Harnessing Rhizospheric Microbes for Mitigating Petroleum Hydrocarbon Toxicity

Abstract

Hydrocarbon pollution resulting from anthropogenic activities related to the petrochemical industry and other natural sources presents a major problem that has crippled environmental sustainability and contributed to food insecurity crisis. Bioremediation which has proven to be an effective and eco-friendly approach with a broad spectrum potential of targeting and removing a wide range of hydrocarbons including known recalcitrant hydrocarbons has been well studied. However, for bioremediation to be successful and complete, eco-restoration must be achieved. A promising approach to restoration of polluted environment is through the utilization of plant rhizospheric microbes in rhizoremediation. Harnessing rhizospheric microbes as potent tools for rhizoremediation has gained considerable attention in the field of environmental science because of the additional benefits it presents in the decontamination of pollutants such as enhanced nutrient delivery, increased microbial diversity, enhanced biofilm formation, enhanced degradation efficiency, plant-microbe interactions and high adaptation to soil conditions for enhanced remediation activity. These group of microbes possess inherent metabolic capabilities that allow them to efficiently degrade or transform a wide range of pollutants, including hydrocarbons, heavy metals, pesticides, and organic contaminants. This review therefore highlights in details environmental pollution and its challenges, remediation of petroleum hydrocarbons with different groups of rhizospheric microbes and the beneficial attributes of rhizomicrobes in bioremediation technology and environmental sustainability.

1. Introduction

Hydrocarbon contamination resulting from activities related to the petrochemical industry constitutes one of the major environmental problems today. Human actions, including unintentional spillage of petroleum substances, inadequately managed waste disposal sites, seepage from subterranean storage facilities, and improper crude oil storage, pose notable environmental hazards which makes environmental cleanup highly mandatory [1]. Based on existing literature, mechanical and chemical methods generally have been used for the purpose of hydrocarbon decontamination from impacted sites, however, reports have shown their limited effectiveness and high operation cost [2]. The use of these approaches in environmental pollution management have also been limited because of their invasive, unsustainable and potential source of pollutant to the environment. Given these circumstances, it becomes crucial to identify and implement cost-effective, swift, environmentally friendly, and sustainable cleanup methodologies with the aim to optimize and expedite the restoration of ecosystems heavily impacted by petroleum hydrocarbon contamination. The ultimate goal is to recover these ecosystems to a state where they can once again support agricultural activities and reestablish ecological balance.

The depuration of petroleum hydrocarbon polluted ecosystems is mandatory in promoting sustainable development and the process of bioremediation forms an integral part of the numerous remediation techniques for the detoxification of polluted terrestrial environments. This bioremediation phenomenon has sparked scientific curiosity because of the numerous benefits it presents. This technology is an appropriate, economical, and environmentally friendly strategy that is quicker, practical, and adaptable in a variety of physical settings for the restoration and rejuvenation of the affected environment [3]. Bioremediation is an evolving technology for the removal and degradation of many environmental pollutants including the products of petroleum industry and it involves the use of microorganisms equipped with catabolic genetic structures capable of complete hydrocarbon mineralization or biodegradation [4]. The bioremediation technology is very flexible and evolving, it accommodates the infusion and incorporation of different biological-based technologies for optimal outcome. In recent times the use of plant-associated microbes to effectively deliver ecorestoration of hydrocarbon polluted environment through bioremediation has gained researchers interest. Effective application of rhizomicrobes for the remediation of hydrocarbons depends mainly on the presence and metabolic activities of plant-associated rhizo- and endophytic bacteria possessing specific catabolic genes required for the degradation of hydrocarbon pollutants [5]. The beneficial application of rhizobacteria is specifically related to phytoremediation and rhizoremediation technologies, although their utilization in bioremediation directly has also been recognized.

Plants and their associated microbes interact with each other whereby plant supplies the microbes with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-microbes can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. Additional benefits obtained by plants from associated bacteria possessing hydrocarbon degradation potential include enhanced hydrocarbon mineralization, a lowering of phytotoxicity as well as evapotranspiration of volatile hydrocarbons [6]. Further understanding of rhizomicrobes and partnerships will lead to enhanced remediation of hydrocarbon-contaminated soils as well as sustainable production of non-food crops for biomass and biofuel production [6]. The application of rhizospheric microbes in collaboration with plants is referred to as rhizoremediation, a branch of phytoremediation.

Phytoremediation is an established remediation strategy that leverages the inherent capacity of plants and their associated microbiomes to either accumulate, degrade, sequester, or stabilize toxic environmental pollutants [7]. Over the last two decades, this approach, involving the utilization of plants and their microbiomes, has been extensively employed to address a broad spectrum of both inorganic and organic pollutants in soil and water environments [8]. Despite being a relatively new technology, phytoremediation has gained traction and garnered interest from an increasing number of researchers as well as companies. Phytoremediation technologies are generally classified into five distinct categories; phytoextraction, phytostabilization, phytotransformation, phytovolatilizaton, and rhizoremediation [5, 9]. For petroleum hydrocarbon-contaminated soil, the most applicable phytoremediation method is known as rhizoremediation [7].

