Overview

Soils are home to some of the most complex and diverse biological communities on Earth. While certain organisms such as earthworms and some insects are observable, the majority of soil life consists of microorganisms invisible to the naked eye. The term “microbiome” refers to the collection of microbes present in a given habitat, which includes bacteria, archaea, protists, and fungi. The soil itself comprises distinct microbial habitats, with the highest microbial abundance and activity typically in the top 10 cm. The rhizosphere, or the region of soil directly surrounding plant roots, is another hotspot of microbial activity.

Soil microbiomes differ across different soils and ecosystems. For instance, forest soil microbiomes differ from agricultural soil microbiomes both in terms of the specific microbial species present but also the abundances of these populations. Certain soil characteristics are very strong determinants of what microbes are present, such as pH, organic carbon quantity and quality, and moisture. Other characteristics, such as temperature or the presence of different plant species, are weaker predictors.

Microbial contributions to soil health

a) Decomposition. Microbes break down dead organic matter (e.g., crop residues, insect carcasses), returning carbon, nitrogen, and other nutrients into the soil. For instance, certain bacteria and fungi can degrade cellulose, which is present in plant cells and the most abundant organic molecule on Earth. These nutrients are either incorporated into living cells, incorporated into dead cells or microbial necromass, or respired as gas. Living and dead microbes typically contribute 1-4% of total soil carbon and 2-6% of total soil nitrogen.

b) Nutrient Cycling: Microbes mediate global biogeochemical cycles of essential soil and plant nutrients including carbon, nitrogen, and phosphorus. To illustrate, some soil and plant-associated microbes (e.g. rhizobia living in legume roots) fix atmospheric nitrogen. Other microbes mediate the transformation of nitrogen between organic and inorganic nutrients through a process called nitrification. Finally, other microbes are responsible for denitrification, which involves the release of soil nitrogen back into the atmosphere in the form of N2O. Different microbial communities carry out these processes at different rates.

c) Greenhouse Gas (GHG) Emissions and Climate Regulation: Microbes play a pivotal role in the decomposition of deceased organic matter and the utilization of carbon from root exudates. During these processes, carbon and nitrogen can either remain stored in the soil or be released back into the atmosphere as CO2, N2O, or CH4. Microbes regulate the movement of carbon between the soil and the atmosphere. When this carbon is protected from microbial activity, it becomes sequestered within the soil thereby increasing soil carbon content. This presents a significant opportunity for agricultural soils to act as carbon sinks, effectively capturing and storing atmospheric carbon which can help mitigate climate change.

d) Soil Structure and Water Retention: Many microbes are capable of producing extracellular polymeric substances (EPS), biofilms, and other “sticky” secretions. These substances serve to bind together soil particles with microbial cells, forming soil microaggregates and macroaggregates. Soil aggregates play a pivotal role in enhancing soil structure and promoting better water infiltration. Furthermore, the substances excreted by these microbes have the added benefit of retaining water, thereby improving water-holding capacity.

e) Plant Growth Promotion. Microbes establish symbiotic relationships with plants that are vital for plant growth and yield. Many of these partnerships involve nutrient exchanges benefiting both parties. For instance, nitrogen-fixing rhizobia colonize legume root nodules, supplying the plant with nitrogen in exchange for carbon. Arbuscular mycorrhizal fungi (AMF) are another important group of microbes that colonize plant roots, enhancing nutrient use. Certain microbes can produce growth-regulating phytohormones like auxin, gibberellin, and cytokinin, further contributing to plant development. Moreover, evidence suggests that symbiotic microbes provide enhanced stress tolerance to crops, enabling them to withstand challenging environmental conditions such as salt, drought, and heat.

f) Disease Suppression. While some pathogenic microbes can indeed cause diseases, the overwhelming majority of microbes are either beneficial or have a neutral impact. Microbes contribute to disease suppression through both direct and indirect mechanisms. Directly, they can produce biocidal compounds, including antibiotics and antifungal agents, which hinder the growth of harmful pathogens. Alternatively, microbes can indirectly combat disease by outcompeting potential pathogens, preventing them from establishing in the soil or colonizing plant roots. These processes are responsible for disease-suppressive soils. 

Management Recommendations

The USDA-NRCS guidelines for preserving and enhancing soil health, as outlined in the General Soil Health recommendations, emphasize the importance of supporting active microbial communities. Practices that foster soil formation and reduce soil loss and erosion are inherently beneficial to microbes. For instance, minimizing soil disturbance through reduced tillage encourages the formation and stabilization of microbial aggregates. Ensuring the presence of living roots throughout the year guarantees a continuous supply of carbon in the form of root exudates which provides food for microbes. The addition of carbon-rich soil amendments, such as compost and manure, further sustains soil microbes. Additionally, there are various commercial microbial products, often referred to as biologicals, designed to enhance soil health processes or act as symbiotic plant growth promoting microbes. While these technologies hold great promise, it’s worth noting that their efficacy can vary widely, particularly across diverse soils and production regions.

Assessment Tools

The USDA-NRCS has developed a soil health and management assessment framework (SMAF), which measures primary indicators of soil health. Other analyses developed by the Cornell Soil Health Laboratory (Comprehensive Assessment of Soil Health or CASH) evaluate additional  biological properties. Standard measurements of biological soil health indicators typically assess microbial abundance or microbial activity. Microbial abundance can be quantified through various methods, including the measurement of microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Alternatively, the abundance of distinct functional microbial groups can be determined using techniques such as phospholipid fatty acid analysis (PLFA), which identifies lipid components found in all cells. Microbial activity, on the other hand, can be evaluated through several approaches. One method, called rapid mineralization, involves measuring the amount of carbon dioxide released when the soil is rewetted and assessed over a 24-hour or 4-day period. Another approach is to quantify enzyme activity, which involves assessing the activity of proteins responsible for catalyzing the decomposition of organic matter substrates.

Recent advances offer additional insights into microbial biodiversity. DNA sequencing methods can provide a comprehensive profile of microbial taxa (species) and community functional potential across different soil samples. This can also include the identification of potential pathogens or specific functional genes related to a biogeochemical process. These technologies are rapidly advancing, and microbial-based measurements of soil biological health are promising solutions for agronomic challenges.