How the soil food network works

Lots of people here have heard of the soil food web, but how many of us actually know or understand how it really works?
What was considered the way the soil food web works has been changed drastically in recent months and so I feel it a great time to give some updated information on just how this primary part of the eco system works.

Most gardeners know that the soil food web is a complete circle of events involving all the organisms that live in the soil, all the diagrams show it as a closed circle (which it is) and these diagrams are scattered about on this site so I'm not going to delve into the known at this time.
If there are questions, I am sure someone that can post up one of the diagrams will do so in this thread.

We all know or should know about bacteria, fungi, nematodes, amoeba, flagellates, ciliates and many of the other microscopic organisms that take dirt and convert it (by their act of being there) into soil which helps plants thrive.
What I want to focus on here is how are those nutrients actually taken up by the plant's roots and what happens both to the plant and to those nutrients that were sucked in by the plant.
It used to be a given that the nutrients plant roots had available were free in space as unused nutrient or left overs from the bacteria breaking them down or out of soil particles and eating what they wanted.
Recently a paper was published that broke this "traditional thinking", while it doesn't turn my community on its head it is rather ground breaking. (some of us were working on this very subject but were beaten to the press)
James F. White, Kathryn L. Kingsley, Satish K. Verma and Kurt P. Kowalski have published this significant paper (you can find it on MDPI or just search for " Rhizophagy Cycle: An Oxidative Process in Plants for
Nutrient Extraction from Symbiotic Microbes")

We now know with fairly good certainty that there is more interaction between plant root and bacteria than previously thought when it comes to nutrient uptake.
The new research shows that plants use their exudates as previously thought, to attract and activate certain bacteria strains to provide the needed nutrient which the bacteria processes.
What happens next is that the exudate attracts these bacteria to infiltrate the roots and once they have, they are literally milked of the nutrients the plant needs, once this has been done the bacteria are pushed back out into the soil so they can rejuvenate and the process can be repeated.
So, what was previously thought of as plant roots simply sucking up left over nutrients is now known to actually be a type of bacteria farming by the plants.
This all takes place in each plant's rhizosphere area and repeated use of the bacteria increases the numbers of that species of bacteria so as to enable greater production of the nutrient each species provides.

This is significant because it goes right along with the mycorrhizae functions of transporting messages from plant root to rhizosphere to inhabiting bacteria and then providing the highway for the migration of those bacteria answering the plants call for nutrients.
It also negates the theory that the bacteria are eaten by other organisms which releases free nutrients which the plants take up through their roots.
However that theory isn't completely wrong since bacteria eaten by other organisms do release free nutrients which other bacteria can take in then migrate into the roots to be "milked" of the nutrients needed by the plant.

I will expand this thread as I have time available


Redhawk

Redhawk's soil threads

Bryant RedHawk wrote:
What happens next is that the exudate attracts these bacteria to infiltrate the roots and once they have, they are literally milked of the nutrients the plant needs, once this has been done the bacteria are pushed back out into the soil so they can rejuvenate and the process can be repeated.

WOW!

Do I have this right? The plants tell the fungi what they need, and don't want. The fungi keeps away the bacteria that the plant does NOT want, protecting the plant. The fungi a'so help make a way for the bacteria to get to the plants roots. Then the bacteria come to feed off the plant's tasty exudates. While the bacteria is there, the roots suck out the nutrients from the bacteria and then release the bacteria.

Thanks Bryant. I'm looking forward to your future installments.

Thanks so much for this.  It's awesome info and amazing to learn.  Keep it coming.

Dr Redhawk,

This is now something my son and I read together! He is going to be a giant plant nerd. I dreamed of him advancing past me, and you have a major role. Thank you for your "bedtime stories"!

Interesting. Plants as ... dairy farmers.

Great thread topic, keen to see how it goes. It seems to be overlooked by many people, probably not very profitable to fund studies that decrease fertilizer sales.

