Biofertilization and Bioremediation—How Can Microbiological Technology Assist the Ecological Crisis in Developing Countries?

Abstract

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. The recent introduction of genetically modified microorganisms into the gamut of biofertilizers and bioremediators requires further studies to assess potential adverse effects in various ecosystems. This article reviews and discusses these two soil correcting/improving processes with the aim of stimulating their use in developing tropical countries.

1. Introduction

Developing countries are facing a series of critical environmental issues due to the mismatch between their pace of development and their role in the global context [1,2]. Given their relatively short history, they have not had sufficient time to catch up with the global pace set by developed nations. Consequently, these countries are already showing signs of the impact of recent industrialization and urbanization [3]. Rapid development, population growth, inadequate responses to climate and environmental risks, and inefficiencies in governance and environmental management pose substantial environmental challenges for developing countries [4].

A significant number of these countries are located in warmer climates, allowing them to become major global food producers and leading to the excessive use of their land for agriculture. Unfortunately, this can lead to biomes that are rich in biodiversity being destroyed to make way for monocultures of food plants, depleting ecosystems and their soils. Additionally, chemical fertilizers introduced into these systems to boost agricultural productivity potentially disrupt the local soil geochemical balance and affect adjacent environments such as rivers, lakes, and coastal areas [5]. Ultimately, this process can lead to imbalances in water bodies, resulting in hyperproductivity and subsequent eutrophication [6].

In this sense, tropical soil ecosystems exhibit a rich tapestry of diversity and complexity, setting them apart from their temperate counterparts. Within the expansive realms of the tropics, a myriad of ecosystems serves as the canvas for diverse microbial niches and evolutionary processes [7]. The relationship between latitude and bacterial diversity is not statistically significant, but communities can be aptly characterized by their ecotypes and functional attributes. Delving into desert soils, where extremes of solar radiation, minimal precipitation, and fluctuating temperatures prevail, one discovers the existence of intricately diverse bacterial communities, a subject briefly touched upon here. In the semi-arid tropical biomes dominated by grassy vegetation, a resilient and dry-adapted bacterial biodiversity coexists harmoniously with plants [7]. Venturing into water-rich tropical environments, encompassing rainforest soils and the sediments of mangroves, unveils an astonishing array of diversity, harboring untapped biotechnological potential. It is noteworthy that tropical soils play a crucial role in providing sustenance for around 40% of the world’s population, with a significant portion residing in developing countries. In Brazil, the application of microbial inoculants, like biofertilizers derived from tropical soils, has yielded substantial improvements in large-scale food production. This particular brand of biotechnology is now being shared by Embrapa (Brazilian Agricultural Research Corporation, Brasilia, Brazil) with tropical nations in Africa. The utilization of tropical soil bacteria extends beyond agriculture, with applications in remediating polluted soils, promoting reforestation, and safeguarding water resources [8]. However, the imperative lies in scaling up these efforts across all tropical regions. Preserving designated areas within the intricate tapestry of tropical ecosystems becomes paramount, ensuring that the invaluable soil microbial gene pool remains intact for the benefit of future generations [8].

Soil, plant, and water-associated microorganisms play a vital role in ecosystem functioning, participating in biogeochemical cycles and degrading organic matter [9]. Over 80 coexisting beneficial soil microorganisms, including photosynthetic bacteria, lactic acid bacteria, yeasts, actinomycetes, and fermenting fungi had been identified by 2014 [10]; with the greater use of DNA-based technologies, this number has increased substantially. These microorganisms can be employed as biofertilizers, to replace the harmful chemicals still being used. Ranipa et al. (2023) [11] noted the role of biofertilizers in sustainable agriculture and reviewed various organisms and their applications. Zhang et al. (2021) [12] investigated the role of arbuscular mycorrhizal fungi in symbiosis with plants, revealing their catalytic effect on organic matter decomposition. This symbiosis was also found to promote soil aggregation and contribute to soil stabilization through mycelial growth, ultimately enhancing nutrient uptake, particularly phosphorus, by plants. Kheirfam et al. (2017) [13] demonstrated that soil crusts enriched with beneficial microorganisms improved soil properties; poor soils could be improved by adding cyanobacteria, for instance. The application of these bacteria proved to be a rapid, long-lasting, environmentally friendly, and cost-effective technique for enhancing soil quality [14]. Liu et al. (2022) [14] demonstrated that the application of biofertilizers resulted in the increased presence of beneficial bacteria, while reducing the population of pathogenic bacteria (such as Leifsonia), within the sugarcane rhizosphere. This shift in microbial communities could help mitigate or hinder the development of diseases.

These examples underscore the significance of biofertilizers, microorganism-based fertilizers, in sustainable agriculture; they have a long-lasting impact on soil fertility [15,16]. In addition, the ability of microorganisms to balance soils and water bodies and to degrade toxic compounds provides them with another important use, commonly referred to as bioremediation.

Biofertilizers and bioremediators are formulations comprising living microbial cells, either a single strain or multiple strains (a consortium), that enhance plant growth by increasing nutrient availability and acquisition and reducing adverse conditions. The term “biofertilizer” has evolved over the past 30 years and has received various interpretations [17]. Macik et al. (2020) [18] pointed out that the most common misconception in this nomenclature arises when microbial inoculants with other beneficial activities (e.g., biopesticides and phytostimulators) are included under the umbrella of biofertilizers. Plant growth-promoting bacteria and rhizobacteria (PGPB/PGPR) may also be distinguished, as not all PGPB/PGPR function as biofertilizers [19]. However, it is worth mentioning that biofertilizers can offer additional direct and indirect benefits for plant growth, including phytostimulation, enhanced tolerance to abiotic stress, and control of plant pathogens [20,21,22].

Thus, taking into consideration the information contextualized above, it is understood that the global demand for food is expected to continue growing at an accelerated pace, a fact that negatively impacts the environment in various ways. On the other hand, the specific environmental characteristics of tropical countries can aid in the improvement of agricultural production techniques and the recovery of more sustainable and effective environments, including biostimulation and bioremediation, which should be further enhanced and more intensively applied. This article provides a brief compilation of data regarding the environmental impacts resulting from unchecked global development, which has led to the indiscriminate use of chemical fertilizers. It highlights the advantages and importance of these “bio-tools” as potential sustainable methods for managing natural resources.

2. 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 [23]. 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 [24] or heavy metals [25], drought [26], salinity [27], and extreme temperature variations [28]. Among these stressors, the release of metals from diverse human activities [29,30,31] 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 [32]. 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 [33]. 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 [34,35,36,37,38]. 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.

