Types and functions of soil microorganisms used for soil improvement and remediation

The soil contains rich and diverse microbial communities with diverse metabolic functions. They are not only drivers of soil nutrient cycling, but also the main bearers of environmental pollutant degradation and transformation. These microorganisms can regulate nutrient cycling, decompose organic matter, inhibit soil borne diseases, improve soil structure, support plant production, participate in atmospheric trace gas metabolism, regulate soil acidity and carbon dynamics, and are crucial for improving soil fertility and carbon fixation. The use of microorganisms to assist in soil improvement and remediation of toxic pollutants is economically efficient and environmentally friendly. Currently, a variety of highly efficient functional microorganisms have been discovered, such as phosphorus solubilizing bacteria (soil monomonas and knot bacteria), fungi (Penicillium, Aspergillus, and Aspergillus), and symbiotic microorganisms (rhizobia and mycorrhizal fungi). They have been successfully applied in soil improvement and remediation, with broad application prospects.
1、 Bacteria
Soil bacteria, as the most abundant and diverse microbial community with diverse biological functions, participate in the process of organic matter degradation in soil environment, release nutrients, drive the biogeochemical cycle of important elements such as carbon, nitrogen, sulfur, and phosphorus in soil, and play an important role in degrading and transforming soil pollutants and improving soil quality. According to the role played by bacteria in soil, they are divided into different functional groups, including nitrogen fixing bacteria, ammonia oxidizing bacteria and nitrite oxidizing bacteria, nitrifying and denitrifying bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria and other bacterial groups with different physiological functions.
Nitrogen is an essential component of all living organisms and a necessary substance for synthesizing key cellular compounds such as proteins and nucleic acids. Nitrogen fixing bacteria can convert atmospheric free nitrogen (N2) into ammonia nitrogen, which is then absorbed and utilized by plants and plays an important role in nutrient cycling. According to the survival mode of nitrogen fixing bacteria, they can be divided into autotrophic (non symbiotic) nitrogen fixing bacteria and symbiotic nitrogen fixing bacteria. There are various types of autotrophic nitrogen fixing bacteria in soil, and nitrogen fixing bacteria have been found in multiple genera such as Proteobacteria, Cyanobacteria, and Firmicutes. These bacteria can independently fix nitrogen and provide a convenient and low-cost source of nitrogen for soil replenishment. They are important biotechnological measures for the recovery of barren soils and completely destroyed soil functions in arid areas. Symbiotic nitrogen fixing bacteria are a large class of bacteria that form a symbiotic nitrogen fixing system with host plants, mainly including rhizobia and cyanobacteria. Rhizobia are the most widely used, and rhizobia legume symbiosis increases nitrogen content in the soil plant system, improves soil nitrogen fertility, and affects soil chemical properties by promoting plant root growth, improving soil structure, and enhancing soil enzyme activity. As an important community in soil, rhizobia can also stimulate other microorganisms with different functions in the soil, allowing more microorganisms in the soil to play a role in remediation.
After the atmospheric free N2 is converted into ammonia nitrogen through the action of nitrogen fixing bacteria, it needs to be further oxidized into nitrate through the ammonia oxidation (nitrite) reaction and nitrification reaction by nitrite oxidizing bacteria. Under the action of these two bacteria, ammonia is oxidized into nitrate, which is then converted into a nitrogen form that can be absorbed and utilized by plants. At present, ammonia oxidizing bacteria have been found in the genera Anammoxoglobus, Anammoximicrobium, Brocadia, Jettenia, Kuenenia, and Scalindua, while nitrite oxidizing bacteria are found in the genera Nitrobacter, Nitrococcus, Nitrospina, Nitrotoga, Candidatus Nitromaria, and Nitrolancea. These nitrifying bacteria convert ammonia into nitrate, providing nitrogen for plants and promoting the entry of exogenous nitrogen fertilizer into soil nitrogen cycling through ammonia oxidation. Denitrifying bacteria reduce nitrate and nitrite to N2O or N2, completing a complete nitrogen cycle. Denitrifying bacteria have been identified in multiple genera such as Pseudomonas, Alcaligenes, Paracoccus, and Bacillus. At present, denitrifying bacteria are still used in wastewater treatment and water purification, which can effectively remove nitrate nitrogen and ammonium nitrogen from water bodies, convert them into nitrogen gas, and improve water quality.
