Soil Microbes
Soil Microbiomes: The Living World Beneath Our Feet
Soil is not simply a mixture of minerals, organic matter, water, and air. It is also one of Earth's most biologically complex habitats. A handful of healthy soil can contain enormous numbers of bacteria, fungi, archaea, protists, viruses, and other microorganisms interacting with one another and with plants, animals, and the physical environment.
Collectively, these organisms and their genetic material form the soil microbiome. Although largely invisible, soil microorganisms participate in many of the processes that allow terrestrial ecosystems to function. They decompose organic matter, recycle nutrients, influence soil structure, interact with plant roots, suppress some diseases, and regulate the movement of carbon and other elements through ecosystems.
Research increasingly shows that soil microbiomes should not be viewed as passive inhabitants of soil. They are active ecological communities capable of influencing crop productivity, ecosystem resilience, greenhouse-gas emissions, plant health, and the long-term storage or release of carbon.
What Is the Soil Microbiome?
The soil microbiome includes a vast range of microorganisms occupying tiny habitats between soil particles, inside aggregates, around roots, and within microscopic films of water.
Major groups include:
- Bacteria, which perform an enormous variety of functions including decomposition, nutrient transformations, nitrogen fixation, and interactions with plant roots.
- Fungi, including decomposers, pathogens, endophytes, and mycorrhizal fungi that form important partnerships with plants.
- Archaea, which can play important roles in carbon and nitrogen cycling.
- Protists, many of which feed on bacteria and other microorganisms and influence microbial food webs.
- Viruses, which infect microorganisms and can alter microbial populations and ecosystem processes.
The composition of these communities varies enormously among soils. Soil acidity, moisture, temperature, organic matter, nutrients, vegetation, land use, depth, and climate all influence which microorganisms survive and how microbial communities function.
At the same time, microbes modify their own environment. Their growth, decomposition, chemical transformations, and interactions with plant roots can alter soil chemistry, nutrient availability, aggregation, and carbon storage.
Roots and the Rhizosphere
One of the most biologically active regions of soil is the rhizosphere, the narrow zone surrounding plant roots.
Plants release sugars, organic acids, amino acids, and many other compounds from their roots. These substances can feed microorganisms and help plants selectively recruit microbial partners.
The relationship is not one-sided. Microorganisms can influence the compounds released by roots and can affect plant nutrition, growth, stress tolerance, and resistance to pathogens.
Studies of crops including maize, soybean, barley, ryegrass, potatoes, peanuts, and other plants show that root-associated microbial communities can differ substantially from those living in surrounding bulk soil.
Plant genotype, breeding history, soil conditions, climate, and previous vegetation can all influence which microorganisms become associated with roots.
Some plants appear capable of consistently selecting beneficial microorganisms even when growing in different soils. These findings raise the possibility that crop varieties could eventually be bred not only for their own characteristics but also for their ability to recruit useful microbial partners.
Soil Microbes and Plant Nutrition
Microorganisms are central participants in nutrient cycling.
Plants require elements such as nitrogen, phosphorus, potassium, iron, and other nutrients, but much of the nutrient supply in soil exists in forms that plants cannot immediately absorb.
Microbial activity can transform these materials into more available forms.
Nitrogen-fixing bacteria can convert atmospheric nitrogen into biologically useful compounds. Other microorganisms participate in nitrification, denitrification, decomposition, and mineralization.
Mycorrhizal fungi extend fungal networks outward from plant roots, effectively increasing the volume of soil from which plants can obtain nutrients and water. These partnerships can be particularly important for phosphorus acquisition.
Other microorganisms can solubilize phosphorus or potassium locked in soil minerals.
Because of these relationships, scientists are investigating whether microbial inoculants, microbial fertilizers, crop rotations, cover crops, and other management strategies could reduce dependence on some synthetic fertilizers while maintaining agricultural productivity.
Climate Change, Carbon and Soil Microbes
Soils contain enormous quantities of carbon, and microorganisms play a central role in determining whether that carbon remains stored underground or returns to the atmosphere.
Microbes decompose plant residues and soil organic matter. During this process they release carbon dioxide through respiration.
Warming can increase microbial activity in many environments, potentially increasing carbon dioxide emissions from soil. The magnitude of this response depends partly on the composition and characteristics of the microbial community.
Research has found that microbial responses to temperature can help explain soil-carbon losses under warming.
Climate change can also alter microbial ecosystems through drought, flooding, heatwaves, changes in precipitation, and other environmental stresses.
Experimental warming has been associated in different studies with changes in bacterial and fungal diversity, microbial metabolism, carbon emissions, antibiotic-resistance genes, and microbial ecological strategies.
Some microbial responses can create feedbacks to climate change. If warming accelerates microbial decomposition and releases more carbon dioxide, atmospheric warming could increase further.
However, microorganisms also contribute to the formation and stabilization of soil organic matter. Understanding the balance between microbial decomposition and microbial contributions to long-term soil carbon storage has therefore become an important area of climate research.
Drought, Heat and Environmental Stress
Soil microorganisms experience the same environmental stresses affecting plants.
Drought can restrict the microscopic water films through which many soil microorganisms move and interact. Heat can alter metabolism and community composition. Salinity and alkalinity can restructure microbial networks and reduce the range of conditions tolerated by some organisms.
Microbial communities can also leave ecological legacies. Long-term exposure to particular precipitation regimes or environmental conditions may affect how microbial communities and plants respond to later drought.