2.1. Agricultural Fertilization

The global human population continues to expand at a concerning rate, giving rise to various issues, including food insecurity [39,40]. 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 [41,42], 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 [43,44,45].

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 [46]. 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 [47]. 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 [48].

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 [49]. Their impact extends to the modulation of microbial communities within the rhizosphere, thus exerting an influence on the soil’s overall ecosystem [50].

The use of biofertilizers enhances both the function and structure of soil microorganisms and has implications for the physicochemical properties of the soil [51]. 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 [52]. 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 [53]. Numerous studies have assessed the impact of microbial inoculants on soil microorganisms [54,55,56]. As early examples, we may cite Upadhyay et al. (2012a) [56], 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) [57], 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.

2.2. 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) [58]. 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 [59]. The global agricultural land area increased from 15.84106 km² in 1983 to 16.79106 km² in 2003 [60]. 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 [61]. 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 [62]. 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.

2.2.1. 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 [63,64]. 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 [66,67]. Carbon dioxide solubility decreases more than that of oxygen with rising temperatures, resulting in reduced carbon dioxide concentration in the chloroplast compared to oxygen [68]. 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 [69].

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 [70]. 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 [71]. 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 [72]. 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 [73,74,75]. 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 [74,75,76]. 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 [77]. 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 [67]. 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 [78].

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 [79]. 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 [80]. For example, the ACC deaminase-producing Paraburkholderia phytofirmans PsJN has been found to support normal tomato development under heat stress [81]; however, this strain has not yet been commercialized [67].

Despite the documented positive effects of biostimulants as mitigators of thermal stress, further research is needed to better understand their mechanisms of action and to develop efficient formulations that can mitigate the impact of heat stress in the recuperation of desertified areas.

2.2.2. 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 [82]. Mitsuchi et al. (1989) [83] conducted a review of both natural and human-induced factors contributing to soil salinization. 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 [84]. Soil salinization affects approximately 30% of total arable land in Mediterranean regions [85]. 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 [86]. Drylands now cover 46% of the world’s land surface, impacting around 250 million people in developing countries [87].

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 [88], promoting plant growth under water stress conditions [67]. Additionally, exopolysaccharides form hydrophilic biofilms, creating a microenvironment that retains water by shielding microbes from drought stress [89] and binding Na+ ions to reduce their uptake by plants [90,91]. Examples of bacteria that produce protective exopolysaccharides include Pseudomonas spp. PF23 [90], Pseudomonas putida GAP-P45 [92], and Bacillus licheniformis [93]. Root capacity can also be strengthened by mycorrhizal fungi [94], leading to increased root biomass, improved soil structure, enhanced water retention, and reduced leaching of mineral nutrients [95,96]. For instance, the arbuscular mycorrhizal fungus, Glomus sp., produces a glycoprotein called glomalin, which enhances soil structure, plant growth, and drought tolerance [97]. 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 [94,98].

In addition to promoting root development, mycorrhizal fungi can improve water absorption through aquaporins [99], a family of integral membrane transporters that facilitate water movement through the cell membrane [100]. For example, Glomus intraradices colonizes common bean plants and mitigates water stress by affecting aquaporin activity and improving water conductivity in the roots [99,101]. 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 [78].

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) [102,103]. 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 [79]. 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 [104,105]. Beneficial microorganisms that possess ACC deaminase activity, such as Achromobacter piechaudii ARV8 in pepper and tomato plants [106] and Pseudomonas fluorescens TDK1 in peanut seedlings [106], 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 [78].

According to Ouyang et al. (2017) [107], 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. These authors suggested that this phenomenon is observed in various bacterial species, such as those falling within the genera Alcaligenes, Sinorhizobium, Serratia, Bacillus, and Arthrobacter. 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 [108]. 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 [109]. Specific commercial products derived from Funneliformis mosseae can enhance plant nutrient and water uptake [67]. 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 [110]. 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 [111]. Despite their promising attributes, there are presently no commercially available products based on these species.

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 [112]. 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 [113]. 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 [114]. Pseudomonas species increase catalase activity in basil plants under water stress [115]. 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 [67]. Ascorbate, peroxidase, and glutathione peroxidase in Pseudomonas species, Bacillus lentus, and Azospirillum brasilense have been utilized to alleviate drought stress [115].

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 [67]. Numerous bacteria can produce osmolytes [116], which often collaborate with osmolytes synthesized by the host plant, such as proline, to reduce osmotic potential and stabilize cell wall components [117]. The phosphate-solubilizing bacterium Bacillus polymyxa, when introduced to specific plants, produces proline, reducing the effects of water stress [118]. 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 [119]. 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 [120]. Although the significance of hormone signaling pathways has been established [121], 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 [122] and increased plant fitness by 2,3-butanediol [67]. Compounds like 1-heptanol, 3-methyl-butanol, and 2-undecanone produced by Paraburkholderia phytofirmans enhance salinity tolerance [123], while butyrolactone and 1-butanol promote root growth and carbon exchange in the rhizosphere [124]. The production of VOCs by Bacillus thuringiensis AZP2 has been instrumental in mitigating drought stress in wheat [125]. 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 [78]. 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.

2.2.3. 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 [67]. 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 [67]. 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 [126], where it is converted into ethylene, leading to symptoms such as wilting, chlorosis, leaf necrosis, fruit and flower loss, and reduced crop yields [79]. Microbial biostimulants, through their ACC deaminase activity, can help to alleviate the stress caused by water stagnation by reducing endogenous ethylene levels [79,127]. Plants inoculated with ACC deaminase-producing strains of Pseudomonas spp. and Enterobacter spp. exhibit reduced anoxia stress and improved germination [67,128]. Pseudomonas and Enterobacter spp. can increase stress tolerance, although they do not specifically protect against waterlogging. Pseudomonas sp. [129] and Streptomyces sp. GMKU 336 [130] 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 [131,132]. Future research should aim to develop more microbial biostimulants and comprehensively explore the potential of existing commercial products for mitigating water stress.

2.2.4. 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 [133]. 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 [134].

An example is the Brazilian Amazon rainforest, which faces a significant threat from the expansion of cattle ranching activities [135,136]. During this process, farmers not only extract valuable timber, but also burn the remaining vegetation and replace it with fast-growing grasses [137]. This slash-and-burn technique alters the physical, chemical, and biological properties of the soil, facilitating the establishment of pastures in the Amazon region [138]. This practice is unsustainable, and pastures experience a rapid decline in productivity, ultimately becoming degraded and abandoned [139]. Under ideal conditions, ’secondary forest’ is gradually formed [140], but studies suggest that deforestation is becoming increasingly common in the Brazilian Amazon region. Even though Carvalho et al. (2019) [141] stated that these secondary forest areas are expanding, covering more than 100,000 km², there is a need for more research on the re-establishment of secondary forests, especially with respect to soil microorganisms and nutrient cycling [142].