Soil microorganisms can also promote the dissolution of insoluble minerals in soil, such as phosphate solubilizing bacteria and potassium solubilizing bacteria, which can convert insoluble phosphorus and potassium in nature into soluble phosphorus and potassium through decomposition or dissolution, and then provide mineral elements that can be absorbed and utilized by plants and other microorganisms. At present, bacteria with phosphorus solubilizing ability have been isolated from multiple genera including Alcaligenes, Agrobacterium, Agromonas, Arthrobacter, Azotobacter, Bacillus, and Beijerinckia. And the distribution of potassium solubilizing bacteria in soil is also very extensive. Currently, bacteria with potassium solubilizing ability have been isolated from many genera such as Acinetobacter, Agrobacterium, Arthrobacter, Azotobacter, Bacillus, Exiguobacter, Klebsiella, etc. Among them, the more extensively studied species include Bacillus subtilis, Bacillus mucilaginosus, and Bacillus edaphicus. They can decompose silicate minerals in soil, have the ability to hydrolyze potassium and phosphorus, and convert them into effective nutrients for plant use. At the same time, these microorganisms can secrete growth hormones and enzymes to promote plant growth and development.
In addition, soil microorganisms also include other bacteria with rich functions, such as sulfide bacteria and anti sulfide bacteria, which complete the oxidation and reduction reactions of sulfur, reduce soil pH, and have a certain effect on the improvement of saline alkali land. It has been found that some bacteria have the ability to reduce sulfates, with typical representatives including Desulfovibrio and Desulfotomaculum. The process of bacterial sulfate reduction can generate highly insoluble sulfide precipitates from heavy metal ions in the environment, and is therefore commonly used for the remediation of heavy metal polluted areas. Some bacteria also have the function of degrading petroleum hydrocarbons, and have good degradation effects on alkanes and aromatic hydrocarbons. There are bacteria with different functions such as microplastic degrading bacteria and antibiotic degrading bacteria in the soil, which can be used for environmental pollution remediation. There are various types of actinomycetes in the soil with different metabolic functions. Among them, Streptomyces, Nocardia, Micromonospora, Actinopales, and Streptosporangium can promote plant growth and improve soil ecology by enhancing the ability of roots to absorb, fix, and transform nutrients.

2、 Fungi
Mycorrhizal fungi, Trichoderma, and some functional fungi are commonly used in soil improvement. Among them, mycorrhizal fungi refer to a large class of soil fungi that can form symbiotic bodies (mycorrhiza) with plant roots. According to the fungi that form mycorrhiza, the types of plants, and the anatomical characteristics of mycorrhizal morphology, they are usually divided into ectomycorrhizal fungi, arbuscular mycorrhizal fungi, ectomycorrhizal fungi, orchid mycorrhizal fungi, and azalea mycorrhizal fungi. Among this category of functional fungi, arbuscular mycorrhizal fungi are the most widely distributed (72%), capable of directly secreting metabolites such as organic acids or various active enzymes such as hydrolytic enzymes, as well as gibberellins, to improve soil physicochemical properties and promote the formation and stability of soil aggregates. Some fungi can also directly absorb or adsorb heavy metal ions in the soil, improving the soil environment. The symbiosis between mycorrhizal fungi and plants can also improve the absorption and utilization of water and nutrients in the soil by plants, and enhance soil fertility.
Trichoderma is a type of fungus belonging to the Deuteromycotina, Hyphomcetes, Hyphomycetalies, Hyphomycetaceae, and Trichoderma genera. It has a wide variety of species and is widely used. Among them, T. harzianum, T. viride, T. atroviride, and T. aureoviride are commonly used in production. Trichoderma has the ability to promote soil nutrient cycling and environmental remediation by decomposing phosphorus, potassium, nitrogen, etc. It can also adsorb heavy metal ions in soil and remediate heavy metal contaminated soil. Trichoderma can also be used for the biodegradation or transformation of pollutants in sewage and sludge, as well as pesticide contamination.
In addition to utilizing a wide range of mycorrhizal fungi and Trichoderma, there are also other functional fungi such as petroleum hydrocarbon degrading fungi and laccase producing fungi. At present, these functional fungi have been screened from multiple genera of fungi, such as Aspergillus, Candida, Fusarium, Mortierella, Mucor, Penicillium, Rhodotorula, etc.
The following table lists some bacteria and fungi used in soil improvement and remediation.