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The soil microbiome: why microbial consortia are displacing monostrains

Microbial consortia or single-strain inoculants: where is soil microbiome science headed?

Timur LEVDA Author of patented developments for the greening of intensive farming and the development of organic agriculture, developer of comprehensive solutions GREENODIN

Declaration of interests: the author is a developer of GREENODIN technological solutions. The scientific conclusions in the article are separated from the description of the author’s product and supported by published sources.

Soil as a living system

Soil is not just a mechanical support for plants or a reservoir of nutrients. It is a complex living system in which the mineral part, organic matter, water, air, plant roots and a huge number of living organisms interact.

Soil microbiota includes bacteria, archaea, fungi, protists, and other microscopic organisms. The concept of soil microbiome is broader: it includes not only the organisms themselves, but also the collection of their genes, metabolites, functions, and interactions with each other, plants, and the soil environment.

It is these relationships that largely determine:

  • transformation of organic matter;
  • the cycle of nitrogen, phosphorus, sulfur and other elements;
  • availability of nutrients to plants;
  • soil structure formation;
  • plant resistance to pathogens, drought, salinity and other stresses;
  • the ability of soil to self-clean and restore.

Modern research on the plant microbiome shows that plant health does not depend on a single “beneficial microbe” but on a complex system of genetic, biochemical, physical, and metabolic interactions between the plant, microorganisms, and the environment [4, 6]. Soil biodiversity supports productivity, nutrient cycling, water filtration, carbon sequestration, and pollutant degradation [7].

“Soil should not be perceived as a passive substrate that we force to work with a new dose of chemicals every time. It is a living system with which we need to build a technologically managed partnership.” — Timur LEVDA

From single strain to microbial community

Microbial inoculants have been used in agriculture for many decades. A large part of such preparations contain one characterized strain of bacteria or fungi.

Examples include representatives of the following genera:

  • Rhizobium and Bradyrhizobium — symbiotic nitrogen fixation in legumes;
  • Azospirillum and Azotobacter — associative or free-living nitrogen fixation;
  • Bacillus and Pseudomonas — nutrient mobilization, growth stimulation and biological control;
  • Trichoderma – suppression of certain phytopathogens and interaction with the root system;
  • arbuscular mycorrhizal fungi – promote the absorption of phosphorus and water.

A single-strain preparation may be the optimal solution when it is necessary to provide one specific function and obtain the most controlled composition.

Advantages of single-strain preparations

Their advantages include:

  • well-studied mechanism of action;
  • easier control of culture purity;
  • the ability to establish a specific titer of viable cells;
  • easier standardization of production;
  • higher reproducibility between batches;
  • lower risk of mutual inhibition of microorganisms;
  • It is easier to establish a cause-and-effect relationship between the introduction of the strain and the result obtained.

Therefore, single-strain inoculants cannot be considered an outdated approach. In many cases, they remain the most accurate and technologically manageable tool.

What is a microbial consortium?

A microbial consortium is a community of two or more microorganisms selected to perform certain functions together.

The different consortium members can:

  • fix atmospheric nitrogen;
  • mobilize phosphorus and potassium;
  • produce organic acids;
  • synthesize auxins and other regulatory compounds;
  • form siderophores;
  • promote the formation of the root system;
  • produce enzymes and antimicrobial substances;
  • compete with pathogens for space and nutrient resources;
  • help other community members survive stressful conditions.

When microorganisms are functionally compatible, an additive or synergistic effect may occur. However, the mere presence of multiple strains in a preparation does not prove synergy.

The effect of the interaction can be:

  • positive;
  • neutral;
  • additive;
  • synergistic;
  • antagonistic.

To scientifically confirm synergy, it is necessary to compare the result of the complete consortium with the effect of each of its components separately and with the corresponding uninoculated control.

“The value of a microbial consortium is not determined by the number of names in the list of strains. It is determined by whether these microorganisms are able to survive together, not suppress each other, and create a measurable functional result for the plant.” — Timur LEVDA

The results showed that multi-strain consortia on average provided greater plant biomass growth than single-strain preparations. A similar trend was observed during bioremediation of contaminated soils.

