communicate.

In just one example a broad bean plant – under attack by aphids – transmitted a signal through its mycorrhizal filaments to other bean plants nearby, signaling those plants to produce a defensive chemical that repelled aphids and attracted wasps, a natural aphid predator. In much the same way yeast builds in a baker’s oven, the symbiotic association between plants and the fungi that colonize their roots is ongoing, albeit this partnership has been building for millions of years.

We take the connection one step further, linking the soil’s microbiome to the human one. To presume that human and soil-bound microbial communities begin and end in isolation is to ignore the mass of data about declining human health, and the wealth of data showing that the health of our soil has a direct effect on the level of our own health through the foods we eat, the water we drink, the air we breathe, even the amount of time we spend outdoors with nature.

Whether you acknowledge that link or not, it’s impractical to ignore the perils of diminishing our greatest natural resource, the soil of planet earth.

The good news is we can reintroduce the microorganisms to the earth. Mapping the soil microbiome – the work of the Earth Microbiome Project – will help identify species that are vital to soil and plant health, in order to replenish the earth.

The Soil Foodweb

“It’s not the soil itself – it’s the soil life that is the most important element.” Geoff Lawton

A World of Microorganisms: the Soil Foodweb

Microorganisms in the soil foodweb make up a living, thriving community. This community includes a wide range of microorganisms, seen and unseen, that grow, eat, reproduce, live and die. It is a busy little world bustling right beneath our feet.

A Busy Community

Because you don’t notice them, you may think they are unimportant. However, this little community makes it possible for us to have clean air and water as well as healthy plants. Within this community live tiny creatures with big jobs to do.

Tiny one-celled creatures such as bacteria, algae, fungi, and protozoa that are too small to see, arthropods, and larger creatures such as earthworms and insects help to break down waste and organic matter from plants and animals. They break down nitrogen and other materials that could become pollutants in our water. They fix nitrogen from the atmosphere so plants can utilize it. The also protect plants from pests that damage crops. In a nutshell, they make the environment as a whole a healthier place for everyone without us even noticing it! And this is just a small sample of what these organisms do.


There are thousands of kinds of bacteria in a spoonful of soil and those bacteria have many jobs. Depending on the type, bacteria may help add organic material to the soil, inhibit organisms that cause disease and protect plant roots from disease which enhances plant growth.

One of the most important jobs of bacteria is the fixing of nitrogen in the soil. Nitrogen is an essential nutrient for plants but it isn’t found in high enough concentrations in the soil. The air, on the other hand, is about 80 percent nitrogen, but that does little to help the plants.

Nitrogen-fixing bacteria take the nitrogen from the air and concentrate it into the roots of certain plants in growths called nodules. There it is converted into a form of nitrogen that the plants can use. If you were to cut open one of these nodules, it would look red inside. That is because of an oxygen scavenging molecule called leghaemoglobin that is only found in these nodules. It serves a similar function that hemoglobin does in our blood, scavenging oxygen to protect the nitrogen-fixing enzyme nitrogenase, which in activated by oxygen.

When the plant and roots decompose, the nitrogen is left in the soil for future plants. Thus the soil is enriched by the bacteria for future generations of plants.


Fungi don’t sound very appealing, but they play an important role in the soil food web. Fungi excrete humus by consuming organic matter. This is why the forest floor is so dark and rich. Leaves and fallen branches are broken down naturally by a fine web of fungi that effectively cleans up what has fallen and turns it into beautiful soil teeming with nutrients.

Fungi are important in soil’s ability to absorb and retain water thanks to fine threads called hyphe that bind soil particles together. Hyphe also release enzymes that break down nutrient molecules, allowing them to be reabsorbed.


Protozoa are similar to bacteria in that they add nitrogen into the soil in a form that plants can use. They also have the job of eating bad bacteria that can cause disease. Being single-celled organisms, they are certainly not at the top of the food chain, however. Protozoa are also food for nematodes, and when they are excreted they become part of the nitrogen and other nutrients in the soil that plants need.


Some types of nematodes can cause problems in the soil, but the good news is that beneficial nematodes think of the bad ones as food. Beneficial nematodes also feed on protozoa, bacteria and other microorganisms. Their waste provides nutrients vital for healthy root growth in plants.


Arthropods are the creepy-crawlies of the soil food web. They can consist of creatures as small as mites to sow bugs, centipedes, spiders, ants, and more. Often these are the critters you think you want to get rid of in your garden, but the fact is, if you see lots of them, you have a robust, healthy garden. Bugs are good!

Arthropods play many different roles in your soil. There are shredders, predators, herbivores and fungal feeders, and all are important for a balanced food web. They keep each other in check and help break down debris, making it easier for other microorganisms to continue the process of breaking down organic materials. They also excrete nutrients in forms that are more easily used by plants.

Soil is bursting with life! You may never look at it the same way again.

The Story of Soil

The soil is the greatest connector of lives, the source and destination of all…Without proper care of it, we can have no life.” – Wendell Berry

It is easy for most of us to look down and take for granted what is under our feet, regarding soil simply as dirt. But did you know it takes up to 400 years to replace just one centimeter of topsoil? Soil is so much more than ‘dirt’. In fact, if it wasn’t here, we wouldn’t be here today. We depend on soil to exist, as does every other living thing on the Earth. Yet we know so little of its journey.