Phosphorus is considered an essential nutrient for plant growth, although it can limit primary productivity in various environments, including tropical and subtropical forests [143] (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 [144,145]. Consequently, many plants rely on the recycling of P from litterfall and microbial P turnover [146].

Land-use changes negatively impact soil P dynamics in the Amazon region [145,148]. 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 [145]. It can also release substantial amounts of nitrogen and P from forest biomass, which can be lost through leaching and runoff [149,150].

There is limited research and information available regarding the effects of secondary forest re-establishment on P dynamics. Existing studies suggest that secondary forest re-establishment has the potential to promote a gradual recovery of soil P [9,151,152]. According to those authors, the increase in plant diversity, the restoration of certain soil physicochemical properties (e.g., pH), and enzymatic activity (e.g., C, N, P, S enzymes) may favor specific bacterial and fungal groups such as P-mineralizing and P-solubilizing microorganisms. These groups play crucial roles in P transformation processes and availability. They are primarily involved in three key soil processes: (i) mineralization, (ii) solubilization, and (iii) immobilization [153] (Figure 3). These microorganisms produce enzymes that break down ester-phosphate bonds, releasing orthophosphate from recalcitrant organic P forms, as explained by Arenberg and Arai (2019) [154]. They possess genes encoding enzymes such as phytase (appA), alkaline phosphatase (phoD), acid phosphatase (olpA), phosphonatase (phnX), and C–P lyases (phn), which can mineralize organic-P compounds in soils [155,156].

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 [155,157]. 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 [158].

Microorganisms involved in P immobilization, on the other hand, can assimilate inorganic P into their biomass, competing with plants for available P [153]. They possess pst and pit transporter genes, which assist in the assimilation of inorganic P under P-limited and P-rich conditions.

The microbial groups involved in P transformations are ubiquitous in soils, but their population and activity are influenced by different environmental requirements [159]. They are also sensitive to disturbances, particularly changes in soil physicochemical properties [160,161]. This is a significant concern; previous studies have indicated that the conversion of pristine forests to pasture in the Amazon region alters soil physicochemical properties and the overall composition of the soil microbial community [125,162,163].

2.2.5. Soil Compaction by Cattle

Cattle trampling of agricultural soil can cause the collapse of larger soil pores, producing smaller pores. This leads to increased soil density and greater resistance to soil penetration, ultimately promoting more soil compaction. This, in turn, hinders the regrowth and renewal of pastures, resulting in reduced overall productivity [164]. Thus, soil compaction is closely linked to significant soil degradation processes, which manifest as reduced soil aeration, diminished water infiltration rates, and an increased risk of flooding and surface runoff [165,166,167,168]. These processes collectively have a negative impact on soil productive capacity [169]. Factors such as soil type, moisture content, and grazing management practices (like stocking rate, stocking density, and timing of activities) can exacerbate this soil compaction [164,170]. It is well-recognized that the risk is heightened when the soil moisture content increases [171,172], as generally occurs in the wet summer seasons, which are thus the most vulnerable to soil compaction.

Currently, there are no reported studies that involve microorganisms and the impact of soil compaction resulting from cattle farming. However, some authors have addressed the use of biochar to mitigate this problem. Biochar is a carbon-rich material produced by the thermal decomposition of organic matter (such as agricultural residues, wood chips, or manure) in a low-oxygen environment through a process called pyrolysis. It is primarily used as a soil amendment to improve soil fertility, enhance water retention, and sequester carbon, thereby contributing to climate change mitigation. Gao and DeLuca (2022) [173] suggested that soil compaction and the consequent reduction in soil moisture and aeration may affect nutrient cycling, hindering natural repopulation with vegetation. There is thus a potential for enhancing nutrient cycling through the addition of specific microbial strains. The above authors noted an increase in soil organic matter and P content with biochar application; the use of microorganisms could further enhance this. Soil biofertilization could also stimulate primary production, leading to bioturbation by roots and detritivorous animals, thus promoting soil aeration. However, specific studies in tropical soils need to be carried out to substantiate this hypothesis. Porous materials can also play a crucial role in substrate enhancement [26,174,175]. Incorporating porous materials into the substrate augments soil porosity, elevates aeration rates [176], provides a conducive environment for microbial communities to thrive [177,178], and fosters the development of plant roots [179].

2.3. Treatment of Polluted Soils (Bioremediation)

The use of industrial effluents to irrigate agricultural crops is particularly prevalent in poor and less environmentally aware countries. This leads to the buildup of toxic substances in the soil with resulting effects on agricultural production and produce. Over the last decade, there has been a consistent growth in the number of publications discussing the application of microorganisms for the remediation of heavy metals and other contaminants in such polluted environments. While bacteria and fungi have been the predominant choices, yeasts and algae are also employed—the latter phylum mainly, but not exclusively, in aqueous environments [180]. Bioremediation usually relies on the metabolic activity of either a single organism or a consortium of microorganisms [181]. In this process, the transformation of contaminants may not provide significant benefits to the cell; in such cases, it is termed non-beneficial biotransformation [182,183]. Numerous studies have demonstrated that many organisms, both prokaryotes and eukaryotes, possess a natural capacity for biosorbing toxic heavy metal ions [184,185]; the biosorption sites may be located on or in the cells, or in the extracellular polymeric layer (EPS) of the microorganisms [186,187,188,189]. Alternative methods of bioremediating heavy metal contaminated soil include the use of microorganisms that change the toxicity of the metal by altering its oxidation state or by methylation [190,191,192,193]. Examples of bacteria, fungi, and yeasts that have been studied and strategically employed in bioremediation applications for heavy metals in soil are shown in

Table 1. Some microorganisms that have been used for bioremediation of heavy metal-contaminated soils.