Myrth Montana wrote:Interesting. Plants as ... dairy farmers.

lol

hau Kola Nicole, well you do indeed have it mostly right, but we now know that the bacteria actually enter the roots and it is while they are inside the root that they are milked of their nutrients and then released by the root and migrate back outside to the soil.
The extreme interaction between the mycorrhizae, root exudates and the bacteria is something that we didn't have proof of previously.
It was thought that bacteria were eaten by fungi and other microorganisms and that excesses of nutrients were what was made available to the plants roots.
The work done by White, Kingsley, Verma and Kowalski shows that plants can and do actually use bacteria the same way we use cows and goats for milk.

Redhawk

My first thought was for the advise to sow in pots with sterile medium! How on earth are plants managing to grow there? Is there anything different at their beginning of life?

It seems too that then bacterias grow in hydroponics? Or what is happening in that case?

Is there anything special we can think of, like when doing culture rotations? How lost are bacterias when their favorite hosts have migrated to another garden? We rotate to starve pests who cannot find their food, but does it starve bacteiras? Do they say how fast they travel?

I have never rotated cultures, as it was not compatible for me with my micro-climates and with companion planting. At least I can drop any guilt (I had none anyway...)!

Xisca Nicolas wrote:My first thought was for the advise to sow in pots with sterile medium! How on earth are plants managing to grow there? Is there anything different at their beginning of life?  

My understanding of growing in a sterilized soil is that growers artificially supply plant food to the growing medium. Scale notwithstanding, this is, in my opinion, not far from industrial agriculture that supplies plant-available food on the surface of dead nor near-dead soil. You simply have an inert growing medium into which you sow and roots grow and you artificially supply plant food. Many houseplants are maintained this way.

I don't believe sterilized soil is a living environment as is healthy soil. Yes, it doesn't have the bad microbial life you want to avoid, but it is absent the mandatory microbial colonies. This breaks the food cycle of plants in soil and thus you have to artificially introduce plant-available food.  When it comes to producing food, even for a single family, I ask why do this when you can enjoy the benefits of healthy soil and all it provides with little intervention on our part.

Thanks for sharing.
Reading the paper, it only studied seed-vector microbes - the endogenous/exogenous organisms naturally on the reproductive material of a plant.
However, the authors hypothesize that any microbe that can colonize and enter a root can be oxidatively digested.

'Rhizophagy' means root-eating and refers to this process of in-root bacterial oxidation.
As well as oxidation, it has also been shown that plant roots secrete protein-degrading enzymes [proteases] to make nutrients in microbes available at the root tips.

However, the amount of nitrogen acquired from rhizophagy was magnitudes smaller than N taken up from soluble N within soil.
Whether rhizophagy involves uptake of other nutrients has not been tested.

Microbes that produce antioxidants are more resistant to oxidation.
Seed-vector microbes often perform poorly when used to inoculate a different host-plant.
There is a tendency for microbes to act similarly on like organisms - grass microbes help other grasses, hurt other plant types.
As well as oxidation resistant microbes that can only be farmed by certain plants.

The part I found most intriguing:

When all bacteria have exited the hair through the tip, hair elongation stops. This
suggests that root hair growth, at least in some cases, is a function of intracellular bacteria.

Rhizophagy Paper

Dan Grubbs wrote:

Xisca Nicolas wrote:My first thought was for the advise to sow in pots with sterile medium! How on earth are plants managing to grow there? Is there anything different at their beginning of life?  

My understanding of growing in a sterilized soil is that growers artificially supply plant food to the growing medium. Scale notwithstanding, this is, in my opinion, not far from industrial agriculture that supplies plant-available food on the surface of dead nor near-dead soil. You simply have an inert growing medium into which you sow and roots grow and you artificially supply plant food. Many houseplants are maintained this way.

