The increasing global demand for food caused by a growing world population has resulted in environmental problems, such as the destruction of ecologically significant biomes and pollution of ecosystems. At the same time, the intensification of crop production in modern agriculture has led to the extensive use of synthetic fertilizers to achieve higher yields. Although chemical fertilizers provide essential nutrients and accelerate crop growth, they also pose significant health and environmental risks, including pollution of groundwater and other bodies of water such as rivers and lakes. Soils that have been destabilized by indiscriminate clearing of vegetation undergo a desertification process that has profound effects on microbial ecological succession, impacting biogeochemical cycling and thus the foundation of the ecosystem. Tropical countries have positive aspects that can be utilized to their advantage, such as warmer climates, leading to increased primary productivity and, as a result, greater biodiversity. As an eco-friendly, cost-effective, and easy-to-apply alternative, biofertilizers have emerged as a solution to this issue. Biofertilizers consist of a diverse group of microorganisms that is able to promote plant growth and enhance soil health, even under challenging abiotic stress conditions. They can include plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and other beneficial microbial consortia. Bioremediators, on the other hand, are microorganisms that can reduce soil and water pollution or otherwise improve impacted environments. So, the use of microbial biotechnology relies on understanding the relationships among microorganisms and their environments, and, inversely, how abiotic factors influence microbial activity.
Biofertilizers and Bioremediators
One of the key elements of fertile soil is the presence of beneficial soil microbiota, which plays a crucial role in enhancing the nutrient pool through biogeochemical processes in the soil. Consequently, it is essential for biofertilizers (microbial inoculants) to be compatible with the soil environment. However, a significant proportion of arable soils worldwide does not offer ideal cultivation conditions due to various abiotic stressors, such as the presence of organic pollutants or heavy metals, drought, salinity, and extreme temperature variations. Among these stressors, the release of metals from diverse human activities poses a substantial threat to the sustainability of crop production systems.
Biofertilizers and bioremediators consist of organic or composite products containing living microorganisms with the ability to enhance biogeochemical cycles and, as a result, increase primary productivity and environmental health. The basic difference between the two lies in their purpose and consequent composition: Biofertilizers are used to enhance crop productivity, while bioremediators are employed for the removal of excessive or toxic compounds. In the particular case of biofertilizers, they are mainly used in agriculture as an alternative to traditional chemical fertilizers, since they can play a significant role in providing essential plant nutrients, such as nitrogen, phosphorus, and potassium, in a more sustainable manner. Various biofertilizer types are available, including nitrogen-fixing varieties, mycorrhizae (fostering symbiotic associations between fungi and plant roots to enhance nutrient absorption), phosphorus-solubilizing bacteria, and liquid fertilizers containing microorganisms that facilitate organic matter decomposition, thus enhancing soil structure and nutrient availability. In comparison to chemical fertilizers, biofertilizers are deemed more sustainable, as they reduce the dependence on harsh chemicals, promote soil well-being, and, in many instances, encourage environmentally friendly agricultural practices. Bioremediators, on the other hand, contribute to the reduction of pollution and the associated environmental impact stemming from conventional agriculture, deforestation of forests with concomitant soil degradation, and the ultimate contamination of soil and water bodies.
Agricultural Fertilization
The global human population continues to expand at a concerning rate, giving rise to various issues, including food insecurity. To ensure the supply of food, it is imperative to enhance crop production through fertile agrosystems. Soil fertility and crop productivity are often used interchangeably; however, they differ significantly. Soil fertility refers to the inherent capacity of soil to provide essential plant nutrients in sufficient quantities, while crop productivity is defined as H/P × Y, where H is acres harvested, P is acres planted, and Y is the yield per acre. Both, however, rely on the availability of essential plant nutrients such as N, P, K, Ca, Mg, S, Cu, Cl, and Si. These nutrients are produced by the natural decomposition of soil organic matter and the addition of chemical fertilizers. Inoculating biofertilizers represent a promising approach for enhancing crop productivity while decreasing reliance on synthetic fertilizers, thereby promoting environmentally sustainable agriculture.
