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Review

Microbial Degradation of Lignocellulose for Sustainable Biomass Utilization and Future Research Perspectives

by
Mengke Chen
1,
Qinyu Li
1,2,
Changjun Liu
1,2,
Er Meng
1,2 and
Baoguo Zhang
3,*
1
Hunan Engineering Research Center of Lotus Deep Processing and Nutritional Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
2
School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
3
Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No.99 Haike Road, Shanghai 201210, China
*
Author to whom correspondence should be addressed.
Sustainability 2025, 17(9), 4223; https://doi.org/10.3390/su17094223
Submission received: 10 April 2025 / Revised: 30 April 2025 / Accepted: 6 May 2025 / Published: 7 May 2025
(This article belongs to the Section Resources and Sustainable Utilization)
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Abstract

Lignocellulose, as Earth’s most abundant renewable biomass, represents a crucial resource for the production of biofuels and biochemicals, it is of great significance for sustainable development. Microbial degradation offers a promising pathway for transforming lignocellulose into valuable products. This review explores the diversity and classification of lignocellulose-degrading microorganisms, focusing on fungi and bacteria and their respective enzyme systems responsible for breaking down cellulose, hemicellulose, and lignin. Key factors influencing degradation efficiency, including environmental conditions, substrate complexity, and microbial interactions, are thoroughly analyzed. Limitations in microbial degradation are also discussed, notably the need for identifying high-activity strains. Additionally, the review outlines future research directions, emphasizing the application of advanced technologies such as genomics, synthetic biology, and machine learning to optimize microbial degradation processes. These insights aim to enhance lignocellulose utilization efficiency, fostering its broader industrial and agricultural applications.

1. Introduction

In recent years, the global focus on reducing greenhouse gas emissions and combating climate change has intensified, leading to a stronger emphasis on sustainable development. Lignocellulose, one of the most abundant renewable biomass resources on Earth [1]. Many solid wastes from crops such as rice husks, straw and rice stalks are rich in lignocellulose. The burning and discarding of these solid wastes lead to the waste of renewable resources and hinder the sustainable utilization of resources. Therefore, the effective utilization of lignocellulose has attracted widespread attention. Lignocellulose, composed of cellulose, hemicellulose, and lignin, is the primary component of agricultural waste and a significant non-food biomass resource, providing an abundant source of C5 and C6 sugars without affecting the food supply [2,3]. Therefore, utilizing lignocellulose as a feedstock to convert it into valuable biomass products, such as biofuels (an alternative to traditional fossil fuels) and other renewable materials, has emerged as a crucial green and sustainable strategy to mitigate global warming while repurposing agricultural and industrial waste [4,5].
The efficient utilization of lignocellulose largely depends on biorefining processes to synthesize biofuels, biomaterials, and other value-added bioproducts. In biorefineries, a critical step in processing biomass is the pretreatment of its basic components (Figure 1) [6,7]. Compared to energy-intensive physical methods, chemical pretreatment with acids, alkalis, and organic solvents is more efficient and adaptable to various types of biomass, making it one of the most promising approaches. However, this method will inevitably generate intermediate toxic by-products. For instance, the initial products of acid pretreatment of hemicellulose, such as hexose and pentose, will further decompose to form furfural and hydroxymethylfurfural, which will inhibit subsequent enzymatic hydrolysis and microbial fermentation. The unfavorable by-products obtained in the alkaline pretreatment process are relatively fewer, but the acid and alkaline pretreatment liquids are highly corrosive, imposing higher requirements on the reaction equipment and causing certain pollution to the environment. Moreover, organic solvents with lower toxicity usually have flammability, volatility, and explosiveness, which not only have a high risk factor but also have a high recovery cost. For the sake of environmental safety, economic efficiency, and the fact that no investment in high-energy equipment is required, low-cost biological pretreatment with fewer chemical additives is gradually replacing chemical methods as a more attractive option [8]. Biological pretreatment primarily utilizes microorganisms and enzymes to degrade biomass in a gentler, more environmentally friendly manner. Compared to enzyme pretreatment, microorganisms offer greater functional diversity and resilience to environmental factors such as temperature and pH, resulting in higher pretreatment efficiency during anaerobic digestion [9].
However, lignocellulosic-based microbial treatment methods also face the challenge of high-cost lignocellulases, as shown in Table 1, for the relevant characteristics of enzyme production processes, which are critical for evaluating the performance of any biotechnological process, and comparing the composition of enzyme production costs derived from these process designs, where raw material and capital-related costs are often the main drivers of enzyme production costs. The data provided in Table 1 indicate that the low-cost cellulase from Trichoderma reesei is obtained through a combination of extremely high enzyme yields, high enzyme titers, and high volumetric productivities. It can be seen that improving process parameters and optimizing the cellulase production process is one of the ways to increase the degradation rate of lignocellulose. However, the most fundamental approach is to screen out high-yield and stable enzyme-producing microorganisms (such as T. reesei, which is a typical lignocellulose-degrading microorganism that secretes a high-level cellulase mixture) to increase the enzyme yield per unit fermentation volume and reduce production costs [10].
In nature, lignocellulose degradation is achieved through the synergistic actions of fungi and bacteria, which secrete cellulases, hemicellulases, and ligninases to break down cellulose, hemicellulose, and lignin, either simultaneously or selectively [17]. In this context, the study of microbial degradation of lignocellulose has become a hot topic in the fields of ecology, resource utilization, and sustainable development. Since the earliest fungal degradation of cellulose, efforts have been made to unravel the microbial degradation mechanism of lignocellulose [18]. However, lignocellulose has an exceptionally complex structure, and its degradation demands the coordinated activity of various microorganisms and a diverse array of degradative enzymes. To date, many microorganisms involved in this process remain poorly classified, and their metabolic pathways are not fully understood. Furthermore, the cooperative degradation mechanisms among different microorganisms require further investigation [19]. This paper reviews recent advances in the study of lignocellulose-degrading microorganisms and enzyme systems, along with an analysis of the various factors influencing lignocellulose degradation. These insights aim to establish a theoretical foundation for the efficient utilization of lignocellulose.

