Soil Microbiome: Functions of a Community

Introduction

Our soils support a tremendous amount of life, including crop roots, insects, earthworms, arthropods, and microorganisms known as "microbes." Microbes are too small to be seen with the naked eye but are the primary force behind nutrient cycling of essential elements, such as carbon, nitrogen, sulfur, and phosphorus. These microbial functions mediate the health of natural ecosystems, agroecosystems, and the Earth’s biosphere. Recently, scientists and farmers alike have increasingly been looking to these nutrient-cycling functions of the microbiome to help improve agricultural sustainability by reducing the application of the expensive and unsustainable resources, such as fertilizers and pesticides.

What is a Microbiome?

The word "microbiome" can be split into "micro-," meaning small organisms, and "biome," meaning ecosystem or environment. Biomes exist on a large scale, such as deserts, tropical rainforests, or tundra, and are unique both because of physical characteristics (temperature, water availability, nutrient profile) and because of the organisms that live there and contribute to essential ecosystem functions. A 'micro' biome is often more complex in terms of species diversity than a large biome, and the residing microorganisms are influenced by environmental factors that vary across different types of soil (pH, nutrient levels, structure, texture, and moisture levels). Thus, different soils have different microbiomes. The groups of organisms defined as microorganisms include members of the domains Bacteria, Archaea, and within the domain Eukarya, those belonging to fungi, and protozoa. Additionally, some groups fall outside of the domains of life, including viruses. This diverse group of organisms encompasses thousands of species, each serving unique functions and contributing to a balanced soil ecosystem.

How do Microbes Contribute to Plant Nutrition?

Indirect Contribution

In the bulk soil, microbes can contribute to nutrient availability for plants because they are the workforce that breaks down organic matter present in decaying plant debris/crop residues, decaying organisms, compost, and animal manure. This is vital because the nutrients in this organic matter are locked up in forms that are unavailable to plants. For example, certain species of fungi typically handle the first round of decomposition of large and complex organic matter like leaf litter or roots decaying in soil. Then, other groups of bacteria can take over and break down the simpler compounds that are exposed by the initial fungal activities. During this dynamic transformation of organic matter, termed mineralization, nutrients that are essential for plants (e.g., nitrogen, phosphorus) are chemically transformed into forms that can be taken up by plant roots.

Direct Contribution

Specific microbes can directly supply nutrients to plants – often in exchange for resources (i.e., carbon-rich compounds like sugars) that plants produce during photosynthesis. A primary example of this direct partnership is a group of bacteria called rhizobia. These bacteria live within knobby outgrowths – called nodules – on the roots of legume plants, such as soybeans, alfalfa, peas, and clover. There, they feed on the carbon sugars that the plant provides. In the nodules, they convert nitrogen gas from the air into forms of nitrogen that the plant can uptake as nutrients (i.e., ammonia and nitrate). Another important direct partnership between plant roots and microbes is the association of plants with arbuscular mycorrhizal fungi (AMF). This group of fungi attaches to plant roots and creates long, thin, root-like structures called hyphae that extend the nutrient-absorbing surface area of the plant and aid in phosphorus and water uptake in exchange for carbon-rich compounds.

Community Function (Why Do We Care?)

As mentioned above, the soil microbiome serves a very important role in agriculture, such as recycling nutrients for plants. This nutrient cycling is considered a "function" of the soil microbial community, which is one of the many services that are provided when the soil microbes interact. Most of these functions are a product of the community at large rather than just one microbe species acting independently.

The microbiome is a living ecosystem in which each species of microbes depends on one another to provide essential resources for survival, thereby creating a tight-knit and complex community. These dependencies between the soil members keep the microbes in a rigid checks-and-balances system that creates relative structure. This structure makes each microbial community unique and dictates the community-level services that are carried out. The diversity, or the variety of different species of microbes in the soil, is an important component of community structure because some microbes can fill similar roles as others. For instance, if one group of microbes is killed off by a disturbance (such as a specific pesticide effect), a diverse community has an increased likelihood that another member could fill in, allowing the community as a whole to continue to function in a similar manner. This quality of consistency and strength in the face of stress is called ecological resilience.

