It all started when I was about 3 years old, at least that’s the first time I remember. It was all my dad’s fault. I was out in the garden with him, and I said I was hungry. He took two steps over a row of beans and a row of spinach and pulled up a couple of carrots. He wiped most of the soil on his pants and handed me one. “It’s just got a few bacteria on it, good for your gut,” he told me as he started munching on the other one. So, I did the same. It was a little gritty, but it was sweet, and that’s how it began.
That carrot didn’t just have “a few bacteria.” Studies done by the USDA found that, on average, there are 22 species of bacteria in an average organically grown carrot. Not on the skin, not in the soil, in the carrot you eat. Those are the same species of bacteria necessary for digestion, and you already have them in your gut.
My Gut Is Full Of Soil Bacteria?
Yes, and fungi, and viruses, and all manner of microorganisms that keep you healthy. You started to populate your intestines with bacteria and other microbes during your journey out of the womb and into the world. You picked up all the bacteria your mother had accumulated, so you started out with a good mix of bacteria. They didn’t make you sick but helped to fend off pathogens. If you were born by C-section you missed out on many of the microbes that would keep you healthy throughout your entire life.
Have you ever noticed that kids crawl around and explore their world with their mouths? Put a kid on a carpet, and you will be picking out carpet fibers from his mouth, put him down on the grass, and it’ll be grass and soil. Which is the most beneficial, synthetic carpet fibers or fresh green grass and soil?
Assuming you don’t use pesticides on your lawn it’s the grass and soil. Why? Your child is enriching his intestinal tract with bacteria in the soil and on the grass, that will keep him well. By the age of three, most children have a complete microbiome in their guts. That microbiome is predominantly influenced by the environment, lifestyle, and diet. According to the National Center for Biotechnology Center, your contribution by way of genetics is less than 8%.
Let’s Look More Closely At What Your Child Ate
Most parents think of bacteria as something to disinfect for. But many studies, such as Protective effects of farming on allergies and asthma: have we learnt anything since 1873? by Douwes et al., have shown that kids who grow up on a farm or with exposure to outdoor animals are far less likely to have asthma, allergies, or autoimmune diseases. What role does the soil bacteria play in keeping your child and plants healthy?
Most soil bacteria protect plants from disease as well as play major roles in soil nutrient cycling. When your child has a healthy gut biome with the right ratio of bacteria, fungi, and other microorganisms, he is as healthy as the soil he ate.
Bacteria are the most abundant microorganism in your soil. According to Jeff Lowenfels in his book "Teaming With Microbes," one teaspoon "…contains a billion invisible bacteria, several yards of equally invisible fungal hyphae, several thousand protozoa, and a few dozen nematodes."
Soil bacteria, though small, are mighty in their functions and multitudes. And most bacteria in your soil are dependent on your plants. Yes, plants control the show.
How Do Plants Control The Soil Bacteria?
Soil bacteria are almost totally dependent on plants for food. Depending on whether those plants are dead or alive, different types of soil bacteria can be found. Bacteria fall into four functional groups.
- Decomposers – they consume simple carbon compounds – root exudates and plant litter – they convert soil organic matter into useful forms for the rest of the soil food web.
- Mutualists – they partner up with plants. Protecting plant roots from pathogens and supplying nutrients in exchange for root exudates.
- Pathogens – not all bacteria are beneficial, but this group is the smallest, and with healthy soil full of decomposers and mutualists, there isn’t much space for them to thrive.
- Lithotrophs – instead of consuming carbon these bacteria obtain their energy from nitrogen, sulfur, iron, or hydrogen. These are usually found around hydrothermal vents such as the mud pots in Yellowstone National Park. This isn’t a bacterium you’re going to find in your garden or field.
The species of bacteria active around a plant’s roots is dependent on what the plant needs.
Mutualist bacterial species have an ebb and flow depending on what root exudates the plant emits. In essence, the plant signals the soil food web what nutrients are necessary for optimal growth at each developmental stage.
Having a strong community of beneficial bacteria in the rhizosphere (the area directly around the plant’s roots) not only wards off root pathogenic bacteria but also creates a shield around the plant leaf, stem, and fruit biomass making it impossible for insects and airborne pathogens to access the plant.
Nature covers the soil with plants even if you haven’t planted anything. Even weeds have their mutualist bacterial species to keep them healthy. As the soil structure changes with the addition of dead and decaying organic matter, the types of weeds change and the mutualist bacterial community changes as well.
Decomposers can be found anywhere organic matter is dead or dying: your compost pile, roots of flowers that are going into dormancy, the rotting log in your woods, the mulch mowed residue in your lawn. Organic matter is everywhere.
As humans, we carry around our own load of bacteria, both in our gut and on all skin surfaces. We are always sloughing off dead skin and with-it dead bacteria, which are never wasted but food for fungi and other microorganisms in the air and soil.
