Organic growing from a microbial perspective



Organic Growing from a Microbial Perspective
To come to a rudimentary understanding of how organic or natural growing really works, one must cast off previous miscomprehensions from the chemical model, that when we fertilize or add compost or other organic matter, we are feeding plants. This is not the case. With true organics one is feeding the microorganisms in the soil which convert organic nutrients into a form which can be assimilated by the roots of plants. According to studies, there are only a very few plant species capable of absorbing only a very few organic nutrients. Most plants are only capable of absorbing inorganic nutrients which are made that way by microbes which live at the root to soil interface, the rhizosphere. So the idea which you have, that you are feeding your plants when they appear to need nitrogen and you feed an organic fertilizer deemed high in nitrogen, is bogus. You are feeding the microbes which feed the plants.

Chemical fertilizers, mostly derived from petroleum are inorganic and can be absorbed by the roots of plants, however they are pollutants, which can cause a die off of and population change of soil microbes [** see addendum below], build up unused residues which run into the water table and, in my opinion, create harmful tissue changes in the plants which humans consume as food and medicine. In addition, I believe, the use of chemical fertilizers promote the incidence of plant pathogens like powdery mildew, erwinia, fusarium, pythium, etc. The grower can end up in a vicious spiraling downward fall as they use one chemical after another to control the effects brought on by the others.

The plant is no passive player in the natural growing game of survival but is the master conductor of this delicately balanced orchestra. The plant receives energy from above the soil in the form of light. This photosynthesis results in the plant’s internal production of carbon. It utilizes this carbon to create and reinforce tissue as it grows, so it is a very valuable commodity. As we all know the plant also requires a form of nitrogen (N) and other macro and micro-nutrients which it receives through the root system. As already stated this N must be in a form which the plant can directly uptake and use, usually a form of ammonia (N). Research has shown that when a plant needs to uptake N from the soil it sends out some of its precious carbon through it’s root system as a feed for bacteria and *archaea which live in the rhizosphere. [* Archaea are prokaryotes indiscernible from bacteria except through specialized testing; usually DNA] There are more complexities involved, such as, that certain plant types attract certain bacteria/archaea types but that is beyond the scope of this portrayal. When the bacterial/archaea population has increased in response to the carbons excreted by the roots, protozoa and bacterial feeding nematodes are attracted to the region, ‘hatch out’ from cysts and eggs respectively and in the case of protozoa multiply rapidly. Protozoa consist of flagellates, amoebae and ciliates. Some protozoa can multiply (divide) every 2 to 4 hours so their numbers can increase in short order. The protozoa and nematodes consume the bacteria/archaea and release, as waste, the ammonia (N) which the roots can then absorb. The multiplication rate of the bacteria/archaea increases in response to this predation and so on. This has been called the microbial loop. Protozoa are particularly good providers as their ‘digestive system’ only utilizes about 30% of the nutrients consumed meaning that roughly 70% is released as the waste which the roots crave. This factor, combined with their short generational time makes them real feeding machines. Undoubtedly there are micronutrients also processed and absorbed in this cycle. There are still many mysteries which research has yet to unfold or are not yet known to this author.

This is not the end. The concert continues. The bacteria/archaea also consume the ammonia (N) which is now bioavailable to them, so are in competition with the plant for these nutrients. Because of this, if there are no predators or insufficient numbers to consume the bacteria/archaea they could potentially lock up the N.  When the plant is growing it is in a vegetative state and requires a large load of available nitrogen (N) so it is advantageous for it to continue this release of carbon and maintain a balance of bacteria/archaea and protozoa, while uptaking just the right amounts of nutrients. Don’t get me wrong. There are other players in this orchestra, either playing subdued roles or waiting their turn to play. There are higher order animals like mites, other microarthropods and worms. There are various forms of fungi, most of which are degraders but some of which are mycorrhizal. These all have roles in breaking down organic matter into a form which can then be mineralized by the plant’s bacteria/archaea team or delivered directly to the roots.