Below are four major services that soil microbial communities provide:

Nutrient Availability

Soil microbial diversity fosters different types of microbes and the partnerships between them that fill critical roles in maximizing the breakdown and recycling of nutrients in the soil. This is because each microbe has unique substrate (food) preferences and capabilities to interact with various organic materials present in the soil. Pieces of organic matter move through the community along an intricate reverse-assembly line in which it is passed down the line and transformed to become available for different species to harvest from. This process feeds a complexity of organisms and converts nutrients into forms that are assimilated by plants.

Soil-borne Pathogen Suppression

The soil microbiome also functions to suppress disease-causing microbes called pathogens. Despite a large proportion of soil microorganisms being essential for soil functions, a minor fraction of them are pathogenic and harmful to crops. In a system in ecological equilibrium, the community of microbes is often capable of suppressing (i.e., controlling) the pathogenicity of these harmful microbes. This is because there is enough competition and internal balance to prevent the pathogens from building up a population big enough to cause disease in plants. However, once the system experiences severe disturbances (intensive use of agrochemicals or practices like soil fumigation), it is common for these pathogens to find room to proliferate and cause damage to crop systems.

Storing Carbon in the Soil

Carbon dioxide (CO₂) is an infamous air pollutant that collects in the atmosphere and causes the phenomenon called the "greenhouse effect," which traps the sun's heat and warms the planet. To reduce and potentially reverse the dangerous effects of climate change, scientists have looked for ways to pull CO₂ out of the atmosphere and put it into "storage." In this sense, the soil is one of the largest carbon storage sources on the planet. In fact, soil accounts for nearly 2,500 billion tons of carbon on Earth (compared to the 800 billion tons in the atmosphere). This is because carbon is an essential component of all living organisms, including microbes. When plants undergo photosynthesis, they convert CO₂ into carbon compounds (such as sugars, lignin, carbohydrates, and cellulose) that make up their tissues. When decaying plant matter is decomposed by microbes, the carbon is then assimilated into the microbial bodies. As microbes produce byproducts or decompose, the carbon they use becomes locked up in organic matter that stays in the soil and out of the atmosphere.

Improving Soil's Physical Structure

The processes of microbial life involve the production of many byproducts, such as polysaccharides, glycoproteins, lipids, and biofilms. These compounds generally form a sort of sticky 'biological glue' that encourages soil particles to bind together. This binding is called aggregation and is critical for maintaining gas flow (aeration) to the soil. This enhanced aggregation can also reverse some of the damage caused by compaction and create larger pore space between soil particles. Increased soil aeration is essential for proper plant root functioning, nutrient cycling, and the activity of larger soil organisms like earthworms and arthropods.

 To summarize, the services of the soil microbial community include:

• Recycling nutrients into the soil from decaying organic matter
• Providing a rich diversity of nutrients that are required for plant growth
• Reducing the ability of pathogenic microbes to take over and cause disease
• Locking carbon in the soil, reducing the amount of CO₂ in the atmosphere
• Improving soil structure through aggregation, which allows for the essential gas exchange required for nutrient cycling and plant root function

The Harm in Community Disruption

The structure of the soil community is dependent on the physical and chemical characteristics of the habitat in which it was formed. Thus, any change in the habitat and resources available to the microbes can disrupt the structure and result in a loss of the checks-and-balances system that keeps the community functioning normally. Major disturbances include environmental events such as flooding, drought, and soil erosion due to wind and water runoff. These events can cause shifts in essential water and nutrients for the microbes. Importantly, specific agricultural management practices can also significantly alter the soil habitat, such as tillage breaking apart soil aggregates, fumigation leading to large-scale soil sterilization, and the indiscriminate use of fertilizers and pesticides causing direct impacts on soil life and shifts in soil salinity or acidification. Further, while pesticides can help eliminate disease-causing microbes, their over-use may create a toxic and inhospitable environment for many of the nonharmful members of the community.