I don't believe sterilized soil is a living environment as is healthy soil. Yes, it doesn't have the bad microbial life you want to avoid, but it is absent the mandatory microbial colonies. This breaks the food cycle of plants in soil and thus you have to artificially introduce plant-available food.  When it comes to producing food, even for a single family, I ask why do this when you can enjoy the benefits of healthy soil and all it provides with little intervention on our part.

Most people probably just use the commercial plant nutrient solutions that only provide a small limited amount of what could be provided by microoganism and the diverse amount of minerals in the soil. I thought hydroponics was all the hype until I learned more about microbiology in the soil and I thought the same as you. How could you possibly recreate the entire food web in a hydroponic system? Well apparently it's possible to get pretty close. Apparently, these microorganisms and microarthopods can live in coir, peat, or rock wool mediums.

There is a good book on how to add biology to the soil and hydroponic systems: https://www.amazon.com/Adding-Biology-Soil-Hydroponic-Systems-ebook/dp/B001PTG6LM

You still have to make good compost and compost tea to develop the bacteria and fungal colonies and apply it to the medium. This could show that plants grown in a hydroponics system could be considered "healthy" enough to compete with soil grown produce. Although we could get pretty close, I'm not convinced we will ever be able to recreate a system that produces plants with the same level of density and diversity of nutrients as plants grown in soil with similar energy costs.

Then plants do not rely ONLY on "milking bacterias" or else they would never grow in comercial sterile medium!

But after all, they want to live and set seed, so they might do so with less than optimum...

Yes this is so important, and weird it took so long to understand.

In aquaponics we know its not just free nutrients, but they must be produced or combined, in addition in animal/mammel biology many processes must happen to make many of the minerals or nutrients available, it only make sense that plants need these same processes but in a more indirect environment. Hence why composting is so important, or a live fertilizer. You can'y expect your plants be health or have a good immune system without good bacteria. Just like our Own guts.

im not entirely sure i understand the finer details . but it backs up what ive always been doing in the garden . what ever you grow in your garden , it always starts with the soil. ive known for a long time now "feed the soil and not the plant" . if you work hard enough on the soil to start with , i dont have to apply fertalizer later . my compost heap is full of all kinds of things that used to be alive. mixed twice before use.
this is all very intresting. but does it mean we need to be doing things different. what we are doing now seems to be working?

In my experience, sterile potting soil doesn't stay that way for long.

Put another way, if you can grow an Effective Microbial solution just by leaving strained rice water or whey out, why does it seem reasonable that potting soil should remain sterile?

I would expect that, in the absence of agents disinfecting the nutrient solution, water system, and air, a hydroponic system would quickly gather unto itself its own bacterial backup band.

So if I am not mistaken, what happens is that soil bacteria carry out their normal functions, finding food in the soil and converting it internally to forms useful to plants. They are then attracted into the root hairs of growing plants, which milk these bacteria in exchange for exudates that the plant doesn't need.

So it's literally the movement of bacteria that is responsible for moving plant food through the soil? Where do the fungi come in?

-CK

It's unclear how microbes enter the root tip. Possibly incomplete cell-walls, fatty acid signalling or invagination - where the plant folds its cells around the microbe. The microbes are subjected to oxidation which kills some of them or makes their cell membrane leaky, then they exit through root hairs.
I think milking is the wrong word as its a bit more destructive and forceful than that.

Plants release exudates to encourage microbes in nutrient limited soils. Some of the microbes fix N.
Fungi is a microbe.
The study only focused on seed-vector microbes, so all of this may or may not apply to generic soil biology or the majority of what we cultivate in compost.

Rhizophagy seems to be a second-order nutrient acquisition mechanism for plants in deficient soils - at least for nitrogen.
Plant hardiness is increased by beneficial microbe interactions both through colony displacement and plant immune system upregulation.

I'm curious about whether rhizophagy is a stabilizer of trace minerals in the soil as they cycle back and forth between microbes and plant in a positive feedback loop.

So far the studies published are very limited in their scope, I'm sure this was done either to produce some rapid results for publication or it might have been limited because of the particular grant the authors received.

