The Symbiotic Dance of Roots and Microbes in Living Soil
Four groups of microorganisms routinely colonize roots, and their ability to enhance plant growth has been documented. These organisms are true plant symbionts.
Living soil includes organic matter like peat, compost, coco coir, manure, and worm castings that provide food for fungi and bacteria. These fungi support a healthy soil ecosystem that improves crop yields and provides resilience against stress, pests and disease.
Roots and Microbes
For more than 300 years, plant biologists have known the benefits of living soil in symbiotic relationships with microorganisms in the soil. These are called mycorrhizae, and they help plant roots get the nutrients and water they need to survive and thrive.
In the last few decades, scientists have learned more about these microbial symbionts and how they work with their host plants. They have found that they can increase crop productivity and yield by a variety of mechanisms including nitrogen fixation, hormone signaling, nutrient acquisition, and stress resistance.
The microbial community in and around root cells (the rhizosphere) is a dynamic and constantly changing mixture of both resident and transient taxa. These microorganisms are largely recruited from the surrounding soil by a wide range of metabolites released by plant roots into the soil. This chemical communication between the microbial community and the plant root plays a key role in many of the symbiotic functions discussed above.
Four groups of microbial symbionts routinely colonize and reside within plant roots: (a) bacteria in the Rhizobiaceae family, including the well-studied rhizobia; (b) arbuscular mycorrhizal fungi (AMF) in the phylum Glomeromycota; (c) specific strains of the ascomycetous fungus Trichoderma; and (d) fungi in the order Sebicales, such as Piriformaspora indica. While these symbionts are phylogenetically distinct and belong to different classes of organisms, they have independently evolved means to internally colonize plant roots and become resident endophytes. Each group produces SAMPs, which are able to induce multiple benefits in their host plants.
Although the root-microbe interaction is complex, researchers can now study this process at a cellular level using modern Minirhizotrons which combine transparent tubes in the soil, miniature video cameras for capturing images of the root system, and automated software for analyzing the data. This technology makes it possible to identify the exact locations of microbial colonization, as well as the time of colonization, in a noninvasive way.
The rhizosphere is a vibrant hub for symbiotic plant-microbe interactions. This understanding will help pave the way for green agriculture, sustainability, and enhanced crop yields through nutrient provisioning, hormonal signaling, outcompeting pathogens, and abiotic stress adaptation.
Nutrient Cycling
Nutrient cycling is the process of transferring elements from the physical environment into living organisms and back again. It’s essential to ecosystem productivity and sustainability. It includes the carbon cycle that regulates Earth’s climate, the nitrogen cycle crucial to plant growth and protein synthesis, and the phosphorus and sulphur cycles needed for aquatic ecosystems. All of these cycles are intricately connected, and altering one element can have unforeseen consequences for other elements.
Bacteria harvest nutrients from the rhizosphere—the narrow region adjacent to and within root tissues. They do so by secreting compounds called metabolites that stimulate the growth of other bacteria that help them digest soil organic matter. In turn, the bacteria release nutrient-rich spores that are transported to other roots, stimulating further microbial growth. The microbial community in the rhizosphere has unique characteristics compared to the surrounding bulk soil, and this distinct microenvironment is an important source of nutrients for plants.
The rhizosphere also contains nutrients from the parent material—rocks, pebbles, sand particles and silts. On a molecular level, these materials contain atoms of iron, boron, phosphorus, and calcium. The bacterium’s metabolites allow them to access these nutrients, which are otherwise inaccessible to the plant.
In addition to the supply of nutrient, symbiotic microbes can provide protection against disease and environmental stresses. Four groups of symbiotic microbes have been identified that inhabit the rhizosphere of most plants: Rhizobiaceae bacteria; arbuscular mycorrhizal (AMF) fungi in the phylum Glomeromycota; and specific strains of fungi in the Ascomycetous order Sebicales, such as the common soil-inhabiting genus Trichoderma and the more rare Piriformaspora indica. All of these groups have documented abilities to positively impact plant physiology and aid in the mitigation of abiotic stress, such as drought, salt and pathogens.