Soil as a living system

Soil is not just a mechanical support for plants or a reservoir of nutrients. It is a complex living system in which the mineral part, organic matter, water, air, plant roots and a huge number of living organisms interact.

Soil microbiota includes bacteria, archaea, fungi, protists, and other microscopic organisms. The concept of soil microbiome is broader: it includes not only the organisms themselves, but also the collection of their genes, metabolites, functions, and interactions with each other, plants, and the soil environment.

It is these relationships that largely determine:

  • transformation of organic matter;
  • the cycle of nitrogen, phosphorus, sulfur and other elements;
  • availability of nutrients to plants;
  • soil structure formation;
  • plant resistance to pathogens, drought, salinity and other stresses;
  • the ability of soil to self-clean and restore.

Modern research on the plant microbiome shows that plant health does not depend on a single “beneficial microbe” but on a complex system of genetic, biochemical, physical, and metabolic interactions between the plant, microorganisms, and the environment [4, 6]. Soil biodiversity supports productivity, nutrient cycling, water filtration, carbon sequestration, and pollutant degradation [7].

“Soil should not be perceived as a passive substrate that we force to work with a new dose of chemicals every time. It is a living system with which we need to build a technologically managed partnership.” — Timur LEVDA

From single strain to microbial community

Microbial inoculants have been used in agriculture for many decades. A large part of such preparations contain one characterized strain of bacteria or fungi.

Examples include representatives of the following genera:

  • Rhizobium and Bradyrhizobium — symbiotic nitrogen fixation in legumes;
  • Azospirillum and Azotobacter — associative or free-living nitrogen fixation;
  • Bacillus and Pseudomonas — nutrient mobilization, growth stimulation and biological control;
  • Trichoderma – suppression of certain phytopathogens and interaction with the root system;
  • arbuscular mycorrhizal fungi – promote the absorption of phosphorus and water.

A single-strain preparation may be the optimal solution when it is necessary to provide one specific function and obtain the most controlled composition.

Advantages of single-strain preparations

Their advantages include:

  • well-studied mechanism of action;
  • easier control of culture purity;
  • the ability to establish a specific titer of viable cells;
  • easier standardization of production;
  • higher reproducibility between batches;
  • lower risk of mutual inhibition of microorganisms;
  • It is easier to establish a cause-and-effect relationship between the introduction of the strain and the result obtained.

Therefore, single-strain inoculants cannot be considered an outdated approach. In many cases, they remain the most accurate and technologically manageable tool.

What is a microbial consortium?

A microbial consortium is a community of two or more microorganisms selected to perform certain functions together.

The different consortium members can:

  • fix atmospheric nitrogen;
  • mobilize phosphorus and potassium;
  • produce organic acids;
  • synthesize auxins and other regulatory compounds;
  • form siderophores;
  • promote the formation of the root system;
  • produce enzymes and antimicrobial substances;
  • compete with pathogens for space and nutrient resources;
  • help other community members survive stressful conditions.

When microorganisms are functionally compatible, an additive or synergistic effect may occur. However, the mere presence of multiple strains in a preparation does not prove synergy.

The effect of the interaction can be:

  • positive;
  • neutral;
  • additive;
  • synergistic;
  • antagonistic.

To scientifically confirm synergy, it is necessary to compare the result of the complete consortium with the effect of each of its components separately and with the corresponding uninoculated control.

“The value of a microbial consortium is not determined by the number of names in the list of strains. It is determined by whether these microorganisms are able to survive together, not suppress each other, and create a measurable functional result for the plant.” — Timur LEVDA

Not every multi-strain drug is SynCom

Synthetic Microbial Communities — SynComs, i.e. synthetic microbial communities, have become a separate area of ​​modern science.

A SynCom is not just a random mix of a few beneficial microorganisms. It is usually a defined and reproducible community of cultured strains, rationally formed to perform a specific function or create a predictable interaction with the plant.