2. Diversity and Classification of Lignocellulose-Degrading Microorganisms

In nature, lignocellulose degradation is a complex and orderly process, involving diverse microorganisms that collaborate to produce enzymes which attack, depolymerize, and degrade lignocellulosic polymers. These microorganisms are both highly diverse and abundant, with the capacity to proliferate rapidly under favorable conditions [20].

2.1. Classification of Fungi in Lignocellulose Degradation

Fungi are the most extensively reported and deeply studied microorganisms in lignocellulose degradation and depolymerization. Research has shown that lignocellulose-degrading fungi can be classified into three major categories—white-rot, brown-rot, and soft-rot fungi—based on the type and extent of degradation they induce [21,22]. These fungi, which produce lignocellulolytic enzymes, exhibit different preferences for the types of enzymes they secrete (Table 2). White rot fungus can effectively degrade lignin, cellulose and hemicellulose, although the degradation rate is slow and the environmental requirements are high, but the comprehensive and in-depth degradation of lignocellulose can achieve efficient degradation in the long-term action process [23]. In particular, basidiomycetes rot fungi are particularly significant in the production of lignin-delyssing enzymes and lignin depolymerization [24,25]. Brown rot fungus can degrade cellulose and hemicellulose, but its ability to degrade lignin is limited; it has strong adaptability to the environment and can also degrade lignocellulose well under the condition of lack of nutrients. Soft rot mainly degrades cellulose and hemicellulose and almost does not degrade lignin. So, the overall effect on lignocellulose is poor, but it has a certain degradation ability to cellulose under high temperature conditions [26,27,28].
Different fungal genera show variations in degradation mechanisms and efficiency, with early studies primarily focusing on aerobic processes. For example, certain enzymes produced by symbiotic fungi associated with termites can degrade lignin in aerobic environments. Recent studies, however, have shown that two anaerobic fungal strains from the genus Neocallimastix demonstrate highly efficient lignin degradation, surpassing the efficiency of termite symbiotic fungi [44]. Among reported lignocellulose-degrading fungi, including species of Aspergillus, Trichoderma, and rumen fungi, the lignocellulose-degrading abilities of rumen anaerobic fungi are particularly notable. This observation suggests that the oxygen requirements of fungi significantly influence their enzyme production capabilities [18,21,45].
Some filamentous fungi, such as Aspergillus and Trichoderma, have been applied in the production of secondary metabolites like lignocellulolytic enzymes (industrial proteins) due to their advantages of being able to ferment on low-cost raw materials and having strong protein secretion capabilities. This has sparked a wave of filamentous fungal modification. However, the basic and applied research on filamentous fungi is highly dependent on gene-editing platforms, and the unique physiological properties of filamentous fungi, such as apical growth, heterokarytic, low homologous recombination efficiency, and lack of genetic screening markers, have brought challenges to the construction of such microbial gene-editing platforms, resulting in the difficulty of large-scale applications of filamentous fungi in industrial production [46,47].