Plants may benefit from these relationships. Research suggests that some microorganisms can increase plant tolerance to drought, heat, salinity, nutrient limitations, and other stresses.
This has encouraged interest in identifying microbial communities capable of helping crops remain productive under increasingly variable climatic conditions.
Agriculture and Soil Management
Agriculture profoundly influences soil microbiomes.
Tillage, fertilizer application, irrigation, crop rotation, crop residues, cover crops, organic amendments, pesticides, and land conversion can all change microbial abundance, diversity, and community structure.
Long-term agricultural experiments show that management practices can produce persistent microbial differences.
Crop rotation can alter bacterial and fungal diversity. Irrigation frequency can strongly influence bacterial communities. Fertilizer regimes can favor particular microorganisms, while changes in soil pH caused by agricultural inputs can indirectly restructure microbial communities.
Converting natural ecosystems to agriculture can also make microbial communities more similar across large geographic areas, a process sometimes described as microbial homogenization.
Conservation and regenerative farming practices are increasingly being studied for their ability to maintain microbial diversity while improving soil health, nutrient cycling, carbon storage, and crop resilience.
Cover crops are particularly important because living roots continue feeding and shaping microbial communities during periods when agricultural soils might otherwise remain bare.
Organic amendments and biochar can also alter microbial activity and community composition, although results depend on soil type, climate, crop, amendment, and management system.
Disease Suppression and Plant Defense
Some soils naturally suppress plant diseases.
This protection may arise not from one beneficial microorganism but from interactions among entire microbial communities.
Microorganisms can compete with pathogens for nutrients or space, produce inhibitory compounds, stimulate plant immune responses, or alter environmental conditions in ways that make disease establishment more difficult.
Competition for resources such as iron can determine whether pathogenic bacteria are able to establish themselves.
Predatory protists can indirectly suppress disease by reshaping bacterial communities.
Some plants actively recruit beneficial microorganisms after encountering pests or pathogens. Soybeans, for example, have been studied for their ability to alter root-associated microbial communities in ways that improve defense.
Soil conditions also matter. Acidification and other environmental changes can weaken naturally disease-suppressive microbiomes.
Understanding these relationships could eventually allow farmers to manage soils in ways that encourage protective microbial communities rather than relying exclusively on chemical disease control.
Microbial Biodiversity
The biological diversity contained in soils is enormous and remains only partially understood.
Different microbial species and strains possess different ecological strategies. Some grow quickly when nutrients become available, while others are adapted to survive long periods of scarcity or environmental stress.
Soil pH is one of the strongest predictors of bacterial-community composition, but climate, vegetation, soil depth, water availability, nutrient concentrations, dispersal, and land use are also important.
Microbial communities can differ greatly between surface soils and deeper layers.
Extreme environments such as deserts contain microorganisms capable of surviving severe water and nutrient limitations. Mountain environments can contain microbial communities structured by elevation, climate, and barriers to dispersal.
Global genomic surveys continue to reveal previously unknown microbial genes and organisms, suggesting that a substantial portion of Earth's microbial biodiversity remains undescribed.
Microbial Networks and Ecosystem Stability
Soil organisms do not function independently.
Bacteria, fungi, archaea, protists, plants, and soil animals form complex networks of competition, cooperation, predation, and resource exchange.
Changes affecting one group can therefore spread through the larger ecological community.
Researchers increasingly study these interaction networks rather than simply counting individual microbial species.
Some evidence suggests that land-use changes, ecosystem development, and environmental conditions can alter both the complexity and stability of microbial networks.
Water availability is particularly important because microscopic water pathways determine whether organisms can reach one another within soil pores.
The extraordinary complexity of microbial communities initially appears to make their behavior almost impossible to predict. Yet modeling research suggests that large microbial communities can sometimes produce predictable collective patterns despite containing thousands of interacting organisms.
Land Use, Degradation and Ecological Restoration
Land degradation can substantially alter soil microbial ecosystems.
Agriculture, mining, pollution, vegetation removal, and other disturbances can reduce or restructure microbial communities.
Restoration projects increasingly recognize that rebuilding vegetation without rebuilding belowground biological communities may leave ecosystems incomplete.
Studies in grasslands, steppes, semi-arid landscapes, forests, mines, and agricultural systems indicate that microbial communities can recover following restoration, although surface and subsurface communities may respond differently.
Plants can play an important role in this recovery by providing organic matter and creating new root-associated habitats.
Trees can also produce distinctive microbial communities beneath their canopies and influence microbial composition within agroforestry systems.
As ecosystems develop, microbial functional diversity may increase, allowing soils to perform a broader range of ecological processes.
Measuring the Invisible Ecosystem
Most soil microorganisms cannot easily be studied using traditional laboratory culturing alone.
Modern molecular techniques have transformed soil microbiology.
Metagenomics allows researchers to sequence genetic material directly from environmental samples rather than growing organisms individually.
Metabarcoding can identify groups of organisms through characteristic genetic markers.
Metatranscriptomics, metabolomics, and other molecular approaches can reveal which genes are active and which compounds are being produced.
Researchers increasingly combine these techniques through multi-omics approaches.
Machine learning, ecological modeling, biosensors, and artificial intelligence are also being developed to interpret large microbial datasets and predict soil processes.
These approaches could eventually make microbial measurements a routine component of soil-health monitoring.
Microbiome Engineering
A rapidly developing field seeks to deliberately manipulate soil microbiomes.