Microbial Inoculum	Heavy Metal(s)	Reference
Bacteria:
Arthrobacter spp.	Cd	[194]
Pseudomonas veronii	Cd, Zn, Cu	[195]
Burkholderia spp.	Zn, Pb, Mn, Cd, Cu, As	[196]
Kocuria flava	Cu	[197]
Bacillus cereus	Pb, Cd, Cr	[198]
Sporosarcina ginsengisoli	As	[199]
Serratia sp.	Ni, Cd	[200]
Enterobacter cloacae KJ-46, E. cloacae KJ-47, Sporosarcina soli B-22, and Viridibacillus arenosi B-21	Cd, Pb, Cu	[201]
Enterobacter cloacae B2-DHA	Cr(VI)	[202]
Brevibacillus parabrevis OZF 5	Cr(VI), Zn	[203]
Cupriavidus metallidurans LBJ and Pseudomonas stutzeri LBR	Pb	[204]
Acinetobacter sp. LSN-10	Mn(II)	[205]
Achromobacter denitrificans, Klebsiella oxytoca, and Rhizobium radiobacter	Cd, Hg, As, Pb, Ni	[206]
Cyanobacteria
Gloeomargarita lithophora and Cyanothece sp.	Sr	[207]
Nostoc minutum and Anabaena spiroides	Pb, Cd, Ni	[208]
Fungi
Simplicillium chinense	Cd, Pb	[209]
Penicillium sp.	Hg	[210]
Penicillium chrysogenum FMS2	Cd	[211]
Aspergillus versicolor	Cr, Ni, Cu	[212]
Aspergillus fumigatus	Pb(II)	[213]
Aspergillus spp.	Cd, Cu	[214]
Gloeophyllum sepiarium	Cr	[196]
Perenniporia subtephropora, Daldinia starbaeckii, Phanerochaete concrescens, Cerrena aurantiopora, Fusarium equiseti, Polyporales sp., Aspergillus niger, Aspergillus fumigatus, and Trametes versicolor	As, Mn, Cu, Cr, and Fe	[215]
Yeasts
Candida tropicalis	Cr(VI)	[216]
Saccharomyces cerevisiae	Pb, Cd	[217]
Saccharomyces cerevisiae	Cd, Hg	[218]
Mixed consortia
Chlorella thermophila SM01, Leptolyngbya sp. XZMQ and Bacillus XZM	As	[219]
Leptolyngbya sp. XZ1 and Bacillus sp. S1	Cd	[220]

.

Rhizobacteria have been suggested to be particularly useful for the bioremediation of heavy metal-contaminated soils; the mechanisms of metal removal include chelation by siderophores, biotransformation (change to a less damaging oxidation number or methylation to reduce toxicity), biosorption and bioaccumulation in the cells, precipitation, ACC deaminase action, and biomineralization [220]. Biotechnological approaches by other microorganisms encompass bioleaching, bioextraction, and bioencapsulation [221,222], although not all of these are applicable to soil in situ.

When a contaminated site contains various pollutants, effective remediation requires a diverse array of microorganisms. Many microorganisms can degrade petroleum hydrocarbons, using them as a source of carbon and energy. The selection of these organisms for bioremediation varies based on the chemical nature of the pollutants and must be made carefully, as they can only thrive in the presence of a limited range of chemical contaminants. The efficiency of the degradation process is linked to the microbial capacity to introduce molecular oxygen into the hydrocarbon and generate intermediates that enter the cell’s energy-yielding metabolic pathways. Some bacteria have chemotactic responses, actively seeking out contaminants [223], while many produce powerful surface-active compounds that emulsify oil in water, aiding its uptake by the cells and hence removal from the soil [224]. Bacteria capable of degrading petroleum products include genera such as Pseudomonas, Aeromonas, Moraxella, Beijerinckia, Flavobacteria, Chromobacterium, Nocardia, Corynebacterium, Streptomyces, Bacillus, Arthrobacter, and Aeromonas, as well as cyanobacteria [221,225], and certain yeasts [32]. One example is Pseudomonas putida MHF 7109 isolated from cow dung, which can be used for the biodegradation of selected petroleum hydrocarbon compounds, including benzene, toluene, and o-xylene (BTX) [186].

3. Genetically Modified Microorganisms for Bioremediation

Genetic engineering is a fundamental method to modify the metabolic pathways of microorganisms and improve their bioremediating activity, increasing efficiency and reducing the time required to produce the required effect. Genetic engineering can be applied to modify microorganisms to exhibit features like accelerated growth, tolerance to extreme environmental conditions and pH fluctuations, and cost-effective cultivation. Omics technologies, e.g., genomics, transcriptomics, proteomics and metabolomics, are being employed to increase our understanding of relevant microbial metabolisms, such as responses to heavy metals and high salt concentrations, and to indicate the appropriate engineering of potential microbial inoculants, with increased resistance and degrading activities for soil pollutants like heavy metals and hydrocarbons [226,227,228]. Perceived hazards in the release of genetically modified organisms (GMOs), however, have led to problems in legislation for their placement on the market [229]. Similarly, care must be taken when releasing genetically modified microorganisms (GMMs), defined as “microorganisms in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination” [230]. For this reason, genetic manipulations included in GMMs may include inbuilt senescence genes, so that unexpected negative interactions with native organisms will be limited [231]. Nevertheless, research on the use of GMMs in soil bioremediation in situ is now rather restricted.

The techniques used in the production of GMMs are beyond the remit of this article, but for those interested, there is a wealth of papers published on this topic [232,233,234,235].

4. 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 [236,237,238]. 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 [239]. Microbial consortia often exhibit multifunctionality and resistance and thus are more efficient than a single microorganism [240]. 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 [241]. Soil type also impacts bioremediation, with sandy soils generally achieving higher levels of pollutant bioremediation than clay [242]. The factors influencing bioremediation and the methods employed for soil remediation, both in situ and ex situ, are discussed by da Silva et al. (2020) [243]. 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 [18,244].

4.1. 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 [245,246]. 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 [247,248,249,250,251].

4.2. 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 [252]. Unsustainable soil management, such as irrigation with brackish water or overapplication of fertilizers, are responsible for some of these [253]. 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 [254]. Salinity reduces the bioremediation of motor oil [255] and petroleum hydrocarbons [256,257] in soil. Nguyen et al. (2021) [258] suggested that salinity exposure may influence Cr(VI) bioremediation. Cr-resistant microorganisms may be able to deal with this problem [193]. There are several examples of the use, or potential use, of halophiles in the bioremediation of polluted environments [234,259,260,261,262,263]. Although still undergoing considerable research effort, the use of halophilic microorganisms for bioremediation in, or of, saline environments appear to be a real possibility [248,259,264]

4.3. 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 [265]. In the case of petroleum hydrocarbon biodegradation, a pH close to neutrality is optimal [266], 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 [267]. Acidophilic methanotrophs, growing optimally at pH 5 or below, have been suggested for the bioremediation of chlorinated volatile organic compounds in groundwater aquifers [268]. It should be noted, however, that biofertilizers themselves may be able to alter soil pH advantageously [269].