For a well-founded classification of a composition into SynCom, it is desirable to have:

  • accurate identification of microorganisms to the species, or better yet, to the strain;
  • a certain ratio of components;
  • confirmation of their pair and group compatibility;
  • description of the functional role of each component;
  • comparison of the complete composition with individual strains;
  • reproducibility of composition between production batches;
  • assessment of stability during storage;
  • confirmation of function in laboratory and field conditions.

Therefore, the term SynCom should not be used solely as a marketing designation for a multi-strain preparation. It is primarily a scientifically based and controlled model of the microbial community.

What modern research shows

One of the most revealing works was a meta-analysis by Xipeng Liu, Siyu Mei, and Joana Falcão Salles, published in 2023 in the journal Applied Soil Ecology [1].

The authors summarized the results of 51 studies conducted in living soil and calculated 796 statistical estimates of the effect.

On average compared to uninoculated control:

  • monostrain inoculations increased plant growth rates by 29%;
  • consortia — by 48%;
  • in bioremediation experiments, monostrains increased the efficiency of the process by 48%;
  • consortia — by 80%.

These figures do not mean that any consortium will automatically be better than any single strain. They show an average trend for the set of studies analyzed. The performance of an individual preparation depends on the composition of the consortium, the crop, the soil, the climate, the application method and the experimental design.

In 2024, another large-scale meta-analysis was published in the journal Nature Ecology & Evolution, covering 335 studies [2].

This work did not directly compare monostrains and consortia. Its goal was to investigate how the introduction of microbial inoculants affects natural soil microbial communities.

Researchers found that inoculants, on average:

  • increased soil microbial biomass;
  • did not cause an overall statistically significant change in alpha diversity;
  • changed the structure and bacterial composition of microbial communities;
  • reduced the complexity of bacterial networks;
  • at the same time, they increased the stability of these networks.

The positive effect on microbial biomass was weakened under environmental stress and enhanced with the use of local inoculants and additional fertilization.

It is important to interpret these results correctly. A change in the structure of the natural microbiome is not yet automatic evidence of long-term colonization of the soil by introduced strains. To draw such a conclusion, it is necessary to separately monitor:

  • survival of introduced microorganisms;
  • the duration of their presence;
  • maintaining the required titer;
  • activity of functional genes;
  • changes after the end of the growing season;
  • repeatability of the effect in the next season.

Thus, modern science confirms the promise of microbial inoculants, but at the same time rejects the simplistic formula: “the more strains, the better the drug.”

Under what conditions can consortia work more effectively?

The potential advantage of consortia is related to several mechanisms.

Functional complementarity

One microorganism can mobilize phosphorus, another can fix nitrogen, and a third can produce growth regulators or suppress pathogens.

Distribution of ecological niches

Different microorganisms may colonize different parts of the root system or utilize different nutrient sources, potentially reducing direct competition.

Cross-feeding

The metabolic products of one member can be used by other members of the community. This interaction is called cross-feeding.

Sequential transformation of substances

A complex organic or mineral compound can undergo several successive stages of biological transformation, each of which provides a separate microorganism.

Functional redundancy

If one strain loses activity due to adverse conditions, another can partially compensate for its function.

Cooperation during colonization

Some microorganisms can form biofilms, change the local environment, or produce substances that help anchor other members of the consortium to the root.

Why a consortium might not work

Introducing multiple strains simultaneously significantly complicates the preparation technology.

Possible problems:

  • competition for the same substrates;
  • secretion by one strain of substances that inhibit another;
  • different reproduction rates;
  • change in strain ratio during storage;
  • unequal resistance to drying, temperature and pH;
  • incompatibility with the carrier material;
  • low adaptation to specific soil;
  • displacement of introduced microorganisms by local microbiota;
  • incompatibility with pesticides, fungicides or concentrated fertilizers;
  • insufficient number of viable cells at the time of application.

That is why modern research is increasingly focusing not on the maximum number of strains, but on the minimum functional composition capable of providing the predicted result.

Not just strains: why the drug matrix is ​​important

The effectiveness of a microbial preparation is determined not only by the properties of the microorganisms. It is equally important in what form they are produced, stored, and applied.