Approaches include:
- adding beneficial microorganisms;
- introducing synthetic microbial communities;
- transplanting microbiomes from healthy soils;
- altering plant varieties to improve microbial recruitment;
- using biochar or organic amendments to favor desirable organisms;
- changing crop rotations and management practices to influence microbial communities.
Researchers have tested microbial inoculants for nutrient acquisition, soil rehabilitation, residue decomposition, disease resistance, microplastic degradation, and crop productivity.
Results are often inconsistent because introduced microorganisms must compete with complex native communities.
Increasingly, researchers are attempting to identify characteristics of existing soil microbiomes that predict whether an inoculation will succeed.
The goal is shifting from simply adding individual "beneficial microbes" toward understanding and managing entire microbial ecosystems.
Soil Microbiomes and One Health
Soil microbiomes are increasingly being considered within the One Health framework, which recognizes connections among environmental, plant, animal, and human health.
Healthy soils support plant production and food systems. Soil microorganisms influence nutrient cycling and crop health and may affect microorganisms associated with plants and food.
Researchers have proposed a possible soil-plant-human gut microbiome axis, although many details of these connections remain uncertain.
Agricultural antibiotics, pollutants, heavy metals, climate change, and land degradation can also alter microbial communities, creating potential consequences beyond individual fields or ecosystems.
For these reasons, some researchers have argued that soil microbiomes should be explicitly considered in environmental and public-health policy.
The Future of Soil Microbiome Research
The science of soil microbiomes is moving from describing microbial diversity toward understanding function.
Important questions include:
- Which microorganisms perform essential ecosystem functions?
- How stable are these functions when microbial species change?
- How do microbial communities respond to warming and drought?
- Can microbiomes be managed to increase soil carbon storage?
- Can beneficial microbial communities reduce fertilizer or pesticide requirements?
- How can farmers reliably manipulate microbiomes across different soil types?
- Which microbial indicators provide meaningful measures of soil health?
- How quickly do microbial communities recover following land degradation?
- How should microbial biodiversity be incorporated into conservation and climate policy?
Advances in genomic sequencing, artificial intelligence, ecological modeling, field experimentation, and long-term monitoring are beginning to make these questions more tractable.
Conclusion
The soil microbiome represents one of Earth's largest and least visible biological systems.
Microorganisms beneath the surface help determine how nutrients move through ecosystems, how plants obtain resources, how diseases spread or are suppressed, how soils respond to drought and warming, and how enormous quantities of carbon are stored or released.
Agriculture can either disrupt or cultivate these microbial communities. Land degradation can simplify them, while restoration can help rebuild them. New technologies are increasingly allowing researchers to observe microbial ecosystems that were largely inaccessible only a few decades ago.
The emerging lesson is that maintaining healthy soil requires more than managing its chemistry and physical structure. It also requires understanding soil as a living ecosystem.
Protecting soil microbial biodiversity may therefore be important not only for soil itself but for agriculture, ecosystem resilience, climate regulation, and the long-term health of terrestrial environments.
Foundations and Big Picture
Examines how soil microorganisms release carbon dioxide through respiration and how warming, moisture changes, and other climate factors may alter this enormous component of the global carbon cycle.
Reviews the complex relationships among plants, soils, and microbial communities and their potential importance for sustainable agricultural systems.
Explains how soil texture, chemistry, nutrients, water, and other properties influence microbial communities while microbes in turn modify soil characteristics.
Describes how the physical organization of soil creates microbial habitats and influences nutrient cycling, carbon storage, plant health, and agricultural productivity.
Connects soil microbial diversity with plant, animal, environmental, and human health through the One Health framework.
Digging into the plant and microbe relationship | Allyson Mann | UGA Today | November 13, 2020
Describes research into the ways plants communicate with and recruit microorganisms living around their roots.
Reviews how climate change affects soil microorganisms and how microbial responses can feed back into greenhouse-gas emissions and ecosystem processes.
Provides an accessible introduction to where soil microorganisms live and how organic matter, pores, roots, water, and soil conditions shape microbial habitat.
Explores the rhizosphere as a highly active microbial ecosystem in which plant roots interact with bacteria, fungi, and other microorganisms.
Introduces soil as a living ecosystem containing enormous populations of bacteria, fungi, protozoa, and other organisms essential to soil processes.
Climate Change, Drought and Soil Carbon
How soil microbes may control the future of our planet | Paul Arnold | Phys.org | March 23, 2026
Explains why microbial decomposition and carbon storage in soils could strongly influence how rapidly atmospheric carbon dioxide rises in a warming world.
| Nichole A. Ginnan et al. | Nature Microbiology | October 30, 2025
Shows that long-term precipitation history can leave microbial legacies in soil that influence how native plants respond to later drought.
Identifies broad functional patterns that help explain how microbial communities respond to environmental change despite their enormous biological complexity.
| Madhav P. Thakur | Nature Ecology & Evolution | June 4, 2025
Discusses evidence that warming can alter bacterial life-history strategies while increasing antibiotic resistance and virulence-related genes in soils.
Uses metagenomic evidence to examine how combinations of global-change pressures alter microbial communities and their functional potential.
| Ashley York | Nature Reviews Microbiology | December 19, 2024
Examines how soil microbial communities respond to drought, flooding, heatwaves, and freezing and what those responses could mean for ecosystem functioning under climate change.