Rhizoremediation is defined as the degradation of organic pollutants through the utilization of plants and their root-associated microbiomes. This technique stands out as a prominent green technology that has attracted widespread global attention due to its potential as a cost-effective and potentially efficient method for remediating soil contaminated with petroleum hydrocarbons (PHCs). In essence, rhizoremediation involves utilizing plants and their associated microbiota to remediate environments inundated by contaminants. In this process, the roots of these plants play a pivotal role by stimulating soil microbes through the release of exudates, promoting the mineralization of organic pollutants into innocuous forms such as H₂O and CO₂. Nevertheless, this multifaceted interaction within the rhizosphere is notably complex, largely due to the numerous biotic and abiotic factors that influence microbial metabolic activities. These factors can exert varying degrees of influence on microbial processes, rendering the efficiency of rhizoremediation somewhat unpredictable. In the practice of rhizoremediation, rhizospheric microbial communities are harnessed for the purpose of biodegrading a wide range of pollutants, spanning from saturates to aromatics. The advantage of rhizospheric microbes in bioremediation over other microbes lies in their close association with plant roots, which provides a unique and favorable environment for their growth and activities. This association enhances the potential of rhizospheric microbes to degrade pollutants efficiently and contributes to their overall effectiveness in bioremediation processes. The rhizomicrobe-mediated bioremediation (rhizoremediation) approach comprises a strong interaction between microbes and the plant root zone, which increases microbial activity in the rhizosphere and aids in the breakdown of organic pollutants through the activation of degradative and catalytic genes.

Research findings have indicated that both rhizospheric and endophytic bacteria have been employed as an inoculation system in soil for the rhizoremediation of polycyclic aromatic hydrocarbons (PAHs) and other hydrocarbon constituents [10, 11]. Nevertheless, when compared to the approach of bioaugmentation, microbe-assisted phytoremediation, specifically rhizoremediation, proves to be notably more efficient for the elimination and breakdown of organic contaminants in polluted soils, especially when coupled with suitable agronomic practices [12]. This efficacy arises from the distinct chemical conditions in the rhizosphere, which differ from those in the bulk soil due to processes induced by plant roots and rhizobacteria [12]. The collaborative impact of plant roots and rhizospheric microbial communities, including the secretion of organic acids leading to a reduction in soil pH, production of siderophores, phytochelatins, amino acids, 1-Aminocyclopropane-1-carboxylate (ACC) deaminase, and other secondary metabolites by plant growth-promoting rhizobacteria (PGPR), has also proven effective in the ecological restoration of polluted sites. This review therefore highlights the role of rhizospheric microbes in hydrocarbon pollution mitigation.

2. Petroleum hydrocarbon (PHC) pollution and its consequences

Petroleum hydrocarbon is a complex class of pollutants typically introduced into the environment as a composite mixture of n-alkanes, branched alkanes, cyclo-alkanes, monoaromatic hydrocarbons (MAHs) and polyaromatic hydrocarbons (PAHs). These diverse hydrocarbon constituents exhibit distinct interactions within the environment, which often depends on their molecular weight and other notable properties. This assortment of hydrocarbon compounds exhibits a broad range in terms of both size and structural configuration, spanning from the smallest, methane (C1), to larger, more complex molecules such as n-C40+ and beyond [13]. In consideration of their chemical structure, petroleum hydrocarbons can be categorized into four principal classes, each characterized by unique traits and composition—namely, the saturates, aromatics, asphaltenes, and resins. Petroleum hydrocarbons in the environment undergo weathering, which may involve physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) influences [14, 15].

Petroleum hydrocarbon exploitation and exploration, production, transportation, and industrialization have exacerbated environmental pollution and its consequences which usually require immediate cleanup to reduce the drastic effect on the environment. Petroleum hydrocarbons are known to cause significant health consequences in humans and other organisms due to their teratogenicity, mutagenicity, carcinogenicity, and toxicity [16]. Hussein et al. [17] proposed that direct consumption or the transfer through food chains (such as soil-plant-human or soil-plant-animal-human), ingestion of contaminated groundwater, and diminished land usability due to soil pollution by PHCs pose substantial risks to both human populations and ecosystems. It is noteworthy that the US Environmental Protection Agency (USEPA) has classified the majority of crude oil constituents as priority contaminants (USEPA, 2009), especially the polycyclic aromatic hydrocarbon group. The contamination of soil with PHCs moving through the food chain can have detrimental effects on human health, potentially leading to severe ailments such as cancer, as well as disorders of the immune and reproductive systems [18].