The Journey

If soil could speak, it would tell you that it has a pretty amazing history with rocky beginnings – quite literally. Soil begins as cold, hard rock. Spewed out by volcanoes, shifted by glaciers, it creates a fast base, rich in minerals, but devoid of life. Over time, rain and ice, varying temperatures, geography and other factors gradually break down its surface into small, even dust-like particles.

These particles accumulate in lakes and streams, rock crevices and surfaces, moving downstream and spreading over vast surfaces, or blown by winds to new locations. This powdery mineral rich base becomes the foundation for life to follow.

Combined with organic materials like leaves, animal waste, insects and organisms, these materials when mixed with moisture slowly start the first inklings of life in the soil. Life cycles upon itself, and so the as plants develop on that mineral base, grow and die, they add more organic matter, slowly, slowly building thin layer upon thin layer of the nutrient rich soil that sustains all life on this planet.

Nature is amazing – she grows just the right plant at the right time to break down the rocky mineral base with its roots, or to supply the nutrients that are deficient in the soil, all the while moving the soil towards richer fertility. The deeper the plant life goes into this mineral rich base, as it breaks it apart and creates more living soil, the denser becomes the growth and the beginning of canopy cover, which in turn creates habitat for richer life and soil.

As the density of the plant material grows, taller and taller plant material blocks out the strong sun so the soil does not heat up as much, creating an even more habitable area for all kinds of life. And this cycle continues – for our forests, to the point that most of the direct sun is blocked and rich, fertile, lush topsoil continues to build on the forest floor.

Very aged topsoil, hundreds of thousands of years old, is very deep, and so nutrient rich it can support any kind of plant growth in abundance.

Soil Is Alive!

Soil has several layers – anywhere from three to six depending on the region it is in. The upper layer is called the topsoil. Topsoil is that fertile rich surface layer of soil with all the nutrients, microbial life and humus needed to sustain a healthy habitat of plants and living organisms. It is a blanket of nature’s finest that is critical to sustaining life. Topsoil is very thin compared to the other layers of earth. It is also relatively fragile and needs to be treated carefully because once it is gone, it is almost impossible to replace.

Topsoil is a living, thriving community – an ecosystem – where there are producers and consumers and a flurry of activity going on all the time. In fact, there is so much life in one gram of soil, 70 to 80 percent of the organisms in it haven’t even been identified yet! You don’t notice much of this activity unless you spend some time on the ground carefully observing what is going on, and even then you only see a very small portion of what is really happening under your feet. This is important to know because healthy, living soil will produce healthy, thriving plants. If the topsoil dies, the things planted in the topsoil will die as well.

And It Can Die

Soil is the living skin of the Earth, and like our own skin, it can be damaged. It is being damaged.

Topsoil dies when it is over-farmed using modern farming practices that involve chemicals and synthetic fertilizers that change the pH of the soil, killing the tiny creatures living in it, making ‘dirt’ that is depleted of nutrients and barren.

Studies have found that weedkillers like Roundup actually compete with plants for important nutrients such as calcium and boron. They also cause a serious imbalance in the beneficial bacteria around the roots of plants that are needed to protect against diseases and parasites.

Soil dies because of deforestation. Over grazing, fires and mass construction also do irreparable damage to our topsoil. These things rape the Earth, forcefully stripping away that vital resource that we can’t simply replace, leaving us with nothing but lifeless dust. The worms are gone. The insects are gone. The microorganisms are gone. So the soil is gone. Forever.

Erosion occurs when topsoil is damaged so badly that it is washed away by wind and rains, and eventually becomes sediment. Today, erosion is removing topsoil at a rate many times faster than it can be replaced world wide.

When acres of topsoil are destroyed, we can’t just make more. Soil is a vital non-renewable resource; it cannot be recreated, it must regenerate itself over time. It takes thousands of years for nature to replace what was lost, but by then it may be too late. It is up to us to learn to manage the gift that has been given to us and not squander it.

If we don’t learn to cherish and nurture the soil we have, the story of soil will have a very sad ending.

And so will the Earth.

7 Ways to Get Back to Nature and Why It Matters

“A little garden in which to walk, an immensity in which to dream, at one’s feet that which can be cultivated and plucked; overhead that which one can study and meditate upon; some herbs on earth and the stars in the sky.”   - Victor Hugo

Once a fringe field, ecopsychology – which explores the relationship between human beings and the natural world – has become mainstream. Of course you always knew a little fresh air and sunshine were good for you, but now there are studies that prove it. Even a simple view of the outdoors helps reduce stress.

In one study, adults were exposed to mild stress and to one of three views: a glass window overlooking grass and trees, a 50-inch plasma television screen showing the same scene in real time and a blank wall. The heart rates of those exposed to the sight of real nature decreased most quickly. People who faced the TV screen fared the same as those looking at drywall.