2.2. Classification of Bacteria in Lignocellulose Degradation

Compared to fungi that are difficult to genetically manipulate, bacteria are more easily genetically engineered due to their rapid growth, simple structure, wide biological activity, and strong environmental adaptability. Cellulose-degrading bacteria are gradually being valued by researchers [48]. In the 1960s, certain bacteria were identified as participants in wood decay, and by the 1980s, studies confirmed that bacteria could degrade lignin fragments, as well as sulfur-containing lignin [49]. As research on bacterial lignocellulose degradation has advanced, it has been found that the diversity and functionality of lignocellulolytic enzymes produced by bacteria are comparable to those of fungi (Table 3). With advances in research on bacterial lignocellulose degradation, it has been found that the diversity and functionality of lignocellulolytic enzymes produced by bacteria are comparable to those of fungi.
Most lignocellulose-degrading bacteria are aerobic, primarily belonging to the Actinobacteria, Proteobacteria, and Firmicutes phyla [63]. Among these, Streptomyces species, members of the Actinobacteria, are among the most extensively studied lignocellulose-degrading bacteria. In addition to Streptomyces, aerobic bacteria such as Bacillus and Pseudomonas are common in soil and have been widely researched [64,65]. However, the extracellular cellulases secreted by aerobic bacteria are often limited in diversity, resulting in lower lignocellulose degradation efficiency in practical applications [66]. In contrast, although anaerobic bacteria grow more slowly, they demonstrate higher lignocellulose degradation efficiency and are less susceptible to contamination from competing microorganisms [67]. For example, Clostridium and thermophilic anaerobes typically exhibit superior lignocellulose degradation capabilities [68,69]. In 2024, Manesh et al. reported the complete genome sequence of an extremely thermophilic, fermentative anaerobic bacterium capable of efficiently degrading lignocellulose under specific environmental conditions [70].
Caldicellulosiruptor bacteria, an obligate anaerobic bacterium and an extreme thermophilic bacterium, C. owensensis cultured on corn cob xylan or xylose could produce cellulase and hemicellulase with high enzyme activity, and the conversion rates of xylan and arabinose were 16.7% and 60%, They showed significant synergistic effects with the commercially available enzyme mixture Cellic CTec2 (Novoyzmes). When natural corn stover and corn cob were sequentially hydrolyzed by extracellular enzymes of C. owensensis and CTec2, the conversion rates of glucan were 31.2% and 37.9%, respectively, which were 1.7 times and 1.9 times higher than each control (hydrolyzed only by CTec2), C. owensensis exhibited enhanced ability to degrade natural lignocellulosic hemicellulose [71].
While research on fungal lignocellulose degradation predominated in the 20th century, scientists have increasingly recognized that bacteria often surpass fungi in adaptability, enzyme thermostability, and pH tolerance. The genome of bacteria is relatively small and the genetic background is relatively clear, and the lignocellulase gene of bacteria can be modified and introduced by genetic engineering, or the genes related to the metabolic pathway that compete for carbon source or energy with lignocellulose degradation can be obtained by genetic engineering, so that they can express specific lignocellulosic degrading enzymes or improve the activity of enzymes. This shift in understanding has led to a growing focus on bacterial applications in lignocellulose degradation [64].
Table 4 summarizes the effectiveness of fungi and bacteria in the degradation of lignocellulose. Overall, fungi and bacteria have their own advantages and different focuses; the different advantages of fungi and bacteria complement each other in the process of lignocellulose degradation, improving the decomposition efficiency of lignocellulose and developing various biotechnology applications. With advancements in biotechnology and genetic engineering, researchers have begun to develop highly efficient, high-activity microorganisms by cloning cellulase genes into bacteria, fungi, and plants, aiming to select ideal strains with high enzyme production [72,73,74]. In the future, constructing microbial systems capable of rapidly degrading lignocellulose and developing engineered strains with high enzyme activity through genetic recombination will become key directions in microbial research on lignocellulose degradation [75,76].

3. Diversity and Classification of Lignocellulose-Degrading Enzymes

Lignocellulose is composed of cellulose and hemicellulose, which are interconnected and tightly encased by lignin, forming a complex, three-dimensional, irregular network [85]. It also contains trace amounts of lipids, proteins, resins, pectin, and inorganic substances [86,87]. Lignocellulolytic enzymes can be categorized by their substrates into cellulases, hemicellulases, and ligninases (Figure 2), which degrade cellulose, hemicellulose, and lignin, respectively, working together to facilitate lignocellulose degradation [88,89].