Crude oil pollution affects humans and other living organisms through diverse routes such as ingestion or inhalation of toxic components, uptake through the food chain, absorption, and dermal contact. The toxic effect of PHC can be acute or chronic. For acute toxicity, the effect is caused by exposure to a high concentration of crude oil over a short-term period while conversely, chronic toxicity refers to the effects that arise from prolonged and continuous exposure to oil pollution. The toxic effect of crude oil whether acute or chronic depends on factors such as the duration of exposure, the concentration of released oil, the resistance of organisms to hydrocarbons, the availability of oil, the bioaccumulation of other oil components, and the level of attention to these factors [19]. In addition, PHC pollution has the potential and capacity to trigger an increase in stress-tolerant microbial populations specifically hydrocarbonoclasitic microbes that exhibit adaptability to the contaminated environment. This phenomenon leads to notable shifts in both the composition and structure of the microbial community, as well as the enzymatic systems within the soil, facilitating the degradation of oil. Also, crude oil pollution has deleterious effects on soil properties, plant anatomy, physiology, growth parameters, and consequently plant development [20]. Crude oil pollution has the capacity to directly pollute terrestrial ecosystems, while the dispersed oil, which remains afloat and spreads across the water surface, exerts its influence on both terrestrial and aquatic environments [21].

From the perspective of the aquatic environment, PHCs pose negative effect on the aquatic organisms and this environment harbors the largest number of living organisms compared to other environmental compartments. Among the consequences of PHC on water include ecological imbalance, and negative effects on aquatic animals, plants, and microorganisms. One of the major occurrences of crude oil pollution in water is bioaccumulation. When organisms are exposed to crude oil, the hydrocarbons accumulate within the tissues and other internal organs which could be transferred to humans through the food chain and subsequently returned back to the environment when the organisms die. Also, the microbial community within the aquatic environment is greatly affected by PHC contamination which leads to a reduction in the microbial diversity, evenness, richness, and structure. This occurs for a number of reasons such as unavailability of nutrients and other growth factors, preventing microbes from assessing essential and rate-limiting building blocks for growth and proliferation, and difficulty in aligning due to the in-conducive highly non-polar conditions which results in rupture of microbial cells when the cytoplasm lipid chain dissolves [22]. The presence of crude oil induces several transformations and alterations in the physical and chemical composition of the environment such as a reduction in biodiversity and soil fertility, alterations in soil pH, and the accumulation of heavy metals [23]. These modifications, combined with varying sensitivities among species, lead to shifts in the microbial community composition. All of these effect on the biotic and the abiotic entities in the environment is contingent upon several factors which include but are not limited to the specific characteristics of the ecosystem and the prevailing environmental conditions, the chemical composition of the pollutant and the composition of the indigenous microbial community [24]. These factors largely determine the impact and influence the PHC would have on the environment. Based on the outlined and aforementioned effects associated with PHC pollution on the environment, the need for developing new tools and improving on existing bioremediation technologies for cleanup and restoration of impacted matrices for ecological sustainability and balance is highly imperative. Table 1 represents the several consequences of hydrocarbon pollution in different environments.

S/N	Environment	Consequence	Reference
1	Soil	The penetration of oil and oil products darkens the upper horizons of soils and leads to mosaic changes in the morphological structure due to the uneven oil distribution in the soil stratum.	[25]
		Hydrocarbon pollution transforms the granulometric composition of soils (an essential genetic and agronomic characteristic that influences soil fertility).	[26]
		Pollution by hydrocarbons lead to the formation of a bituminous crust in the upper layers of soils, thus hindering plant growth and deep-water penetration	[27]
		Pollution with oil and oil products causes an increase in the content of organic carbon in soils.	[28]
		Petroleum hydrocarbons can alter soil pH and nutrient availability, affecting its chemical properties.	[26]
		Fires caused by the explosion of oil tankers, oil installations, leakages from oil pipes and pipeline vandalism leads to burning of the organic matter composition of soils.	[29]
		Petroleum hydrocarbons can influence soil biological properties by altering microbial activity, diversity, and composition.	[26]
		Soil contamination by crude oil changes the group and fraction composition of humus, as well as the quantity and proportion of macro- and microelements in the soil.	[28]
2	Microbes	Crude oil penetration causes changes in the total quantity and organization of the microbial population.	[26]
		Crude oil pollution reduces the population of microorganisms and bacteria that assimilate mineral nitrogen forms	[30]
		The introduction of hydrocarbons in soils kill or inhibit many microbial species, thereby altering the functionality of the microbial community and thus disturbing the ecosystem	[23]
		Petroleum hydrocarbon contamination lowers the variety and evenness of a microbial population.	[23]
3	Water	Crude oil and petroleum products form a waterproof film on water that prevents the oxygen exchange between environment and water causing damages to plants, animals, and human beings.	[31]
		Pollution from hydrocarbon leaks and oil spills in the maritime environment disrupts the balance of the marine ecology.	[32]
		Floating organisms, notably algae and zooplankton, are particularly vulnerable to harm when they come into contact with hydrocarbons in water.	[31]
		Petroleum products touching sea birds in water bodies deprives them of their ability to fly as well as dissolves the oil on their feathers, resulting in super-cooling and, eventually, death.	[32]
		Hydrocarbons can accumulate in aquatic bodies, potentially affecting aquatic ecosystems.	[23]
4	Air	A larger percentage of the flared gas released is methane leading to increase in the amount of greenhouse gases (GHGs) in the atmosphere, hence increasing the global warming potential	[33]
5	Plants	Hydrocarbons in soil restrict plant mobility through the soil matrix, preventing plants from obtaining sunlight, water, and nutrients.	[23]
		Byproducts of hydrocarbon combustion, specifically aldehydes negatively impact plant photosynthesis.	[33]

Table 1.