The complex interactions of the rhizosphere are vital to healthy soils and the overall health of all living things. However, human activities significantly disrupt these natural processes. Excessive fertiliser use can cause nutrient runoff into water bodies, resulting in eutrophication and harming aquatic life; deforestation reduces soil organic matter; and fossil fuel combustion changes atmospheric nitrogen levels, all of which affect nutrient cycling and ecosystem function.
Nutrient Retention
Soil serves a number of essential functions, from providing a medium in which plant life can grow to recycling and storing organic matter (such as this farmer using a probe to check the depth of soil organic matter or SOM), supplying water, regulating temperature and pH, sheltering animals like groundhogs and bumble bee colonies, and retaining vital nutrients such as carbon, nitrogen, phosphorus, iron, and zinc. Soils also protect plants from disease and stress.
Soils are home to a diverse community of microorganisms, including bacteria and fungi, some visible to the naked eye and others too small to see, such as amoebae, roundworms (nematodes) and mites. These organisms decompose organic matter – such as dead plant material, crop residues and dung – into nutrients the plants can uptake for growth and development.
Several groups of microbial symbionts are known to symbiotically associate with roots, enhancing plant growth. The most well-known are the rhizobia, bacteria in the family Rhizobiaceae that form nodules on legumes, such as soybeans and alfalfa. These nodules convert atmospheric nitrogen gas, N2, into ammonia, NH3, an essential plant nutrient. Another group of microbial symbionts, arbuscular mycorrhizal fungi, or AMF, are fungi that penetrate and colonize the inner surface of root cells, without damaging the cell walls. This symbiotic association is responsible for enhanced nutrient uptake in roots and a general increase in plant productivity.
Researchers are still learning how to exploit the full potential of these symbiotic associations for improving world food supplies and climate change mitigation. Promoting greater rates of photosynthesis that translate into larger and deeper root systems requires changes in farming practices and agricultural policy, as well as research to understand microbial biochemical activities and rhizosphere elasticity.
To better understand these interactions, Los Alamos scientists are collaborating with colleagues worldwide to create and share data that will lead to a more complete understanding of the microbial communities associated with roots. They are working to standardize the way microbiome data is collected and shared, and to help educate scientists to make these datasets more usable. This work is being conducted through the National Microbiome Data Collaborative, a project funded by the U.S. Department of Energy and the National Science Foundation.
Disease Prevention
Many of the bacteria and fungi that co-evolved with plant roots are primary decomposers, but some also help with other tasks. They can detoxify harmful chemicals, suppress disease organisms and even produce products that might stimulate plant growth. They are essential to all life on Earth.
One of the oldest and most widespread symbiotic relationships is between plants and root-associated fungi, called mycorrhizae. The fungi send out thin threads, called hyphae, that can take up water and nutrients from small spaces in the soil that would be otherwise inaccessible to the plant. The fungi receive energy from the plant in return, for example by converting atmospheric nitrogen to nitrates that can be used by the plant to grow. Most land plants, including most of the crops that we eat, form mycorrhizae with their roots.
Other symbiotic microorganisms that closely associate with plants include the nodules of Rhizobiaceae bacteria on legumes, which convert atmospheric N2 to NH3, and the endophytic fungi that colonize most plant species, including crop species. In addition to improving plant productivity, these symbiotic associations can enhance resistance to pests and environmental stressors such as drought or salt.
These symbiotic microorganisms also provide an important barrier against the pathogens that cause plant diseases. For a fungal or bacterial pathogen to infect and kill a plant, it must first enter the rhizosphere. The mycorrhizae of some plants, including most legumes, block the pathogen from entering the rhizosphere. Other fungi, such as those in the genus Aspergillus, secrete an enzyme that breaks down the chemical compounds that make up a plant cell wall, allowing the pathogen to invade.
Buck Hanson and his Los Alamos colleagues collect hundreds of bacteria and fungi from various soils, growing them in petri dishes with carefully adjusted nutrients to determine their metabolic functions. They then test whether a particular microbe can boost a plant’s ability to take up certain nutrients, such as nitrogen or phosphorus. Their research is part of a Department of Energy Science Focus Area program on Bacterial-Fungal Interactions in Living Soil.
