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Review

Role of Natural and Modified Clay Minerals in Microbial Hydrocarbon Biodegradation

by
Lei Li
* and
Chunhui Zhang
School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, China
*
Author to whom correspondence should be addressed.
Minerals 2025, 15(11), 1120; https://doi.org/10.3390/min15111120 (registering DOI)
Submission received: 23 September 2025 / Revised: 24 October 2025 / Accepted: 25 October 2025 / Published: 27 October 2025
(This article belongs to the Section Clays and Engineered Mineral Materials)
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Abstract

Microbial hydrocarbon degradation mediated by natural/modified clay minerals represents an eco-friendly and economically viable remediation strategy for hydrocarbon contamination. However, its effects are not always positive as they depend on multiple factors, including clay mineral types, modification methods, microbial species, and hydrocarbon substrates. This review systematically synthesizes existing fragmented studies concerning the impacts of natural clay minerals, modified clay minerals (acid/alkali/thermal/organic/metal ion), and clay minerals containing composite materials on microbial hydrocarbon biodegradation. Based on current findings, future research should prioritize the following recommendations: (1) avoid using concentrated strong acids in acid activation; (2) exclude metal cations that induce strong adsorption (reducing hydrocarbon bioavailability) or trigger excessive interlayer hydrolysis (some trivalent cations) in metal cation modification; (3) eliminate biologically toxic agents during organic modification; and (4) expand understanding of alkali/thermally modified clay minerals and clay mineral-containing composite materials in this direction. Natural/modified clay mineral-mediated microbial degradation is a highly promising remediation technology for hydrocarbon contamination and poised to advance and achieve breakthroughs through continuous synthesis of knowledge and innovation.

1. Introduction

Hydrocarbons, indispensable strategic resources for modern societal development, play a pivotal role in global industrial operations, economic propulsion, and innovation-driven growth. However, hydrocarbon contamination poses a severe environmental challenge, persistently threatening ecosystems and public health [1]. Hydrocarbon contamination originates from diverse sources [2], with industrial and petroleum activities estimated to accidentally release 1.7 × 106–8.8 × 106 metric tons of oil annually into the environment [3], leaving numerous contaminated sites requiring remediation. Additionally, natural sources such as volcanic activity, marine oil seeps, and biogenic emissions [2] continuously contribute hydrocarbons to the environment. These contaminants endanger residents in affected areas by polluting groundwater, crops, and air [4,5]. Their accumulation in soils disrupts soil structure and fertility, leading to arable land degradation, reduced crop yields, and biodiversity loss [6]. Recent studies confirm significant contaminant migration between groundwater and hosting soils [7,8]. Current methods for treating hydrocarbon contaminations include biological, physicochemical, chemical, and physical (thermal, electrical (electromagnetic), and acoustic (ultrasonic)) treatment approaches [9].
Natural biodegradation is typically enhanced via the addition of nutrients, such as oxygen, nitrogen, phosphorous (biostimulation), or specialist microorganisms (bioaugmentation) [9]. Clay-mediated microbial hydrocarbon degradation has emerged as one of the most promising biostimulation approaches due to its eco-friendliness, cost-effectiveness, and demonstrated effectiveness. Clay minerals typically exhibit key properties, such as a large specific surface area [10], high cation exchange capacity [11], swelling behavior [12,13], fine particles [14], and unique microstructures [15], which collectively create favorable conditions for microbial degradation. Firstly, these properties enable clay minerals to provide nutrient provision, physical protection, microenvironment regulation (moisture and pH control), and metabolic enhancement (catalysis and electron transfer) [16]. Additionally, clay surfaces serve as attachment sites for hydrocarbons and microorganisms, further forming oil–clay–bacteria aggregates with the aid of the sticky extracellular polymeric substances [17], a process that ultimately promotes microbial degradation. Finally, fine particles of clay minerals may act as surfactants and stabilize the oil–water interface, thus leading to the formation of what is known as Pickering emulsions [14]. The biodegradation of Pickering emulsions depends on the physicochemical interactions (attraction or repulsion) between clay particles and bacteria.
Despite these advantages, the inherent hydrophilicity of clay mineral surfaces under most natural conditions [18,19] can hinder hydrocarbon adsorption. Owing to the structural properties of clay minerals that inherently facilitate their modifications [18,19], various modification techniques have been explored to optimize clay-mediated microbial hydrocarbon degradation, including acid/alkali activation, thermal/metal cation/organic modification, and engineered clay-containing composite materials. Unlike conventional modified clay materials used in environmental remediation—which primarily focus on pollutant adsorption [19,20,21]—this approach must also account for microbial activity. Inappropriate modifications may enhance hydrocarbon adsorption, but simultaneously reduce bioavailability [22] or introduce biotoxicity [23], ultimately impairing hydrocarbon degradation efficiency.
While clay-mediated microbial hydrocarbon degradation generally yields positive outcomes, negative effects have also been documented. This review systematically synthesizes fragmented existing research to elucidate the dual regulatory mechanisms of natural/modified clays in either stimulating or inhibiting hydrocarbon biodegradation, thereby providing guidance for future studies.