Consequences of hydrocarbon pollution on the environment.

3. Plant growth promoting rhizobacteria in bioremediation

Plants and their associated microorganisms play a vital role in remediation processes, effectively removing pollutants from the environment. During plant development, a symbiotic relationship forms between the soil, plants, and microbes. This connection is established when plant root secretions called rhizodeposits stimulate the microbial community in the rhizosphere. This class of microorganisms are referred to as plant growth promoting microbes because they are responsible for promoting the growth of plants through different mechanisms and providing the plant with selective properties to support healthy development [34]. Such properties include enhanced nutrient uptake, promoting essential nutrient availability, phytostimulant production, biocontrol of phytopathogens, and conferring resistance to abiotic stresses on the plant. Plant growth-promoting rhizobacteria (PGPR) are essential in this co-evolution, displaying both antagonistic and synergistic interactions with microorganisms and the soil. Microbial rejuvenation through plant growth promoters can be achieved through various direct and indirect methods, including stimulating root growth, bio-fertilization, and rhizoremediation among others [35]. Again, the symbiotic and non-symbiotic relationships between microbes and plants make them strong candidates for rhizoremediation technology [36]. It is worthy to note that PGPR enhance plant growth and increase plant resistance to biotic and abiotic stresses through diverse mechanisms. A primary mechanism in hydrocarbon rhizoremediation is rhizodegradation, which establishes plant-microbe interactions and the role and function of rhizomicrobes in hydrocarbon degradation [37].

These interactions, occurring within the plant’s root region, results in the production of primary compounds like organic acids, amino acids, and carbohydrates, as well as secondary metabolites such as phenolic compounds, alkaloids, and terpenes. These substances influence the rhizosphere microflora, affecting microbial populations and metabolic activities in the area [38]. Furthermore, it’s important to note that plant roots release oxygen, oxygenating soil pores and creating a suitable environment for aerobic organisms. This aeration facilitates rhizodegradation, an essential aspect of pollutant removal by plants and their associated microbes.

According to Divya and Kumar [39], rhizoremediation encompasses both spontaneous occurrences and deliberate interventions involving microorganisms aimed at enzymatically degrading environmental pollutants within the soil matrix. Even in adverse environmental conditions, the presence of PGPR within the rhizosphere fosters substantial increases in plant biomass within polluted soils. It is increasingly evident that the mutualistic interplay between plants and rhizospheric bacteria profoundly increases the efficacy of phytoremediation. Through the augmentation of plant growth and the stimulation of augmented root biomass production, the introduction of PGPR has demonstrated notable enhancements in the removal of recalcitrant organic pollutants such as polycyclic aromatic hydrocarbons and creosote compounds. In rhizodegradation, plants play an indirect role in the phytoremediation process by creating a conducive environment for the proliferation of microorganisms within the rhizosphere. These microorganisms possess the capability to enzymatically degrade or mineralize harmful substances to innocuous forms. Several rhiziobacteria have been successfully implicated in bioremediation/rhizoremediation of PHCs and this is information is presented in Table 2.

Microorganism	Hydrocarbon	Reference
Marinobacter sp.	Total petroleum hydrocarbon	[40]
Pseudomonas aeruginosa	Aromatics	[41]
Dietzia sp.	Aliphatics	[42]
Sphingomonas paucimobilis strain EPA 505	Benzo (a) pyrene (BaP)	[43]
Pseudomonas and Burkholderia	Naphthalene	[44]
Mycobacterium vanbaalenii	Anthracene and naphthalene	[11]
Pseudomonas aeruginosa	Naphthalene	[45]
Bacillus sp.	Benzo(a)anthracene	[45]
Bacillus stratosphericus, Bacillus subtilis, Bacillus megaterium, and Pseudomonas aeruginosa.	Polycyclic aromatic hydrocarbons (PAHs)	[46]
Pseudomonas putida	Naphthalene	[47]
Promicromonospora sp.	Total petroleum hydrocarbon (TPH)	[48]
Klebsiella sp. D5A	Petroleum oil	[49]
Pseudomonas putida UW3,; Azospirillum brasilense Cd and Enterobactor cloacae; CAL2	Polycyclic aromatic hydrocarbons (PAHs)	[50]
Kurthia sp.	PAH	[11]
Sphingomonas sp.	Polycyclic aromatic hydrocarbons (PAHs)	[51]
Pseudomonas sp	TPH	[52]
A. lipoferum 59b, A. brasilense Sp 7, and A. brasilense Cd	Protocatechuate, 4-hydroxybenzoate, and catechol	[53]
Pseudomonas gessardii strain LZ-E	Naphthalene	[54]

Table 2.

Rhizospheric bacteria implicated in petroleum hydrocarbon degradation.