4.4. 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 [270,271]. For example, when petroleum degrading bacteria (PDB) Acinetobacter radioresistens KA5 and Enterobacter hormaechei KA6 were inoculated into soil containing indigenous microorganisms, the level of petroleum breakdown was considerably lower than that achieved by the PDB alone [272]. 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. The negative effects of one pollutant on the degradation of another are discussed and exemplified by Olaniran et al. (2013) [273], but double bioremediation is achievable, although perhaps not at maximum efficiency. In the case of metal-contaminated soils, one approach is to use metal-resistant microorganisms. Roane et al. (2001) [195] isolated four bacterial strains of different genera that reduced soluble Cd levels in the contaminated soil and also supported the degradation of 500-μg ml⁻¹ 2,4-D by the cadmium-sensitive 2,4-D degrader Ralstonia eutropha JMP134, while Wani et al. (2023) [204] 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 [274], as well as the most widespread hydrocarbons [273].

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 [275,276]. As eloquently articulated by Neidhardt (1999) [277], 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 [278].

4.5. Oxygen Levels

The biodegradation process is directly related to the available oxygen content in the environment. Most bioremediation systems run under aerobic conditions [279]. Often, however, in aquatic sediments, sludges or compacted soils, for example, there is limited oxygen available. With the impossibility to aerate the environment, the use of anaerobic decomposers or facultative organisms can be more effective [280]. Ji et al. (2014) [281] investigated how the activities of microorganisms were influenced by the presence of dissolved oxygen (DO) in polluted river water. Their study revealed that the removal efficiency of different substances, such as chemical oxygen demand, total phosphorus, and ammonia nitrogen, increased with higher levels of DO, showing improvements of 4.59%, 18.18%, and 34.34%, respectively, suggesting that this bioremediation works even under aerobic conditions.

Petroleum-contaminated sludge is a particular problem in coastal wetlands, where costly physicochemical treatment is currently the norm [282]. Anaerobic bioremediation, utilizing sulfate-reducing bacteria, denitrifying bacteria, iron and manganese reducing bacteria, and, particularly, methanogenic bacteria, is more economical, although it is currently less efficient than aerobic bioremediation [283]. Intermittent oxygen supplies may also be useful in some cases. For example, Chen et al. (2023) [283] found that intermittent microoxygenation facilitated codegradation of trichloroethane and toluene; the main bacterial genera responsible for the dechlorination were Dehalococcoides and, mainly, Dehalogenimonas. One possibility could be the use of cyanobacteria, which can grow anaerobically under the correct conditions and produce oxygen by photosynthesis. Their potential as biofertilizers in green technology is discussed by Bhuyan et al. (2023) [284].

4.6. Soil Moisture

The soil moisture content is also an important factor in accelerating biogeochemical processes. Soil that is excessively waterlogged is not suitable for microbiological treatment [285]. The moisture level in the soil impacts the movement of water and soluble nutrients in and out of microorganisms, and excessive moisture diminishes oxygen levels during the aerobic process [286] and hence bioremediation [287]. With this effect of soil moisture in mind, Naorem (2022) [288] considered the potential effects of climate change on biodeterioration efficiency. Bahmani et al. (2018) [289], using laboratory experiments and various moisture levels in hydrocarbon-contaminated soil, developed a mathematical model for this process. They defined a first-order rate equation for the removal of total petroleum hydrocarbons (TPH); this equation held good between a specific moisture value at which the constant is zero and that at which the constant reaches its maximum.

ν dθ/dt = q_in-q_out (1) q_in= 0 (2) q_out = APET (θ-θr /θsat-θr)

where ν = volume of beaker, θ = water content, q = volumetric flow rate of water, A = surface of beaker, PET = potential evaporation (constant during their experiment at 0.00495 m day⁻¹), θr = residual water content, and θsat = saturation water content.

In their study, the best TPH removal from a sandy clay soil was achieved by adjusting the water to 60% capacity and adding water every 2 days. This moisture level was higher than that quoted by other workers. For example, Kumari et al. (2023) [290] suggested 35%. However, Zeng et al. (2023) [291] and Norozpour et al. (2023) [292] suggested 60% and 70–80%, respectively. These authors were all working with PAH-contamination.

4.7. 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 [293]. 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 [81]. Microbes that consume oil rely on these essential nutrients to thrive, and they are typically present in limited quantities in natural settings [294,295].

Cavazolli et al. (2023) [296] used DNA sequencing techniques to investigate the bacterial populations of soil co-contaminated with heavy metals and hydrocarbons. Bioremediation was carried out using meat and bone meal (MBM) as nutrient addition and cyclodextrin (Cdx) as a surfactant to release previously unavailable nutrients. After 12 weeks, only Cdx had increased bacterial diversity more than the control soil; MBM accelerated the change in populations, but the final diversity after 12 weeks was not altered. Oil-degrading groups of bacteria increased in prevalence during the procedure, but the hydrocarbon and heavy metal levels were not determined. The effects of the addition of any specific nutrient, or nutrients, to contaminated soil are difficult, perhaps impossible, to predict and should be carefully monitored.

4.8. Pollutant Complexity

The release of diverse chemical pollutants into the environment by industries can disrupt the delicate equilibrium of ecosystems. Anthropogenic pollutants in particular tend to exhibit greater complexity and heightened resistance to degradation, necessitating the use of specific bioremediating strains capable of withstanding the toxicity of substances such as metals and hydrocarbons [297]. It has been suggested that GMOs and mixed strains of microorganisms may be the preferred route for future treatment of complex pollutants [298,299]. While the potential of GMOs in bioremediation is substantial, its practical application is circumscribed in various ways [300] and the discussion above (Section 3) points out the problems of this approach.

Li et al. (2020) [301] suggested that fungi may be more appropriate for the degradation of complex pollutants. Fungi may oxidize pollutants extracellularly using laccases, manganese peroxidases, and lignin peroxidases, or intracellularly using cytochrome P450, reductive dehalogenases, and nitroreductases [302]. Recently, innovative remediation techniques have been proposed, including the utilization of extracellular and/or cell-free enzymes, together with metabolomics and proteomics to study the response of the microorganisms to complex and mixed pollutants [302,303]. Using a single microbial species in a bioremediation treatment for complex molecules is unlikely to achieve success. Microbial consortia are now being intensely studied to find species that can survive and work together. The engineering of microbial consortia is discussed by Li et al. (2021) [304]; they considered two main approaches: “bottom-up” and “top-down”. Interactions between microorganisms include antagonism and symbiosis; the bottom-up approach involves reconfiguring negative interactions to ensure co-survival and continued activity. The top-down approach involves modifying the environment to compel the organisms to perform the desired activities; this is not an easy option because of the complexity of the microbial interactions. The bottom-up approach requires a detailed knowledge of the metabolism and interactions of the consortium members. New omics techniques have allowed this to become a less onerous and more achievable goal and will assist the development of consortia for the bioremediation of complex pollutants such as PAHs.