2. Natural Clay Minerals

According to existing research, montmorillonite exhibits a stimulating effect on microbial degradation of hydrocarbons, regardless of the degraders (microbial consortia from different locations or specific microorganisms) or the types of hydrocarbons (heavy oil, crude oil, saturated hydrocarbons, aromatic hydrocarbons, or specific hydrocarbons) (Table 1). Additionally, although studies on vermiculite, nontronite, and bentonite are limited, they all demonstrate a stimulatory effect (Table 1). Palygorskite and saponite show either stimulation or neutral effects (neither stimulation nor inhibition), whereas kaolinite exhibits variable effects—either stimulation or inhibition—depending on degradation conditions (hydrocarbon types and degraders) (Table 1). This variation may be attributed to differences in the structural characteristics and surface properties of the clay minerals (Table 2 and Figure 1).
Montmorillonite is a 2:1-type clay mineral (composed of two layers of silicon–oxygen tetrahedra and one layer of aluminum–oxygen octahedra), characterized by large specific surface area, strong cation exchange capacity, and high expansibility (Table 2). Typically, a high specific surface area facilitates the adsorption of microorganisms and hydrocarbon molecules, thereby enhancing bioavailability. The high cation exchange capacity and water-swelling characteristics, inherent to its 2:1-type layered structure, collectively indicate the presence of abundant exchangeable cations. These cations serve a dual purpose: they can be utilized by microorganisms to stimulate metabolic activity and enhance bioactivity, while also providing crucial support for the adsorption processes of both microorganisms and hydrocarbon molecules. In contrast, kaolinite is a 1:1-type clay with tightly bonded layers via hydrogen bonds, resulting in high bond energy that prevents water molecules from entering the interlayer space. Thus, kaolinite exhibits no expansibility, small specific surface area, and weak cation exchange capacity (Table 2 and Figure 1). The properties of other clay minerals fall between those of montmorillonite and kaolinite. For instance, vermiculite, which also possesses a 2:1 layered structure but exhibits a lower cation exchange capacity, and fibrous-structured minerals like palygorskite and attapulgite all demonstrate distinct specific surface areas and cation exchange capacities (Table 2). From this, we can infer that among natural clays, 2:1-type clays with larger surface areas and stronger cation exchange capacities are more likely to enhance microbial hydrocarbon degradation.
However, a more detailed study revealed that illite could stimulate Pseudomonas stutzeri in degrading 45 aromatic hydrocarbons in heavy oil while inhibiting its degradation of 50 other aromatic hydrocarbons and all 64 saturated hydrocarbons. This observation aligns with the structural variations of hydrocarbons [24]. Unlike typical 2:1 clays, illite contains fixed K+ ions in its interlayer space, leading to low specific surface area and weak cation exchange capacity (Table 2)—properties closer to kaolinite. The differential effects of illite on microbial degradation of various hydrocarbons suggest that the influence mechanisms of clay minerals may be more complex than currently observed, necessitating simultaneous consideration of factors such as clay type, hydrocarbon structure, microbial degraders, and environmental variations.
Researchers are spurred by three key challenges: pursuing higher degradation efficiency, solving practical engineering problems, and tackling complex hydrocarbon contamination in various environments. These challenges motivate their investigation into how modified clay minerals (Figure 1) affect the microbial degradation process.
Table 1. Effects of natural clay minerals on microbial hydrocarbon degradation.
Table 1. Effects of natural clay minerals on microbial hydrocarbon degradation.
YearClay
Mineral		SubstrateDegraderEffectRef.
1997Mixed clayCrude oilMicrobial
community		Stimulation for saturated hydrocarbons (23%), neutral for aromatic hydrocarbons[25]
2005KaoliniteHeavy oilMicrobial
community		Stimulation[26]
2005MontmorilloniteHeavy oilPseudomonas aeruginosa + microbial communityStimulation[27]
Kaolinite
2009MontmorilloniteHeavy oilMicrobial
community		Stimulation (62.9%–78.4%)[28]
2009VermiculiteNaphthalene, anthraceneMicrobial
community		Stimulation (11%–77%)[29]
2013MontmorilloniteCrude oilMicrobial
community		Stimulation (30%)[30]
2014MontmorilloniteSaturated
hydrocarbons		Microbial
community		Stimulation (78.4)[31]
PalygorskiteStimulation (75.9%)
SaponiteNeutral
KaoliniteInhibition (5.5%)
2014SaponiteCrude oilMicrobial communityStimulation (9%–12%)[32]
2014KaoliniteCrude oilMicrobial communityInhibition (−1%)[33]
PalygorskiteStimulation (17%)
SaponiteNeutral
MontmorilloniteStimulation (22%)
2014MontmorilloniteCrude oilMicrobial communityStimulation (22%)[22]
2014MontmorillonitePhenanthrene and dibenzothiopheneMicrobial communityStimulation (28%–43%)[34]
2016BentoniteCrude oilMicrobial communityStimulation[35]
Kaolinite
2017PalygorskitePhenanthrene(C14)Burkholderia sartisoliStimulation (66%–69%)[36]
2017MontmorillonitePhenanthrene(C14)Burkholderia sartisoli +
microbial community		Stimulation (8% and 5% for montmorillonite and saponite)[37]
Palygorskite
2017MontmorillonitePolycyclic aromatic hydrocarbons (PAHs)Microbial communityNeutral for low-weight PAHs, stimulation for high-weight PAHs[38]
Saponite
2017MontmorilloniteAromatic hydrocarbons in crude oilMicrobial communityStimulation[39]
Saponite
Palygorskite
KaoliniteInhibition
2018KaolinitePhenanthreneSphingomonas sp. GY2BStimulation (13%)[40]
2018NontroniteCrude oilAlcanivorax borkumensisStimulation (12.3%)[41]
2018BentoniteAromatic hydrocarbons and cadmium contaminated soilMicrobial communityStimulation (23.6%)[42]
2018PalygorskiteCrude oil contaminated soilMicrobial communityStimulation (12.3%)[43]
2023IlliteHeavy oilPseudomonas stutzeriInhibition (−5.1%–9.8%)[24]
Table 2. Structure and properties of different natural clay minerals [41,44,45].
Table 2. Structure and properties of different natural clay minerals [41,44,45].
Clay TypesStructural FeaturesSize Range (Typical, µm)Zeta Potential (Typical, in Water, mV)Property
Kaolinite1:1 layered (T-O) with strong hydrogen bonds between layersDiameter: 0.2–2
Thickness: 0.05–0.2		−40–−20Low cation exchange capacity, small specific surface area
Montmorillonite2:1 layered (T-O-T) with octahedral alumina sandwiched between tetrahedral silica sheetsDiameter: 0.1–1
Thickness: 1 (monolayer)		−40–−25High cation exchange capacity, expandable interlayers, and adsorption dominated by cation exchange
BentoniteParticle Size: 1–100 (raw ore)−50–−20
Vermiculite2:1-type, negatively charged surfaces Flake Diameter: –1–10 (raw ore)Negative charge
(variable, often close to −25)		Moderate cation exchange capacity
Palygorskite2:1 (T-O-T) layer chain with zeolitic water channelsLength: 0.5–5
Diameter: 10–50		−30–−15Fibrous, high specific surface area, M-OH groups
Attapulgite
SaponiteTrioctahedral 2:1 smectiteDiameter: 0.01–1−50–−30Swelling properties
Nontronite2:1-typeDiameter: 0.1–1−50–−30High specific surface area, belonging to Fe–smectite
Illite2:1 layered with K+ locked in interlayersDiameter: 0.1–5 µm
Thickness: 10–50 nm		−40–−25Low cation exchange capacity due to fixed K+, limited specific surface area
Minerals 15 01120 g001
Figure 1. Schematic of modification mechanisms of clay minerals (acid, alkali, thermal, organic, and metal cation modification) [18,20,21,46,47]. Note: 1. Acid activation: Dissolution of crystal framework with leaching of interlayer cations, resulting in enhanced surface acidity, specific surface area and porosity. 2. Alkali activation: Cleavage of Si–O–Si bonds generates reactive Si–O− sites through depolymerization of inert siloxane bonds accompanied by interlayer expansion creating new adsorption sites. 3. Thermal modification: Removal of physically adsorbed water and bound water leads to formation of silanol groups, followed by silylation reaction. 4. Organic modification: Intercalation of organic molecules expands interlayer spacing while replacing surface/interlayer cations, introducing hydrophobic adsorption sites. 5. Metal cation modification: Substitution of native interlayer ions with new metal cations.
Figure 1. Schematic of modification mechanisms of clay minerals (acid, alkali, thermal, organic, and metal cation modification) [18,20,21,46,47]. Note: 1. Acid activation: Dissolution of crystal framework with leaching of interlayer cations, resulting in enhanced surface acidity, specific surface area and porosity. 2. Alkali activation: Cleavage of Si–O–Si bonds generates reactive Si–O− sites through depolymerization of inert siloxane bonds accompanied by interlayer expansion creating new adsorption sites. 3. Thermal modification: Removal of physically adsorbed water and bound water leads to formation of silanol groups, followed by silylation reaction. 4. Organic modification: Intercalation of organic molecules expands interlayer spacing while replacing surface/interlayer cations, introducing hydrophobic adsorption sites. 5. Metal cation modification: Substitution of native interlayer ions with new metal cations.
Minerals 15 01120 g001