Pizarro-Tobías et al. [51] also reported an in-situ field scale combined bioremediation and rhizoremediation study in a semi-arid environment previously contaminated with oil refinery sludge. The treatability study involved the application of bioaugmentation approach using a consortium of PGPR for plant growth and polycyclic aromatic hydrocarbon-degrading bacteria as well as a combination of this consortium with pasture plants. The increased plant growth supported the evolution of indigenous microbiota with hydrocarbon-degrading potentials to facilitate the removal of the toxic PAH compounds according to the principle of rhizoremediation.

However, Singha and Pandey [55] have recommended that a more detailed evaluation of the efficiency of biostimulation and bioaugmentation with eligible plant-microbe combination under toxic environmental conditions is required. Also, modification of microbiomes utilizing genetic engineering/recombination technology to improve biodegradation of contaminants is an upcoming and effective strategy that could also be exploited for optimal bioremediation activities. Based on this recommendation, a recent study conducted by Bhuyan et al. [56] investigated the application of bioaugmentation and biostimulation in synergy with rhizoremediation. The hydrocarbon-degrading bacterial strains also known as hydrocarbonoclastic bacteria were obtained from the rhizosphere of plants growing in regions of Assam, India, contaminated with crude oil and these bacteria exhibited characteristics that promote plant growth. To assess the ability of the bacterial consortium to facilitate rhizodegradation, two separate pot experiments were conducted using a combination of either Azadirchta indica or Delonix regia plants and the selected bacterial consortium, consisting of five hydrocarbon-degrading bacterial isolates (Rhodococcus ruber BB-VND, Pseudomonas aeruginosa BB-BE3, Ochrobactrum anthropi BB-NM2, Gordonia amicalis BB-DAC and Pseudomonas citronellolis BB-NA1). Additionally, NPK fertilizer was added to the soil to stimulate biodegradation. After 120 days of planting, the A. indica + consortium + NPK treatment demonstrated a PH degradation rate of up to 67%, while the same treatment with D. regia yielded a 55% degradation rate. Significant modifications in both plant and soil enzyme activities were also observed which resulted in an increased/enhanced degradation of PHCs in the soil-contaminated area. The shift in the bacterial community composition was evident, with A. indica treatment leading to a 35.35% increase in the relative abundance of Proteobacteria, a 26.59% increase in Actinobacteria, and a 20.98% increase in Acidobacteria. In contrast, D. regia treatment resulted in a 39.28% increase in Proteobacteria, a 35.79% increase in Actinobacteria, and a 9.60% increase in Acidobacteria. Predicted gene functions indicated a shift towards the breakdown of xenobiotic compounds. This study suggests that a combination of plant-bacterial consortium and NPK biostimulation represents a promising approach for bioengineering the rhizosphere microbiome to effectively remediate crude oil-contaminated sites, addressing a significant global environmental challenge. The rhizoremediation strategy with plant-microbe interactions has also been reported to show prospects in field conditions [5, 57].

4. The role of arbuscular mycorrhizal fungi (AMF) in bioremediation

Arbuscular mycorrhizal fungi (AMF) engage in mutualistic partnerships with the roots of approximately 80–90% of vascular plant species, potentially comprising up to half of the overall microbial biomass in soil. These fungi have been recognized as a valuable resource for improving phytoremediation efforts, as their mycelial networks extensively traverse the subterranean environment, serving as a connecting link between plant roots, the surrounding soil, and microorganisms within the rhizosphere [58]. This class of rhizospheric microorganisms (AMF) confer advantages to plant growth due to their capacity to augment the water and nutritional status of their host plants through the acquisition and transport of phosphate, nitrogen, and micronutrients. Consequently, numerous studies have demonstrated the ability of mycorrhizae to enhance plant biomass in soils contaminated with PHCs. This class of rhizospheric fungi establish extensive mycelial networks, ranging from approximately 81 to 111 meters per cubic centimeter of soil, which is orders of magnitude longer than the root systems of the host plants [59]. Furthermore, AMF hyphae possess small diameters, typically ranging from 2 to 15 micrometers. These characteristics allow them to explore a significantly larger soil volume and gain access to areas, including fine soil pores that are typically beyond the reach of plant roots. Consequently, this enhances the contact between mineral nutrients present in the soil and the plant roots (Figures 1 and 2).

Figure 1.

Environmental fate of petroleum hydrocarbon in soil [23].

Figure 2.

Mechanism of pollutant removal by rhizomicrobes [60].

Numerous research studies have documented that the formation of arbuscular mycorrhizal symbiosis can lead to both quantitative and qualitative alterations in the chemical compounds released by plant roots. For instance, Hage-Ahmed et al. [60] conducted an experiment demonstrating that when the roots of Solanum lycopersicum (tomato) were colonized by F. mosseae, the root exudates contained a higher concentration of sugars but a lower concentration of organic acids compared to non-mycorrhizal tomato plants. Furthermore, it was observed that the establishment of mycorrhizal associations modified the chemical composition of the root exudates, which serve as a nutrient source for microorganisms residing in the mycorrhizosphere, thereby influencing microbial biodegradation processes. Depending on the specific characteristics of the root exudates, different plant species may shape the structure of the rhizosphere microbial community in distinct ways. In a study conducted by Joner et al. [61] utilizing phospholipid fatty acid profiles, it was demonstrated that arbuscular mycorrhizal fungi (AMF) had the capacity to alter the composition of the microbial community in soil contaminated with polycyclic aromatic hydrocarbons (PAHs), and the researchers proposed that the microflora associated with mycorrhizal symbiosis might be responsible for reducing PAH concentrations in the mycorrhizosphere. Mycorrhizal roots have the natural capacity to modulate the genetic structure of the microbial rhizospheric community towards biodegradation of recalcitrant hydrocarbons by releasing higher levels of phenolic compounds, such as morusin, morusinol, and kuwanon, which share similar chemical structures with PAHs and can activate genes involved in pathways for the degradation of contaminants [59].

