Unsurprisingly to eco-farmers, many of the phytohormones plants need are actually created by microbes — and these can be measured and cultivated by growers
More than a century ago, Japanese researchers were working to understand a “foolish seedling disease” in rice, so called because infected seedlings towered over their healthy neighbors. These abnormally leggy and weak seedlings had been driven to their abnormal height by the fungus Gibberella fujikuroi. Subsequent lab cultures of the fungus induced the same gangliness in rice seedlings, even if the fungus itself had been killed off. In time, the compound responsible for this excessive elongation was isolated and named after the offending fungus.
Chemists clarified that this “gibberellin” was not one but a class of compounds that induced a similar stem elongation in numerous plant species beyond rice. The fungal isolate was found effective at inducing rosette-forming plants to bolt and at enabling dwarf mutants to grow tall like their non-dwarf relatives. These observations led to the hypothesis and eventual discovery that gibberellins, though initially isolated from their namesake fungus, are compounds properly native to plants themselves and key to plants’ own growth regulation.
As the discovery of gibberellins makes clear, soil microbes were known to produce substances that influence plant growth even before these microbes were recognized in plants.
Around the same period that gibberellins were being studied as a fungal isolate, another class of molecules was the first to be recognized as growth regulator molecules native to plants. These “auxins,” from the Greek verb meaning “to grow,” were soon found to be usefully produced by yeasts and bacteria as well, providing a ready source of the substances for experimentation.
From the very start, then, it has been understood that the regulation of plant growth is not entirely the purview of plants. Numerous microbes place their thumbs on the scales of plant growth, for good and for ill. Pathogens like Agrobacterium tumefaciens hijack the plant’s growth regulation machinery to induce the tumors we know as crown gall and to parasitize the plant’s resources and energy. In contrast, the famous teammates of the legume family produce growth-regulating compounds in order to nodulate the plant roots, enabling a mutually beneficial trade in NH4 and sugars.
Many other plant hormones — signaling molecules by which plants direct diverse aspects of their growth, immunity and stress responses — have been discovered, as have other microbial friends and foes capable of synthesizing these hormones and markedly altering crop performance, resilience and health.
As new soil microbiome tests empower farmers to assess their own soil critters’ capacity to produce and deliver plant hormones, I write this article with three goals in mind:
- To provide a handy reference guide for plant hormones themselves.’
- To elucidate how each hormone is connected to soil life, enabling us to perceive an underappreciated set of services provided by soil microbes.
- To demonstrate via these connections the impossibility of conceptualizing and managing the life of the crop in isolation from the life of the soil
A Plant Hormone Caveat
Before we get into the hormones themselves, a quick caveat: hormones are difficult to encapsulate in a nutshell. A hormone is a tiny molecular signal that enables one area of the plant to communicate with another. There are myriad behaviors that plant cells are capable of expressing at any given time, but hormones play a crucial role in determining which genes are being expressed, which enzymes are produced, and which needs are prioritized at any given moment.
By design, these tiny messengers can set off widely varying physiological responses depending on (1) what plant tissue is concerned, (2) the concentration of the hormone, (3) the synergistic or antagonistic influence of other phytohormones (referred to as “crosstalk”), and (4) the growth stages of the plant, to name the principal few. Nonetheless, we can get an awful long way by understanding some of the core jobs of each hormone.
Plant hormones may be classed somewhat artificially, but usefully, into two groups: those principally related to growth promotion and those related to stress responses. I say “artificially” because there is much overlap between these buckets, but we’ll need to make some simplifications in order to get a handle on how our crops grow and behave.
Growth-Promoting Phytohormones
There are three primary growth-promoting phytohormones that growers should be aware of.