Much of the transport mechanisms are already well known such as the fungal interactions with bacteria via the fungi being a sort of super highway for other organisms to travel along.
This is where the mycorrhizae shine, they are either wrapped tightly to the exterior of the root or they are inside the root cells both having extended tendrils that connect the exo species to the endo species of particular plants.
This is how the bacteria get inside the roots, they travel along the fungal network arriving at the exomycorrhizae and then continue along to the endo mycorrhizae.
My study is indicating that depending on what compounds are included in the exudate, those bacteria that prefer that food are the primary respondents to the exudate and this results in more of those bacteria concentrating around the roots via the fungal network.
When no fungal network is present (exo or endo mycorrhizae) the bacterial response is far slower to reach the root if they do so at all.

It should be noted that testing for nitrogen is fast and simple in the chemistry world and probably why it was chosen by the authors for their article.
Since N is usually found as compounds of ammonia and it is within the plant that these compounds are processed to free up the nitrogen it is reasonable to expect the plant to utilize bacteria as the transport mechanism.
Silica is one of the necessary minerals that seems to be directly brought in by capillary action, where as iron and other atoms might need a carrier (bacteria) to get these nutrients into the root system for transport up the phylum to the leaves.

There are limits to how effective hydroponics and aquaponics can be for transporting nutrients into plant root systems since both methods reduce the root mass of the plants in these growing mediums.
If the particular nutrient is not in the solution, no matter how many bacteria or fungi there are, they can't transport it to the plant because it simply isn't available to them. This is why vegetables grown with these methods seem to always be less nutrient dense than those grown in very healthy soil.
Until adjustments are made and the mechanisms are fully understood, it will be nearly impossible for plants grown in these alternate mediums to be able to not only receive all the nutrients but also to be able to sequester them in the fruits of the plants for humans to consume.
The day is coming since there is a lot of work being done by those dedicated to these discoveries, they just aren't there yet is all.

Redhawk

This is incredible! It reminds me of the human body and the vascular system. The soil as interstitial tissue, the fungi as veins, microbes as blood products, and plants as organs. There are forces of physics, hydrolic and osmotic pressure that make the whole process of cellular respiration (Oxygen and nutrients going from vessels to tissues and then empty blood cells making the journey to refill) very passive. I wonder if this.... could we call it soil web respiration, is a very passive process as well, each piece involved simply following a natural chemical or physic pressure or stimuli.

I'm not going to be able to look at my garden the same!

Kelly B.

That is a fairly good analogy Kelly.

To expand on that idea the fungi hyphae could also be considered a neural network that is also capable of acting like the leukocytes in the human blood stream.
The exomycorrhizae not only help transport bacteria called for by the plant exudates but they also send electrical signals along the fungal network that have the affect of drawing more beneficial organisms to their vicinity.
If a predatory nematode that isn't beneficial should show up, the fungi will literally wrap around the nematode, and the fungi will then start the devouring process.
Fungal networks have been found that are hundreds of square miles in area covered and it is thought that the network discovered in the Sierra Nevada Range above Los Angeles might be found to stretch all the way to the Canadian Border, the study to find out if this is the case is in progress now.

Bacteria will migrate from the soil up a plants main stalk(s) where they also can act as protectors, attaching to certain insects, scales and other plant malady causing organisms for the purpose of breaking down those organisms to use them for food, the affect for the plant is protection.

Plants that are healthy will not be sought out by pests animals as readily as those plants that are not getting the nutrition they need, these "sick" plants send out chemical messages that attract the insects that love to feed on the plant, these "sniffles" can be in the form of exudates, pheromones released through the stomata to the air and through electrical messages that travel through the fungal network as well as the root surrounding soil. These are the reasons composts teas are usually recommended to be sprayed on the trunks, branches and leaves of plants.

Redhawk

This is all amazing! Discovering the anatomy and physiology of the plants is turning out to be quite mind-blowing.