Pathogenic bacteria are always around us in the air and soil but can be kept at a minimum. People, not plants, control the number of pathogens found in our soil and our gut. The key to healthy plants, and people, is maintaining a strong community of beneficial soil microorganisms. Healthy soils and healthy humans have beneficial microorganisms that protect them from pathogens..
When toxic chemicals are sprayed on a field, pathogenic bacteria have an easier time reestablishing themselves because the toxic spray kills off all bacteria and fungi, creating voids in the soil food web. Nature will fill those voids, even if it’s not beneficial to the crops you want to thrive. Pathogenic bacteria can become dominant, thus leading to crop disease, insect infestation, and spraying of more toxic chemicals.
The pathogenic bacteria cycle can be broken by incorporating beneficial microorganisms, cover crops, and no-till ag practices in unproductive fields. Human health can be improved by eating more organic fruits and vegetables grown in healthy soil containing these beneficial microorganisms that inoculate your gut.
Bacteria play many roles in your farm ecology. Beneficial soil bacteria are already in your soil but often imbalances create deficiencies that attract disease, insect pests, and pathogenic bacteria. Adding beneficial biology will benefit your plants and will not displace indigenous beneficial organisms.
Functions Of Soil Bacteria
Usually, we think of soil bacteria as out there in the field, and it only gets in the house when we track in mud. But those bacteria are all around us, in us, and in our food.
Soil bacteria not only fertilize the soil with their dead bodies, they are food to their predators. When consumed, the predators use what they need and then excrete the excess as waste. That waste is in a plant-soluble form and available for the plant to aid in growth.
Cycling nutrients and water to plants, soil bacteria are necessary for plant growth and health. The soil has many nutrients, but most are not in plant digestible form. Bacteria are the first microorganisms to begin the “mineralization” of those nutrients. If you feed the soil, the soil will take care of your plants.
One of the major essential elements for all living organisms is iron. Most soil and water have abundant iron but it’s not usually in a plant-soluble form. Soil bacteria secrete siderophores, which are iron-chelating compounds. The bacteria transport iron across cell membranes. A side benefit of removing iron from the soil is that many pathogenic bacteria also need iron and the plant gets the iron first.
"Iron has several roles within a bacterial cell. It is required to render active many different proteins and enzymes in a variety of metabolic processes. It is also essential for expression of many key virulence determinants. Without iron, it is almost impossible for bacteria to establish themselves within the host and cause disease."
Plants form mutualistic relationships with bacteria based on plant needs. Soil bacteria that are “allowed” access to the interior of the plant root are called “Endophytic Bacteria.” Like all bacteria they are microscopic one-celled organisms that start their lives as soil bacteria.
A small subset of the bacteria in the rhizosphere has the characteristics beneficial for the plant. The endosphere microbiota are assembled by the plant but microbial competition and cooperation also come into play. It’s a complex process of becoming an endophytic bacterium.
The Functions Of Endophytic Bacteria
Bacteria that spend at least part of their lives in the plant fulfill a number of functions for the plant. The study of endophytic bacteria (EB) is relatively new, and most information on function is coming from labs. Soil scientists are aware there may be more roles of EB but field testing is in its infancy. Tests for efficacy are not keeping up with biological farming. These are the benefits of endophytic bacteria soil scientists have discovered to date.
- Promote plant growth by providing plants with nutrients
- Produce various plant hormones to aid growth and fruiting
- Increased cold stress tolerance
- Better drought tolerance
- Nitrogen cycling within the plant
- Strengthening of the plant’s immune system
- Prime plants for faster defense responses against pathogens
Bacteria are amazing and fill many roles in agriculture.
Perhaps by working with nature, instead of against her, you can start a greener revolution in your fields.
Remember that little girl who ate bacteria? She’s still eating carrots from the garden, chock full of bacteria but usually washed – grit isn’t what it used to be. Like hers, your gut can benefit the greatest by not peeling your potatoes or root crops – why throw out all those beneficial bacteria?
Your Gut And Your Soil
Soil has contributed to the human gut microbiome – the human digestive system has changed over time from the diet of hunter-gatherers to today’s fast food. Soil bacteria and gut bacteria are incredibly similar.
In recent decades contact with soil and bacteria has become less frequent. With the modern lifestyle and change in nutritional consumption our gut microbiomes are becoming less diverse than ever before. Commercial agriculture, with an emphasis on synthetic fertilizers, has decreased soil microbiology and the nutritional quality of the food we eat. These actions have led to adverse effects on both soil health and human health.
Isn’t it time to reconsider our relationship with the soil and the foods we eat?
Note: This blog highlights the role of the bacteria in the food web. There are more microorganisms that are important for the food web and that interact with the bacteria.