| Auxin Key functions: Get big, tall, and well-rooted -Auxin signals cells to expand—to get bigger and longer—and thereby governs the direction of growth: -In roots, auxin accumulates on the lower side, inhibiting growth there and causing the root to bend downward. -In shoots, auxin masses in the shade, causing those cells to elongate, bending the stem toward the light. -If the shoot is uniformly shaded, auxin inhibits branching and directs all energy into growing straight up in search of direct sunlight. -Stimulates root initiation and favors root growth over shoot growth -Directs root branching -Key to root colonization by rhizobia and mycorrhizae In short: Auxins help plants chase light and get tall; they favor root growth and branching. |
| Cytokinin Key function: More cells! -Stimulates cell division and differentiation in seed embryos, the shoot meristem (the area of active growth where new cells find out what kind of cell they will be), lateral buds, and roots -Regulates seed germination and seedling development -Promotes shoot growth over root growth -Key in nitrogen mobilization from old cells to young ones -Delays leaf senescence by maintaining chlorophyll Crosstalk with other hormones: -The auxin:cytokinin ratio is of definitive importance -High auxin/low cytokinin tends toward root growth on the macroscale (positive associations with mycorrhizae and other endophytes) and cell elongation on the microscale. -Low auxin/high cytokinin promotes shoot growth on the macroscale and cell division on the microscale -Cytokinin also promotes lateral growth against auxin’s vertical campaign In short: Cytokinins help multiply cells, make plants branch out, and keep things green. |
| Gibberellin Key function: Successful transitions -Gibberellic acid (GA) induces many growth stage transitions: germination, spring regrowth, bolting, flowering, fruiting, etc. -It breaks seed dormancy to trigger germination and breaks winter bud dormancy in woody plants -While auxins initially elongate cells in primary growth by loosening cells walls, GA is primarily responsible for rapid shoot and branch elongation (such as bolting) later on -GA is involved in the transition from vegetative meristems to floral meristems -Promotes pollen development and pollen tube growth -Stimulates fruit growth and development In short: gibberellin is a hormone of transitions. Time to sprout! Time to flower! Time to fruit! |
Microbes that Produce Growth-Promoting Hormones
With that trifecta of growth promoting hormones in our hip pocket, let’s turn to the tiny critters that are able to produce them. Why do these microbes possess this talent? And why do plants outsource hormone manufacturing, a job that they are perfectly capable of themselves?
Auxins are produced by a wide range of bacteria and fungi for plants, as well as for their own purposes. While there is evidence that cytokinins regulate growth and secondary metabolite production in some microbes, it is such a key phytohormone that most microbial production involves plants. In fungi, gibberellic acid has been noted to promote mycelial growth, spore germination, and production of chitosan, but gibberellin synthesis is particularly notable in plant-associated fungi, both beneficial and pathogenic, as with the gibberellin-driven disease of rice seedlings we mentioned above. Bacterial producers seem to mainly synthesize gibberellin for the benefit of their plant partners.
There are a handful of bad actors that employ their powers to take advantage of the plant: corn smut, ergot fungus, crown gall, Ralstonia, and root-knot nematodes to name a few. Their motives are obvious. But what advantage is there to the beneficial organisms? Principally, sugar!
The plant is exceptionally good at sugar production, thanks to the awesome power of photosynthesis. Microbes are particularly good at very efficiently producing organic molecules like auxin, cytokinin and gibberellin. Thus does the plant focus on massive sugar manufacturing, microbes focus on cheap hormone manufacturing, and the two carry on a mutually beneficial trade. Microbes, with their vested interest in increasing the output of their sugar daddy, serve as short-order cooks to the plant — filling orders not just for hormones, but for nutrients as well.
There are further benefits to plants with a strong brigade of hormone-producers. Microbes experience the world on a smaller scale than the plant, and as such are more acutely sensitive to conditions micrometer by micrometer across the root zone. Their signaling represents an intelligence network communicating with the plant about threats and opportunities. “Rich pocket of nitrogen right here! Send root hairs this way!” Like avid couponers hunting for a sale, plants benefit from reconnaissance intel about nutrient troves.
When present in the rhizosphere, auxins produced by microbes mainly influence root architecture, which helps plants access more nutrients and water. This takes a load off of the apical meristem for synthesis and transport. This is particularly useful in nutrient-poor soils or stressful environments where plants struggle to produce enough hormones themselves, and where they need that intelligence network to guide them to invest precious resources where they’ll have an ROI.
Our agricultural soils are stressful to plants. Best to ensure you have hormone-makers on call. Plants that have the option to trade a bit of sugar for ready-made phytohormones are at an advantage over those that don’t have the option. A soil microbiome with a robust capacity to synthesize these three plant-growth-promoting hormones is a soil well-staffed with plant helpers. Conversely, a microbiome lacking such skills means compromised yields — or else the burden of compensating for missing microbes falls on the farmer.
To take it one step further, microbes that have chosen the survival strategy of hitching themselves to plants’ wagons are often not solely hormone factories. Phytohormone production is frequently an indicator of critters that promote plant growth in other ways, be they nutrient cyclers, pathogen suppressors, stress mitigators or otherwise.
When using a microbiome analysis, the most important time for seeing medium to high indices for auxin-, cytokinin-, and gibberellin-producing microbes is from planting throughout its life of nutrient uptake. Once the sugar spigot shuts off, organisms whose survival strategy revolves around teaming up with plants will take a dirt nap until the next crops comes a-callin’ for assistance.