Petroleum hydrocarbons are known to cause a shift in diversity, functionality and reduction in the population of microbial communities within the rhizosphere as a result of its toxic components. This pollutant tends to affect majority of the AMF groups within the rhizosphere, however the Glomeraceae group are the most dominant in such environment. In a report by Kong [62], the roots and rhizospheric soils of two plant species, Eleocharis elliptica and Populus tremuloides, which naturally grow in sedimentation basins with significant petroleum contamination from a former petrochemical plant in Quebec, Canada, influenced the diversity of arbuscular mycorrhizal fungi (AMF) which resulted in each individual plant hosting fewer than five AMF operational taxonomical units (OTUs) across all the studied sites. The detected OTUs were predominantly from the Glomerales order. Notably, the genus Rhizophagus was the most prevalent taxon among all sequences analyzed in the research and it exhibited a clear correlation with the highest levels of contamination. This strong connection between Rhizophagus and elevated contamination levels underscores the significance of this genus in utilizing AMF for bioremediation purposes.

Similarly, the predominance of the Glomeraceae has been reported in various studies. In a report by Hassan et al. [63]. Glomeraceae was the predominant group in a soil polluted with petroleum. They described Glomeraceae as a ruderal group (i.e. one that is quick to colonize disturbed areas), which might benefit from allocating more biomass to plant roots than to surrounding soil, to limit damage from external disturbances. A recent study at a former petrochemical plant revealed that the contaminant concentrations in soil affected the AMF community structure, and that different AMF families dominated at each level of contaminant concentration. These authors found that the most contaminated soil was dominated by three phylotypes closely related to Rhizoglomus irregularis whereas these operational taxonomic units (OTUs) represented a small proportion only of the AMF sequences in uncontaminated and moderately contaminated soil. Table 3 showcases other selected AMFs and their degradation activity against PHCs.

Microorganism	Hydrocarbon	Reference
Phanerochaete Chrysosporium	Anthracene, pyrene, acenaphthene	[41]
Penicillium funiculosum	Total petroleum hydrocarbon	[64]
Beijerinckia	anthracene
Penicillium, Candida spp	PAHs	[65]
Pleurotus eryngii	Napthalene	[66]
Penicillium janthinellum strain SFU 403	Pyrene	[67]
Aspergillus terreus	Naphthalene and anthracene	[68]
Glomus intraradices	TPH	[69]
	Anthracene	[70]
Rhizophagus custos	Phenanthrene and dibenzothiophene	[71]
F. mosseae	Chrysene and dibenz[a,h]anthracene	[61]
R. irregularis	Anthracene	[72]
F. mosseae	Phenanthrene, pyrene	[73]
R. intraradices	Phenanthrene, pyrene,; dibenz(a,h)-anthracene	[74]

Table 3.

Some selected AMF with petroleum hydrocarbon degradation potential.

The co-inoculation of AMF and PGPR also holds significant ecological importance in terms of mitigating pollution and supporting a sustainable environment [34]. In a study by Dong et al. [69], it was noted that co-inoculating the PGPR Serratia marcescens BC3 and AMF Glomus intraradices had a positive impact on plant growth, antioxidant enzyme activities, and the microbial populations in the root zone of soil contaminated with petroleum. The research further pointed out that the combined inoculation resulted in a 72.24% reduction in the breakdown of total petroleum hydrocarbons compared to the individual inoculation of either AMF or PGPR. Xun et al. [75] investigated the potential of PGPR and AMF in remediating petroleum-contaminated saline-alkali soil. The findings revealed that petroleum stress hindered plant growth by triggering the accumulation of free proline and malondialdehyde (MDA), along with alterations in the activities of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase. Furthermore, soil quality was enhanced, as evidenced by increased enzyme activities (dehydrogenase, sucrase, and urease). Moreover, a high rate of hydrocarbon degradation was observed, indicating that co-inoculation with AMF and PGPR could help plants tolerate harmful hydrocarbon contaminants, improve soil structure, and remediate saline-alkali soil polluted with petroleum hydrocarbons. Recent research studies have also highlighted the promising potential of AMF and PGPR in pollution control [76, 77].