3. Acid-Activated Clay Minerals

Acid-activated clay minerals are prepared by washing or treating the clay minerals with strong inorganic acids (e.g., sulfuric or hydrochloric acid [30]) or organic acids (e.g., stearic acid [48]). This chemical treatment, termed acid activation, acid washing, or dissolution, involves proton exchange between the acid and interlayer cations (e.g., Mg2+, Al3+, Fe3+), followed by partial dissolution of the clay crystalline framework through cation leaching. The resulting product exhibits enhanced surface acidity, specific surface area, and porosity [21,48,49,50,51] (Figure 1). Under natural environmental conditions, the acid attack (e.g., acid mine drainage) on clay mineral can also lead to the formation of acid-activated clay minerals [52].
Although acid-activated clay mineral possesses a greater specific surface area, most studies demonstrate that microbial hydrocarbon degradation is instead inhibited (Table 3). This phenomenon may result from the concurrent pH reduction in the biodegradation system induced by acid-activated clay mineral, where the inhibitory effect of surface acidity dominates over the stimulatory effect of increased surface area. This explains why successful stimulation of microbial hydrocarbon degradation was achieved under conditions of lower acid concentration [37] and weaker acidity [48] (Table 3).
In fact, acid-activated clay minerals are widely applied in environmental fields due to their enhanced specific surface area, which facilitates the adsorption of hazardous substances (e.g., heavy metals and organic pollutants) [21]. However, when considering microbial degradation, their potential impacts on microbial metabolic activity must be carefully reevaluated. Current research suggests that modifying clays with low-concentration inorganic acids, organic acids, or surfactant-combined modification approaches [53] may be more microbially friendly and could potentially stimulate hydrocarbon biodegradation.
Table 3. Studies on the effects of acid-activated clay minerals on microbial degradation of hydrocarbons.
Table 3. Studies on the effects of acid-activated clay minerals on microbial degradation of hydrocarbons.
YearClayAcidModification MethodsHydrocarbonDegraderResultRef.
2013MontmorilloniteHClClay:HCl (3 mol/L) = 1:3 (w/w),
70 °C for 45 min		Saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes in crude oilMicrobial communityInhibition[54]
2013MontmorilloniteHClClay:HCl (3 mol/L) = 1:3 (w/w),
70 °C for 45 min		Steranes, diasteranes, and hopanesMicrobial communityNo effect[30]
2014MontmorilloniteHClClay:HCl (3 mol/L) = 1:3 (w/w),
70 °C for 45 min		C1-phenanthrenes,
C1-dibenzothiophenes,
C2-phenanthrenes,
C2-dibenzothiophenes		Microbial communityInhibition (−6%)[34]
2014Montmorillonite
Palygorskite Saponite
Kaolinite		HCl2 mol/L HCl for saponite, 3 mol/L HCl for palygorskite and montmorillonite, 4 mol/L HCl for kaolinite (70 °C for 45 minCrude oilMicrobial communityInhibition (−13%, −13%, −8% and −13% for acid-activated montmorillonite, palygorskite, saponite, kaolinite)[33]
2014Montmorillonite
Palygorskite Saponite
Kaolinite 		HClClay:HCl (3 mol/L) = 1:3 (w/w), 70 °C for 45 minSaturated hydrocarbonsMicrobial communityInhibition[31]
2017MontmorilloniteHClClay:HCl (3 mol/L) = 1:3 (w/w), 70 °C for 45 min11 polycyclic aromatic hydrocarbonsMicrobial communityInhibition[39]
Palygorskite
Saponite
Kaolinite
2017Palygorskite
Saponite		HClClay:HCl (0.5,1 and 3 mol/L) = 1:3 (w/v)
75 °C for 45 min		PAHsMicrobial community +Only the 0.5 mol/L HCl treatment showed stimulation[37]
Burkholderia sartisoli
2018MontmorilloniteStearic acidStirred in 0.91% (w/v) stearic acid (ethanol-water, 1:1 v/v) at 50 °C for 4 hPhenanthreneSphingomonas sp. GY2BStimulation[48]