The most effective way to have populations of growth-promoters on hand, therefore, is to have living roots in that soil as much as possible, with tight rotations, cover cropping, intercropping, and so on. If you are a compost producer, consider planting crops in your compost during the maturing phase. Numbers of phytohormone producers tend to be abysmally low in most compost due to the absence of plants from the system.
Stress-Response and Growth-Inhibiting Phytohormones
In addition to the three growth-promoting phytohormones, here are three other hormones — created by both plants and microbes — that help plants respond to stress and, sometimes, inhibit growth.
| Abscisic Acid (ABA) Key functions: The front brakes of the car -Calls the plant to rationing, austerity and frugality when resources are scarce, conditions are poor, or winter is coming. -Roots produce abscisic acid when water is limited. Right there, it enhances the roots’ ability to transport water. The hormone also travels to the leaves where it shuts the stomata, preventing water loss. Closed stomata means no gas exchange, so photosynthesis grinds to a halt. -ABA tells buds and seeds to hold their horses until the opportune scenario arrives to sprout. -ABA calls off unsustainable growth and factors into anti-viral immunity as well. Crosstalk: -While auxin, cytokinin, and gibberellin say, “Greenlight! Grow, grow, grow!” abscisic acid says, “Slow, slow, slow! Something ain’t right! Be cautious!” -In dry conditions, abscisic acid induces the gathering of auxin on the underside of roots, causing them to bend down at a steeper angle in search of water. |
| Ethylene Key functions: Promotes leaf and flower senescence and abscission — i.e., to wind down active growth and wrap up the season. -Ethylene responds to mechanical stressors (e.g., bending, wounding, pressure, compaction) -Ethylene triggers the opening of flowers, the ripening of fruit, and even the formation of the hooked stem that germinating seeds use to push their way through the soil -Ethylene contributes to plant adaptation to saline conditions, chill, drought, and flood, reducing reactive oxygen species and avoiding excess stunting -In short, you can think of ethylene as a finisher (flowering, ripening, abscission) and a caretaker (healing wounds, responding to abiotic stressors). Crosstalk: Auxins and ethylene work cooperatively to form root hairs and ripen fruit, and against one another when it comes to lateral root growth and leaf senescence. |
| Salicylic Acid: Key function: Plant defense -Provides plant defense — particularly in systemic acquired resistance against biotrophic pathogens — critters that keep plant cells alive to continuously feed on their resources, such as root knot and cyst nematodes, rusts, downy and powdery mildews. -One way salicylic acid achieves this is by employing a scorched earth policy. Biotrophs depend on the cells they invade staying alive, but salicylic acid initiates programmed cell death, depriving the enemy of the spoils of war -Salicylic acid is the 911 dispatcher responsible for non-lethal crimes |
Please note that this article, in order to focus on those hormones that microbes produce, must omit three other very important phytohormones: jasmonic acid (defense against insects and cell-killing pathogens), strigolactones (key to establishing symbiosis) and brassinosteroids (a growth partner to auxin, cytokinin, and gibberellin).
Microbes that Produce Stress-Response Hormones
Some microbes produce abscisic acid to conduct their own response to osmotic or oxidative stress. Bacterial allies like Achromobacter, Bacillus and Pseudomonas produce ABA to support the plant’s own stress adaptation, leading to a more resilient crop.
High numbers of these hormone synthesizers mean your soil offers your crops enhanced stress tolerance — especially drought, salinity and nutrient deficits. It is a capacity particularly worth building in regions of unpredictable precipitation. The faster a plant can react to water variability, the more efficiently it uses water. Abscisic acid producers have also been linked to reduced uptake of heavy metals and significant yield improvements in vegetable crops.
Ethylene is a special case. While there are a handful of microbes known to produce ethylene, far more influential on crop resilience are organisms that reduce ethylene production in the plant by synthesizing an enzyme known as ACC-deaminase.
Part of the process of creating ethylene is the production of a compound called ACC. ACC, on its way to be turned into ethylene, can be intercepted by the enzyme which, as the name usefully denotes, snips an amine off the ACC and prevents its conversion into ethylene. Had the ethylene been produced, it would push the plant to put the brakes on photosynthesis, growth, and protein synthesis — affecting both yield and quality. Microbes that curb that stress response enable the plant to maintain growth even in the face of stress. This signaling effectively convinces crops that conditions aren’t actually all that bad.
