Living Soil by Tim Wilson of Microbe Organics

Tim wilsonTim Wilson explains beautifully his perspective on the soil. The microbes in the soil. Such an interesting article even  if you have only a slight interest in soil.

the following is an excerpt.  please go here for full and original post.

The term ‘living soil’ is getting a lot of lip service these days, however a living breathing moving soil is a thing to behold and great to grow with. It just gets better as it becomes more alive.

I’d like to try describing to you what this means. A living soil is comprised of a large variety of creatures, mostly microscopic and single celled. Part of this life is the plant itself but billions of life forms which support this plant and microcosm are arranged hierarchically at a level in the soil to which they have evolved for optimum survival and the wholistic function of their universe.

There are multiple interfaces in the soil. There are millions of small pores throughout, millions of various particles interfacing as aggregate; sand, clay, silt, rock, organic matter, humus and thousands or millions of roots interfacing these.

Besides these areas of contact or buffer, there are some broader distinct fields of transpiration between life forms which thrive within certain steadfast environmental conditions. This is why, as horticulturists, we may achieve living soil through minimal soil disturbance or no-till.

cropped-0031.jpgTo describe these fields, first lets talk about the soil’s surface. Soil scientists call this the detritusphere, not a very complex name when you consider what detritus encompasses. So here is where stuff falls; everything from leaves to poop and this is where the greatest velocity and frequency of decomposition occurs. The detritus is principally carbon based. The elements of oxygen, nitrogen, light and moisture combine with the microorganisms evolved to this environment to do their job of degradation through consumption. These organisms are specialized to use the components and fuel available in the top layer of the soil, let’s say the top one to three inches dependent on soil type.

At a lower depth they would not function similarly because the fuel would be lacking. The material processed as waste by these microbes is then passed down to the next set of microorganisms evolved to process that modified substance.

If the raw detritus is worked into the soil, without first being degraded by surface dwellers, then the subsurface microbes can become overwhelmed (if I can use such an expression for microbes) with the task and can easily use up any and all nitrogen at hand decomposing this organic matter, thereby depriving local plants of this nitrogen. This can result in what some refer to as nitrogen lock out or lock up.

The next interface is where openings are created by earthworms, nematodes and other larger creatures, rather comically called the drilosphere by scientists. This is an area where some of the previously described material is conveyed by the bugs n’worms along with bug n’ worm poo and bioslime. The bioslime created is important for binding particles and contributing to aggregation. Obviously these create unique passage ways for certain sized organisms, air and water.

Branching off of these passages and stretching into the entire area which we call our living soil is a myriad of various sized openings and caverns. This area is referred to as the porosphere. This is where the meat and potatoes of the soil grows, is stored and is hunted. It is this zone which interfaces with the roots, which as most know, is called the rhizosphere.

Of critical importance is the conjoining matter, the particles or chunks which comprise the soil itself. These pieces once bound together by bacterial and fungal ‘bioslime’  is referred to as aggregated material and how they cohese is what forms the aggregatusphere (another complex term ;>). The aggregation is bound by fungal hyphae, roots and various gel-like polymers and carbohydrates excreted from plants and creatures alike.

When the gardener/horticulturist first mixes their soil, they can have some pretty good control over the size of pores created, balanced with decomposed/aged/composted organic matter.

The various sized particulate creates the multitudinous openings and caverns which make survival habitats for certain small organisms like bacteria and archaea and hunting grounds and habitat for some larger organisms like protozoa, nematodes and rotifers. These spaces flow with water and air allowing bacteria, archaea and fungi to mine the stored/sequestered nutrients, from vermicompost, compost, humus, clay/rock and other organic matter, which are then passed via the rhizosphere in a number of ways to the roots. There are miniature pockets of water bound to soil particles which are necessary to the survival of many microorganisms.

Methods of Nutrient Assimilation in the Rhizosphere
There are a variety of ways in which plants uptake nutrients organically/naturally. The majority of relevant current research indicates that most nutrients are derived from the predation of bacteria and archaea by protozoa and nematodes. The waste produced by the larger organisms is in ionic form, being directly taken up by the roots. In addition to this there are mycorrhizal associations between certain types of fungi and roots whereby the fungi provide the roots with nutrients and receive nutrients in exchange.

The most active protozoa contributing to this nutrient loop are flagellates and naked amoebae, however ciliates and testate amoebae cycle nutrients to a lesser degree in an aerobic soil. As the flagellates and naked amoebae consume bacteria/archaea they utilize somewhere from 10 to 40% of the energy intake for sustenance, dependent on species. The excess is excreted in a (ionic) form directly available to the roots of the plants. This means a plant can receive a whopping 60 to 90% nutrient bonus from this exchange.