4. Alkali-Activated Clay Minerals

Acid activation may enrich clay minerals with H+ ions, creating an environment potentially incompatible with microbial growth [33]. In contrast, alkaline cations may stimulate microbial colonization by forming cation bridges between clay mineral surfaces and bacterial cells [28]. These cations may also enhance the retention of polycyclic aromatic hydrocarbons on clay surfaces through electrostatic attraction or cation–π bonding [46,53,55]. Additionally, acid activation primarily removes Mg2+ or Al3+ ions, but does not dissolve Si [56,57]. Conversely, alkali activation exhibits stronger corrosion capability toward metal cations and can disrupt Si–O–Si bonds [58], generating new Si–O− active sites by breaking inert siloxane linkages [59] (Figure 1). Furthermore, the alkali-activated clay mineral biotite may develop new adsorption sites due to interlayer expansion [60] (Figure 1). Although acid activation generally increases the specific surface area of clay minerals more significantly than alkali activation, the aforementioned advantages make alkali-activated clay minerals a promising research direction for hydrocarbon biodegradation.
Unfortunately, current research on the effects of alkali-modified clays on microbial hydrocarbon degradation remains limited. To date, only Biswas et al. have reported the influence of NaOH (0.5–3 mol/L)-activated palygorskite and saponite on phenanthrene degradation by a microbial community (supplemented with Burkholderia sartisoli) [37]. Their results demonstrated that NaOH-activated palygorskite and saponite simultaneously enhance bacterial growth and polycyclic aromatic hydrocarbon biodegradation [37]. Unlike acid-activated clay minerals, even high-concentration alkaline activation (3 mol/L) of clays does not inhibit microbial growth, highlighting a key advantage of alkali activation.

5. Thermally Modified Clay Minerals

The purpose of thermally modifying clay minerals, similar to other modification methods, is to regulate the properties of clay materials to enhance microbial hydrocarbon degradation. A key advantage of thermal modification is that it does not require chemical agents, which may have harmful environmental impacts [61] or unknown ecological effects.
Thermal modification is considered a simple, mild, cost-effective, yet efficient technique for modifying clay minerals [62]. Thermal modification entails heating natural clay minerals to a target temperature for a specified duration. Studies confirm that this process markedly alters the distribution of hydrated species on clay surfaces and modifies key reactive sites, thereby influencing surface-mediated reactions such as adsorption [18] (Figure 1). For palygorskite, both physisorbed and zeolitic water can be removed at temperatures up to 200 °C [63], resulting in enhanced specific surface area. Structural hydroxyl groups begin decomposing above 400 °C, causing progressive lattice distortion. Subsequent irreversible dehydration and Mg-OH dehydroxylation above 750 °C induce channel shrinkage, ultimately leading to complete structural collapse at 1000 °C and transformation into amorphous phases with minimal specific surface area [21,64]. For smectite, the specific surface area exhibited a monotonic decrease with increasing preheating temperature, concomitant with substantial alterations in phase composition and structural integrity. Thermal modification above 149.85 °C (423 K) induced desorption of surface-adsorbed gases and physisorbed water, thereby exposing additional free active sites and enhancing the material’s adsorption capacity [65] (Figure 1). Thermal modification of bentonite and kaolinite induces significant modifications in their surface properties. The specific surface area of bentonite initially increases at 100 °C through desorption of physisorbed water and volatile impurities [66]. However, progressive heating to 500 °C leads to substantial specific surface area reduction [67] resulting from sequential dehydroxylation processes: initially in kaolinitic minerals, followed by montmorillonitic minerals at 750 °C [68]. The extent of specific surface area variation is governed by the mineralogical composition and geological provenance of the clay materials, whereas structural transformations exhibit strong dependence on thermal exposure duration [69].
Although studies on pollutant adsorption by thermally modified clays are abundant [18,21], research applying such clays to microbial hydrocarbon degradation remains scarce. Biswas first investigated the influence of thermally modified palygorskite on the viability of polycyclic aromatic hydrocarbon-degrading bacteria (Burkholderia sartisoli) [62], finding that the maximum viability was imparted by the palygorskite product obtained at 400 °C, while dissolution of Al from products heated above 500 °C posed inhibitory effects on bacterial growth in aqueous media [62]. Extending these findings, subsequent research on phenanthrene degradation by Burkholderia sartisoli revealed that 400–modified palygorskite exhibited reduced binding sites, weakening phenanthrene sequestration in its surface and pores, consequently increasing total phenanthrene biomineralization by 20–30% (p < 0.05) [36].