Cell-free systems have also been investigated for the bioremediation of pollutants such as organophosphate pesticides [305], aromatic polymers like chlorophenols [306], and nitrile and amide-based xenobiotics [307]. The immobilization of the enzymes on a suitable, and economic, material can be advantageous to ensure their continued activity, but the support must be carefully chosen to prevent any reduction in efficacy [308]. Screening of microorganisms for enzyme activities, in addition to being used for the identification of potential enzymes to be extracted or engineered, could also be used in place of laboratory biodegradation tests for detection of efficient functional isolates for bioremediation procedures [309].

5. Risks to Ecosystem Health: Impact on the Local Biota

In theory, biofertilization and bioremediation approaches should lead to minimal or well-controlled consequences concerning factors such as dispersal, persistence, alterations to microbial function and biogeochemical cycles, and shifts in the ecosystem communities [310]. A substantial area of concern lies in the potential impact of introduced microorganisms on the existing microbiome, which may result from direct ecological interactions, be they cooperative or antagonistic in nature. Invasive, alien species are bad for ecosystems, since they may reduce biodiversity and disrupt food chains, including our own. Species from other regions that establish self-sustaining populations in an invaded area are referred to as naturalized species. Among naturalized species, those that quickly spread beyond the site of their initial introduction in the invaded region are classified as invasive, as described by Richardson et al. (2000) [311], Pyšek et al. (2004) [312], and Blackburn et al. (2011) [313]. For instance, the chestnut blight fungus entered North America surreptitiously through contaminated nursery stock [314], leading to the demise of four billion trees over a span of 40 years. Especially in tropical regions, like South Asia and South America, plant invasions are one of several factors that threaten the local biodiversity. The economic and social challenges resulting from plant invasions are on the rise across all continents. The expenses directly associated with the harm caused by invasive species are thirteen times greater than the costs incurred for their management [315].

Finally, biological invasions rank as the fifth most significant driver of global environmental change, according to IPBES 2019 [316]. Approximately 14,000 taxa, constituting about 4% of the world’s flora, are recognized to have naturalized from the global plant species pool [317,318]. Among them, around 2500 species have been identified as invasive, with the Asteraceae family contributing the highest number of naturalized taxa [319]. Escalating international trade has led to a global increase in the number of invasive species [320].

The phenomenon of horizontal gene transfer has also been identified as a relevant consideration [321,322,323]. Horizontal gene transfer involves the transfer of genetic information between organisms, facilitating the dissemination of antibiotic resistance genes among bacteria, excluding those passed from parent to offspring. This process contributes to the evolution of pathogens [323]. For instance, the simple use of manure as an organic fertilizer in agriculture introduces fecal bacteria, along with their plasmids and antimicrobial resistance genes, into the soil. The exchange of genetic material, which includes plasmids [324] and even entire genomic segments, is particularly prevalent in the rhizosphere—an area rich in microbial activity. Such exchanges have been observed even between species that are quite distantly related. There have, for example, been documented cases of gene transfer between Pseudomonas putida and E. coli facilitated by the TOL plasmid (pWW0) [324]. Macedo et al. (2022) [325], through a microcosm study involving E. coli, recorded the successful transference of a broad host range plasmid to soil and manure bacteria by conjugation [326]. Similar instances of plasmid transfer have been witnessed within various strains of Azotobacter vinelandii. Martínez-Carranza et al. (2019) [327] suggested that A. vinelandii may have a polyphyletic origin, with a genomic resemblance to the pathogenic bacterium P. aeruginosa. This hypothesis opens up the possibility of horizontal transfer from P. aeruginosa to A. vinelandii of genetic information encoding pathogenicity [327].

It has been suggested that microorganisms may influence ecosystem biodiversity or induce infections in humans, animals, or plants, thereby having an adverse environmental impact. As a response to this concern, the European authorities have tried to protect humans, plants, animals, and the environment by developing European Regulation (EU) 2019/1009 [328] on biofertilizers.

Our current understanding suggests that plants are not isolated entities; instead, they exist in association with a diverse range of microbes [329]. Introduced microorganisms can indirectly alter resident microbial communities by influencing plant physiology and morphology via the acquisition of nutrients, reduction of plant stress, and suppression of plant diseases. For instance, some plant growth-promoting microbes are known to modify root architecture and exudation [330], which can impact rhizosphere communities [331,332]. In mixed plant communities, indirect effects on the resident microbiome could also occur if the introduced microorganism induces changes in plant diversity and composition, as has been seen with some AMF inoculants [331,332].

Inoculation with rhizobia, commonly used in biofertilizers, has shown significant effects on soil and plant-associated microbial communities in soybean [333], alfalfa [334], and common bean crops [335]. These effects can extend beyond the rhizosphere. Field inoculation of Phaseolus vulgaris with two native rhizobia strains (separately or combined) altered the structure and increased the phylotype richness of bacterial communities in the bulk soil [336]. Changes in microbial structure can result from both positive and negative interactions of rhizobia with the rhizosphere microbiome. The close relationship between root endophytes and root tissues facilitates the exchange of nutrients between plants and microbes [337]. For instance, Azospirillum, a bacterial genus known for its free-living organisms with nitrogen-fixing capabilities, among other plant growth-promoting traits, has shown variable effects on the resident microbiome [337]. Inoculation of maize with A. lipoferum induced a shift in the composition of rhizosphere bacterial communities lasting for at least one month [338]. However, variable results were observed when inoculating the same or other crops with A. brasilense [339,340], even though this bacterium can induce physiological and morphological changes in the root system.

According to Trabelsi and Mhamdi (2013) [337], the effects of Azospirillum inoculation on rhizosphere microorganisms are likely driven by nitrogen dynamics, although a wide array of factors are involved. While rhizobia and Azospirillum have been more widely studied regarding their effects on the resident microbiome, research on other taxa, such as Pseudomonas sp., remains limited, even though they could potentially modify both bacterial and fungal communities [341,342].