When the plant receives its signal from the upper world, above the soil, that it is time to switch gears and produce flowers and or fruit, its nutrient requirement changes. Although the mechanics are not well known to this author, studies indicate that the plant then increases the uptake of the ammonia (N) (bioavailable nitrogen) and reduces or stops excreting the carbon which feeds the bacteria/archaea. This effectively starves the bacteria/archaea which will react by dying or becoming dormant. This of course results in a similar reaction by the protozoa and bacterial feeding nematode population. The mycorrhizal fungi previously mentioned is then triggered into increased growth and production. Studies have indicated that the transference of bioavailable phosphorus and potassium to the roots occur mainly as a function of arbuscular mycorrhizal fungal hyphae in symbiotic relationship with the roots of the plant. The fungal hyphae (microscopic strands) grow right into the root cells and exchange nutrients. In exchange for carbon, once again released by the plant, the fungal hyphae delivers the required bioavailable nutrients to the root system. The fungal structure derives these nutrients from organic matter and food sources in the soil, some naturally processed by the other players as previously mentioned. It is my hypothesis  that the form of carbon released to stimulate the mycorrhizal activity is of a varied molecular structure from that released to promote the bacteria/archaea population previously discussed, however I have no direct data to substantiate this. There are often different types of bacteria which accompany mycorrhizal fungi, adhering to the fungal hyphae in a symbiotic relationship. It is thought that these bacterial species function to exchange nutrients with the fungi as well as to protect the fungal hyphae from consumption by other microbes and even contribute to the protection of the plant from pathogenic fungi. There are other types of mycorrhizal fungi (ectomycorrhizal) which encapsulate roots rather than entering them but these are mostly associated with trees in the temperate and boreal regions.
So you see it is quite a complex arrangement which the plant conducts or controls and there are many facets which yet remain a mystery.

** Addendum to Organic Growing From a Microbial Perspective

Okay, since I wrote Organic Growing from a Microbial Perspective I’ve received feedback which clearly outlines the need to explain the ‘chemicals killing beneficial soil microbes thing’, the role of NPK ratings as well as the pollutants statement. This feedback is justifiable. Please bear with the redundancy of the following. It reflects my attempt to be thorough.

It may be so, that some beneficial microbial life is out and out killed by chemical fertilizers but the more likely cause of death occurs over an extended period which I’ll attempt to explain.

There are bacteria/archaea that will happily feed on chemical fertilizers. Indeed, there are bacteria that will ‘feast’ on diesel fuel. It is more likely that the use of chemical fertilizers negatively effect soil biota over a period of time. Chemical N (for example) is (to my knowledge) delivered to the roots of plants in ionic form, bypassing the whole microbial nutrient loop, which occurs through degraded organic matter being delivered in several processes; one major way being by bacterial/archaeal [sic] predation by protozoa (& bacterial feeding nematodes). It follows logically that if chemical fertilizers are used over an extended period (days? months? years?) that the microbial nutrient cycle will slow and/or cease.

The other side to this is that plants emit compounds from their roots which feed bacteria/archaea and fungi (of species conducive to their survival[?]) as an active participant in this microbial nutrient loop. Logically, if the plant is receiving direct feed ionic nutrients it is likely to slow and/or cease this process.

I compare this to a patient receiving intravenous feeding for a period of time and then needing to slowly adjust to real food again when the IV is discontinued.

The effects over a period of time (days? months? years?) will likely cause a die off of soil biota of a particular microbial consortia but may stimulate the growth of another microbial consortia (possibly/probably not as balanced and beneficial as the natural one), possibly causing disease.

I hypothesize another factor that may have effect is that when the plant is an active participant in the microbial nutrient cycle it ‘decides’ what nutrients it requires in time shifts unknown to us. If we are using chemical fertilizers quite likely much goes unused by the plant or is absorbed by the plant unnecessarily, perhaps promoting disease. The unused chemicals pass into the groundwater and streams or into the atmosphere. We’ve all heard the detriments around that and this is the pollution to which I refer.

What about NPK in Natural Growing?

I’ll try to write something up which illustrates the difference between nutrient processing and utilization from a chemical and natural (or organic) standpoint (for want of a better word). The following information and opinion is stated by me and is derived from the citations and links provided. I use the words ‘apparently’ and ‘appears’ because I believe knowledge and science is fluid. I also don’t pretend to understand everything perfectly and may need correcting. Just because we know the Earth is not flat does not mean we know everything about it.