3.1. Cellulose-Degrading Enzymes

Cellulose, the primary component of lignocellulosic biomass, is a polymer of D-glucose molecules linked by β(1–4) bonds. It mainly exists in two forms: crystalline cellulose, which is unbranched, and amorphous cellulose, which is more readily hydrolyzed by enzymes [92]. This is shown in Figure 2; cellulase is responsible for depolymerizing and hydrolyzing cellulose into cellobiose and glucose. Rather than a single enzyme, cellulase is a complex system composed of endoglucanases, exoglucanases, and β-glucosidases [91]. Endoglucanases act on the amorphous regions of cellulose, while exoglucanases target the crystalline regions, creating new reactive ends and producing cellobiose or glucose. Finally, β-glucosidase hydrolyzes cellobiose into two glucose molecules, thus completing cellulose degradation [93,94].
In recent years, the discovery of oxidases (LPMOs) has further expanded the mechanism of cellulose degradation. LPMOs are a type of copper ion dependent oxidase that can break glycosidic bonds in polysaccharides through oxidation, thereby depolymerizing difficult to degrade biomass and exposing more binding sites to glycoside hydrolases (GH), thereby accelerating the hydrolysis of cellulose and chitin [95]. Recently, a metallooxidase enzyme named CelOCE has been reported due to its unique catalytic ability, which is different from the mechanism of action of LPMO, CelOCE acts on the C1 terminal of cellulose to produce cellobionic acid in the form of oxidative cleavage, instead of traditional cellobiose or glucose, which makes it have a stronger synergistic effect in the process of cellulose degradation. When CelOCE interacts with commonly used fungal degrading enzyme systems in industry (such as the cellulase secreted by Trichoderma reesei), the overall sugar release efficiency increases by 21%. Among them, the saccharification efficiency of crystalline cellulose and amorphous cellulose increases by 8% and 12.5%, respectively, significantly improving the cellulose conversion efficiency [96].
Current research indicates that fungi, bacteria, and some protozoa are the primary microbial sources for cellulose degradation. Fungi possess a more complete cellulase system and exhibit high degradation activity, which is why most cellulose degradation studies focus on fungi. For instance, Trichoderma reesei, Rhizopus, Trichoderma viride, and Penicillium are widely utilized for cellulase production [97]. Aerobic fungi and bacteria primarily secrete free extracellular cellulases for degradation, while certain anaerobic fungi utilize cellulosome complexes to achieve this process. Fungal hyphae can directly penetrate host cells and secrete cellulases, enabling more efficient cellulose degradation [98]. Anaerobic bacteria also employ cellulosome complexes for cellulose degradation, albeit through a slightly different mechanism. These bacteria assemble cellulosomes composed of functional proteins that attach to the cell surface, enabling cellulose to swell and degrade under bacterial action. Well-studied cellulose-degrading bacteria include Actinomyces, Fibrobacter, and Cellulomonas [99]. Among these, Clostridium thermocellum has demonstrated an exceptionally high cellulose utilization rate, with its cellulosome showing significantly greater specificity for crystalline cellulose compared to most other bacteria (Figure 3) [100]. Microorganisms that utilize cellulosomes for cellulose and hemicellulose degradation either anchor these complexes to the cell membrane via scaffold proteins or deploy free-floating cellulosomes to carry out the degradation process [101].

3.2. Hemicellulases

In lignocellulose, hemicellulose is interconnected with cellulose and lignin through hydrogen and covalent bonds, creating a tightly structured complex [103]. Hemicellulose is a heterogeneous polysaccharide composed of various sugar units, including xylose, mannose, galactose, arabinose, glucose, and uronic acids. Its primary component is xylan, a pentose polymer that can be biodegraded into monosaccharides and acetic acid. Due to the structural diversity of xylan, its degradation enzyme system is complex, comprising enzymes such as endo-β-1,4-xylanase, which hydrolyzes xylan into xylooligosaccharides, and β-xylosidase, which releases xylose residues from the non-reducing ends of xylooligosaccharides [101]. Additionally, various accessory enzymes, such as α-arabinofuranosidase, α-glucuronidase, β-mannanase, and α-galactosidase, act on xylan side chains to facilitate its depolymerization (Figure 2) [90].
Fungi, particularly Aspergillus and Trichoderma species, are known for producing a wide variety of hemicellulases, secreting a complete set of enzymes that enable efficient hemicellulose degradation [104]. Furthermore, the hyphae of filamentous fungi can penetrate host cells and produce hemicellulases, enhancing the degradation process [105]. Trichoderma reesei, a typical filamentous fungus, secretes high levels of xylanases along with additional enzymes that degrade xylan side chains, demonstrating a strong capacity for hemicellulose degradation [106,107].
The mechanism of hemicellulose degradation in bacteria differs from that in fungi. Aerobic bacteria secrete limited amounts of hemicellulases, with intracellular enzymes also contributing to the degradation process. In contrast, anaerobic bacteria utilize cellulosome-like structures for hemicellulose degradation (Figure 3) [89,100,102]. Although bacteria generally exhibit lower hemicellulose degradation capacity than fungi, their resilience enables them to survive and maintain enzyme production under extreme conditions. Examples include thermophilic xylanases produced by Bacillus species at 60–70 °C, alkali-stable xylanases from B. pumilus, and cold-adapted xylanases from Paenibacillus species PXLY1 [108].