As I have indicated previously the plant is not necessarily passive in this process. Studies show that plants emit certain carbons from their roots which attract and feed specific types of bacteria/archaea. Once these bacteria/archaea begin to divide, they begin pigging out on the adjacent organic matter (using organic acids) and the population explodes, thereby stimulating a resultant protozoa population explosion. Talk about a return on your investment.

We should not leave the bacterial feeding nematode out of this. They also cycle nutrients via the microbial nutrient loop in similar fashion by predation of bacteria/archaea and excreting bio-available nutrients. One difference is that they require about 50 to 70% of the energy intake for sustenance, however they are much, much larger. I suppose that due to their size, they cannot get to some spots that protozoa do. The other consideration is that bacteria can multiply every 20 minutes and protozoa every 2 hours, while nematode eggs take 4 to 7 days to ‘hatch’. Tough to do the math.

Roots also exude various organic acids like carbonic acid, citric acid, malate, oxolate and several others. These acids solubilize sequestered nutrients into an ionic form which they can assimilate. [e.g. dissolved organic nitrogen (DON); phosphorus; (DOP)] Some bacteria and archaea (besides the nutrient loop previously described) excrete similar acids which degrade organic matter and provide nutrients directly to the roots or the soil solution (an area in the rhizosphere where nutrients are in solution) and some fix atmospheric nitrogen and are symbiotic with legumes.
[note: fungi also excrete similar organic acids to release/degrade nutrients from organic matter]

Where does CEC (cation exchange capacity) come into this picture? The CEC is your soil’s capacity to hold nutrients. It is based on your soil components having a negative charge and holding on to positively charged nutrients. Various types of clay like bentonite, organic matter and sphagnum peatmoss have excellent CEC.

It is this researcher/gardener’s understanding or hypothesis that the nutrients which are held in place in the soil are released by the various types of acids (citric, carbonic…others) mentioned previously. These acids are exuded by bacteria, archaea or roots to create hydrogen ions which then displace (exchange for) into the soil solution, the nutrient ions required by the plant. In the case of bacteria/archaea which have consumed these nutrients, they are themselves consumed by protozoa and nematodes which they expel as waste in ionic form nutrient immediately available to the plant, as previously described.

It appears that this method of uptaking the desired nutrient is more ‘economically’ viable for the plant. Rather than expending its precious resources to mineralize (release) these nutrients, the bacteria, archaea, protozoa and nematode pull it off for her.

Soil Composition?
In my opinion, the number one method of nutrient uptake listed above that the horticulturist can influence is the predation of bacteria/archaea by protozoa (and perhaps nematodes). By ensuring a good soil base with a variety of pore sizes but with lots of adequate drainage, moisture retaining substance and composted organic matter, one will provide good habitat and hiding spots for these organisms to flourish.

When creating your soil mix bear in mind that you wish to create long lasting spaces or pores of various sizes so it is best to include some very slow to decompose organic matter and some rock or sand-like particles along with some of your faster degrading compost to see you through your first season as your soil matrix comes to life.

I won’t get into specific ingredients, as others are better able to list these. Besides, I’m a believer in using what is close at hand, easily available and cheap.

There is another sphere of influence in the soil which I feel is of importance and that is the interface between stone/rock and the upper portions of the soil. For container growing there is going to be variance in accord with your container size and depth and the way you wish to arrange things. I do believe that there are groups of microorganisms (bacteria/archaea & fungi) which work at certain depths with limited to no oxygen which mineralize nutrients from stone, rock and rock powders. In similar fashion to the surface dwellers, the nutrient waste which they process is  passed up the chain and then to the roots. Within this hypothesis there may be some logic in placing a layer of small stones or gravel in the bottom of a container. Of course this makes more sense in a larger, deeper container.

Anecdotally, I surmise that a variety of colors of rock/stone is beneficial. This is more of a gut feeling and is derived from the idea that as humans we assimilate more vitamins and minerals by choosing diversely colored foods.

I hope I have conveyed that allowing microbes to live and function hierarchically at their optimum position undisturbed is how a horticulturist best achieves living soil. By leaving soil undisturbed fungal hyphae circuitry remains established, mycorrhizal colonization of roots takes place more quickly, networks of microbial nutrient exchange stay in optimum position.

Of course it is a decision which each grower must make on their own, balancing what is feasible and convenient to the space available and to their lifestyle and ability. I can attest that my experience with this method of container growing is that the soil just seems to get better with each season.