Microbial inoculants play a crucial role in accelerating the decomposition process, which results in the release of these essential nutrients. This, in turn, leads to an overall increase in crop productivity. As the global population currently stands at around 8 billion people and is projected to reach 9.7 billion by 2050, there is a pressing need to produce 321 million tons of food to feed this growing populace. However, relying solely on chemical fertilizers is no longer a sustainable solution due to their cost and detrimental effects on soil health. The emphasis is shifting toward cost-effective, environmentally friendly, and sustainable biofertilizers, which not only enhance the physical, chemical, and biological properties of the soil but also boost crop yield per unit area.
Biofertilizers are also gaining attention for their potential use in challenging environments, such as those with elevated temperatures, saline soils, water scarcity, fluctuating pH levels, and the presence of environmental stressors like protein and heavy metal contaminants. Their impact extends to the modulation of microbial communities within the rhizosphere, thus exerting an influence on the soil’s overall ecosystem.
The use of biofertilizers enhances both the function and structure of soil microorganisms and has implications for the physicochemical properties of the soil. The effects of introducing plant growth-promoting rhizobacteria (PGPR) can be quite variable, impacting indigenous microbial populations in various ways. Some remain unaffected, while others may experience either stimulation or inhibition of their growth. For instance, the probiotic strain Stenotrophomonas acidaminiphila BJ1 was found to increase the bacterial population in the rhizosphere of Vicia faba in chlorothalonil-polluted soil. Numerous studies have assessed the impact of microbial inoculants on soil microorganisms. As early examples, we may cite Upadhyay et al. (2012a), who reported positive effects on the growth and antioxidant status of wheat under saline conditions when inoculated with two PGPR strains, Bacillus subtilis SU47 and Arthrobacter sp. SU18, and Gangwar et al. (2013), who observed enhanced root length, shoot length, root dry weight, and shoot dry weight of Mung Bean (Vigna radiata L.) following dual inoculation with plant growth-promoting Pseudomonas putida and Trichoderma viride.
Afforestation and Biostimulation
Afforestation involves the establishment of trees on land that has not been previously managed for forests or has been without forests for a minimum of 50 years (United Nations Framework Convention on Climate Change). It serves as a crucial restoration method for reclaiming abandoned agricultural and degraded land. A substantial portion of today’s agricultural land was once covered by forests. The ever-increasing human population and the rising need for food and fiber has led to the expansion of agricultural activities, resulting in the conversion of forested areas into agricultural land. The global agricultural land area increased from 15.84106 km2 in 1983 to 16.79106 km2 in 2003. As depicted in Figure 1, the escalating demand for agricultural land has caused the world to lose approximately one-third of its forests over the centuries.
The growing human and livestock population, uncontrolled extraction of forest resources, frequent forest fires, and mining operations have all contributed to soil erosion, diminished fertility, reduced moisture levels, and declining forest productivity. These issues create a multitude of challenges in ecosystem restoration. Consequently, soil-residing microbial inoculants play a vital and integral role in our soils, primarily by enhancing plant growth through nutrient accessibility, nitrogen fixation, the mobilization of otherwise unavailable nutrients, and the production of antifungal substances. More specifically, deforestation for cattle production brings a series of impacts to the soil. Soil degradation can be classified as one of the most perilous human activities on the Earth’s surface, due to the fact that soil is not immediately renewable. When deforestation reaches a stage that makes reoccupation by secondary forest impossible, the soil becomes exposed or occupied by low grasses, leading to changes in several abiotic factors that may result in desertification. Factors such as inappropriate temperature and salinity can make it impossible for the reestablishment of plant ecological succession, thus preventing the recolonization of deforested areas. Below, some impacts of deforestation on the abiotic parameters of the soil are listed, mentioning how the application of biofertilizers can contribute to the environmental restoration process. It should be taken into consideration, however, that the majority of studies on biostimulation are related to agriculture, with limited tests conducted on native species in tropical forests.
