Microbe diversity delivers resilience and is a principal driver of soil and plant
health
This article will address what microbe population diversity is and why it is important and will include practical and actionable strategies to increase your soil microbe population diversity.
Defining Diversity
Healthy soils should have 600 to 1,000 microbe species and populations of 1-10 billion per gram.
Diversity is much more than the number of different species; it also concerns the types of microbe life. It is more about the variety in the phylum and classes than it is about the total number of species. There are 266 Bacillus species, but if your soil had all of them but not much else, it would not be a diverse, balanced or resilient population.
Microbial Diversity Is Key
The reason plants need diversity is that it confers resiliency on the microbe community to reliability deliver plant-beneficial functions. The important plant-beneficial microbe functions that need to be ensured through microbial diversity include:
- Nitrogen fixing, cycling, and plant delivery (in L-amino acid form);
- Phosphorus solubilization;
- Chelation of potassium, calcium, magnesium, manganese, iron, copper and zinc;
- Plant hormone production (e.g., auxins, cytokinins, gibberellins, jasmonic acid);
- Plant metabolites (over 20,000 plant physiology triggering and regulating compounds);
- Soil structure aggregation for increased water infiltration rates, water holding capacity and gas exchange;
- Chemical residue degradation;
- Carbon cycling and sequestration;
- Crop residue decomposition;
- Plant immune system elicitors and support;
- Plant pathogen suppression through competition and direct predation; and,
- Plant pathogen quorum sensing suppression.
Disruptions to Diversity
A healthy soil with a diverse microbe population has dozens of different microbe species to perform each of the previously listed plant-beneficial functions. Average production soils have 5 to 10 percent of the diversity and 1/100th to 1/1,000,000th the population of a healthy soil.
Read that last line again. Soils with that much loss of diversity and population are fundamentally broken, both functionally and ecologically. When analyzing customers’ soils, we often find that even well-farmed regenerative soils lack fungal diversity after 20-plus years. The narrowing of the population diversity and reduction in population size is the result of an accumulation of adversity. It does not happen all at once but is successive in impact. Adversity that narrows microbe diversity and reduces population sizes comes from a myriad of sources, including:
- Lack of available carbon;
- Tillage;
- Salt accumulation;
- Soil solarization;
- Significant soil nutrient imbalances or absences;
- Significant nutrient availability interference — e.g., chloride or aluminum;
- Too acidic or alkaline soil;
- Anaerobic conditions caused by cementation, compaction or waterlogging;
- High-dose synthetic fertilizer applications and non-liquid salt-based fertilizers;
- Pesticides (especially systemic ones);
- Poor water quality (salts, pH, bicarbonates); and,
- Insufficient plant genus diversity in crop rotations and cover cropping.
Some microbes are very sensitive to one or more of these adversities and therefore rapidly disappear. Other microbes will be tolerant of some or most of these. As community diversity narrows, the interdependent support between the different microbes dwindles, and microbes that were previously enduring will also successively disappear. The lack of fungal diversity, even on many regenerative soils, can be attributed to fungicide-treated seeds, GMO plant varieties, and/or systemic pesticide use. These practices all disproportionately disadvantage fungi.
Plant species tend to have tight associations with a subset of 50 to 100 rhizosphere microbe species. GMO varieties appear to have associations with fewer species, thus contributing to diversity reduction. Plants can further narrow the microbe diversity by selectively supporting the same species to do their favored functions.
This narrower microbial diversity means that when a plant experiences an abiotic stressor event such as heat, drought or pests, the complement of other microbe species needed to respond may not be present and may result in significant yield loss. In fields managed to restore microbe diversity, crops exhibit little or no stress during an adverse event while adjacent untreated fields are suffering significant losses.
Healthy Soils and Biological Balance
You can tell a healthy, living soil by its rich, earthy smell. When you dig into a soil and it lacks this smell, it is a sign that the soil biology is significantly impaired. The earthy smell is volatile organic compounds that microbes use to communicate between themselves and plants, between different microbe species, and within species.
Several hundred VOC compounds have been identified, marking it as an important microbe function that could potentially be considered a language. VOCs between microbes and plants can trigger or moderate plant physiology and processes, such as sodium uptake and immune responses. Communication between microbe species can coordinate complex functions like chemical residue break down. They are also used as a weapon between species that can epigenetically turn off gene sequences in a competitor to be able to enzymatically process a food or even to reproduce – this is an important pathogen biocontrol function.