To simplify things I’ll restrict the discussion to the plant’s use of nitrogen (N). The forms of N which plant roots are able to uptake are in ionic form or soluble. These soluble forms of N are ammonium (NH4+) and nitrate (NO3-). Very simply stated these soluble forms of N are instantly available in chemical N and there is no need for any bacterial/archaeal (B/A) mineralization to make them available to the roots of plants. There is some indication that some soluble ammonium is utilized by B/A and mineralized into nitrates, however this appears (to me) somewhat an opportunistic occurrence (from the B/A perspective). So yes we can concur that B/A eats and thrives on some chemically provided ions but this action is not a necessary one for the plant to uptake exactly the same ions as are being consumed by the B/A. In certain circumstances the B/A will be in competition with the plant for these nutrients. So it appears that plants can grow in this fashion without interaction by mineralizing B/A. It appears that the chemically provided ions (soluble N) completely bypass the microbial nutrient cycle.

With natural or organic growing, N ( R-NH2 ) for the plant is contained (sequestered) in a non-soluble (non-ionic) form in organic matter (or in the case of the gardener; compost and other soil foods). It is true that there are certain known bacteria (and now some archaea) which directly fix and supply ionic forms of N to the roots of plants and this is an area where ‘we’ are still learning so all is not known by any stretch. However soil scientists have discovered and it is common knowledge (as knowledge goes) that the bulk of NH4+ and NO3- are delivered to the roots of plants by protozoa (flagellates, amoebae and ciliates). This occurs in a complex network ostensibly, controlled in large degree by the plant. The plant releases compounds from the roots which feed B/A, thereby increasing the B/A population. The B/A consumes/processes forms of R-NH2 or forms which are pre-degraded by fungi and or other B/A. The B/A further multiply with a good supply of food and their large population encourages the excysting (hatching from cysts) and dividing of protozoa. The protozoa prey upon the B/A and in an approximate 30 minute period complete the excretion of NH4+ and/or NO3- available to the roots of the plants. Apparently protozoa only utilize 30 to 40 percent of the nutrient consumed  making 60 to 70% available to plants and many have a division cycle of 2 hours so the efficiency of this nutrient delivery system is considerable. Just as it began, the microbial N cycle can be rapidly shut down by chemical emissions from the plant. It is apparent that the nutrient needs of the plant can change within short periods (perhaps in hours). There is much yet unknown, however I hypothesize that even disease control may be effected by a sudden reduction of N in the rhizosphere. This is certainly something which cannot be effectively manipulated by chemical N applications.

My goal in writing this was to illustrate the stark differences between the use by a plant of chemically provided ions and those derived through the microbial nutrient cycle. I believe I have succeeded. There are other ways which plants obtain N, such as through fungal interactions but that is nature; always have a back up.

I did fail to find information detailing the effects of chemical soluble N on protozoa populations. Although we humans have great confidence in our ability to mimic natural molecules sometimes we discover it is the subtle variances going unnoticed which end up having the greatest effects.

Some References; 
Email me if you wish to track down these references.

Protozoa and plant growth:  2003;
the microbial loop in soil revisited;     Michael Bonkowski;
Rhizosphere Ecology Group, Institut für Zoologie, Technische Universität Darmstadt,
Darmstadt, Germany

Soil microbial loop and nutrient uptake by plants: a test
using a coupled C:N model of plant–microbial interactions
Xavier Raynaud Jean-Christophe Lata
Paul W. Leadley
Plant Soil
DOI 10.1007/s11104-006-9003-9

The mycorrhiza helper bacteria revisited; 2007 P. Frey-Klett, J. Garbaye and M. Tarkka
Interactions Arbres/Micro-organismes, Champenoux, France;
UFZ-Department of Soil Ecology, Helmholz Centre for Environmental
Research, Halle, Germany

Modern Soil Microbiology; 2nd edition 2007 – Chapter 6 – Protozoa and Other Protista in Soil
Marianne Clarholm, Michael Bonkowski, and Bryan Griffiths