Temperature
Once soil is exposed by deforestation, the direct incidence of sunlight on the soil surface causes an increase in ambient temperature. This affects plant physiology by increasing respiration rates and leaf transpiration, altering photosynthate allocation. The enzyme ribulose bisphosphate carboxylase/oxygenase (Rubisco), which produces organic carbon from the inorganic carbon dioxide in the air (Figure 2), is one of those affected.
At high temperatures, Rubisco’s affinity for carbon dioxide decreases, while its affinity for oxygen increases. Carbon dioxide solubility decreases more than that of oxygen with rising temperatures, resulting in reduced carbon dioxide concentration in the chloroplast compared to oxygen. Additionally, plants close their stomata to reduce water loss through evapotranspiration when temperatures rise. Stomatal closure leads to a rapid decline in carbon dioxide concentration, while the oxygen concentration increases, limiting photosynthesis and increasing photorespiration.
Heat stress triggers complex molecular, biochemical, and physiological responses in plants [66], leading to the synthesis of heat shock proteins, reactive oxygen species (ROS), osmoprotectant compounds, amino acids, sugars, and sulfur compounds. Consequently, heat stress stimulates oxidative stress and ROS production, which are detected by histidine kinases and heat stress factors (Hsfs). Redox-sensitive transcription factors downstream from these signals are activated through the mitogen–activated-protein kinases signaling pathway, subsequently turning on other transcription factors (e.g., BF1c and Rboh) to trigger the expression of genes involved in the synthesis of antioxidant enzymes. However, although ROS accumulate during abiotic stresses, such as heat, ROS themselves are toxic and can react with cell components; the classical response to heat stress involves Hsfs, HSPs and various levels of ROS. The heat shock response is a complex and finely tuned system.
Hormonal signaling plays a significant role in heat stress responses, with ethylene acting as a major gaseous phytohormone. Ethylene is involved not only in processes like senescence, development, and plant physiology but also in plant responses to various abiotic stressors, including heat, salinity, and drought. The protection of plants against heat stress can be enhanced by microbial biostimulants. For instance, the synthesis of enzymes that degrade ROS, such as superoxide, catalase, peroxidases, and dismutase, can improve heat stress tolerance in plants. This enhancement can be observed in plants colonized by beneficial bacteria like Pseudomonas and Bacillus, as well as mycorrhizal fungi like Septoglomus deserticola and Septoglomus constrictum. Some available biostimulants contain P. fluorescens and P. aeruginosa, which contribute to improving soil quality and heat stress tolerance, working as bioremediators and phytostimulators and enhancing soil fertility. Similarly, Bacillus spp. have been developed not only as biopesticides but also in the form of biostimulant products. While these microorganisms are utilized in various commercial treatments, whether individually or in combination, their potential to mitigate heat stress is not always highlighted as one of their benefits.
The use of microorganisms capable of reducing ethylene emissions holds promise, because decreasing ethylene levels during stressful situations could help plants avoid the detrimental effects of heat stress. Bacteria that possess 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity appear to be particularly promising, including species like Bacillus subtilis BERA 7, Leclercia adecarboxylata MO1, Pseudomonas fluorescens YsS6, and Pseudomonas migulae 8R6. For example, the ACC deaminase-producing Paraburkholderia phytofirmans PsJN has been found to support normal tomato development under heat stress; however, this strain has not yet been commercialized.
Salinity
Soil serves as a reservoir of biodiversity, but the worldwide issue of soil salinization poses a significant threat to crop cultivation, affecting all living organisms and hindering the achievement of sustainable development goals, particularly in ensuring food security. Salinity in soil can be attributed to a variety of natural and human activities. Reduced water availability and osmotic pressure in saline soil are indicated by poor seed germination, leaf wilting, and in extreme instances, the death of plants. Of the various human-induced factors, salinization resulting from deforestation was considered to be prevalent. In saline soil, the accumulation of solutes reduces the osmotic potential of the liquid phase, limiting water absorption by plant roots. Soil salinization affects approximately 30% of total arable land in Mediterranean regions. Drought stress and the resulting soil salinization are major contributors to desertification in overexploited regions, affecting soil biodiversity and composition and leading to plant deterioration, reduced soil coverage, and subsequent soil erosion. Drylands now cover 46% of the world’s land surface, impacting around 250 million people in developing countries.
