Environment Celebration Institute

Biological Permaculture – Part 1

October 17, 2016

This series of articles focuses on how permaculture management practices can alter, influence, and change biology in the soil, otherwise known as the Soil Food Web. The author has spent her life delving into these creatures in the soil and how they affect plant production. A complex web of life exists on all plant surfaces, both below and above ground. Soil, it turns out, is all about life.


2016 Douglas Gayeton / Lexicon of Sustainability





This is an introduction to the organisms that live in soil and to the Research Farm in California we started in June of 2015. If it was the general public reading this article, considerable time would have to be spent explaining that soil is actually a living entity. All sorts of organisms, each doing highly specific jobs for plants, are present in soil, and must be present, to keep plants healthy. Luckily, most permaculture folks already know that, so we can move right along!

Yet, perhaps permaculture people haven’t fully put together the fact that any disturbance to the soil will impact the organisms in that soil, and many will be killed with any disturbance. Hold on – what’s a disturbance? Anytime the soil is mixed, moved, or upset, if something outside the normal system is added, that is a disturbance. Is that good, or bad? It depends on your point of view. For example, a disturbance that kills many of the organisms that stop weed seeds from being able to germinate and grow would be a good thing, from a weed’s point of view. But from a grower’s point of view, that disturbance would be a bad thing, because weeds start winning. Disturbance can result in exactly what we want, or can wipe out all the things we are trying to improve. Eye of the beholder, right?

If we disturb soil constantly and never let the beneficial organisms recover, eventually we drive that soil into the condition of becoming dirt. Weeds adore dirt, diseases adore dirt, and pests like that condition more than anything else. But why? If we fix whatever was destroyed by those disturbances, then can we eliminate weeds, diseases or pests? Yes.
Really? What fixes those problems? The answer is….. life! Of course, it has to be beneficial life. Who are these organisms, how do you select for conditions that select for beneficial organisms, from a human point of view, as opposed to, conditions that select for diseases, pests, parasitic, weeds and “bad guys”?

In soil (not dirt), plants require the right balance of bacteria, fungi, protozoa, nematodes, microarthropods, earthworm or enchytraeids, spiders, and macroarthropods. Googling these creatures and learning about them in detail can be very useful to proper garden biology. Here is a brief introduction to get you started.


These organisms can be round (cocci) or rod (bacillus) shape, and be 1 micrometer (one millionth of a yardstick in size) or up to 5 to 8 micrometers in size. They clump
in various ways: chains, grape-like clusters, or pyramids. They hold onto surfaces by making glues for the express purpose of not washing away from their food sources.
Disease-causing bacteria (the “bad guys”) require reduced oxygen,
or anaerobic conditions, because they can out-compete beneficial organisms. When conditions allow plenty of oxygen to diffuse into the area, aerobic organisms will win, because their enzymes function better when there is plenty of oxygen around, and the disease organisms lose.

Many disease-causing bacteria look quite different from beneficial aerobic bacteria, and thus are good indicators that other disease- causing bacteria which do not
have distinctive shapes, are also present and functioning. Spirilla (stiff corkscrew shape which spins), spirochete (move like snakes), and vibrio (comma shape) are bacteria with a unique appearance, signaling that it is dirt, not healthy soil.


Beneficial fungi grow as strands or filaments, called hyphae. In general, beneficial fungi are wide diameter (wider than 3 micrometers), colored (tan, red, yellow, pink, purple, gold, brown, black), and have uniformly spaced septa. Beneficial fungi require aerobic conditions in order to flourish, while not-beneficial fungi, which are mostly yeasts and disease-causing oomycetes, are only competitive when oxygen is low. Disease-causing fungi are narrow in diameter, clear, and do not have uniformly spaced septa (the internal cross walls that divide the hyphae into separate cells). Beneficial fungi utilize more complex food resources than bacteria, so when selecting for a higher fungal biomass, woody materials high in cellulose, lignins, terpenes, and tannins should be added to the compost, soil, or potting mixes.

Bacteria and fungi: Two strands of fungal hyphae and a number of bacteria, including small, medium, and large cocci (round), and small and larger rod-shape bacteria. The rich brown color, and uniform septa in the fungal hyphae indicate they’re likely quite bene cial for plant growth. (in 1/16,000th of a drop of a 1:5 dilution of a compost)





All protozoa eat bacteria, in rare instances they can eat algae and each other. Two types of protozoa grow best in aerobic conditions: flagellates and amoebae. Ciliates are the protozoa that flourish in reduced oxygen conditions and thus are indicators of disease organisms growing, and conditions that will harm plants. Because the concentration of nutrients in bacteria are so much greater than inside protozoa, the excess nutrients from the bacterial biomass will be released to the plant in available forms of those nutrients.



Bacterial-feeding nematodes eat bacteria, fungal-feeding nematodes eat fungi, predator nematodes eat other nematodes, and root-feeding nematodes attack unprotected roots of plants. The beneficial nematodes contribute to plant nutrition by releasing the excess nutrients in the bodies of their prey in plant- available forms. Root-feeding nematodes are the “bad guy” nematodes, of course. Usually, the different types of nematodes are identified by the structure of the nematode’s mouthparts.