6. Metal Cation-Modified Clay Minerals

Metal cation-modified clay minerals are typically synthesized through cation exchange reactions by replacing interlayer cations in natural clays with target metal cations (Figure 1). Specifically, when this process occurs in montmorillonite, the resulting product is termed homoionic montmorillonite [22,34,70]. During clay formation, octahedral Al3+ undergoes isomorphous substitution by lower-valence cations (Fe2+, Mg2+, and Mn2+), creating a permanent negative charge imbalance in the layered structure. This charge deficiency is compensated by the intercalation of hydrated exchangeable cations such as Na+, Ca2+, and K+. These weakly bound cations display dynamic exchangeability with external solution-phase ions, endowing clay minerals with dual capabilities: natural sequestration of metal/inorganic cations from external environments, and engineered modification through targeted cation exchange reactions with organic/inorganic species [19].
Under normal circumstances, both Gram-negative and -positive bacteria possess a relative negative charge on their cell surface due to the presence of proton-active functional groups (e.g., hydroxyl, carboxyl, phosphoryl, and amide groups) [71]. This facilitates adsorption by combining with the positive charges on clay mineral surfaces, thereby enhancing hydrocarbon bioavailability. The cation modification process can neutralize the negative charges on clay surfaces, altering their structural and physicochemical properties, which in turn affects microbial–hydrocarbon interactions [72,73]. On the other hand, exchangeable divalent cations exhibit a “local bridging effect,” which explains why certain clay mineral samples are more effective in promoting the biodegradation of crude oil hydrocarbons [28]. Certain hydrocarbon compounds, particularly aromatic hydrocarbons containing π-electrons, can form cation–π interactions with metal cations [55] (Figure 1). This molecular interaction enhances the adsorption of hydrocarbons into clay minerals, potentially increasing their microbial bioavailability and thereby facilitating biodegradation.
Metal cation modification exhibits both promotive and inhibitory effects on microbial hydrocarbon degradation. For instance, Zn- and K-montmorillonites strongly adsorb hydrocarbons, potentially reducing hydrocarbon bioavailability to microorganisms and thus suppressing biodegradation (Table 4). However, Na-, Ca-, and Fe-montmorillonites with relatively high surface area and cation exchange capacity were observed to stimulate hydrocarbon biodegradation [22] (Table 4). Although the “local bridging effect” of clay minerals are critical factors enhancing hydrocarbon biodegradation [28], the interlayer trivalent cations—which impart the most significant local bridging effect (a promotive factor)—also induce the highest degree of interlayer water hydrolysis (an inhibitory factor). Under such conditions, the hydrolysis of interlayer water by trivalent cations, which generates protons and increases medium acidity [74,75], is hypothesized to inhibit hydrocarbon biodegradation (Table 4).
Wang et al. [77] proposed that metal cation-modified clay minerals can form efficient electron transfer networks with microorganisms, thereby enhancing the degradation process. Concurrently, specific cations (e.g., Fe3+) can stimulate the activity of key enzymes such as peroxidases and dioxygenases. These combined effects synergistically promote microbial hydrocarbon degradation. The variations in electron transfer efficiency induced by different metal cations, along with their differential stimulation of enzymatic activity, collectively contribute to the observed macroscopic differences in microbial hydrocarbon degradation efficiency across various metal-modified clay minerals.

7. Organically Modified Clay Minerals

Most natural aluminosilicate clays exhibit strong hydrophilicity, leading to low adsorption capacity for hydrophobic hydrocarbons. However, through surface modification with organic compounds, these materials can be engineered to achieve significantly enhanced sorption performance for hydrocarbons. The resulting functionalized materials are termed organically modified clay minerals [19]. In environmental applications, the most commonly used chemical agents for organic modification of clays include surfactants, polymers, and organosilanes [18,20]. Interlayer cations are crucial in surfactant modification due to their ability to exchange with organic cations, facilitating surfactant intercalation into clay interlayers. Some surfactants also adsorb onto clay surfaces, creating additional adsorption sites [78] (Figure 1). Since clays are inherently negatively charged, cationic surfactants are more widely studied than anionic or non-ionic types. Common cationic surfactants include quaternary ammonium salts, quaternary phosphonium salts, pyridinium salts, amino acid-based surfactants, and imidazolium salts. Modifiers such as cetyltrimethylammonium and hexadecyltrimethylammonium bromide significantly enhance the hydrocarbon adsorption capacity of modified clay minerals [79]. The replacement of interlayer cations by cationic surfactants introduces new functional groups, increasing available adsorption sites [80] (Figure 1).
Polymer modification is recognized as one of the most effective approaches to significantly enhance the adsorption performance of clay minerals by introducing functional groups (e.g., hydroxyl, carboxyl, and amino) onto clay surfaces or interlayers through dissociation or polymerization processes [81,82]. This modification enables the formation of specific interactions between clays and contaminants, thereby achieving strong adsorption or even selective adsorption. Organosilane modification is typically achieved by grafting organosilanes onto clay [83]. The alkoxy groups of organosilanes undergo hydrolysis to form silanol groups, which then participate in condensation reactions with the clay. Silanol groups can also form hydrogen bonds with hydroxyl groups on the clay surface [84]. The diverse functional groups of organosilanes provide clay with broader functionalization possibilities [85].
However, the influence of organically modified clay minerals on microbial hydrocarbon degradation does not always yield satisfactory outcomes (Table 5). This is primarily due to the need to balance adsorption performance with biological activity, as most chemical modifiers exhibit varying degrees of toxicity to microorganisms. Hexadecyltrimethylammonium (HDTMA) bromide and didecyldimethylammonium (DDDMA) bromide are two chemical compounds extensively tested for enhancing hydrocarbon biodegradation through organoclay modification (Table 5). Overall, organically modified clay minerals exhibit both stimulatory and inhibitory effects on microbial crude oil degradation, with neither outcome being uncommon (Table 5).
The inhibition of microbial hydrocarbon degradation by organically modified clay minerals may be attributed to four primary mechanisms. First, the desorption of chemical modifiers (e.g., HDTMA, DDDMA) from the organoclay may desorb toxic compounds that suppress microbial activity [23]. Second, the enhanced hydrophobicity of organically modified clay minerals results in strong adsorption of hydrocarbons onto the clay surface, significantly reducing their bioavailability [54]. Third, organic cations compete with hydrocarbon molecules for adsorption sites, thereby limiting microbial access to the hydrocarbons. Fourth, the replacement of interlayer cations during organic modification eliminates the “local bridging effect” that originally facilitated microbial interaction with nutrients, consequently diminishing microbial metabolic activity [31].
In positive cases, most studies utilized various chemical modifiers for clay mineral modification (e.g., octadecylamine, palmitic acid, among others). The enhanced biodegradation of hydrocarbons primarily resulted from microbial-friendly properties, most suitable adsorption (neither excessive nor insufficient), pH regulation, stimulation of microbial enzyme activity, and other contributing factors [47]. It is evident that the effectiveness of organically modified clay minerals is influenced by a combination of multiple factors, including but not limited to the type of organic modifier, modification method, hydrocarbon species (and other co-contaminants), and microorganisms. This field warrants further systematic investigation and exploration.