Plant tolerance to drought and salinity can be enhanced by microbial biostimulants through various direct and plant-mediated processes. For example, microbial biostimulants can produce bacterial exopolysaccharides that improve the soil structure by forming micro- and macroaggregates, promoting plant growth under water stress conditions. Additionally, exopolysaccharides form hydrophilic biofilms, creating a microenvironment that retains water by shielding microbes from drought stress and binding Na+ ions to reduce their uptake by plants. Examples of bacteria that produce protective exopolysaccharides include Pseudomonas spp. PF23, Pseudomonas putida GAP-P45, and Bacillus licheniformis. Root capacity can also be strengthened by mycorrhizal fungi, leading to increased root biomass, improved soil structure, enhanced water retention, and reduced leaching of mineral nutrients. For instance, the arbuscular mycorrhizal fungus, Glomus sp., produces a glycoprotein called glomalin, which enhances soil structure, plant growth, and drought tolerance. Similarly, ascomycetes (P. glomerata LWL2, Exophiala sp. LHL08, P. formosus LHL10, and Penicillium sp. LWL3) colonize cucumber plants, enhancing leaf development and chlorophyll content under drought stress.
In addition to promoting root development, mycorrhizal fungi can improve water absorption through aquaporins, a family of integral membrane transporters that facilitate water movement through the cell membrane. For example, Glomus intraradices colonizes common bean plants and mitigates water stress by affecting aquaporin activity and improving water conductivity in the roots. G. intraradices, often found in commercial products, is typically formulated in combination with various beneficial bacterial and fungal strains but is available in single formulations.
Microbial biostimulants offer various supplementary benefits when it comes to alleviating the effects of drought stress in associated plants. These advantages encompass the enhancement of antioxidant defenses, the synthesis of protective osmolytes such as glycine betaine as well as phytohormones, and the emission of volatile organic compounds (VOCs). Drought stress often triggers increased ethylene production, which impedes plant growth. Microbial biostimulants, like Pseudomonas fluorescens, can address this issue by reducing aminocyclopropane-1-carboxylic acid (ACC) levels, consequently restricting ethylene production and mitigating ethylene-mediated inhibition. Numerous microbial species, including Staphylococcus sp. Acb12, Staphylococcus sp. Acb13, Staphylococcus sp. Acb14, Bacillus, Achromobacter, Klebsiella, and Citrobacter spp., also synthesize ACC, offering the potential to alleviate the consequences of drought and salt stress. Beneficial microorganisms that possess ACC deaminase activity, such as Achromobacter piechaudii ARV8 in pepper and tomato plants and Pseudomonas fluorescens TDK1 in peanut seedlings, can assist in mitigating these unfavorable impacts. Furthermore, Achromobacter spp. and Pseudomonas spp. are recognized for their ability to stimulate plant growth and enhance soil quality.
Microbial biostimulants have the ability to biosynthesize indole acetic acid (IAA), which serves to stimulate the growth of plants and the proliferation of their root systems when they are exposed to drought stress. The bacterium Pseudomonas chlororaphis TSAU13, renowned for its ability to produce IAA, can bolster the resistance of cucumber and tomato plants to drought and salinity when introduced in salt-stressed conditions. Similarly, the mycorrhizal fungus Funneliformis mosseae elevates IAA concentrations in the roots, fosters the development of root hairs, and stimulates the growth of orange plants experiencing drought stress. Specific commercial products derived from Funneliformis mosseae can enhance plant nutrient and water uptake. Microorganisms proficient in producing cytokinins and gibberellins can alleviate water stress by promoting stomatal opening and encouraging shoot growth in conditions of restricted water availability. Plant growth-promoting rhizobacteria (PGPR) of the Acinetobacter, Pseudomonas, and Burkholderia genera can generate gibberellins and can augment the growth of cucumber plants under salt and drought stress.