Reports evidence that experimental warming increased the diversity of metabolically active soil bacteria, potentially changing ecosystem functioning.
Describes efforts to incorporate microbial processes more accurately into models that predict soil carbon dynamics and future climate change.
| Research team | Communications Earth & Environment | 2024
Finds that microbial biodiversity helps maintain multiple soil and agricultural ecosystem functions under elevated carbon dioxide and warming.
Shows that differences among soil microbial communities help determine how strongly soil respiration responds to higher temperatures.
Examines relationships among warming, microbial activity, soil organic matter, and the release or stabilization of soil carbon.
Reviews ways soil microorganisms contribute to climate feedbacks and considers management strategies that could enhance carbon storage or reduce emissions.
| Research team | The ISME Journal | 2023
Shows how extreme heat and drought altered bacterial, fungal, and viral communities in cropland and grassland soils.
| Andrew T. Nottingham et al. | Nature Microbiology | September 5, 2022
Finds that experimental warming reduced microbial diversity in tropical forest soil while increasing carbon dioxide emissions more strongly than expected.
| Haitao Wang et al. | ISME Communications | August 25, 2022
Examines how summer drought changes microbial community composition and metabolic functioning in carbon-rich peat soils.
Investigates global patterns in carbon contained within soil microbial biomass and the environmental factors associated with changes over time.
| Erin E. Nuccio et al. | The ISME Journal | 2022
Shows that plant-associated fungi can help nearby bacterial communities recover from water limitation and maintain microbial functioning.
| Xue Guo et al. | Nature Ecology & Evolution | March 25, 2019
Reports that warming accelerates changes in bacterial and fungal biodiversity through time in experimental grassland soils.
| Mark A. Bradford et al. | Nature Ecology & Evolution | January 14, 2019
Uses evolutionary theory to explain broad differences in the temperature sensitivity of microbial respiration across soils from different biomes.
Finds that microbial responses to higher temperatures can help explain why warming causes carbon losses from soils.
Roots, Rhizosphere and Plant-Microbe Partnerships
Reports research suggesting beneficial microorganisms may help crops tolerate salt stress as soil salinization becomes a growing agricultural problem.
Describes evidence that microbes associated with maize and sorghum may influence how these major crops cope with heat.
Examines how soil bacteria alter their physiology and behavior when confronted with stressful environmental conditions.
Reports evidence that crop plants can consistently favor beneficial microbial partners even when grown in different soils.
| Yang et al. | Frontiers in Microbiology | March 22, 2024
Compares root and rhizosphere microbiota in healthy potatoes and plants infected with the soil-borne pathogen Rhizoctonia solani.
| Cristiana Paina et al. | Scientific Reports | March 8, 2024
Shows that ryegrass genotype, nitrogen availability, and season all influence the composition of its associated soil microbiome.
| Research team | Nature Reviews Microbiology | 2024
Reviews strategies for harnessing plant-associated microorganisms to improve crop nutrition, stress tolerance, disease resistance, and agricultural sustainability.
| Research team | Nature Communications | 2024
Separates plant-driven and environmental effects on active rhizosphere bacteria during short-term drought.
Investigates how proximity to plant roots can produce major shifts in microbial diversity and community structure.
| Xianheng Fu et al. | Frontiers in Plant Science | October 12, 2023
Shows that fine-scale bacterial genetic diversity helps sustain microbial populations across the gradient from maize roots to bulk soil.
| Jan Helge Behr et al. | Frontiers in Plant Science | August 28, 2023
Reports that a beneficial microbial consortium improved winter rye nutrition and performance while altering rhizosphere bacterial communities.
Describes experiments showing that soil microorganisms can alter plant drought responses through mechanisms more complicated than previously assumed.
| Yufan Lu et al. | Frontiers in Plant Science | June 22, 2023
Finds that arbuscular mycorrhizal fungi improve maize phosphorus acquisition while restructuring bacterial communities around the roots.
| Liqun Song et al. | Frontiers in Plant Science | May 30, 2023
Examines how root-knot nematode infestations are associated with changes in bacterial communities surrounding cucumber-family crops.
| Hugo A. Pantigoso et al. | Journal of Applied Microbiology | June 26, 2022
Reviews plant-microbial partnerships in the rhizosphere that help plants acquire phosphorus, nitrogen, iron, water, and other resources.
| Research team | FEMS Microbiology Ecology | February 23, 2022
Examines how pathogen infections and plant development alter bacterial and fungal communities associated with soybean roots, soil, and leaves.
| Ning Ling, Tingting Wang and Yakov Kuzyakov | Nature Communications | February 11, 2022
Synthesizes hundreds of datasets to identify broad differences between bacterial communities in rhizosphere and bulk soils.
| S. Emilia Hannula et al. | Nature Communications | September 28, 2021
Shows that microbial legacies left behind by previous plants can persist in soil and roots and influence later plant growth.
| Ankit T. Hinsu et al. | Scientific Reports | August 31, 2021
Tracks peanut rhizosphere microorganisms from before planting through harvest under field conditions.
| Erqin Li et al. | Nature Communications | June 22, 2021
Demonstrates that bacteria can rapidly evolve more beneficial relationships with plants when living in the rhizosphere.
| Antonio Castellano-Hinojosa and Sarah L. Strauss | Scientific Reports | May 12, 2021
Identifies shared bacterial groups and functions across agricultural crop rhizospheres and explores microorganisms that may drive these communities.
| Alonso Favela, Martin O. Bohn and Angela D. Kent | The ISME Journal | March 10, 2021
Shows that the breeding history of maize has affected its ability to recruit microorganisms from surrounding soil.