8. Clay Mineral-Containing Composite Materials

The core objective of material modification lies in performance enhancement, yet its achievable ceiling remains fundamentally governed by the intrinsic physicochemical properties of clay minerals. Contemporary research has progressively shifted toward developing clay-incorporated composite systems for enhanced microbial hydrocarbon degradation, where clay minerals transition from serving as primary matrices to functional additives. This paradigm shift has spurred the creation of composite materials containing clay minerals. These composites effectively overcome the inherent limitations of pristine clay minerals. Examples include clay mineral–biochar composites and nano-attapulgite–hydrophilic urethane foam hybrids (Table 6). These clay-containing composite materials typically exhibit not only the hydrocarbon-degrading microbial enhancement effects characteristic of natural/modified clays, but also incorporate additional practical functionalities. These include engineered capabilities such as marine surface flotation [41] or integration into filtration systems [89] to facilitate microbial hydrocarbon degradation.
Biochar, a porous and carbon-rich solid material produced through pyrolysis of biomass under oxygen-limited conditions, has garnered significant attention due to its eco-friendly nature and cost-effectiveness [90,91]. It exhibits large surface area, chemical durability, and excellent adsorption capacity. The influence of biochar on microorganisms is generally manifested in three aspects: microbial biomass, microbial activity, and microbial abundance and diversity [92]. Successful cases have been reported regarding the combination of biochar with clay minerals in enhancing microbial degradation of hydrocarbons [93], demonstrating considerable potential that warrants further attention.
Table 6. Studies on the effects of clay mineral-containing composite materials on microbial degradation of hydrocarbons.
Table 6. Studies on the effects of clay mineral-containing composite materials on microbial degradation of hydrocarbons.
YearClay MineralsMain CompositionPreparation MethodMechanism and ResultRef.
2003MontmorilloniteTrimethyl octadecylammonium cation, polylactideNanocomposites were prepared by melt extrusion of polylactide and montmorillonite modified with trimethyl octadecylammonium cationThe hydroxyl groups at the edges of silicate layers induce heterogeneous hydrolysis of polylactide, accelerating its biodegradation.[94]
2015VermiculiteEcobrasTM (polyester and starch), tetrabutyl phosphonium bromideDifferent formulations were mixed and melted at 140 °C for 8 minHigh cation exchange capacity and porous structure promote microbial colonization, ensuring material integrity while significantly enhancing microbial immobilization and polymer degradation capabilities.[95]
2016BentoniteCationic surfactant, palmitic acidMix cationic surfactant and bentonite, add mixture to ethanol-dissolved palmitic acid (ethanol–water mixture (1:1)), stir 4 h at 25 °CSurface engineering enables carboxyl-specific cadmium adsorption to reduce toxicity while retaining phenanthrene bioavailability on hydrophobic surfaces, offering a solution for Cd-PAHs co-contamination.[53]
2018NontroniteNa-carboxymethyl cellulose, organoclay (Tixogel VP)Mixing, forming, and sterilizationNontronite flakes enhances oil biodegradation (by Alcanivorax borkumensis) primarily through physical adsorption and sustained nutrient supply in marine oil spill remediation.[41]
2019Nano attapulgiteHydrophilic urethane foamsIncorporation of nano-attapulgite during hydrophilic urethane foam formation to create porous matrix (200–500 μm)Enhanced surface area, improved mass transfer performance, and enriched hydrocarbon-degrading bacteria consortium achieved 99.73% COD removal and 97.48% ammonium nitrogen removal efficiency.[89]
2021NontroniteNa-carboxymethyl cellulose, talc, organoclay (Tixogel VP)Mixing raw materials with different formulations, ultrasonic dispersion, drop-casting molding, drying and peelingMaintains long-term buoyancy stability in saline water, reduces oil film coverage to 6% within 5 weeks, and simultaneously enhances microbial growth by 44%–162%[96]
2023Clay (unspecified type, collected from Liaohe Estuarine wetland, China)BiocharMix clay, 15% biochar (reed straw pyrolyzed at 600 °C for 3 h under oxygen-limited conditions), 3% Na2SiO3, and 3% NaHCO3, then press into composite particles.Immobilized Flavobacterium mizutaii sp. and Aquamicrobium sp. to remove ammonia nitrogen and petroleum hydrocarbons[93]
2024AttapulgiteAlginateAdding 1% (w/v) CaCl2 to a solution containing polyvinyl alcohol (1% w/v), sodium alginate (2% w/v), and attapulgite (1% w/v) after microbial inoculationImmobilized microbial cells provide the optimal degradation environment[97]