Following exposure to drought stress, the production of abscisic acid (ABA) increases, leading to stomatal closure. In soybean plants, the introduction of Pseudomonas putida H-2-3 decreases abscisic acid (ABA) levels, reducing the impact of drought stress. P. putida is commonly used in conjunction with B. subtilis to enhance soil fertility, rather than specifically for alleviating drought stress. Similarly, the inoculation of lettuce with Glomus intraradices leads to a reduction in ABA concentration and increased resistance to salt. ABA and water scarcity typically lead to increased ethylene production, which can inhibit plant development.
Water stress leads to the generation of reactive oxygen species (ROS) and subsequent oxidative damage to lipids, nucleic acids, and proteins. Many microorganisms can counteract the effects of elevated ROS by either producing antioxidant compounds or increasing the activity of antioxidant enzymes, such as peroxidases and catalase, in plants. Pseudomonas species increase catalase activity in basil plants under water stress. Similarly, Pseudomonas species, Bacillus lentus, and Azospirillum brasilense are microbial bioinoculants that have been employed individually or in consortia to mitigate drought stress in crops. Ascorbate, peroxidase, and glutathione peroxidase in Pseudomonas species, Bacillus lentus, and Azospirillum brasilense have been utilized to alleviate drought stress.
The accumulation of osmocompatible solutes is a strategy employed by plants to combat water stress, allowing the buildup of inorganic and organic solutes in the vacuole and cytosol, respectively. This lowers the osmotic potential of the cell and maintains turgor pressure in water-stressed conditions. Numerous bacteria can produce osmolytes, which often collaborate with osmolytes synthesized by the host plant, such as proline, to reduce osmotic potential and stabilize cell wall components. The phosphate-solubilizing bacterium Bacillus polymyxa, when introduced to specific plants, produces proline, reducing the effects of water stress. Betaine, produced by osmotolerant bacteria such as Streptomyces tendae F4 in the rhizosphere, can work in conjunction with the betaine produced by the host rice plant, increasing its tolerance to water stress. Despite these promising results, Bacillus polymyxa is not yet available as a commercial product.
Some bacteria can interact with plants through volatile organic compounds (VOCs), which can induce stress adaptation responses related to mineral uptake, water conservation, and root growth. Although the significance of hormone signaling pathways has been established, the underlying mechanisms of VOC-mediated interactions between plants and microbes under extreme conditions remain largely unexplored. Microbial VOCs can have positive effects on plants, such as the synthesis of osmoprotectants and regulation of stomatal closure and increased plant fitness by 2,3-butanediol. Compounds like 1-heptanol, 3-methyl-butanol, and 2-undecanone produced by Paraburkholderia phytofirmans enhance salinity tolerance, while butyrolactone and 1-butanol promote root growth and carbon exchange in the rhizosphere. The production of VOCs by Bacillus thuringiensis AZP2 has been instrumental in mitigating drought stress in wheat. The future development of VOCs for plant promotion will likely depend on the identification of stress-induced signaling pathways.
Although numerous microorganisms have demonstrated the ability to protect plants from water stress, only a limited number of commercial biofertilizers are available. Many of these are based on combinations of microorganisms, including Azospirillum brasilense, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus licheniformis, Cellulomonas cellasea, Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas stutzeri, Streptomyces albidoflavus, Glomus species, and Trichoderma species. These microorganisms exhibit not only the capacity to mitigate water stress but also the ability to enhance plant yields through the production of exopolysaccharides and the enrichment of nutrients and soil organic matter. The development and production of more universally applicable commercial products, effective across various ecosystems, will greatly contribute to the mitigation of water stress in plants.