5. Benefits of rhizomicrobes in bioremediation

The advantage of rhizospheric microbes in bioremediation over other microbes lies in their close association with plant roots, which provides a unique and favorable environment for their growth and activities. This association enhances the potential of rhizospheric microbes to degrade pollutants efficiently and contributes to their overall effectiveness in bioremediation processes. The rhizomicrobe-mediated bioremediation (rhizoremediation) approach comprises a strong interaction between microbes and the plant root zone, which increases microbial activity in the rhizosphere and aids in the breakdown of organic pollutants through the activation of degradative and catalytic genes. It is an ecofriendly, cost-effective, clean, and green approach for the removal of environmental pollutants. Here are some key advantages/benefits of rhizospheric microbes in bioremediation.

5.1 Enhanced nutrient availability

The rhizosphere is a zone rich in organic matter and nutrients due to the release of root exudates by plants. This creates a favorable environment for microbial growth and activity, providing rhizospheric microbes with a continuous source of nutrients [78]. The abundance of nutrients in the rhizosphere can enhance the metabolic capabilities of these microbes and improve their efficiency in degrading pollutants. Root exudates and other organic substances generated by plants enrich the rhizosphere. Rhizospheric bacteria uses these exudates as a source of nutrients, which promotes their growth and metabolic activity [79]. The metabolic potential of some of these rhizomicrobes includes nitrogen fixation, phosphate solubilization and other activities that promote nutrient availability and uptake.

Because of the abundance of carbon in hydrocarbons, as well as the drastic reduction in rate limiting nutrients required for microbial growth after a crude oil spill, the rate and value of biodegradation have been slowed due to limited access to these nutrients, notably phosphorus and nitrogen. The development and functionality of bacteria that digest hydrocarbon compounds is greatly aided by the addition of nitrogen and phosphorus (biostimulation) [80]. This increased nutritional availability in the rhizosphere can encourage the growth and activity of microorganisms that break down pollutants. Rhizospheric bacteria control the availability of nutrients for plants and the soil microbial population by taking part in the geochemical cycling of nutrients, particularly nitrogen, phosphorus, and other micronutrients such as iron, manganese, zinc, and copper.

5.2 Root-induced changes

The root system alters the physicochemical characteristics of the soil immediately around it which confers a positive influence on the growth of specific microorganisms. These changes can also induce the expression of certain microbial genes responsible for [81]. Rhizodeposition, also referred to as root exudates, is the driving force behind the transformation of the rhizosphere environment. It encompasses a wide array of compounds released and discharged from the roots, comprising water-soluble exudates, shed cells, mucilages, lifeless tissues, and gaseous components. Soil microorganisms capable of utilizing these organic substrates tend to multiply within the roots and rhizosphere. Therefore, the makeup of exudates and other rhizodeposits will have an impact on the organization of the microbial communities adjacent to the roots of the plant. Researchers have demonstrated that root exudates aid in the recruitment of beneficial microbes directly from the soil, alter the genetic structure of the microbe based on the long-term exposure and constituent of the exudate and lastly, encourage inoculant proliferation [82, 83, 84].

Higher levels of phenolic compounds such as morusin, morusinol, and kuwanon which share similar chemical structures with PAHs can activate genes involved in pathways for the degradation of PAH-related contaminants in microbes within the rhizosphere. Mycorrhizal roots, for instance, have the natural ability to modify the genetic structure of the microbial rhizospheric community towards biodegradation of recalcitrant hydrocarbons [85].

5.3 Increased microbial diversity

The rhizosphere supports a diverse microbial community comprising bacteria, fungi, archaea, among others [86]. This high microbial diversity can be advantageous in bioremediation, as different microbial species may possess complementary metabolic pathways, enabling the breakdown of a wide range of pollutants. The presence of diverse microbial species can also contribute to the resilience and stability of the remediation process. Variation in interactions that occurs within the rhizosphere is responsible for the enormous diversity of microbes within the region. Understanding the diverse interaction strategies used by plants and their adhering microorganisms will promote plant growth and soil remediation procedures.

5.4 Enhanced biofilm formation

Rhizospheric microbes often form biofilms around plant roots. Biofilms provide a protective microenvironment for microbes, allowing them to withstand adverse conditions and access pollutants efficiently [87]. Biofilms enhance cellular communication and facilitate the exchange of genetic materials [88]. Various genera of microorganisms, including bacteria, fungi, algae, and archaea, have the capability to adhere to different surfaces and form stable biofilm structures. The formation of these biofilms relies on specific environmental factors, the presence of electron acceptors/donors, and nutrient concentrations.

Biofilm-immobilized cultures serve as highly efficient biological tools for removing pollutants in bioremediation and biotransformation processes. These structures exhibit remarkable tolerance to toxic compounds, even when substrate concentrations would be lethal to other microorganisms.

Biofilms promote the removal of pollutants and biodegradation by the accumulation of microbial biomass and immobilization of environmental pollutants. Additionally, biofilms contain exopolymeric substances (EPS) that include molecules with surfactant or emulsifier properties. These substances enhance the bioavailability of hydrophobic compounds such as hydrocarbons thereby facilitating mineralization [89].