3.3. Lignin-Degrading Enzymes

Lignin is the most recalcitrant component of lignocellulose, composed of a three-dimensional network of phenylpropane monomers linked by ether bonds, which makes it highly stable [109]. Additionally, lignin tightly encases cellulose and hemicellulose, shielding them from degradative enzymes and significantly reducing the overall efficiency of lignocellulose degradation [110]. Lignin degradation depends on microbial enzymes, including laccases, peroxidases, and accessory enzymes, which collectively depolymerize lignin into smaller molecular units, such as guaiacyl, syringyl, and p-hydroxyphenyl units [111,112].
Laccase is a multicopper oxidase that oxidizes phenolic and non-phenolic compounds, thereby promoting lignin degradation [113,114]. Peroxidases, including lignin peroxidase (LiP), manganese peroxidase (MnP), and versatile peroxidase (VP), are also critical to lignin degradation. Lignin peroxidase, with its high redox potential, is particularly effective in degrading lignin and other hard-to-degrade macromolecules, making it one of the most widely applied lignin-degrading enzymes [115,116]. In addition, several accessory enzymes, such as β-etherases, dehydrogenases, and decarboxylases, contribute to lignin depolymerization and mineralization. Research has shown that fungi, particularly white-rot fungi, possess a strong lignin-degrading capacity. White-rot fungi produce hyphae capable of penetrating cellulose barriers and secreting extracellular enzymes, significantly enhancing lignin degradation efficiency [117]. In some termite–fungal natural symbiosis systems, fungi can improve the efficiency of enzymatic hydrolysis and saccharification through synergistic effect with enzymes. Liao’s research team constructed a synergistic pretreatment lignin system using laccase (La), which decomposes lignin phenolic units in termite gut, and ant nest fungus (Te). After treating the lignin model compound alkali lignin, the maximum activity of lignin peroxidase (LiP) produced by laccase (La) and Te increased by 43.3% and 58.5%, respectively, compared to untreated alkali lignin samples, Laccase pretreatment strengthened the modification of alkali lignin functional groups and the destruction of physical structure by Te, the maximum enzymatic adsorption capacity of alkali lignin after pretreatment was 51.5% lower than that of untreated alkali lignin, and the conversion rate of subsequent enzymatic hydrolysis was 71.5% higher than that of untreated alkali lignin samples due to the significant reduction in non-productive adsorption. It was proved that the synergistic effect between laccase and fungus could effectively change the physicochemical properties of alkali lignin and promote the subsequent enzymatic hydrolysis and saccharification of lignocellulose [118].
Although fungi have traditionally been regarded as the primary producers of lignocellulolytic enzymes, the recalcitrant nature of plant biomass limits the efficiency of fungal enzyme production, thus constraining the commercial potential of lignocellulose conversion [119]. In contrast, bacteria are more adaptable to changes in pH and temperature, exhibit faster growth rates, and are well-suited to genetic engineering applications, making them ideal candidates for future lignocellulose degradation research [120]. Moreover, the complexity of bacterial lignocellulolytic enzymes makes them better suited for executing the sequential steps in bioconversion processes, and bacterial enzymes are easier to manipulate genetically than fungal enzymes. Consequently, research on cellulose-degrading enzymes is gradually shifting its focus toward bacterial sources [121,122]. Current research on lignocellulose-degrading microorganisms and their enzyme production conditions has become a major focus. Classifying and analyzing these microorganisms and enzymes provides a crucial theoretical foundation for efficient lignocellulose degradation, alternative fossil fuel production, agricultural waste recycling, and enhanced environmental sustainability [123].