Another study showed that hospitalized patients with window views of nature needed less pain medication and spent fewer days in the hospital than those who faced a brick wall. A nature view from a prison cell reduced inmates’ need for health care. And residents of public housing projects who lived near trees showed benefits like more civility, more studiousness, and less aggression.

How do we get back to nature and a healthier lifestyle? Here are seven tips:


If you need to find the idyllic meadow of your childhood before you can commit to your hike, you’re not going anywhere. Keeping in mind that time spent in nature hugely reduces stress, give yourself a break and find a park nearby. Anyplace will do. 


Turn your outdoor activity into a game by foraging for food. There are MeetUp groups all over the country that connect people looking to pick apples or forage for morels or fennel heads. Always be responsible – don’t overharvest and be certain you know the identity of your plants. Here’s a guide. 


Meetings can be toxic to creativity and morale, so professors at Washington University in St. Louis came up with “Meetings on the Move.” The idea is to replace conventional sit-down meetings with outdoor walk-and-talk gatherings. The change of scenery often spurs better ideas. 


There is no better way to enjoy nature than to get involved in preserving it. You can find stretches of highway or trails to adopt through your local department of environmental conservation or park service. 


De-clutter, make a few bucks and enjoy the birds chirping. With free ads on Facebook and Craigslist, this one’s no-brainer. But do check up on local signage regulations; taping your sign to that light pole could blow your whole day’s profits. 


There are entire communities devoted to treasure hunts. That’s right, participants go looking for oddities and objects that are stashed away. Geocaching has items hidden in containers all over the world, you track them down using GPS at whatever speed and level of difficulty you like. 


Much of this site is devoted to educating you about the ways in which modern agriculture and landscape techniques have compromised the health of not only the planet but each individual on it. It would be remiss not to encourage you to spend time in real nature by creating your own natural space, whether it’s to put plants in your windowsill, on your patio, or in the ground around your home. And this is where you can make a real difference. To help clean everything from the air you breathe to the water you drink, be sure to use organic soil and fertilizers. Here are some tips on starting your own garden no matter what your lifestyle.

DID YOU KNOW Fall is the best time to take care of your lawn?

“Autumn is a second spring when every leaf is a flower.” ― Albert Camus

The importance of Fall lawn care is often overlooked, but now is the time to get your lawn in the shape-for-success next year.

You may not have irrigated your lawn during the Summer and it went dormant (yellow/brown). But, when the Fall rains come back your lawn will come back to life. With limited nutrients in the soil it will struggle to fill in and weeds will try to take over. This is the perfect time to get your lawn back into shape. Hendrikus has the Organic fertilizer, seed and soil amendments to make your lawn healthy for the long Fall and Winter ahead.

Here are our two recommended programs for bringing life to your soil and lawn so that it carries through the Winter and has nutrients ready for when it reawakens next Spring.

Program 1: Increasing Fertility with Minor Lawn Renovation

  • Aerate lawn with power or foot aerator to break up thatch layer and allow nutrients to get to the roots easier.
  • Remove largest patches of weeds with garden trowel, rake, or shovel.
  • Over-seed bare areas in existing lawn with Hendrikus Turf Seed, making sure seed makes contact with the soil.
  • Fertilize lawn with Seasons 8-0-4 or Spring Nitrogen 10-0-2 at 10# per 1000 square feet.
  • Apply AxisDE (diatomaceous earth) to wettest areas in non-irrigated lawns, and to both wettest and driest areas in irrigated lawns.
  • Spray HuMagic Liquid on lawn with a tank sprayer at 6oz to 8oz per 1000 square feet.
  • Apply a light top dressing of mulch on bare areas in lawn to help hold in moisture for seed germination.
  • Lightly water lawn to dampen mulch and seed. Keep seed moist with light afternoon watering for the first 7-10 days to promote germination. Dry seed will not germinate.
  • Apply Calpril lime to raise pH 3 weeks after fertilization at 20# – 40# per 1000 square feet.


Program 2: Increasing Fertility with Full Lawn Renovation

  • Aerate lawn with power aerator to break up thatch layer and allow nutrients to get to the roots easier.
  • Remove any excess grass & thatch with rake or power rake (dethatcher).
  • Remove all existing weeds with garden trowel, rake, or shovel.
  • Over-seed with Hendrikus Turf Seed at 8#’s per 1000 square feet. Make sure seed makes contact with the soil.
  • Fertilize lawn with Seasons 8-0-4 or Spring Nitrogen 10-0-2 at 10# per 1000 square feet.
  • Apply AxisDE (diatomaceous earth) to entire lawn at 100# – 150# per 1000 square feet with a fertilizer spreader and rake or stiff broom into the soil.
  • Spray HuMagic Liquid on lawn with a tank sprayer at 6oz to 8oz per 1000 square feet.
  • Apply a light top dressing of mulch on bare/thin areas in lawn to help hold in moisture for seed germination.
  • Lightly water lawn to dampen mulch and seed bed. Keep seed moist with light afternoon watering for the first 7-10 days to promote germination. Dry seed will not germinate.
  • Apply Calpril lime to raise pH 3 weeks after fertilization at 20# – 40# per 1000 square feet.