The carrier or matrix of the drug can affect:

  • protection of cells from drying out;
  • pH stability;
  • access to oxygen;
  • water activity;
  • maintaining viability;
  • sticking to seeds or soil particles;
  • gradual release of microorganisms;
  • local availability of organic carbon;
  • delivery of microorganisms to the rhizosphere.

Therefore, not only liquid inoculants, but also solid carriers, granular systems, encapsulation, cell immobilization, and organo-mineral matrices are promising.

In particular, the scientific literature considers biochar as a potential carrier for the immobilization of microorganisms. Its properties depend on the raw material, pyrolysis temperature, porosity, pH and surface chemistry. Therefore, the use of any material as a microbial carrier requires individual verification and cannot be considered effective automatically [8].

For a granular preparation, the following are particularly important:

  • temperature at the granulation and drying stage;
  • the moment of introduction of microorganisms;
  • residual moisture of the granule;
  • osmotic load;
  • acidity of the environment;
  • contact with mineral salts;
  • preservation of the titer after production;
  • titer retention at the end of the stated shelf life.

“In microbial technology, it is not enough to find a useful strain. You also need to deliver it to the soil alive, preserve its function, and create conditions under which it can interact with the root and not die on the way to the field.” — Timur LEVDA

GREENODIN GRAY in the context of modern microbiome technologies

GREENODIN GRAY should be positioned not as an ordinary microbial inoculant, but as a complex organo-mineral-biological system.

The product concept is a combination of:

  • organic component;
  • functional mineral matrix;
  • nutrients;
  • humic and other biologically active components;
  • complex of beneficial microorganisms.

In such a system, the mineral and organic matrix should not only supply individual nutrients. It can potentially act as a medium for the delivery, localization, and maintenance of the biological component after it is introduced into the soil.

This is fundamentally different from the approach in which microorganisms are considered as an isolated additive to traditional fertilizer.

At the same time, GREENODIN GRAY’s compliance with the principles of modern microbiome engineering should be confirmed not by the total number of declared microorganisms, but by specific indicators:

  1. Identification of microorganisms at least to the species, and for the main components – to the strain.
  2. Determining the functional purpose of each microorganism.
  3. Research into pair and group compatibility.
  4. By determining the titer of viable cells or spores.
  5. Titer control immediately after production and at the end of the shelf life.
  6. By testing the effects of granulation and drying.
  7. Determination of compatibility with organic and mineral matrix.
  8. By comparing the complete composition with individual functional components.
  9. Conducting field experiments with control and a standard feeding system.
  10. By studying the impact on the natural soil microbiome.

The scientifically correct positioning of GREENODIN GRAY should sound like this:

GREENODIN GRAY is a complex organo-mineral fertilizer with a biological component, designed to maintain soil fertility, increase the efficiency of nutrient use, and create favorable conditions for plant interaction with beneficial microorganisms.

It is appropriate to call it SynCom only after confirming the specific composition, compatibility, reproducibility, and functional interaction of the included strains.

“Our goal is not simply to introduce as many microorganisms as possible into the soil. GREENODIN’s task is to combine a living component with a functional organo-mineral matrix and create conditions in which biological processes become part of a controlled technology for soil nutrition and restoration.” — Timur LEVDA

Biologization does not mean giving up mineral nutrition

Microbial inoculants cannot be considered as a universal complete replacement for mineral fertilizers.

Microorganisms do not create phosphorus, potassium, calcium, or magnesium from nothing. They can:

  • convert individual compounds into more accessible forms;
  • increase the utilization rate of nutrients;
  • improve the development of the root system;
  • reduce the loss of some elements;
  • support the plant during stress;
  • promote the accumulation and transformation of organic matter.

However, the removal of nutrients by the crop must be compensated for in accordance with the agrochemical balance.

Therefore, it is advisable to implement microbial preparations and organo-mineral systems as part of an integrated system that includes:

  • soil analysis;
  • calculation of nutrient removal;
  • organic and mineral sources of nutrition;
  • plant residues;
  • sideral crops;
  • crop rotation;
  • minimizing the degrading impact of cultivation;
  • biological inoculants;
  • monitoring results in dynamics.