9. Discussion

While clay minerals exhibit a range of unique properties and functions (as detailed in the Introduction), their fundamental role in the process of microbial hydrocarbon biodegradation is essentially mediated through influencing bioactivity and bioavailability. Alterations in bioavailability are primarily exerted by affecting the adsorption sites or states (e.g., aggregation or dispersion) of both microbial cells and organic hydrocarbon molecules.
The adsorption of microorganisms onto the surfaces of natural clay particles enhances the availability of essential mineral nutrients, water, and cations. This process also improves microbial resilience against pH fluctuations and mitigates other adverse environmental influences [98]. Within a certain threshold, these combined effects increase overall bioactivity, thereby stimulating the microbial degradation of hydrocarbons. Furthermore, the formation of biofilms promotes the development of clay–microorganism aggregates, which further enhances bioactivity. However, when the concentration of mineral particles increases beyond a specific value [99] or microbial accumulation becomes excessive, the diffusion of nutrients and gases to the interior cells can be impeded [100], leading to a decline in bioactivity. Additionally, the adsorption of organic substrates (such as proteins, peptides, amino acids, polysaccharides, nucleic acids, and nucleotides) onto clay mineral surfaces can render them less accessible for microbial utilization [100], which also suppresses microbial bioactivity. Clay particles adsorb not only microbial cells but also organic hydrocarbon molecules, leading to the formation of clay–microorganism–hydrocarbon aggregates. Under such conditions, an increase in bioactivity is typically accompanied by a corresponding enhancement in bioavailability. Moreover, Pickering emulsions, stabilized by clay particles, increase bioavailability by effectively dispersing hydrocarbon molecules.
Currently, clay modification techniques are typically only capable of enhancing a specific aspect of clay mineral properties and often fail to concurrently and significantly improve both bioactivity and bioavailability during microbial hydrocarbon biodegradation. For instance, acid activation significantly increases the specific surface area, thereby enhancing bioavailability. However, the concomitant increase in acidity often inhibits microbial bioactivity. Thermal modification can enlarge the specific surface area and create additional adsorption sites, which improves bioavailability. Conversely, this process may release toxic aluminum species that are detrimental to microorganisms, thereby reducing bioactivity. Additionally, excessively high temperatures can paradoxically reduce the specific surface area. Organic modification introduces hydrophobic adsorption sites, increasing the sorption capacity for hydrocarbons and thus bioavailability. Nevertheless, the potential desorption of some organic agents introduces toxic compounds that suppress bioactivity. Moreover, excessively strong adsorption of organic molecules can hinder their subsequent microbial degradation, ultimately limiting bioavailability. Cationic modification introduces additional cations that promote the adsorption of both microorganisms and hydrocarbon molecules onto the clay particle surfaces, thereby enhancing bioavailability. However, certain cations exhibit overly strong adsorption, which can conversely restrict bioavailability. Furthermore, some trivalent cation-modified clays can increase medium acidity, inducing biotoxicity and consequently reducing bioactivity. Research on alkali-modified clays is relatively limited. Currently, they do not appear to exhibit the significant drawbacks mentioned above. Their ability to increase specific surface area and create adsorption sites warrants further investigation within a broader range of conditions.
Based on the current understanding of modified clays, a comprehensively efficient and ideal modification method remains an area for continued exploration. However, current strategies can strategically leverage the distinct advantages of various modification techniques to address specific pollutants or practical contamination scenarios. For instance, montmorillonite is suitable for the bioremediation of hydrocarbon-contaminated soil in most general cases. For polycyclic aromatic hydrocarbon contamination, clays modified with metal cations (e.g., Na+, Ca2+, Fe3+) are more appropriate. If the goal is solely to concentrate hydrocarbon pollutants in soil without considering microbial biodegradation, acid-activated clay minerals may be considered. In marine environments, composite materials capable of floating on the sea surface while simultaneously adsorbing microorganisms and providing them with nutrients present a more suitable option.

10. Conclusions

This review systematically summarizes current research on natural/modified clay minerals and clay-containing composite materials in microbial hydrocarbon degradation. Several failure scenarios of modified clay minerals have been delineated, which may provide insights for future research and applications: (1) use of high-concentration inorganic acids, (2) application of trivalent metal cations causing excessive interlayer hydrolysis, (3) employment of biologically toxic organic modifiers, and (4) specific metal ion- and organic compound-modified clays demonstrate excessively strong hydrocarbon adsorption capacity, thereby reducing microbial bioavailability. Regarding the less explored direction of alkaline and thermal modification, preliminary theories and limited experimental reports indicate significant potential. Furthermore, clay mineral composites incorporating emerging materials like biochar and nanomaterials demonstrate broad developmental prospects. These materials not only meet practical engineering requirements but also adapt to complex contaminated environments, warranting in-depth exploration.

Author Contributions

Methodology, formal analysis, investigation, writing—original draft, writing—review and editing, L.L.; writing—review and editing, project administration, funding acquisition, C.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This work was financially supported by the National Natural Science Foundation of China (52170096), the Erdos City Science and Technology Cooperation Major Project (2022EEDSKJZDZX015–2), and the Fundamental Research Funds for the Central Universities (Top Innovative Talents Fund of CUMTB) (BBJ2024051).

Data Availability Statement

Not applicable.

Acknowledgments

The content of this review originated from the doctoral dissertation of the corresponding author, Li Lei, completed at the China University of Petroleum (Beijing) under the supervision of Wan Yunyang.

Conflicts of Interest

The authors declare no conflicts of interest.