Soil protozoa: an under-researched microbial group gaining momentum
Marianne Clarholm
Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences (SLU), Box 7026, S-750 07 Uppsala, Sweden
Soil Biology & Biochemistry 37 (2005) 811–817

David C. Coleman
University of Georgia

I created a PDF from a write up I found on the WSU website. I created this without permission but I believe the authors won’t mind. I think some may find it helps to clarify the NPK cycle, etc.
NPK Cycle
The link for the write up is

How to Apply All This to Horticultural Activities

You say, okay so that’s how it works but how do I apply that to my growing situation? The answer is pretty simple really. You need to assure that there is organic matter, mostly in the form of composted plant and animal (manure) substances in or on your soil for a microbial inoculant and food source. Additionally you can add microbial foodstocks such as diluted fish hydrolysate and molasses and kelp meal, alfalfa meal and rock phosphate and other clay and rock powders if available. It is very good to include rock phosphate in your composting process if you are making your own. Rock phosphate in the compost adds a long lasting source of phosphorus for microbes to draw from. At time of planting it is highly beneficial to place some mycorrhizal fungi spores in the hole or on the root system. You can research the best strain of fungi for the plants you are growing and purchase the spores from a number of suppliers. [ ] You may also consider seeding companion edible mushrooms which provide a dual benefit of cycling nutrients to your plants and providing your breakfast. You may research this at the site. The rest is governed by the plant, as previously discussed, assuming that all the necessary components are available from the organic matter and additional foodstocks provided. In my opinion manipulation of the pH is not a wise practice in natural growing unless dramatic acidity or alkalinity are measured. Soil with a healthy microbial population tends to self regulate the pH. One should disturb the soil as little as possible so as to leave fungal growth and strands intact. I realize this is challenging when growing in containers. I have run trials where wooden bins were constructed (2’x3’x1.5’ deep) where soil was successfully left intact after annual plants were harvested and replanted over several seasons. In between plantings composting worms were introduced to help consume the residual dead roots and plant matter. The worms were later trapped out. Compost tea was applied regularly to boost the soil microbial population. Over time there developed something of a miniature ecosystem complete with mushrooms, rove beetles and other beneficial bugs. If you are growing in smaller containers it is a good idea to provide a high volume of quality compost and or vermicompost at the onset.

Some people grow herbs and edible produce in containers organically. Because this has been practiced extensively utilizing chemical fertilizers, there is a period where growers have flushed the soil with copious amounts of water, the thought being that they are removing the harsh or harmful chemicals from the plant tissues. Too late! Those chemicals are already integrated into what you plan to put on your dinner plate or in your medicinal tea or pipe. At least that’s my opinion. If you have grown your produce naturally allowing the plant to be in control, this flushing routine is not only unnecessary but sort of stupid. Since plants are not able to uptake organic nutrients, what exactly would you be flushing away? You might instead be water logging your soil and roots.

Using Compost Tea

The use of compost tea (CT) is one of the best ways to inoculate your soil with the beneficial microbes you wish to have for optimum health of your plants. It is also good if your supply of compost or vermicompost is limited, as it multiplies those microbes, we have been discussing, by the millions. Remember the protozoa I mentioned earlier? Well you can brew an aerated compost tea specifically to have a large population of protozoa, usually mostly flagellates. If you have a good quality compost or vermicompost, protozoa will already be present, often in a resting cyst. If you have an efficient aerated brewer you can pretty much count on having a high flagellate (protozoa) population combined with bacteria/archaea and fungal hyphae (not mycorrhizal) at 36 to 44 hours brew time (65 to 72 degrees F). If you have a microscope you can examine the CT periodically to be sure that the microbial population is optimum. The use of aerated compost tea also provides the opportunity to manipulate microbial populations for specific purposes by using various recipes and brew times. You may wish to have high bacterial or fungal numbers for pathogen/disease control or have soil or plants that require a higher population of a microbial type. I have a lot to learn yet of fungal species which can grow in compost tea so until I have learned to identify the species occurring I’m cautious about some of the tricks employed to stimulate fungal hyphae growth in compost. Better to count on good quality compost and vermicompost with natural occurring quantities and species of fungi and use known mycorrhizal and mushroom spores in the soil.

As always, I am open to correction or refinement of what I have written.



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