“The future of agriculture does not lie in the formal opposition of chemical and biological. It lies in reducing unproductive losses, restoring the natural mechanisms of the soil, and making precise use of every resource.” — Timur LEVDA

Where is soil microbiome science headed?

1. Rationally formed SynCom

Science is moving from randomly combining beneficial strains to creating controlled communities with defined distribution of functions.

2. Microbiome engineering

The goal is not only to introduce individual microorganisms, but to control the processes of formation, functioning, and restoration of microbial communities.

Microbiome engineering combines microbial ecology, systems biology, genomics, synthetic biology, and soil science [3].

3. Selection of solutions for a specific field

The direction, sometimes referred to as precision microbiome, involves selecting the microbial composition taking into account:

  • crops and varieties;
  • soil type;
  • рН;
  • organic matter content;
  • availability of phosphorus and nitrogen;
  • humidity;
  • climatic stresses;
  • predecessor;
  • fertilizer systems;
  • composition of the local microbiome.

4. Multi-omics

To study microbial systems, the following are increasingly being combined:

  • metagenomics;
  • metatranscriptomics;
  • metabolomics;
  • proteomics;
  • sequencing of individual strains;
  • analysis of functional genes.

This makes it possible to investigate not only the presence of microorganisms, but also what functions they actually perform.

5. Artificial Intelligence and Mathematical Modeling

Algorithms can be used to:

  • predicting the compatibility of microorganisms;
  • search for functionally complementary strains;
  • analysis of large metagenomic data sets;
  • modeling of metabolic interactions;
  • predicting the consortium’s response to soil conditions.

However, such models must be tested experimentally.

6. New delivery systems

Promising directions are:

  • solid media;
  • granulated preparations;
  • cell immobilization;
  • encapsulation;
  • biofilm compositions;
  • organo-mineral matrices;
  • separate application of microorganisms after the thermal stage of production.

7. Integration with precision agriculture

In the future, microbial preparations may be applied in a differentiated manner – depending on soil mapping, moisture, pH, nutrient availability, and plant condition.

Checklist for choosing a modern microbial drug

Before purchasing and using the drug, it is advisable to find out:

  1. Are specific species or strains of microorganisms specified?
  2. Is the titer stated in CFU/g or CFU/ml?
  3. Is the titer guaranteed at the end of the shelf life?
  4. Has the absence of external contamination been checked?
  5. Has the compatibility of the consortium components been confirmed?
  6. Are there laboratory and field tests?
  7. Were the experiments conducted with proper control?
  8. Has the drug been tested on an appropriate culture?
  9. Do the test conditions correspond to the soil type of the specific farm?
  10. Are the transportation and storage temperature requirements known?
  11. Is the product compatible with pesticides, fungicides and fertilizers?
  12. Is the interval between chemical and biological treatment defined?
  13. Is the method of application clear?
  14. Does the preparation correspond to the real nutrition system of the farm?
  15. Has the safety of the included microorganisms been assessed?

FAQ

What is the soil microbiome?

It is a system of microorganisms, their genes, metabolites, functions, and interactions with plants and the soil environment. It participates in nutrient cycling, organic matter transformation, soil structure formation, and plant resilience.

What is PGPM?

PGPM — Plant Growth-Promoting Microorganisms — are microorganisms capable of directly or indirectly supporting plant development.

Possible mechanisms include:

  • nitrogen fixation;
  • phosphorus mobilization;
  • production of phytohormones;
  • formation of siderophores;
  • reducing the impact of certain pathogens;
  • stimulation of the root system;
  • increasing stress resistance.

Is a consortium always better than a monostrain?

No. Meta-analyses show that, on average, consortia can provide a stronger effect. But this is not a universal rule.

A well-chosen single strain can be more effective than an incompatible multi-strain mixture. Functions, compatibility, titer, carrier, culture, and conditions of use are crucial.

Is every multi-strain drug a SynCom?

No. SynCom assumes a defined, reproducible and rationally formed composition with confirmed interactions and functions.

Can microbial consortia completely replace mineral fertilizers?