Arbuscular mycorrhizal fungi (AMF) biofertilizers are the most widely used and readily available, despite insufficient evaluation of ecological risks associated with their field application [332,343]. The introduction of non-native AMF can impact indigenous AMF communities in various ways, such as displacing them and reducing their diversity [344] or altering their composition [345], although these effects on the native AMF community may not always be evident [346]. In a study conducted by Jin et al. (2013b) [347], a diverse AMF inoculum had a less pronounced positive impact on plant fitness but had a milder influence on the composition of subsequent AMF communities. In addition to affecting native mycorrhizal fungi, introduced AMF can disrupt other soil microbial communities, especially those associated with their extraradical mycelium, known as the mycorrhizosphere [337].

The influence of AMF on soil microbial communities appears to be variable and is influenced by multiple factors [348,349,350]. For instance, among the principal factors influencing microbial activity lies the microbial capability to reduce organic materials, utilizing them as sources of energy. The average oxidation state of carbon in a contaminant represents an effective energy source for aerobic heterotrophic organisms. A heightened oxidation state, consequently, correlates with a diminished energy yield, thereby offering a reduced energy output for microbial degradation. The outcome of any biodegradation undertaking is contingent upon various factors, encompassing microbial dynamics (population diversity, enzyme activities, and biomass concentration), substrate attributes (physical and chemical properties, molecular concentration, and structure), and an assortment of environmental determinants (pH, moisture content, temperature, electrical conductivity, availability of electron acceptors and carbon, and energy sources). These parameters exert an influence on the adaptation period of microorganisms to the given substrate. The concentration and molecular structure of contaminants wield substantial influence over the feasibility of bioremediation practices and the nature of microbial metamorphosis, determining whether the compound will function as a primary, secondary, or co-metabolic substrate [351].

Notably, bacteria residing in the mycorrhizosphere have demonstrated plant growth-promoting activity and are believed to work in synergy with AMF [352]. The impact of non-AMF fungal inoculants has received less attention, but there is evidence that endophytic fungi [353,354] and Trichoderma spp. [287] can induce changes in local microbial communities.

The impact of introduced microorganisms on existing microbial communities’ hinges, to some extent, on their abundance, survival, and persistence within an ecosystem [355]. This intricate relationship implies that the very traits that contribute to successful plant growth promotion also elevate the risk of ecological invasion. Surprisingly, there is a dearth of comprehensive studies that delve into the consequences of large-scale, repeated inoculations, as well as the enduring effects, both in the long term and across subsequent crops [322,337]. Hart et al. (2018) [333] emphasized the significance of long-term repercussions, particularly concerning AMF inoculants. The assessment of the establishment and endurance of AMF inoculants is compounded by their complex genetic makeup. These concerns become all the more alarming when considering that the effects of inoculation may linger, even as the population of introduced microorganisms diminishes [339]. One of the underlying mechanisms responsible for these enduring “legacy” effects is the phenomenon of plant–soil feedback. This is more likely to occur when the introduced microorganism has a symbiotic relationship with or a strong affinity for a specific plant, potentially affecting non-target plants within the agroecosystem [335,355].

The diverse outcomes witnessed when introducing microorganisms through inoculation into the resident microbiome imply a multifaceted interplay of influencing factors, notably including the host plant [349]. Correa et al. (2007) [342] found that a plant’s genetic makeup exerts control over the genetic and physiological responses of phyllosphere and rhizoplane bacterial communities to A. brasilense seed inoculation. Rhizosphere bacterial communities were found to respond differently to A. brasilense at distinct growth stages of the crop, displaying more pronounced effects during the jointing stage than the grain-filling stage [356].

The resident microbiome susceptibility and buffering capacity can vary considerably depending on its diversity [357,358] and the presence of specific antagonistic or synergistic taxa [359,360]. Environmental conditions, such as soil moisture [352,360] and light intensity [348], may emerge as pivotal factors in regulating the influence of introduced microorganisms.

In general, it appears that the majority of studies investigating the effects of biofertilizers tend to place emphasis on structural attributes rather than functional aspects [338]. Recognizing the functional implications of these alterations is of paramount importance, as they exert a direct influence on ecosystem operation and well-being. To tackle the complexities of these ongoing dynamics and foresee microbial responses in natural conditions, multidimensional omics and advanced data analysis serve as indispensable tools [357,361]. The question remains as to the lasting environmental impact of introduced microorganisms, encompassing their potential for long-term and legacy effects. Additionally, there is a need for more in-depth exploration regarding genetically modified microorganisms, encompassing considerations of metabolic load [362] and the associated risks of horizontal gene transfer and dispersion [363,364]. Diverse inoculants may emerge as a more environmentally benign alternative, as implied by studies on AMF or Bacillus spp. [77].

Bioremediation as a method presents its own set of constraints. The microbial breakdown of specific chemicals may lead to the creation of intermediary substances that not only prove more toxic but also exhibit greater mobility than the original compound. For example, the reductive dehalogenation of TCE can result in the accumulation of vinyl chloride, a highly toxic and carcinogenic byproduct. Hence, bioremediation is a technology demanding extensive research and a comprehensive understanding of microbial processes prior to its implementation; failure to do so could have even more severe repercussions for the ecosystem than the initial contaminant itself [365].

6. Economic Feasibility

Their affordability, environmental compatibility, and ability to enhance soil organic matter position microbial technologies as an effective approach to promoting sustainable agriculture. The improved cost-effectiveness and overall economic viability have demonstrated the potential of biofertilization, encouraging farmers to consider its adoption in the future [366]. In response, various companies have developed a range of biofertilizers that are widely utilized in the market. AgriLife^®, for example, has introduced fifteen biofertilizer products targeting nutrient enhancement through nitrogen fixers, phosphate solubilizers, and potassium-, ferrous-, sulfur-, manganese-, and zinc-mobilizing microbes. Each biofertilizer is tailored to address specific nutrient needs and contains a unique bacterial strain [367].

TagTeam^®, a multi-functional inoculant, is specifically designed for legume crops. It enhances phosphate utilization and nitrogen fixation through the combined action of Penicillium bilaii and rhizobia strains. Available in both granular and liquid forms, TagTeam is suitable for application on soybeans, peas, dry beans, lentils, and chickpeas [368].

JumpStart^®, a notable product, utilizes Penicillium bilaii, a fungus that improves phosphate availability for plants. By colonizing plant roots, P. bilaii releases organic compounds into the soil, breaking the bonds between phosphate and other elements, thus increasing phosphate accessibility for plants while deriving nutrients from the host plant in a symbiotic relationship. This biofertilizer is particularly effective for crops such as canola, wheat, and legumes [369].