4. Factors Influencing Lignocellulose Degradation

4.1. Impact of Environmental Factors

Environmental factors are pivotal in determining the efficiency of microbial lignocellulose degradation, as they directly influence microbial growth and enzyme activity [124]. Microbial populations and activities are controlled by physical, chemical, and biological factors during degradation, such as moisture, aeration, pH, temperature, and the presence of inhibitors, as well as the coexistence of other microorganisms [125]. Among them, the water content and oxygen concentration in the environment determine the population density and life activities of eutrophic and anaerobic organisms [126]. The water content can directly affect the degradation of lignocellulose by affecting the growth and reproduction of microorganisms on the one hand, and the structure of lignocellulose itself on the other hand. By analyzing the effects of different moisture content on the mechanical properties of wood, Li used a mild method to remove amorphous substances (hemicellulose and lignin) from wood cell wall to varying degrees, and when discussing the effects of different water states on the crystalline structure of cellulose and its interaction with amorphous substances, it was found that, in the absolute dry state, the contraction of amorphous substances exerted tensile force on the crystalline structure of cellulose. Changes in the physicochemical environment of the wood cell wall will affect the interaction between amorphous substances and water, and the water in the cell wall will enter the amorphous substances to swell and release the tensile force on the crystalline structure. As the moisture content increases, the amorphous areas of the wood swell, and the water molecules fill the tiny gaps in the wood, making the fibers more orderly and improving the resistance to external damage [127]. Towey et al. also found that stable biomass with less than 20% moisture content was associated with a lower risk of degradation over time. At humidity above 20%, biomass degradation is common, and hemicellulose is the most severely degraded part of biomass feedstock [128].
Oxygen concentration control needs to be very strict in the process of microbial fermentation and enzyme production, usually most microorganisms undergo aerobic reproduction in the early stage, and enzyme production and metabolic activities need to be carried out under anaerobic conditions in the later stage, lignocellulose is usually pretreated before microbial degradation, and the production of some toxic by-products such as organic acid products formic acid, acetic acid, and furfural in the process of lignocellulose pretreatment will inhibit the enzymatic hydrolysis and fermentation of microorganisms [129]. Feng used directional acclimation to select strains with high tolerance to lignocellulose hydrolysate inhibitors, and studied the process engineering control strategy of micro-aeration to alleviate the adverse effects of inhibitors on microorganisms, and the results showed that the use of constant rate and ORP-regulated aeration strategies effectively improved the tolerance of cells to a variety of hydrolysis inhibitors, which fully demonstrated the importance of oxygen to microbial fermentation [130].
Temperature and pH are often significant factors affecting the growth and degradation capabilities of microorganisms. Different microorganisms have their own temperature and pH preferences; generally, bacteria prefer a near-neutral pH, while fungi favor acidic pH [131,132]. After Wang inoculated the selected lignocellulosic flora into media with different initial pH (5.0~11.0) from different carbon sources (filter paper, corn straw, straw straw, and wheat straw), the pH changed rapidly to neutral and gradually stabilized, and the carbon source substrates reached a high weight loss rate [133]. Most enzymes secreted by microorganisms are proteins with charged side-chain groups, which are pH-dependent, and during electron transport, H+ concentration affects the cleavage of chemical bonds, the formation of enzyme-substrate complexes, and thus, the enzyme catalytic rate [134,135]. Many important proteins undergo pH-dependent conformational changes that lead to “on-off” switching of protein functions, which are essential for regulating life processes and have a wide range of application potential. Yao et al. reported a pair of cellulose assembly modules, including adhesive proteins from Clostridium acetobutyrate and dockerin, discovering a new novel pH-dependent change in protein interactions, unlike known pH dependent protein conformational changes, which are controlled by sensing pH changes to achieve an “on-off” switch. At pH 4.8 and 7.5, the two cohesion binding sites on the dockerin switch from one to the other, and the bound dockerin rotates 180°, resulting in a switch between the two interaction sites at different pH conditions [136]. Miao’s research team found that Guizhou Trichoderma NJAU4742 can perform rice straw fermentation normally under different initial pH values (3.0~9.0), but its growth rate and extracellular enzyme activity are significantly improved under acidic conditions. The results of proteomic analysis clearly showed that the secreted lignocellulase had a tendency to be co-distributed according to the environmental pH, which led to the pH-dependent classification of lignocellulase in NJAU4742, and most of the functional lignocellulases were regulated differently by the environmental pH and could accelerate the degradation of biomass by increasing the environmental pH through environmental alkalization. When pH < 4, NJAU4742 strain increased the environmental pH to the optimal range through alkalization, achieving rapid degradation of rice straw [137].
The effect of temperature on enzymes is extremely significant, as it can change both the stability of enzymes and the kinetic and thermodynamic characteristics of enzymes. Most enzymes remain active in the range of 5 to 50, and their activity increases with increasing temperature [138,139]. The number and activity of microbial communities also increased with the increase in temperature in the mesophilic range. Zavala et al. tested the effect of temperature on the degradation of sawdust feces by aerobic microorganisms from several temperatures in the thermophilic range, and found that the optimal temperature for microbial degradation of feces was in the high temperature range close to 60 degrees Celsius. The enzyme activity is significantly reduced at 70 degrees Celsius, and some organic matter can be slowly degraded in the moderate temperature range [140]. In addition, the different ratios of carbon (C) and nitrogen (N), which are essential elements for microbial growth, affect the amount of nutrients absorbed by microorganisms, which in turn affects the activity of enzymes produced by microorganisms [132,141].