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Table 4. Studies on the effects of metal cation-modified clay minerals on microbial degradation of hydrocarbons.
Table 4. Studies on the effects of metal cation-modified clay minerals on microbial degradation of hydrocarbons.
YearClayMetal
Cation		Modification MethodHydrocarbonDegraderResultRef.
2013MontmorilloniteK+,
Ca2+,
Zn2+,
Cr3+		200 mL of 0.5 mol/L chloride solutions (KCl, CaCl2, ZnCl2, CrCl3) added to 5 g montmorillonite, shaken 24 h, centrifugationSaturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes in crude oilMicrobial communityCa-montmorillonite: stimulation; Cr-montmorillonite: inhibition; K- and Zn-montmorillonite: neutral[54]
2013MontmorilloniteK+,
Na+,
Ca2+,
Fe3+		200 mL of 0.5 mol/L chloride solutions (KCl, NaCl, CaCl2, FeCl3) added to 5 g montmorillonite, shaken 24 h, centrifugationSteranes, diasteranes, and hopanesMicrobial communityStimulation:
K-montmorillonite (4%), Na-montmorillonite (28%–33%), Ca- (49%–58%), and Fe-montmorillonite (49%–58%)		[30]
2014MontmorilloniteNa+, K+, Mg2+, Ca2+, Zn2+, Al3+, Cr3+, Fe3+200 mL of 0.5 mol/L chloride solutions (NaCl, KCl, MgCl2, CaCl2, ZnCl2, AlCl3, CrCl3, FeCl3) added to 5 g montmorillonite, shaken 24 h, centrifugation11 Aromatic compoundsMicrobial communityK- and Zn-montmorillonite: no stimulation; Ca- and Fe-montmorillonite: stimulation[76]
2014MontmorilloniteNa+, K+, Ca2+, Zn2+, Cr3+, Fe3+200 mL of 0.5 mol/L chloride solutions (NaCl, KCl, CaCl2, ZnCl2, CrCl3, FeCl3) added to 5 g montmorillonite, shaken 24 h, centrifugationC1-phenanthrenes, C1-dibenzothiophenes, C2-phenanthrenes, C2-dibenzothiophenesMicrobial communityStimulation:
K-montmorillonite (18%–25%), Ca- (48%–63%), and Fe-montmorillonite (48%–63%)		[34]
2014MontmorilloniteNa+, K+, Mg2+, Ca2+, Zn2+, Al3+, Cr3+, Fe3+200 mL of 0.5 mol/L chloride solutions (NaCl, KCl, MgCl2, CaCl2, ZnCl2, AlCl3, CrCl3, FeCl3) added to 5 g montmorillonite, shaken 24 h, centrifugationCrude oil hydrocarbonsMicrobial communityNa- (21%), Ca- (29%), Mg- (21%), and Fe-montmorillonites (28%): stimulation; K- (−9%), Zn- (−6%), Al-, and Cr-montmorillonites (−3%): inhibition[22]
2018Montmorillonite,
kaolinite,
pyrophyllite		Na+, Fe3+100 mL of 0.1 mol/L chloride solutions (NaCl and FeCl3) added to 5 g clays, ultrasonic treatment 10 minPhenanthrenePantoea agglomeransStimulation:
Na-montmorillonite (14.9%) > Fe-montmorillonite (13.8%) >Fe-kaolinite > Na-Kaolinite > Fe-pyrophyllite > Na-pyrophyllite		[72]
2022MontmorilloniteNa+, Ni2+, Co2+, Cu2+, Fe3+Solid/water ratio of 1:20 (NaCl, 0.1 mol/L; NiCl2, 0.5 mol/L; CoCl2, 0.5 mol/L; CuCl2, 0.5 mol/L; FeCl3, 0.033 mol/L); shaken at 160 rpm for 2 hPyreneMycobacteria
strain NJS−1		Stimulation:
Fe-montmorillonite (33.6%) > Na-montmorillonite ≈ Co-montmorillonite > Ni-montmorillonite ≈ Cu-montmorillonite		[77]
Table 5. Studies on the effects of organically modified clay minerals on microbial degradation of hydrocarbons.
Table 5. Studies on the effects of organically modified clay minerals on microbial degradation of hydrocarbons.
YearClayOrganic ModifierModification MethodHydrocarbonDegraderResultRef.
1995SmectiteHDTMA bromideMix HDTMA bromide and smectite, stir 16 h at 23 °CNaphthalenePseudomonas putida, Alcaligenes sp.Stimulation only for Pseudomonas putida[86]
2004BromideHDTMA bromideAdd solution of HDTMA bromide to the stirred bentonite suspensionPhenolMicrobial communityInhibition[23]
2013MontmorilloniteDDDMA bromideAdd DDDMA bromide to montmorillonite/saponite suspension, stir 24 hSaturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes in crude oilMicrobial communityInhibition[54]
2013MontmorilloniteDDDMA bromideAdd 100 mL of DDDMA bromide solution (5.17 g) to 1500 mL clay suspension (50 g), stir 24 hSteranes, diasteranes, and hopanesMicrobial communityNo stimulation (−1%)[30]
2014Montmorillonite, Saponite DDDMA bromideAdd 100 mL of DDDMA bromide solution (5.17 g) to 1500 mL clay suspension (50 g), stir 24 hSaturated hydrocarbonsMicrobial communityInhibition[31]
2014Montmorillonite, SaponiteDDDMA bromideAdd sufficient DDDMA bromide to montmorillonite/saponite suspension, stir 24 hCrude oil hydrocarbonsMicrobial communityOrganosaponite: no stimulation; organomontmorillonite: inhibition (−12%)[32]
2014MontmorilloniteDDDMA bromideAdd 100 mL of DDDMA bromide solution (5.17 g) to 1500 mL clay suspension (50 g), stir 24 hC1-phenanthrenes, C1-dibenzothiophenes, C2-phenanthrenes, C2-dibenzothiophenesMicrobial communityStimulation (8%–23%)[34]
2015BentoniteCationic surfactant, palmitic acidMix cationic surfactant and bentonite, add mixture to ethanol-dissolved palmitic acid (10.99 g in 1000 mL ethanol–water mixture (1:1)), stir 4 hPhenanthreneMicrobial communityStimulation:
microbial count (10%–43%), respiration (3%–44%; enzymatic activities (68%)		[87]
2016BentoniteCationic surfactant, palmitic acidMix cationic surfactant and bentonite, add mixture to ethanol-dissolved palmitic acid (10.99 g in 1000 mL ethanol–water mixture (1:1)), stir 4 hPhenanthreneMycobacterium gilvum VF1Neutral[88]
2017Saponite,
Montmorillonite		DDDMA bromideAdd sufficient DDDMA bromide to clay suspension, stir 24 hPolycyclic aromatic hydrocarbonsMicrobial community (Alcanivorax-dominated)Organosaponite: stimulation; organomontmorillonite: inhibition[38]
2018BentoniteCationic surfactant, palmitic acidMix cationic surfactant and bentonite, add mixture to ethanol-dissolved palmitic acid (10.99 g in 1000 mL ethanol–water mixture (1:1)), stir 4 hPolycyclic aromatic hydrocarbonsMicrobial communityStimulation (13.3%)[42]
2020BentoniteCationic surfactant, palmitic acidMix cationic surfactant and bentonite, add mixture to ethanol-dissolved palmitic acid (10.99 g in 1000 mL ethanol–water mixture (1:1)), stir 4 hPolycyclic aromatic hydrocar-bonsMicrobial communityStimulation: modulates microbiota structure, enhances growth, and boosts respiration[47]
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Li, L.; Zhang, C. Role of Natural and Modified Clay Minerals in Microbial Hydrocarbon Biodegradation. Minerals 2025, 15, 1120. https://doi.org/10.3390/min15111120

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Li L, Zhang C. Role of Natural and Modified Clay Minerals in Microbial Hydrocarbon Biodegradation. Minerals. 2025; 15(11):1120. https://doi.org/10.3390/min15111120

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Li, Lei, and Chunhui Zhang. 2025. "Role of Natural and Modified Clay Minerals in Microbial Hydrocarbon Biodegradation" Minerals 15, no. 11: 1120. https://doi.org/10.3390/min15111120

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Li, L., & Zhang, C. (2025). Role of Natural and Modified Clay Minerals in Microbial Hydrocarbon Biodegradation. Minerals, 15(11), 1120. https://doi.org/10.3390/min15111120

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