In most intensive systems, no. They can increase the efficiency of nutrient use, partially mobilize them from the soil, and support the root system. But the removal of elements by the crop requires compensation.

Why is the field effect often lower or more unstable than the laboratory effect?

In the field, microorganisms are affected by:

  • drought;
  • temperature;
  • рН;
  • local microbiota;
  • pesticides;
  • salt concentration;
  • organic carbon deficiency;
  • method and deadline for payment.

Therefore, the result of a laboratory experiment cannot be automatically transferred to the production field.

How is GREENODIN GRAY related to current trends?

GREENODIN GRAY combines an organo-mineral matrix with a biological component. This format corresponds to the transition from the isolated use of microorganisms to the creation of complex systems for their delivery and functioning.

At the same time, scientific confirmation of the benefits of the product must be based on research into composition, titer, compatibility, stability, and results of controlled field trials.

Conclusions

The soil microbiome can no longer be considered a simple collection of individual bacteria and fungi. It is a complex system whose functions are formed through the interaction of microorganisms with each other, the plant, and the soil environment.

Single-strain inoculants remain an important and scientifically sound tool. Their advantages are controllability, reproducibility, and the ability to specifically deliver a specific function.

Microbial consortia have significant potential due to functional complementarity, niche sharing, cross-feeding, and possible functional redundancy. Meta-analyses show that on average they can provide a stronger effect than single-strain inoculants.

However, the number of strains is not an independent criterion of quality. Effectiveness is determined by their compatibility, viability, stability, adaptation to the soil, production technology and delivery system to the rhizosphere.

The future of agricultural microbiology is associated with rationally formed SynComs, microbiome engineering, multi-omics, mathematical modeling, precise selection of drugs for field conditions, and the creation of functional carriers.

In this context, it is advisable to develop GREENODIN GRAY as a complex organo-mineral-biological system in which nutritional, mineral, organic and microbial components are not simply mixed, but technologically coordinated with each other.

“The next stage in the development of biologics is the transition from a list of useful components to proof of their joint work. It is the measurable interaction between the matrix, microorganisms, soil and plant that should become the basis of new generation technologies.” — Timur LEVDA

List of sources used

  1. Liu X., Mei S., Falcão Salles J. Inoculated microbial consortia perform better than single strains in living soil: A meta-analysis. Applied Soil Ecology. 2023. Vol. 190. Article 105011. DOI: 10.1016/j.apsoil.2023.105011.
  2. Li C., Chen X., Müller C. et al. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nature Ecology & Evolution. 2024. Vol. 8. P. 1270–1284. DOI: 10.1038/s41559-024-02437-1.
  3. Jansson J.K., McClure R., Egbert R.G. Soil microbiome engineering for sustainability in a changing environment. Nature Biotechnology. 2023. Vol. 41. P. 1716–1728. DOI: 10.1038/s41587-023-01932-3.
  4. Trivedi P., Leach J.E., Tringe S.G., Sa T., Singh B.K. Plant–microbiome interactions: from community assembly to plant health. Nature Reviews Microbiology. 2020. Vol. 18. P. 607–621. DOI: 10.1038/s41579-020-0412-1.
  5. Compant S., Samad A., Faist H., Sessitsch A. A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. Journal of Advanced Research. 2019. Vol. 19. P. 29–37. DOI: 10.1016/j.jare.2019.03.004.
  6. Berg G., Rybakova D., Grube M., Köberl M. The plant microbiome explored: implications for experimental botany. Journal of Experimental Botany. 2016. Vol. 67, No. 4. P. 995–1002. DOI: 10.1093/jxb/erv466.
  7. FAO, ITPS, GSBI, SCBD, European Commission. State of Knowledge of Soil Biodiversity: Status, Challenges and Potentialities. Rome: Food and Agriculture Organization of the United Nations, 2020.
  8. Bolan S., Hou D., Wang L. et al. The potential of biochar as a microbial carrier for agricultural and environmental applications. Science of the Total Environment. 2023. Vol. 886. Article 163968. DOI: 10.1016/j.scitotenv.2023.163968.

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