Many physiological and physicochemical factors in biofilm mode make bacterial cells resilient and have an impact on bioremediation, such as bacterial nutrition, oxygen competition, pH and temperature conditions. Catabolite suppression by other organic compounds can reduce pollution degradation gene expression. However, biofilm-associated cells exhibit unique gene expression, which is frequently regulated by quorum-sensing systems or dormancy. This can lead to increased sensitivity to pollutants [90]. The advantage of biofilms over artificially immobilized and encapsulated cells is that the constituent cell’s high density and tolerance is obtained naturally. Thus, biofilm formation is thought to be a natural strategy of microbes to build and maintain a favorable habitat in stressed situations [89].

5.5 Enhanced degradation efficiency

Rhizospheric microbes have evolved to utilize plant-derived compounds efficiently, which can also enhance their ability to metabolize and degrade pollutants with similar chemical structures [90]. For the detoxification or reduction of the hazardous effects of PHCs in the environment, PGPR primarily employs techniques such as biomineralization, biotransformation, biosorption, and biodegradation. Microbes in this complex rhizosphere system take carbohydrates, alcohols, vitamins, proteins, and amino acids as nutrients from plant root exudates for growth and enhanced biodegradation activities [91].

5.6 Facilitation of phytoremediation

In combination with phytoremediation, where plants absorb and store pollutants, rhizospheric microbes can further enhance the breakdown of these pollutants into less toxic forms [92]. Most plants have symbiotic relationships with ectomycorrhizal fungi and/or arbuscular mycorrhiza, supports soil remediation. Furthermore, rhizosphere microorganisms such as bacteria, fungi, and nematodes can consume hydrocarbons as sources of energy and carbon, playing a critical role in the rehabilitation of contaminated soils. Bacteria are the most active hydrocarbon degraders and these bacterial groups catabolically employ naphthalene and phenanthrene or other hydrocarbons as the sole source of carbon and energy, whereas molecules that are less soluble in water, such as anthracene, pyrene, and fluoranthene, are used as growth supplies [93].

The ectomycorrhizal fungi and other rhizospheric bacteria work within the root system to enhance plant absorbent surface. They also assist in nutrient recycling and are often more resistant to abiotic stress, such as oil spill pollution. The plant roots also must be able to acclimatize and withstand the pollutants for removal to be effective [94]. Furthermore, in order to promote acclimation, growth, and development of the plant, the roots must interact with the different physical, chemical, and biological components of the impacted soil. After the acclimatization stage, the organic pollutants begin degradation through the action of microorganisms in the rhizosphere this is usually favorable for plant growth since the hydrocarbons become less toxic or harmless [93].

5.7 Plant-microbe interactions

Rhizospheric microbes have co-evolved with plants, leading to a range of beneficial interactions between the two. Plants can release specific exudates that attract and stimulate the growth of certain microbial species, which can contribute to the biodegradation of contaminants [95]. These plant-microbe interactions can create a mutualistic relationship, where plants benefit from the microbial breakdown of pollutants, while microbes gain access to nutrients released by the plants. Rhizomicrobes, such as AMF for example, are important contributors to the conversion or degradation of hazardous pollutants in the plant community [96]. “Mycorrhiza” refers to the symbiotic association between fungal cells and the roots of vascular plants. Mycorrhizal fungi decompose organic pollutants by producing organic acid and secreting numerous enzymes that hydrolyze phosphorus and nitrogen molecules [91]. They can actually act as filters for plants, using their mycelium to block hazardous chemicals. Plants respond by providing sugars and other critical macromolecules for fungal growth and maintenance.

5.8 Adaptation to soil conditions

Rhizospheric microbes are well-adapted to the specific soil conditions in the rhizosphere. They have evolved mechanisms to survive and thrive in the presence of various stressors, including pollutants [97]. This adaptation allows rhizospheric microbes to maintain their activity even in contaminated environments, making them suitable candidates for bioremediation applications. When soil becomes contaminated with hydrocarbons, the number of indigenous hydrocarbon-degrading microorganisms rapidly increases and begins to adapt to and metabolize (degrade) the pollutants. Studies have shown that this strategy is effective in degrading 25% of hydrocarbon pollutants in soil and sometimes even more [98]. Based on their unique metabolic pathways, the indigenous microorganisms use hydrocarbon pollutants as the sole carbon and energy sources during this process [99].

6. Conclusion

In light of the highlighted increasing threats posed by hydrocarbon pollution to both environmental sustainability and food security, the imperative for the development of effective and eco-friendly remediation approaches cannot be over-emphasized. Bioremediation has emerged as a highly promising alternative due to its proven capacity to target a broad range of hydrocarbons and sustainable features. However, the utilization of rhizospheric microorganisms as potent agents for bioremediation offers more distinct advantages in enhancing the efficiency of bioremediation which surpasses the capabilities of microorganisms present in the bulk soil. These microorganisms, in addition to their pollution-degrading capabilities, exhibit other valuable attributes that foster and sustain bioremediation, seamlessly also complementing phytoremediation techniques. These attractive qualities gives the rhizospheric microbes the selective advantage to not only remediate hydrocarbon polluted soils but also promote ecorestoration and sustainability of the environment. Ongoing research and innovation in this field are poised to offer even more effective and comprehensive solutions for addressing the underlying challenges associated with petroleum hydrocarbon pollution and environmental degradation in the years ahead.