Examines shifts in the microbial community surrounding the roots of a leguminous plant under changing environmental conditions.
| Research team | Scientific Reports | 2021
Connects strawberry rhizosphere microbiomes with cultivar differences in nutrient uptake and resistance to soil-borne pathogens.
| Xuefang Zheng et al. | Scientific Reports | August 13, 2020
Tests a microbial restoration substrate designed to improve plant growth and rebuild rhizosphere bacterial communities in continuously cropped tomato soil.
| Qin Han et al. | The ISME Journal | April 27, 2020
Links differences in soybean rhizosphere microbial communities with the effectiveness of nitrogen-fixing rhizobial symbioses.
Some domesticated plants ignore beneficial soil microbes | Holly Ober | Phys.org | March 10, 2020
Reports evidence that domestication may have altered the ability of some crop plants to obtain benefits from associations with soil microorganisms.
Shows that microorganisms around plant roots can influence the chemical compounds plants release into surrounding soil.
| Research team | Scientific Reports | 2020
Finds that barley varieties adapted to different environments recruit distinctive bacterial communities around their roots.
| Research team | Nature | 2020
Shows how members of the bacterial genus Variovorax can maintain normal root development within complex plant microbiomes.
Describes research aimed at identifying highly effective microbial partners that could improve crop performance while reducing dependence on agricultural inputs.
Cropping Systems, Fertilizers and Soil Management
Introduces research examining how soil microorganisms simultaneously influence crop production, nutrient cycling, carbon storage, and other agroecosystem functions.
Explores combining microbiome analysis, bioengineering, and regenerative farming practices to improve soybean productivity in difficult soils.
Reports that vineyard management practices can alter microbial communities well below the soil surface rather than only in the cultivated topsoil.
Finds that agricultural management can encourage microbial functions associated with protecting crops from pests and pathogens.
| Chong Li et al. | Nature Communications | November 27, 2025
A global meta-analysis finds that crop rotation affects bacterial and fungal diversity differently, with outcomes influenced by crop type and soil conditions.
Examines seasonal changes in soil microorganisms and maize production following use of fertilizer supplemented with beneficial bacteria.
Finds that adding organic materials to urban agricultural soils can restructure microbial communities while improving soil conditions and crop quality.
Uses machine-learning analysis to show that farming practices affect both microbial community assembly and interactions at different soil depths.
| Dan Gao et al. | Scientific Reports | September 12, 2024
Investigates how years of continuous cultivation alter bacterial and fungal communities in medicinal-plant soils on the Qinghai-Tibetan Plateau.
Examines how agricultural land use reshapes soil microbial and fungal communities compared with less intensively managed ecosystems.
Investigates how farmers' understanding of soil microorganisms influences decisions about organic amendments, soil disturbance, and other management practices.
| Susumu Morigasaki et al. | Scientific Reports | April 30, 2024
Shows how different fertilizer programs and crop-development stages produce predictable shifts in bacterial communities in long-managed buckwheat fields.
| Ziheng Peng et al. | Nature Communications | April 29, 2024
Shows that conversion of natural ecosystems to agriculture makes soil bacterial communities increasingly similar across geographic regions.
| Bufan Zheng et al. | Scientific Reports | April 24, 2024
Examines how bacterial diversity and carbon metabolism change from surface farmland soils into deeper soil layers.
| Aura L. García-Serquén et al. | Scientific Reports | February 17, 2024
Examines how traditional potato tillage practices in the Peruvian Andes influence bacterial diversity, composition, and microbial functions.
| Samiran Banerjee et al. | Nature Communications | January 6, 2024
Finds lower fungal diversity, fewer rare fungi, and increased biological homogenization in cultivated European soils.
| Research team | Nature Communications | 2024
Finds that conservation agriculture can protect soil health, microbial communities, and crop production during long-term experimental warming.
| Shikha Singh et al. | Scientific Reports | August 25, 2023
Compares long-term tillage, fertilizer, crop rotation, and residue-management systems and their effects on bacterial communities in dryland wheat soils.
| Research team | Field Crops Research | December 1, 2022
Shows that long-term controlled-release nitrogen fertilizer altered microbial community networks associated with wheat productivity and soil fertility.
| Letusa Momesso et al. | Soil & Tillage Research | October 2022
Examines how cover crops and nitrogen management shape soil microbial communities in tropical no-till agriculture.
| Research team | Applied Soil Ecology | August 2022
Studies fertilizer practices, crop yield, bacterial communities, and fungal communities in a Kenyan paddy rice system.
| Research team | Ecological Indicators | July 2022
Finds that fertilizer treatments affected bacterial communities more strongly than fungi in sandy farmland, with soil pH emerging as a major driver.
| Research team | Agriculture, Ecosystems & Environment | May 1, 2022
A global meta-analysis examines how crop diversification, tillage, and fertilizer type affect total microbial, bacterial, and fungal abundance.
| Martina Kracmarova et al. | Environmental Microbiome | March 28, 2022
Uses long-term experiments to examine microbial effects of two decades of fertilizer and crop-rotation practices in Czech agricultural soils.
| Research team | Applied Soil Ecology | January 2022
Shows that diversified crop rotations reshape root, rhizosphere, and bulk-soil microbiomes while altering carbon and nitrogen cycling.