4.2. Impact of Substrate Characteristics

The complexity and degradability of the substrate structure can directly affect the ease of microbial degradation [142]. The enzymatic catalytic degradation of fibrous polysaccharides is one of the key links in the biorefining of lignocellulose, and the pretreatment of lignocellulose to destroy the recalcitrant characteristics of substrates is a necessary way to achieve efficient enzymatic hydrolysis and saccharification of lignocellulose. The cellulose glycation of lignocellulose is affected by various physical and chemical factors related to substrates, and Cui et al. reviewed the influence of physical properties such as polymerization, crystallinity, hydrogen bond strength, and enzyme reachable area, as well as chemical properties such as lignin, hemicellulose, wax, and inorganic substances on the enzymatic hydrolysis of cellulose from the aspects of substrate resistance [143]. Among them, the inorganic substances in lignocellulose include K+, Mg2+, Ca2+, Al3+, Mn2+, Fe3+, Cu2+, and Zn2+ plasma and compounds affect the degradation of lignocellulose by promoting or inhibiting the enzyme activity of hydrolase enzymes, and other factors affect the degradation of lignocellulose by hindering the degree and range of contact between cellulose and enzymes.
In addition to the complex structure of lignin affecting the degradation efficiency of lignocellulose, Wang et al. suggested that the content of natural (untreated) lignin and the degree of lignin removal and xylan removal by pretreatment were also substrate factors affecting lignocellulosic degradation [144]. Vikman et al. studied the degradation effect of pulp and paper products with different lignin content at different compost temperatures in a controlled composting test, and found that lignin would hinder the biodegradation of samples, mechanical pulp with high lignin content had better biodegradability at lower temperatures, while kraft paper with low lignin content had good biological degradation performance at different temperatures, and kraft paper greatly improved microbial activity, increasing the proportion of sample carbon converted to microbial biomass carbon at lower temperatures [145].
Therefore, in order to change the complex structure of lignocellulose and make lignocellulase play a more efficient role, lignocellulosic is often pretreated with biomass by physical methods (grinding, extrusion, and thinning), chemical methods (acids, alkalis, organic solvents), and biological methods, so as to break up its compact structure and reuse the carbohydrates in it [146,147,148]. In the pretreatment process, hemicellulose is easily degraded into oligosaccharides and dissolved in the system, so that the hydrogen bond connection with cellulose is weakened, which increases the accessibility of cellulose to cellulase, which is conducive to improving the saccharification efficiency of cellulose. The removal of lignin collapses the cell wall skeleton structure, increases the porosity and specific surface area of the material, and exposes more cellulose skeletons [146,147]. The use of different pretreatment methods can lead to different structures of phenolic compounds during lignin degradation, especially the differences in functional groups and side chains have a significant impact on the structure–activity relationship between phenolic compounds and their inhibition of hydrolysis [149]. Chemical pretreatment can effectively degrade lignin and hemicellulose in plant cell walls, achieve component separation, and expose cellulose microfibrils [150,151], while the mechanical grinding process will break the hydrogen bonds in the cellulose microcrystalline region, significantly reduce the particle size and crystallinity of lignocellulose materials, and improve their enzymatic hydrolysis properties [152,153]. At present, changing the internal structure of lignocellulose through a variety of pretreatment methods to improve the degradation performance of lignocellulose is the difficulty and breakthrough point of lignocellulose degradation.

4.3. Impact of Microbial Diversity

The deconstruction of lignocellulose is accomplished by a variety of microorganisms under different environmental conditions, and different species of microorganisms from different sources have different degradation abilities [154]. Most of the microorganisms with lignocellulose degradation ability are derived from agricultural and forestry soils, surface leaf decay, animal rumen, and ruminant feces [155], and the growth and reaction conditions of these microorganisms and their enzymes are within the normal range. Recently, some extreme microorganisms living in extreme environments have received high attention from researchers. These extreme microorganisms naturally grow in harsh environments and can effectively adapt and function under extreme conditions. They still have high stability in the face of pH, temperature, and other conditions that are not conducive to microbial survival in industrial processing. The extreme enzymes they produce can remain stable under extreme reaction conditions and can serve as biocatalysts for various reactions, these characteristics help extreme microorganisms become excellent microorganisms for adapting to the development of biorefinery industry [156]. The recently discovered cellulase derived from the thermophilic isolate Geobacillus sp. R7 can achieve saccharification of waste biomass corn stover and grassland cordyceps within 36 h, and its hydrolysis ability is not inferior to commercial cellulases, the cellulase hydrolysate was fermented by brewing yeast ATCC 24860, the ethanol production is 0.45–0.50 g per gram of glucose, and the glucose utilization rate exceeds 99%. Prove that Geobacillus sp. R7 can ferment lignocellulosic substrates into ethanol in one step, which can be used to consolidate the development of biotechnology [157]. In addition, the extreme enzyme produced by Thermotoga neapolitana is able to digest 29% cellulose from untreated Korean straw, resulting in biohydrogen at 2.3 mol/g straw [158].
In lignocellulose-rich environments, protist biomes have been excavated by metaomics techniques to show genetic diversity in lignocellulosic degradation [159], and some soil bacteria (mostly actinomycetes or proteobacteria) and archaea can degrade lignin by secreting laccase and peroxidase in wood-boring insects such as termites or in compost [160,161]. In addition to the well-studied bacteria and fungi, some unicellular eukaryotes (Chlamydomonas, dinoflagellae), protists (flagellates, Oxomonas), and certain invertebrates (e.g., plant parasitic nematodes, cockroaches, and termites) have been found to carry cellulase genes that express endogenous cellulases [159,162]. Among them, termites have also been found to have symbiotic microorganisms in their intestines, including protozoa, spirochetes, actinomycetes, fungi and bacteria, which play a role in the digestion of lignocellulose in the intestine, so there are more and more studies on the synergistic degradation and utilization of lignocellulose in termites and microbial symbiotic systems. Mo et al. revealed the process mechanism of synergistic degradation of lignocellulose by cultured termites and symbiotic microorganisms of cultured termites. Young worker ants can quickly open the carbon–carbon chemical bonds of lignin and use the sugars on the hemicellulose side chain as food, completely removing the external physical barriers of cellulose and hemicellulose in the polysaccharide components, while fungi and bacteria in the nest can shear the polysaccharide components to oligosaccharides that are easier to degrade and utilize, and the elderly worker ants feed on oligosaccharide-rich bacterial beds for food [163].
The efficiency of the conversion of biomass in the natural biological system far exceeds people’s expectations, and it is found that a single strain has the problem of weak enzyme production ability and single species, and the single strain with strong lignocellulose degradation ability can be combined with each other to construct a multi-strain composite strain, which can improve the degradation ability and stability of lignocellulosic degrading enzyme. Hao et al. randomly combined eight lignocellulosic-degrading bacteria to obtain a composite strain LXB, which exhibited at 36.4% lignocellulose degradation rate after 168 h, and found that LXB was involved in lignocellulose degradation of cellulosic enzymes, hemicellulase, and ligninase in a high state of expression, and LXB could degrade harmful exogenous substances, thereby contributing to the overall detoxification process [164]. Different species of microorganisms have different degradable capacities, and by analyzing microbial diversity, we can better understand the complexity of the degradation system and further improve the degradation efficiency of lignocellulose by taking advantage of the synergies between complex and diverse microbial communities [165,166].