Flooding, Water Pooling, and Heavy Precipitation
The root systems of trees help stabilize the soil, which, in turn, reduces the risk of flooding and erosion; trees also play a crucial role in soaking up excess water during the rainy season. However, when trees are removed from the environment, heavy rains, typical of tropical countries, can have severe consequences. Precipitation washes away essential topsoil and the nutrients in it. Flooding impacts approximately 13% of the Earth’s surface, and it is anticipated that the frequency and intensity of heavy rainfall events will increase globally in the future. Heavy floods and rain result in water stagnation, causing root anoxia and hypoxia. When roots are subjected to flooding, they produce substantial amounts of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) synthase, which is involved in ethylene production. ACC oxidase, another enzyme required for the final step in ethylene biosynthesis, depends on oxygen for its catalytic activity. ACC is transported to the aerial parts of the plant through the xylem, where it is converted into ethylene, leading to symptoms such as wilting, chlorosis, leaf necrosis, fruit and flower loss, and reduced crop yields. Microbial biostimulants, through their ACC deaminase activity, can help to alleviate the stress caused by water stagnation by reducing endogenous ethylene levels. Plants inoculated with ACC deaminase-producing strains of Pseudomonas spp. and Enterobacter spp. exhibit reduced anoxia stress and improved germination. Pseudomonas and Enterobacter spp. can increase stress tolerance, although they do not specifically protect against waterlogging. Pseudomonas sp. and Streptomyces sp. GMKU 336 can increase chlorophyll content, plant growth, biomass, adventitious root formation, and leaf area, while reducing ethylene levels. S. lydicus WYEC 108 and Streptomyces K61 are beneficial bacteria often used against biotic stresses. Future research should aim to develop more microbial biostimulants and comprehensively explore the potential of existing commercial products for mitigating water stress.
Imbalanced Nutrient Recycling
Forest degradation has profound effects on nutrient cycles. Along with its impact on ecosystem functions, it is exacerbated by changes in terrestrial environments. The primary anthropogenic influences on forests are logging and excessive pollution loads. Both processes have detrimental effects on the soil which subsequently hinder the natural regeneration of the forest. The harm inflicted on forest soils jeopardizes the potential restoration of the original plant community, because environmental fluctuations become deregulated. The soil’s ability to regulate environmental fluctuations relies on the continuous cycling of organic matter and sustained fertility. Disruption in forest nutrient cycles hampers effective land management, including sustainable landscape management.
Phosphorus is considered an essential nutrient for plant growth, although it can limit primary productivity in various environments, including tropical and subtropical forests (Figure 3). These regions typically have soils with high levels of iron and aluminum oxides due to intense weathering processes, which are exacerbated by the heavy rainfall and high temperatures in these areas. Fe and Al oxides can bind P, making it less available to plants. Consequently, many plants rely on the recycling of P from litterfall and microbial P turnover.
Land-use changes negatively impact soil P dynamics in the Amazon region. This is because the conversion of pristine forests to pasture using the slash-and-burn method alters P lability and increases P levels in more recalcitrant pools. It can also release substantial amounts of nitrogen and P from forest biomass, which can be lost through leaching and runoff.
P-solubilizing microorganisms can also produce and release organic acids like oxalic acid, malic acid, formic acid, citric acid, and gluconic acid. These acids can solubilize recalcitrant inorganic-P forms in soils. They possess genes such as GCD (encoding glucose dehydrogenase) and the cofactor PQQ gene (encoding pyrroloquinoline quinone) that regulate the solubilization of unavailable inorganic P forms.
Microorganisms involved in P immobilization, on the other hand, can assimilate inorganic P into their biomass, competing with plants for available P. They possess pst and pit transporter genes, which assist in the assimilation of inorganic P under P-limited and P-rich conditions.