It is important to keep it alive through additions of organic matter, topdressed and I believe a minimum volume of 5 gallons and 14 inches depth is important. A larger volume is likely better. Allowing the soil to be populated by small arthropods, nematodes and perhaps earthworms is of great value.

In parting I’d like to avoid any confusion between the distinct areas of the soil habitat I’ve discussed and a recent popularized growing method involving nutrient layers. The level of soil (top 2 to 3 feet) in which most plants grow, naturally or agriculturally is quite homogenous as I have described above and raw nutrients are naturally added at the surface as I have described and not frequently via surprise layers or spikes.

I’ve listed some references and reading resources below.

1/ A Hierarchical Approach to Evaluating the Significance of Soil Biodiversity to Biogeochemical Cycling

2/ MH Beare, DC Coleman, DA Crossley Jr, PF Hendrix, EP Odum
Plant & Soil Journal; 170; 5-22, 1995 ; Netherlands

3/ Regulation of soil organic matter dynamics and microbial activity
in the drilosphere and the role of interactions with other edaphic functional domain
George G. Browna, Isabelle Baroisa, Patrick Lavelle
Eur. J. Soil Biol. 36 (2000) 177-198

4/ The role of biology in the formation stabilization and degredation of soil structure
JM Oades; Dept. of Soil Science, University of Adelaide, Australia – 1992

5/ Resource, biological community and soil functional stability dynamics at the soil–litter interface
Manqiang Liu ⇑, Xiaoyun Chen, Shi Chen, Huixin Li, Feng Hu
Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agriculture University, Nanjing 210095, China 2011

6/ Microbial diversity and soil functions
Dipartimento della Scienza del Suolo e Nutrizione della Pianta, Universita` degli Studi di Firenze, 50144 Firenze, Italy
European Journal of Soil Science, December 2003, 54, 655–670

7/ The Rhizosphere: An Ecological Perspective – Edited by Z.G. Cardon & J.L. Whitbeck. B. M. McKenzie – 2008

8/ Modern Soil Microbiology, Second Edition by Jan Dirk Van Elsas (Editor), Van Elsas Van Elsas, Janet K Jansson (Editor) – 2006

9/ Organic acids in the rhizosphere – a critical review
David L. Jones
School of Agricultural and Forest Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, UK Plant and Soil 205: 25–44, 1998.

10/ Interactions between rhizosphere microorganisms and plants governing iron and phosphorus availability
Petra Marschner, University of Adelaide David Crowley University of California, Riverside, USA and Zed Rengel The University of Western Australia, Australia   2010

11/ A Link Between Citrate and Proton Release by Proteoid Roots of White
Lupin (Lupinus albus L.) Grown Under Phosphorus-deficient Conditions?
Yiyong Zhu, Feng Yan, Christian Zörb  and Sven Schubert
Plant Cell Physiol. 46(6): 892–901 (2005)

12/ Soil Science Extension
North Carolina State University
NC Certified Crop Advisor Training
Steven C. Hodges

13/ Organic acids in the rhizosphere and root
characteristics of soybean (Glycine max) and cowpea
(Vigna unguiculata) in relation to phosphorus uptake in
poor savanna soils
African Journal of Biotechnology Vol. 7 (20), pp. 3620-3627, 20 October, 2008

14/ Role of root derived organic acids in the mobilization of nutrients from the rhizosphere David R Jones & Peter R Darrah; Cornell & Oxford Universities
Plant & Soil Journal; 166; 247-257 1994

15/ The role of root-released organic acids and anions in phosphorus transformations in a sandy loam soil from Yantai, China
African Journal of Microbiology Research Vol. 6(3), pp. 674-679, 23 January, 2012

16/ Nutrient uptake among subspecies of cucurbita pepo L. Is Related to Exudation of Citric Acid – Martin PN Gent, Zakia D Parrish & Jason C White
American Soc. Of Horticultural Science 130(5); 782-788, 2005

17/ Root exudates as mediators of mineral acquisition in low-nutrient
Felix D. Dakora & Donald A. Phillips Plant and Soil 245: 35–47, 2002.

18/ Nutrient Management for Fruit & Vegetable Crop Production
Peter M. Bierman and Carl J. Rosen
Department of Soil, Water, and Climate
University of Minnesota

19/ Protozoa and plant growth:
the microbial loop in soil revisited
Michael Bonkowski
Rhizosphere Ecology Group, Institut für Zoologie, Technische Universität Darmstadt,
Schnittspahnstr. 3, D-64287 Darmstadt, Germany – 2003


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