Microbes both produce salicylic acid and push plants to make more of it, lighting the signal fires for the plant to muster its defenses before the enemy catches it unawares. They even utilize it in direct combat with pathogens, disrupting biofilm production, interfering for the pathogens’ quorum sensing, and leading to an accumulation of reactive oxygen species — a form of biochemical warfare.
A soil testing with an elevated microbial capacity to synthesize ACC-deaminase, abscisic, and salicylic acid is a soil in stress-fighting form. Crops in such soil are better equipped to cope with stress, whether from a pathogen or from inhospitable conditions.
Why the Dependence on Microbes?
When I was first learning all of this, I began to wonder: Why are plants so dependent on the camaraderie of microbes to be persuaded to push through stress and keep growing?
Did you notice my reductive assumption? My question assumes plants and microbes are separable entities in nature — but nature never separates the two. They are designed and adapted to be intimate, responsive partners in surviving and thriving!
A crop’s dependence on microbes to evaluate the severity of stressors is advantageous for at least four reasons:
- Subsidiarity: Microbes are more immediately attuned to the microenvironment in the rhizosphere, where conditions can vary greatly even over small distances. They may detect subtle soil chemistry changes, such as nutrient availability or pH, more quickly or accurately than plant roots can. Microbes can rapidly adapt and signal to the plant based on highly localized soil conditions.
- Redundancy: Plants have evolved with multiple overlapping mechanisms for survival. This redundancy ensures that if one pathway or response fails or is suboptimal, another can compensate. Microbial modulation of plant stress responses adds an extra layer of flexibility and resilience in fluctuating environments.
- Energetic efficiency: Maintaining a full range of hormonal responses to every possible environmental cue is energetically costly. Plants often operate under resource constraints, especially in stressful environments (read: farms). By relying on microbial partners, plants can focus on core growth functions while microbes handle more localized stress responses.
- Signal + solution: The same microbes that signal are those that remediate stress and enable the adaptation. It makes sense that plants then would rely on and trust the signal-makers.
Testing for These Microbes
For many years, this information would be interesting, but not testable — not actionable. Now, farmers and agronomists use soil DNA testing to measure the capacity of the bacteria and fungi to perform functions key to plant and soil health, including producers of auxin, gibberellin, cytokinin, abscisic acid, salicylic acid and the ethylene production regulator ACC-deaminase. This is a groundbreaking new set of insights on soil performance.
Here are some considerations to bear in mind when interpreting test results:
Genes, not hormones
Always bear in mind with DNA testing that you are seeing organisms that produce the hormone, not the hormone itself. That is, what your microbiome can do, not necessarily what it is doing this instant. For example, Bacillus licheniformis can synthesize auxins and consequently contributes to that metric, but it is possible that the crop has asked it to prioritize nutrient acquisition just now.
It is certainly vital to know what your soil can’t do. I may not need abscisic acid right now, but I want microbes on hand to synthesize it if I anticipate stress down the line.
Hormones are multi-modal by design
For instance, salicylic acid can induce a systemic immune response to biotrophic pathogens, but it can also be a key signal dealing with salinity, or in establishing beneficial symbiosis. Test strategically, pairing a problem area with a nearby, healthy point of comparison.
Growth stage matters
Growth-regulating hormones have different influences at different stages of the plant life cycle. Early auxin drives root growth. Late auxin inhibits it.
Therefore hormone-producing microbe data should be interpreted in light of growth stage and field observations of crop response.
Microbes have their own agenda
Not all microbially produced phytohormones are intended for the plant. Microbes produce some phytohormones for their own adaptive purposes — to enhance their own survival, outcompete rivals, or establish niche dominance. Some bacteria produce salicylic acid to suppress the growth of competing microbes or to enhance their own resistance to stress.
The Bottom Line: Context Matters!
I have seen night-and-day soil DNA results that clearly depict a widespread revival of the plant-beneficial fraction of the crittersphere — or its glaring absence. Other tests required more piecing together of observations before the story came into focus. Look at the totality of the report, especially the disease and stress adaptation metrics. Naturally, the more paired crop-test snapshots you have on your own operation, the more insight you’ll get out of these indicators.
We need to appreciate that our crops’ built-in capacities to optimize growth and combat threats are greatly augmented when their support crew is present and active in the soil — much as an athlete performs to a higher level with trainers, sports medicine professionals, nutritionists and managers.
Furthermore, now that these support roles are measurable and quantifiable, we can track them, learn how they respond to our management decisions, and get our soil labor force to work with us, not against us. The more labor that plant growth-promoting microbes do for our crops, the less labor and expense we need to expend to pick up their slack. They want to go to work. We just need to provide adequate working conditions.