• Flooding and tillage can create anoxic (lacking oxygen) conditions that kill microbes requiring oxygen and limit nutrient cycling that needs gas exchange to occur (such as the conversion of ammonia into nitrate).
• Drought can restrict available soil water and eliminate drought-sensitive microbes.
• Erosion results in a loss of organic matter and nutrient resources present in the topsoil.
• Over-application of fertilizers such as ammonium nitrate or potassium chloride, which are salt-based, can lead to soil salinification.
• Application of ammonium-based fertilizers can acidify (lower the pH of) the soil. The pH of the soil is one of the most important physical characteristics determining which microbes can survive there.
• Pesticides contain toxic compounds that inevitably kill more than just the targeted pathogenic microbe. Heavy use reduces diversity and ultimately disrupts the microbiome’s structure and function.

In the face of disturbances such as those mentioned above, the survival of various microbial species may become inhibited. If important steps along the assembly line are missing, many of the "products" along the chain cannot be produced. This can lead to a breakdown of the dependencies that are crucial for the structure of a healthy soil community.

Management to Support Soil Microbial Communities

The way a farm is managed has a huge impact on the health and structure of the soil microbiome. Holistic management with soil biology in mind can help protect the microbiome by aiming for two goals: first, by reducing the amount of disturbance that occurs, and second, by promoting community diversity, which allows for greater resilience in the face of stressful environmental conditions.

Reducing Disturbance

Strategies to reduce the occurrence of disturbances to the soil microbiome include keeping the soil covered with living plants or mulch (reduces temperature and moisture fluctuations), reducing tillage (maintains soil aggregation), controlling erosion, and minimizing the use of pesticides when possible or searching for other sustainable options.

Promoting Diversity

Due to the complexity of microbial communities, it isn't possible to manage just one microbe to either prevent disease or maximize nutrient cycling. Instead, the best way for farmers to enhance the services provided by the soil microbiome is by promoting the diversity of the microbiome in an indirect manner. This is done by ensuring that there are adequate and diverse resources to support microbial diversity and community resilience. Management strategies such as cover cropping and intercropping help reduce erosion and ensure that there are constant inputs of diverse plant root-derived substrates into the soil. Additionally, the use of organic amendments, such as manure, crop residues, and compost, provide organic matter that holds a wide range of nutrients that support a diverse community of microbes.

Soil, even when degraded due to previous poor management, is teeming with dormant microbes and needs only to be nurtured to be restored as a living community. Under careful management, with time, the soil community can be rehabilitated and regain crucial functions to support plant growth for generations to come.

Take-Home Messages

1. Soil is a living ecosystem with complex communities of microorganisms.
2. These communities can provide valuable services in agriculture, such as improving nutrient cycling, soil fertility, pathogen suppression, carbon storage, and soil structure.
3. The interconnectedness of the community creates a tight checks and balances system, which creates a structure that promotes multiple beneficial functions.
4. The services provided by the microbiome can be prevented by disturbances that topple the balance and restrict community function.
5. Diversity within the system creates ecological resilience, which protects the community from becoming imbalanced in the event of a disturbance.
6. Management strategies to protect the health of the microbiome should be aimed at increasing organic matter inputs and minimizing disturbance to the soil.
7. Soil microbes are better able to maintain balance and functionality when management is aimed at protecting the soil ecosystem rather than just seeing it as a nonliving resource.

Additional articles to explore on the topic of soil microbes:

1. Understanding and Managing Soil Microbes
2. Soil Microbes in Organic Cropping Systems 101
3. Management of Soil Microbes on Organic Farms

References

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Jayaraman, S., Naorem, A. K., Lal, R., Dalal, R. C., Sinha, N. K., Patra, A. K., & Chaudhari, S. K. (2021). Disease-Suppressive Soils-Beyond Food Production: a Critical Review. Journal of soil science and plant nutrition, 21(2), 1437–1465. doi.org/10.1007/s42729-021-00451-x

Ontl, T. A., & Schulte, L. A. (2012). Soil carbon storage. Nature Education Knowledge, 3(10), 35.

Wang, J., Peñuelas, J., Shi, X., et al. (2024). Soil microbial biodiversity supports the delivery of multiple ecosystem functions under elevated CO2 and warming. Communications Earth & Environment, 5(1), 615. doi.org/10.1038/s43247-024-01767-z