Microarthropods eat fungi for the most part, and release plant-available nutrients. Larger arthropods (macroarthropods) generally eat smaller microarthropods, and because nutrient concentrations are the same in the larger arthropods as compared to the microarthropods, there is no release of plant-available nutrients in this interaction. But all of these larger organisms help to form larger pore spaces in the soil, which are critically important in maintaining water in the soil. The large scale construction workers are necessary for a healthy soil just as much as bacteria and fungi, which focus on smaller-scale structure.

It’s only necessary to identify the functional group, rather than genus or species, when trying to understand the role and function of bene cial nematodes. Here is a bacterial-feeding nematode’s mouth at bottom right and tail to the left. Fungal-feeding nematodes always have a simple spear in their mouths; predatory nematodes have teeth; and root-feeding nematodes have spears that are complex, almost always with knobs on the proximal end.


More about the consequences of having the beneficial organisms work together in the next installment!






One of 14 test plots on the new farm. Biological amendments where added to rows on the left.


As I have worked with growers over the years, I have often set up scientific trials to document the process of conversion from dirt to soil, or from conventional ag to biological ag. From what I’ve seen, if the growers understand that soil is all about life, and that the easy way to replenish life is to make good thermal, worm, or static compost where all the organisms needed can be grown, then in six months or less, that entire farm was converted to this biological approach. If the growers didn’t really want to change their ways, just can’t comprehend that soil life is what has to be nurtured, then they returned to the toxic chemical management system once again.

Regardless of whether the farmer converted or didn’t, science always lost out. The farm went biological or reverted to conventional long before the required 2 to 3 years of documentation to satisfy scientific journals was achieved. When farmers realize the benefits, see how easy it is to achieve, quickly the farm goes biological. If the farmer can’t overcome the fear instilled by fertilizer salesmen, then the whole farm is back to conventional methods all too soon. Farmers are working hard to keep their farm, make a profit, send the kids to college, and not working as hard to document a scientific theory.

Doing all the measurements required to document the benefits of good biology isn’t cheap either. Just one farm, working with just one crop, requires a budget of about a quarter of a million dollars to measure weed reduction, water use reduction, improved soil tilth, improved nutrient cycling, reduced disease and pest damage, improved nutrient content in the produce, and increased yields. So, it seemed a hopeless cause to get the science done right.

However, we were finally lucky enough to find funders (Thank you, funders!) who wanted to give us the chance to do the science. They donated half the money to buy the farm, and the other half of the funds were from Nature’s Solutions. The farm is near Berry Creek, elevation about 3,600 feet in the Plumas National Forest, and about 40 miles from Oroville, California. Most of the 59 acre farm is conifer (cedar, pine), oak, chestnut, manzanita, madrone, and dogwood forest. There are numerous seasonal springs on the property, and three good- size ponds. We have bear, deer, fox, coyotes, puma, raccoon, birds galore, chickens, cats, and a dog.

Late in May of 2015, we started the odyssey of putting in replicated trials on the farm. We started with a small kitchen garden and small scale, hand-turned compost piles in June, 2015. We implemented controls A) no biological additions B) just compost extract applied C) just compost applied D) and both compost and extract applied in three of the large raised bed rows.

We didn’t realize when we bought the farm how much Roundup had been used on the property. We had to throw away two nearly full containers the previous owners had stored in the shed. Compaction was horrible in all the soils on the farm, from the bare soil areas where Roundup was used extensively, to the garden areas with flowers. As a demonstration that highly compacted soil and overuse of chemicals may prevent establishment of beneficial organisms, we applied these treatments to the surface of the soil, without mixing or turning the biology into the soil.

During the first year of working on the farm, we have detected very little improvement in biology in the soil, although the plants have clearly demonstrated improvement – increased size, less insect damage, reduced weeds, and higher yields. Quite a few people have come to train and visit during our first year. Despite not having a full growing season in 2015, not having fully mature compost, and suffering effects from residues of Roundup and other toxic chemicals in the soil, we grew almost all the vegetables we needed to feed ourselves.
During this last winter, we built the hoop house for starts and the chicken houses for egg production. We planned the expansion from just the kitchen garden to larger production fields, as well as a food forest, from a small scale/ hand- turned composting operation to a composting operation requiring a self-propelled turner. A storefront in Oroville was found to serve as an outlet for some of the farm’s products.

In 2016, we have expanded from a small kitchen garden to just over an acre of production land, and have started the process of opening light gaps in the forest where we will plant under-story trees later this fall. We plan on growing shade-requiring and shade-tolerant cherries, raspberry, blueberry, herbs, mushrooms, possibly coffee, and tea. Our first harvest this year demonstrated that the “plus- biology” management improved pea production, root depth, and reduced weeding, disease and insect attack as compared to no-addition of biology.

We are just getting underway with the “biological permaculture” system, and hopefully, over time, people will stop by to see new projects, see what we are doing differently than other farms, or come to train with us. Our purpose here is to demonstrate the easiest, fastest way to convert from toxic agriculture to life-supporting agriculture. We all need to work together to spread this knowledge far and wide. For life begins in the soil. Stay tuned for more.

For a list of upcoming courses and online classes by Dr. Ingham visit www.environmentcelebration.com

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