RhizoMyco^® is another innovative biofertilizer containing a blend of eighteen species of endo- and ectomycorrhizae. along with growth-promoting agents. Offered in soluble or injectable forms, it provides a broad spectrum of benefits by improving nutrient absorption and expanding root systems [370].

RhizoMyx^®, a widely recognized endomycorrhizal inoculant, is formulated to enhance plant performance by fostering root nodule development and increasing the availability of essential nutrients [371].

Despite the relatively high availability of biofertilizers on the market, their accessibility to small-scale farmers in Brazil, for example, remains limited. This is primarily due to a lack of promotion and insufficient information on the subject. Additionally, Brazilian environmental agencies have limited knowledge about this technology, which creates a series of barriers to its effective use across the country.

In Brazil, theoretically, it is mandatory to present a list of organisms comprising the microbial strains used in biofertilizers. However, since living organisms cannot be patented or registered by private entities in Brazil, laboratories often do not disclose the actual composition of their products when obtaining licenses. Furthermore, the inability of regulatory agencies to verify the declared composition allows for the practice of misinformation, significantly hindering the development of products by small laboratories.

Finally, the aim of this article is to promote the use of biotechnologies not only by large producers but also by family farmers in developing countries. It is understood that the widespread dissemination of these technologies, both for agricultural production and for bioremediation projects in soils and aquatic environments, is essential to raise awareness among environmental stakeholders about the various possibilities to be explored in this field of research.

7. Challenges and Most Recent Developments

Although not yet standard in wastewater treatment systems (WWTS), bioremediation is being increasingly considered for this purpose. It can reduce toxins that are not removed by standard treatment [372], including microplastics [373]. The concept of the circular economy requires a sustainable approach for reusing, recycling, and recovering materials, particularly relevant for wastewater treatment, where current methods are less than perfect. Colla et al. [374] discussed the achievements and potential achievements of the circular economy in the management of agricultural wastes, and Arias et al. [375] provided an integrated review of life cycle assessments, economic aspects, and social analysis with respect to the circular economy as applied to waste treatment processes. Bioremediation techniques could offer a path toward more environmentally acceptable waste treatment [376,377]. A recent paper combined the techniques of bioremediation and biofertilization: Schmuck et al. [377] considered the advantages of using municipal wastewater as a valuable source of raw materials and suggested that microalgae (e.g., Chlorella) be included in WWTS to produce value-added products, such as lipids and carbohydrates. This forms part of the concept of biorefineries, converting municipal wastewater into useful products such as fertilizers and bioenergy [378,379]. Finally, the use of microbe-mediated nanoparticles for the control of pollution (e.g., metals) was cited as an example of an emerging technological use of microorganisms [380].

Although these biotechnologies promise extremely desirable improvements for the agroindustry, there are considerable challenges in the development of their routine use. The biofertilizer market could be revolutionized by genetic engineering, which promises products tailored to specific crop requirements, but the gap between development and routine use is still large [381]. Problems such as the necessary long-term survival of the added microorganisms, especially if conditions are, or become, adverse [382], might be solved by genetic engineering; however, the complex interactions between introduced and native microorganisms are more difficult to tackle and will vary depending on the environment into which the new organisms are introduced. It is difficult to envisage specific bioremediating organisms for each type of soil and local environmental conditions. These are not the only problems to be overcome; perhaps even more challenging is the current attitude of the public, who not only has a negative attitude to agrochemicals in current use, but also, in many cases, a distrust of DNA engineering. There will have to be rigorous vetting, followed by education and effective marketing before these new biotechnologies become acceptable worldwide.

8. Future Directions and Policy Implications

As indicated in this article, the extensive availability of data on soil stimulation and remediation biotechnology reflects advances primarily made by developed countries, whose results often address objectives different from the needs of developing countries, particularly those with hotter climates. These advances are also likely focused on market-oriented goals, which are far removed from the public policies required for socio-environmental sustainability.

The use of biotechnology on various scales should not be solely profit-driven but also serve as a tool for social welfare, especially for the underprivileged segments of society, which constitute the majority in the social pyramid of poorer countries. As previously illustrated, the use of biotechnology in small-scale family farming communities in Brazil is still in its early stages, despite its significant importance to national organic agriculture production [383]. Therefore, promoting the broader use of biostimulants is essential in this sector. On the other hand, few examples exist of projects focusing on the revitalization of environments inhabited by low-income populations, where the lack of sanitation infrastructure leads to issues such as domestic sewage disposal, resulting in environmental imbalance through the disruption of microbial trophic networks. This disruption breaks the critical links represented by sensitive microbiotic species, neutralizing the cooperation among diverse microorganisms within a specific strain. Consequently, this leads to the accumulation of organic matter, anoxia, and other phases stemming from the overload of decomposing material.

One of the key potential social challenges that could be addressed through nutrient recycling bio-stimulation methods is the development of alternative sanitation techniques for areas where installing domestic waste collection networks is financially unfeasible. Notable examples include streams running through impoverished urban communities in large metropolitan areas such as Rio de Janeiro. In these regions, the steep topography of favelas makes conventional sewage systems impractical. The possible introduction of bioremediators as a method to purify these water bodies could facilitate the degradation of organic waste from low-income households using the streams as sewage outlets. This, in turn, could result in nutrient recycling that fertilizes downstream water bodies, such as bays or beaches. The theoretical benefits are numerous, including improved water quality and increased productivity in estuarine environments.

It is understood that various other initiatives could be undertaken to integrate biotechnology into government projects. However, the primary obstacle remains the limited technical capacity of the governmental agencies responsible for implementing public policies. At this juncture, it becomes evident that, as proposed in this article, the widespread dissemination of microbiotechnological techniques within governmental technical departments is of the utmost urgency. To achieve this, a partnership between academia and the government in developing public policies may be the most effective path forward.

9. 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.

The vast majority of articles published on the effects of using microorganisms in bioremediation, particularly studies on the use of microbial strains in the remediation of natural environments, have revealed a range of methodological limitations, like the use of known and secure microbiota species, the use of host species with short-life cycles, the control and manipulation of mineral nutrients level in soil, and the appropriate combination of micobial species and host plant. It is essential to bear in mind that the majority of this research has been conducted in temperate climates. This article proposes that the environmental conditions of tropical regions could offer an advantage for the utilization of this more ecologically sustainable technology, which could usefully be employed to tackle problems in developing countries.