Environmental Parameters Influencing Microbial Fertilization and Bioremediation in Soils
Bioremediation involves harnessing microorganisms, including bacteria, algae, and fungi, as well as plants, to expedite the breakdown, alteration, elimination, immobilization, or detoxification of diverse physical and chemical contaminants in the environment. Microorganisms can employ metabolic pathways to accelerate biochemical reactions that break down pollutants. For bioremediation to be effective, microorganisms must be supplied with the necessary energy and nutrients to support their growth. Various factors, including physical, chemical, biological, soil type, carbon and nitrogen sources, and the type of microorganisms (whether single or a consortium), influence the efficacy of bioremediation. Microbial consortia often exhibit multifunctionality and resistance and thus are more efficient than a single microorganism. These may be natural microbial communities. For instance, carbon, one of the most crucial nutrients, was found to enhance in situ bioremediation by increasing natural consortium metabolic activity and expediting the breakdown of existing pollutants. Soil type also impacts bioremediation, with sandy soils generally achieving higher levels of pollutant bioremediation than clay. These factors include microbial population, contaminant accessibility, and the physicochemical characteristics of the environment (Figure 4). The same considerations apply to the use of biofertilizers. Extra activities involved may be the excretion of phytohormones, the suppression of phytopathogens, and the protection of plants from various types of stress.
Temperature
An important physical factor that significantly influences the survival of microorganisms as well as the degradation of pollutants is temperature. For example, in cold regions such as the Arctic, the natural degradation of oil is slow, creating a greater reliance on microbes to remediate oil spills. In these conditions, sub-zero temperatures can freeze the transport channels of microorganisms, hindering their ability to carry out metabolic processes. Temperature also has a direct impact on the turnover of enzymes involved in degradation, which may vary depending on the pollutant. The physiological properties of microorganisms are influenced by temperature, which can either accelerate or decelerate the bioremediation process. Higher temperatures generally promote increased microbial activity up to a certain limit, and this activity typically decreases if temperatures rise or fall abruptly, eventually ceasing altogether at temperature extremes. However, extremophilic microorganisms, i.e., thermophiles and psychrophiles, are active in extreme environments such as the tropics and polar regions and can be used in bioremediation and biofertilization in such areas, as well as in other extreme environments.
Salinity
One of the factors that can limit bioremediation and that could be tackled by the use of extremophiles is salinity. Salt levels in soils used for agriculture are rising because of natural and anthropic activities. Unsustainable soil management, such as irrigation with brackish water or overapplication of fertilizers, are responsible for some of these. Hypersaline soils not only reduce plant growth but also limit the possibilities of bioremediation. Non-saline soils have been shown to have approximately four times higher total petroleum hydrocarbon biodegradation compared to saline (1% NaCl) soils. Salinity reduces the bioremediation of motor oil and petroleum hydrocarbons in soil. Cr-resistant microorganisms may be able to deal with this problem. There are several examples of the use, or potential use, of halophiles in the bioremediation of polluted environments.
PH
The acidity, alkalinity, and basicity of a compound influence microbial metabolism and the bioremediation process. Soil pH, similarly, has an impact on nutrient availability as well as enzyme activity. Soil pH can be used to predict microbial growth since even slight pH variations have a notable effect on metabolic processes. In the case of petroleum hydrocarbon biodegradation, a pH close to neutrality is optimal, but this will clearly vary depending on the pollutant and the microorganisms. For example, modeling the removal of the antibiotic, azithromycin, from contaminated soil by various fungi showed pH to be the most important physicochemical parameter, with the optimum pH being 5.5. Acidophilic methanotrophs, growing optimally at pH 5 or below, have been suggested for the bioremediation of chlorinated volatile organic compounds in groundwater aquifers. It should be noted, however, that biofertilizers themselves may be able to alter soil pH advantageously.