| Research team | Molecular Ecology | 2022
Tracks changes in bacterial and fungal communities as conventionally managed farmland is converted to organic agriculture.
| Research team | Agriculture, Ecosystems & Environment | January 1, 2022
Studies how strategic tillage, crop-residue retention, and fertilizer management influence soil microorganisms and microbial functions.
| Yanli Xiong et al. | Scientific Reports | October 11, 2021
Studies bacterial-community and soil-property changes through an annual ryegrass-maize rotation system in southern China.
| Haoran Li et al. | Scientific Reports | August 19, 2021
Finds that irrigation frequency had a stronger effect than nitrogen fertilizer on bacterial abundance, diversity, and community composition in wheat soil.
| Peina Lu et al. | Scientific Reports | November 16, 2020
Finds that biofertilizer and decomposed straw altered bacterial communities while improving oat production in saline-alkaline soil.
Examines bacterial-community and nutrient changes under different climate-smart cereal production practices.
| Yao Su et al. | Scientific Reports | April 14, 2020
Examines how more than a decade of different straw-return practices altered bacterial and fungal communities in wheat-corn rotations.
| Research team | Scientific Reports | June 20, 2019
Compares microbial responses in topsoil and subsoil to organic and inorganic amendments and investigates relationships with plant productivity.
Disease Suppression and Biological Control
Surveys research connecting microbial community structure with pathogen suppression, crop health, and broader soil ecosystem functioning.
Describes mechanisms through which beneficial soil bacteria can stimulate plant defenses and reduce vulnerability to disease.
Reports evidence that soybean plants alter their root-associated microbiome in ways that can improve resistance to an important agricultural pest.
| Bin Huang et al. | Frontiers in Microbiology | October 21, 2024
Compares chemical, organic, and bio-organic fertilizers and their effects on rhizosphere bacteria, root disease, crop quality, and yield.
| Mengmeng Zou et al. | Scientific Reports | June 26, 2024
Examines how heavy metals and other environmental conditions combine to structure bacterial communities in polluted paddy soils.
| Zhaokai Sun et al. | Frontiers in Microbiology | May 22, 2024
Compares microbial communities across land-use types and identifies human activity as an important driver of microbial change.
Investigates how grafting can change the root-zone environment and microbial community in ways that reduce crown gall disease.
Identifies soil microorganisms associated with plant resistance to parasitic organisms and explores their possible use in biological control.
| Research team | Frontiers in Microbiology | February 29, 2024
Examines how soil properties influence microbial enrichment and potential microbial biomarkers in healthy versus diseased plants.
| Research team | Nature Communications | 2024
Shows that predatory soil protists can indirectly reduce bacterial wilt disease in tomato by restructuring rhizosphere microbial communities.
Investigates the ecological factors that cause some root-associated microbial communities to suppress plant pathogens more effectively than others.
Shows that soil acidification can weaken naturally occurring microbial defenses against disease-causing Fusarium fungi.
| Research team | Frontiers in Plant Science | April 6, 2023
Reviews beneficial bacteria adapted to arid and nutrient-poor soils and their potential uses in plant growth promotion and biological control.
| Research team | The ISME Journal | 2023
Links banana resistance to Fusarium disease with recruitment of particular pathogen-suppressive fungi into the rhizosphere.
Tests whether transferring a diverse rhizosphere microbiome can improve disease resistance in barley grown in microbially depleted soil.
| Research team | Soil Biology and Biochemistry | April 2022
Shows how amendments to acidified agricultural soil can restructure rhizosphere microorganisms, enhance pathogen suppression, and alter plant defenses.
| Research team | Environmental Microbiome | January 6, 2022
Finds that agricultural intensification changes bacteria, fungi, and protists while reducing the complexity of microbial interaction networks.
| Research team | Nature Microbiology | 2020
Finds that competition for iron among rhizosphere bacteria can determine whether pathogenic bacteria are suppressed and plants remain healthy.
Reports that the composition of microbial communities surrounding roots can strongly influence whether plants resist or succumb to disease.
Describes research showing that disease suppression can depend on interactions among entire microbial communities rather than a single protective species.
Microbial Biodiversity, Networks and Biogeography
Fantastic soil microbes and where to find them | University of Sydney | Phys.org | June 10, 2025
Highlights the extraordinary diversity of microorganisms living in soil and efforts to understand their distributions and ecological functions.
| Daan T. P. Kinsbergen et al. | npj Biodiversity | March 30, 2025
Investigates biological and environmental factors controlling microbial diversity in a heavily grazed natural ecosystem.
| Ernest D. Osburn et al. | Nature Communications | August 11, 2024
Maps broad global patterns in the potential growth rates and ecological strategies of soil bacterial communities.
| Erika Buscardo, József Geml and Laszlo Nagy | Communications Earth & Environment | June 17, 2024
Examines seasonal shifts in the ecological processes responsible for assembling fungal communities in Amazon rainforest soil.
Examines the survival strategies that allow microbial communities to persist in extremely dry and nutrient-poor desert soils.
Describes how soil chemistry and environmental conditions favor bacteria with different growth, resource-use, and survival strategies.
| Research team | Scientific Reports | March 21, 2024
Shows that even relatively short restoration efforts can begin rebuilding bacterial communities in degraded semi-arid soils.