VOC communication within a species is referred to as “quorum sensing.” Quorum sensing is when species use VOCs to determine their population size in proportion to other species present. When a potential plant pathogen species senses it is dominant, it can epigenetically switch the mode of reproduction and metabolism of the species.
We now know that potential plant pathogen species are benign or even beneficial in their normal species balanced state, but they may switch to plant pathogen behavior if not in balance. This imbalanced species condition is common in soils with depleted microbe diversity, and thus we see an increase in the frequency and severity of pathogen outbreaks. If microbe diversity is maintained, potential plant pathogens remain benign or beneficial. This is why we often see even chronic disease problems go away as we reestablish healthy, diverse soil biology.
Completely eliminating a potential pathogen species to control a disease is not a practical or even realistically achievable goal, yet this is exactly what conventional chemical pesticide products promise. If a pesticide is effective on the pathogen, it has also likely killed off much of the rest of the microbe community, destroying diversity and eliminating the checks and balances that keep potential pathogens from becoming a problem. When microbial diversity is destroyed by a pesticide, it is likely that when the biology community starts to come back, it will be out of balance and there will inevitably be another runaway pathogen problem. In order to break this cycle we need to restore all of the soil biology and diversity — not just a few species.
Many biocontrol microbial products assume that their microbes will eliminate the targeted pathogen by competition for food or habitat or direct antibiosis. Again, elimination is not a reasonably achievable or sustainable goal in a natural system. Knowing that these potential pathogen species are actually beneficial at low populations and that they contribute to diversity, keeping other pathogens in check means that elimination is not even a desirable goal.
The easiest and most reliable method for pathogen control is to increase the population of other microbes around the potential plant pathogens. Through this strategy, the quorum sensing of those potential pathogens never reaches concentrations that trigger their adaptation to become pathogenic. It is likely that quorum suppression is a more important mode of action in controlling plant pathogens than the total benefit achieved from competition for food, competition for habitat, or direct predation.
One last note regarding diversity and suppression: some species of nematodes can become plant pests if there are not enough bacteria and fungi to feed on. These “switcher” nematodes leave plants alone as soon as the soil microbe population and diversity are sufficient to support them.
Strategies and Opportunities to Increase Microbe Diversity
To build soil microbe diversity:
- Reduce farming practices that adversely affect microbes, especially fungi (e.g., tillage, systemic pesticides, fungicide-treated seeds, non-liquid fertilizers, bare soils);
- Feed microbes diverse and complete food sources (proteins — fish or plant hydrolysates — seaweed, humates, carbohydrates, vitamins, minerals, etc.);
- Use broad-spectrum microbe inoculants (not just products with a few species) in seed treatments; at pre-plant, planting and other crop growth stages; or in crop residue decomposition;
- Rotate between or use multiple different microbe inoculants;
- Select healthy seeds with good endogenous microbes (living inside the seed) — see my article in the Acres U.S.A. January 2024 issue, “Seeds of Success”;
- Establish green belts, hedge rows or riparian buffer areas as sources of undisturbed biology to recolonize into the field;
- Cover crop with diverse genera (not just different species);
- Build structure to house microbes (e.g., compost, wood chips, humates, biochar);
- Apply composts from different source materials or different geographic areas;
- Inoculate your compost after the thermophilic phase is completed;
- Reintroduce higher trophic level life (from your compost if possible), which supports microbe diversity and colonization (e.g., earthworms, beneficial nematodes, millipedes, roly-polies), which all carry their own biology as well as spread it in the soil for you.
Of course, not all of these strategies for increasing diversity work for every farm, but the more of them you can fully or even partially implement, the more diversity, function and resiliency you will have and the more of the benefits you will reliably and consistently capture.
Conclusion
I am often asked, “How long do you have to keep applying microbe inoculants?” This is complex, but the core concept is that once you achieve and maintain microbe diversity, it becomes a self reinforcing community that will be resilient to stay in balance. Once that stable diversity is established and maintained, the need for reintroduction of outside biology should become minimal or even unnecessary.
Until then, diverse species microbe inoculants and foods will be important tools to building soil diversity and enjoying the benefits of a high-functioning and balanced soil biology.
David Olson is the owner of Sustainable Growing Solutions, LLC (sgs-ag.com). He is a 6th-generation California farmer and 2nd-generation scientist and agronomic consultant. SGS emphasizes the integration of organic inputs and biological products to create healthy soil and plants.