Microbiological Diversity
Quite apart from the microorganisms added to attain the desired effect, the resident microbiota will have a large part to play in the final outcome of a bioremediation or biofertilization treatment. There will be competition between the autochthonous and the added species, as well as between the indigenous microorganisms themselves. When two different types of pollutants require removal, or when biofertilization is the aim, the choice of augmenting microorganisms becomes much more complex; antagonistic or highly competitive interactions must be closely monitored. In the case of metal-contaminated soils, one approach is to use metal-resistant microorganisms. It is reported that Brevibcillus parabrevis OZF5 removed both Cr and hydrocarbons from contaminated soil, enhancing growth of beans. Microbial surfactants, such as surfactin, rhamnolipid, and sophorolipids, may also be used to augment the bioremediation of various pollutants, including DDT, atrazine, hexachlorocyclohexane and cyprodinil, as well as the most widespread hydrocarbons.
Finally, it must be noted that any change in the structure of the microbial community can result in shifts not only in temperature adaptation at the community level but also in growth strategies: copiotrophs can promptly respond to favorable environmental conditions and proliferate rapidly when labile carbon sources are available. In contrast, oligotrophs display gradual, sustained growth under conditions of low carbon and nutrient availability, finally yielding a higher biomass per unit substrate. When the primary objective is growth, delving exclusively into individual enzymes and genes, or even isolated pathways and mechanisms, is insufficient. There comes a point where one must return to the holistic perspective of the entire cell and consider the coordinated orchestration of various processes. When several microbial species are mixed, the community must work together to grow and become active in the bioremediation/biofertilization process in a symbiosis.
Nutrient Availability
Nutrients play a crucial role in influencing the growth of microorganisms and the rate of biodegradation. Enhancing the soil C:N:P ratio can significantly enhance biodegradation efficiency, particularly when vital nutrients like nitrogen and phosphorus are provided. When these nutrients are present in low concentrations, the degradation of hydrocarbons is constrained. The addition of extraneous nutrients, such as glucose, can augment pollutant removal by stimulating microbial activity. The introduction of nutrients is particularly important for bioremediation activities in cold environments; it can boost the metabolic activity and diversity of microorganisms and, consequently, the rate of biodegradation. Microbes that consume oil rely on these essential nutrients to thrive, and they are typically present in limited quantities in natural settings.
Conclusions and Perspectives
Currently, developing countries are going through particular historical phases compared to those experienced by developed nations. This is due to both globalization, which defines their role in the global context, and their geographical characteristics, which directly influence their ecological, cultural, and productive dynamics. Consequently, they are currently grappling with issues stemming from their rapid industrialization, lacking the necessary infrastructure and cultural maturity to address the adverse effects of development. On the other hand, their natural attributes bestow upon them advantages that have not yet been fully harnessed. The warm climate, coupled with increased sunlight and more intense weathering, results in higher primary productivity and, thus greater biodiversity, which could serve as a key to their sustainable development. Throughout this review, we briefly discussed characteristics related to the communities of microorganisms in nature, as well as the effects of microbial coexistence. It becomes evident that there is a direct relationship between environmental health and the microbial balance. The targeted use of these microorganisms can lead to beneficial effects on ecosystems. Introducing microbial strains into low-quality soils, which are typically unfavorable for plant growth, has several benefits. It not only enhances soil fertility, boosts nutrient cycling, and mitigates soil salinity, but also enhances the profitability of cash crops and fosters the sustainability of farming practices. Thus, the key to sustainable development lies in the proper management of these biological tools. Understanding the product of the interaction between microorganisms and environmental factors is essential for the development of cost-effective, sustainable environmental management techniques.
Bioremediation is a burgeoning technology that can be employed in conjunction with other physical and chemical treatments to comprehensively address a wide range of environmental pollutants. In addition to helping to solve a range of other environmental issues, further in-depth studies on its other uses should be undertaken to fully explore the potential of microbial biotechnology, which appears to offer a sustainable approach to environmental pollution management. It is imperative to establish a synergistic relationship between the environmental influences on the fate and behavior of environmental contaminants and the selection and efficacy of the most suitable bioremediation technique, as well as other pertinent methods, to ensure the efficient and successful execution and monitoring of bioremediation processes.
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