Shows that both climate and limits on microbial dispersal contribute to patterns of microbial diversity along mountain environments.
| Research team | Nature Communications | 2024
Finds that soil fungal composition—particularly mycorrhizal and endophytic fungi—is strongly associated with forest carbon storage across Europe.
Builds a large genomic resource revealing extensive previously unexplored microbial diversity and genetic potential in soils.
Compares bacterial ecological strategies across biomes and shows how environmental conditions select microorganisms with different survival and growth traits.
| Research team | Nature Communications | 2023
Links stable plant communities with distinctive patterns of interaction between fungal and prokaryotic soil networks.
| Research team | Nature Ecology & Evolution | 2023
Identifies global water-availability thresholds associated with abrupt changes in bacteria, fungi, protists, soil animals, and ecosystem functions.
Finds that even over relatively short geographic distances, differences in soil acidity can strongly structure bacterial communities.
Compares bacterial communities in surface and deeper soils and shows that depth and elevation create distinct microbial habitats.
Explores soil protists, an often overlooked group of microorganisms that prey on bacteria and help regulate microbial food webs and nutrient cycling.
| Colin Averill et al. | Nature Ecology & Evolution | April 22, 2021
Shows that predicting bacterial and fungal community composition becomes easier at broader spatial and taxonomic scales.
| Lu Luan et al. | Nature Communications | December 17, 2020
Finds that organism size influences the ecological processes assembling microbial and nematode communities from regional to global scales.
| Samuel Bickel and Dani Or | Nature Communications | January 8, 2020
Uses ecological modeling to explain how microscopic water conditions in soil help generate bacterial diversity across global biomes.
Describes one of the early large-scale efforts to map how bacterial communities vary among soils across Britain.
Land Use, Restoration and Ecosystem Development
Examines how combinations of plants and microorganisms can help rebuild soil communities and improve severely disturbed mine soils.
Shows that microbial-community characteristics can help indicate how well soils perform multiple ecological functions simultaneously.
Finds that microbial functional diversity expands as ecosystems develop, linking microbial succession to changing soil processes.
Shows that ecological restoration can affect surface and deeper microbial communities differently and that restoration outcomes depend on ecosystem type.
Finds that agricultural land use can make microbial functions increasingly similar across landscapes even when taxonomic differences remain.
Examines how trees influence bacterial and fungal communities within two diversified agroforestry systems.
Reports that ecosystem restoration can rebuild microbial communities lost or altered by land degradation in semi-arid landscapes.
Examines how land-use change alters the network of interactions among microorganisms in temperate grassland soils.
Shows how microscopic water films, carbon resources, and soil structure determine where bacteria can live and interact within soil pores.
Explains how both living microbial biomass and the remains of dead microorganisms contribute to long-term soil carbon dynamics.
Nutrient Cycling and Functional Microbes
Identifies bacteria capable of making mineral nutrients more available and demonstrates their potential to improve nutrient uptake by maize.
Examines links between fungal-community composition and nitrogen and phosphorus transformations in plantation soils.
Investigates how reducing nitrogen fertilizer influences nitrogen-fixing microorganisms in an intercropped soybean-maize system.
Reviews the often underestimated role of soil archaea in transformations of nitrogen and carbon in agricultural ecosystems.
Reports that compounds associated with vitamin B12 can alter microbial growth patterns and change the composition of soil communities.
Examines how biochar-based fertilizers alter microbial communities and how those changes contribute to nutrient cycling and soil functions.
Shows that different forms of nitrogen fertilizer can reshape soil protist communities in rice-growing soils.
Links concentrations of trace metals and micronutrients with differences in microbial community composition and functional potential.
Synthesizes evidence showing how biochar additions affect microbial abundance, diversity, and activity under different soil and environmental conditions.
Describes evidence that microbial communities use multiple biochemical pathways to process carbon, affecting how carbon moves through soils.
| Tang Haiming et al. | Scientific Reports | April 16, 2020
Examines how manure nitrogen additions affect microbial use of different carbon compounds in rice rhizosphere and non-rhizosphere soils.
Methods, Modeling and Microbiome Engineering
Reviews emerging technologies that could allow farmers and researchers to monitor microbial activity and soil health with much greater precision.
Examines how increasing salinity and alkalinity restructure microbial ecological networks and alter the range of conditions occupied by different taxa.
Uses multiple molecular techniques to investigate how disrupted soil microbiomes contribute to declining blueberry performance under continuous cropping.
Discusses research suggesting that highly diverse microbial systems may display predictable collective behaviors despite containing many individual species.
| Krisy Gashler | Cornell Chronicle | December 17, 2025
Describes research showing how microbes temporarily increase the molecular diversity of soil organic matter while decomposing plant residues.
Evaluates a microbial fertilizer designed to accelerate crop-residue decomposition while improving soil communities and maize productivity.
Tests an engineered microbial community designed to degrade microplastics and examines its effects on fungi and metabolism around barley roots.
| Penn State | Penn State University | November 4, 2025
Describes a technique for identifying which dormant soil microorganisms become metabolically active near plant roots.
Identifies bacteria adapted to degraded sandstone environments and evaluates their potential use in microbial inoculants for soil restoration.
| Marcin Musiałowski et al. | Scientific Reports | September 29, 2025
Presents a two-step metabarcoding strategy intended to improve measurements of bacterial and fungal biodiversity in complex soil samples.
Reviews strategies for deliberately manipulating microbial communities to restore functions lost in disturbed agricultural soils.
Describes a simplified modeling approach for predicting changes in microbial metabolism as environmental conditions vary.
| Loredana Canfora and Massimo Pugliese | Frontiers in Microbiology | October 30, 2024
Reviews research into how environmentally friendly farming practices influence soil microbiome composition and functioning.
| Elisa Clagnan et al. | Frontiers in Microbiology | October 24, 2024
Reviews how culturing techniques and metagenomic sequencing can be combined to preserve and exploit useful soil microorganisms.
| Research team | Frontiers in Microbiology | March 25, 2024
Synthesizes three decades of research on the effects of soil microorganisms on plants, nutrient cycling, soil properties, and ecosystem functioning.
Shows that characteristics of existing soil microbial communities can help predict whether crops will benefit from inoculation with beneficial mycorrhizal fungi.
| Linkun Wu et al. | Frontiers in Plant Science | September 5, 2023
Surveys research on root exudates, microbial recruitment, rhizosphere assembly, plant health, and communication between roots and microorganisms.
| Olivera Topalović et al. | Frontiers in Plant Science | 2023
Reviews biological and environmental factors controlling interactions among plants, bacteria, fungi, protists, nematodes, and other rhizosphere organisms.
| Food and Agriculture Organization | FAO | September 7, 2022
Introduces FAO's major review of soil microbiomes and their implications for crop production, food systems, climate, and environmental health.
| Lucian Constantin Dincă et al. | Applied Sciences | January 24, 2022
Reviews evidence on how mineral fertilizers, manure, organic amendments, and other fertilizer strategies alter soil microbial communities.
Soil Microbes, One Health and Broader Applications
Reviews how beneficial bacteria, fungi, and other microorganisms associated with legumes could support nutrient efficiency, stress tolerance, and climate-resilient farming.
Uses metagenomic analysis to show how agricultural land conversion can make microbial communities more alike across landscapes in Brazil's Cerrado.
Examines possible connections among microorganisms in soils, plants, foods, and the human gut and discusses what is known and still uncertain about these links.
Reviews the importance of soil microorganisms for ecosystem resilience, sustainable agriculture, environmental quality, and long-term soil stewardship.
Shows that relationships between microbes and ecosystem functions vary with soil depth and can be altered by agricultural land use.
Reviews how microbial processes can be incorporated into climate-smart agriculture to increase productivity, nutrient efficiency, and resilience.
Introduces research on using microbial communities and mycorrhizal fungi to improve plant nutrition under drought, heat, and other climate stresses.
Explains why researchers believe soil microbial health should be considered alongside human, animal, plant, and ecosystem health.
Argues that policies addressing human, animal, and environmental health should explicitly recognize soil microbial communities as a foundational component.
Shows how antibiotic residues from livestock production can interact with warming to disrupt microbial communities and ecological processes in soil.
Agricultural Applications and Emerging Research
| Penn State University | Penn State University | 2026
Describes research into rhizobial bacteria, legume rotations, nitrogen fixation, and ways beneficial soil microorganisms might reduce fertilizer requirements.
| Earlham Institute | Earlham Institute | August 26, 2025
Describes a major project examining how land management, soil microbial processes, and carbon storage might contribute to net-zero goals.
| Rachel Kibui and Manoj Kaushal | Alliance of Bioversity International and CIAT | July 14, 2025
Examines soil microbial diversity in smallholder farms in western Kenya and its potential importance for soil fertility and climate resilience.
| Penn State Research | Pennsylvania State University | June 10, 2025
Describes research into sorghum root chemistry, soil microorganisms, and their potential role in crop tolerance to environmental stress.
| Christine Yu | Penn State University | May 29, 2025
Includes research examining how microbial-community dynamics influence production of the powerful greenhouse gas nitrous oxide in soils.
| University of Queensland | UQ News | April 9, 2025
Reports field trials testing fungal endophytes as a way to improve soybean productivity while increasing stable carbon stored in agricultural soils.
| Joslyn Neiderer | Penn State Research | April 8, 2025
Describes research into rebuilding microbial communities after soils have been disrupted or cleared in high-value cropping systems.
| Anna Zarra Aldrich | UConn Today | March 26, 2025
Explores how interactions between biochar and soil microorganisms could improve nutrient cycling, carbon storage, and climate-smart agriculture.
| Sarah Richards et al. | Penn State Extension | March 6, 2025
Explains how cover crops can influence microbial abundance, diversity, fungal communities, and other biological indicators of healthy agricultural soil.
| Carolyn Blais | MIT J-WAFS | January 15, 2025
Describes research in the United States and Kenya aimed at developing microbial communities capable of supplying maize with biologically fixed nitrogen.
| John Innes Centre | John Innes Centre | January 15, 2025
Reports discovery of a plant signaling mechanism that can increase partnerships with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi.
| Amy Calabretta | University of Idaho | December 1, 2024
Examines how different cover-crop mixtures affect soil microbial communities and subsequent wheat production.
| Niranjana Rajalakshmi | University of Arizona News | November 19, 2024
Describes efforts to combine microbial measurements and artificial intelligence to improve representation of soil carbon processes in climate models.
| Amanda Morris | Northwestern Now | June 11, 2024
Shows that soil bacteria release different amounts of carbon dioxide depending on which chemical components of plant material they consume.
| Kristy Borrelli et al. | Penn State Extension | 2021
Provides an accessible overview of soil bacteria, fungi, archaea, protozoa, viruses, microbial diversity, and ways agricultural management can influence them.