5. Conclusions

As the most abundant biopolymer on the earth, lignocellulose has great potential for making advanced materials such as nanomaterials, multifunctional composite materials, and sensing materials due to its advantages of easy water treatment, excellent biodegradability, and compatibility with living organisms [167,168,169]. The degradation and application of lignocellulose has been a research hotspot in recent years, among which the degradation of lignocellulose by microorganisms is the most concentrated, and its efficiency varies with different ecosystems and microbial species. Microorganisms such as fungi and bacteria each exhibit unique advantages and adaptive capabilities in this process. A key strategy for lignocellulose degradation is enzymatic hydrolysis [170]. However, the rapid degradation of lignocellulosic biomass relies on the successful identification and selection of microbial strains capable of producing highly active lignocellulolytic enzymes [171,172,173].
Currently, screening and cultivating strains with high lignocellulase activity is an effective approach for efficient lignocellulose degradation and for enhancing the added value of agricultural by-products. A deeper understanding of how microbial species, enzyme systems, and ecological adaptability impact lignocellulose degradation efficiency will help optimize microbial degradation processes and improve the utilization of lignocellulosic resources [174].
To date, research on lignocellulose-degrading microorganisms and their enzyme systems—including degradation mechanisms and influencing factors—remains limited. In particular, detailed pathways and enzyme systems of microorganisms under specific environmental conditions are not yet fully understood. Future research in microbial lignocellulose degradation will likely focus on identifying and selecting additional strains with enhanced lignocellulose-degrading capabilities. As high-throughput technologies continue to advance, future studies can increasingly leverage metagenomics, transcriptomics, and proteomics to further explore enzyme system structure and function and to uncover the underlying mechanisms of lignocellulolytic enzymes. Synthetic biology was used to optimize the degradation ability of microorganisms, and specific lignocellulase genes were edited by genetic engineering; the high redox potential laccase (∼780 mV) produced by Trametes versicolor is one of the most studied enzymes in this enzyme family. Some studies have found that using the CRISPR/Cas9 system to knock out, silence, and destroy the target laccase gene can seriously affect the expression and activity of laccase, thus revealing the importance of the expression and metabolism of the target laccase gene in fungi [175,176]. Fan used genome walking technologies such as degenerate primer PCR, TAIL-PCR and RT-PCR technology to clone and obtain a laccase gene lac48424-1 and its full-length cDNA sequence from the strain Trametes sp.48424, and cloned the upstream regulatory sequence of laccase gene promoter by SEFA-PCR and other genome step technologies, predicting that there were multiple cis-acting DNA regulatory elements that may be involved in transcriptional regulation. Yeast recombinant laccase protein was successfully purified from Pichia pastoris transformants expressing LAC48424-1 laccase gene [177]. The research on the acquisition, physiological functions, and expression regulation of laccase gene resources is extremely important for enriching the molecular biology theory of white rot fungi and improving related biotechnology methods, and will be a future research focus.
At the same time, artificial intelligence (AI) and automation technology are introduced to optimize the microbial degradation process, and monitor the activity of enzymes and the growth status of microorganisms in real time to achieve accurate control of the degradation process. At present, artificial intelligence is accelerating the change in the research and development of the biological fermentation industry. Not only can AI use big language models (LLM) to analyze the scientific literature, extract biological process features, and provide accurate data support for subsequent research, it can also analyze the sequence and structure of enzymes through deep learning models such as AlphaFold2 (AF2), DLKcat, DeepSeek, etc., accurately predict the activity and catalytic efficiency of metabolic enzymes, and reduce the cost of experimental screening. AI can also simulate fermentation processes in different environments, monitor real-time fermentation data through AI+Internet of Things (AIoT), intelligently adjust production parameters, achieve precise control, improve enzyme production, further enhance the degradation efficiency of lignocellulose, promote the practical application of microbial degradation of lignocellulose in industry and agriculture, and thus achieve efficient utilization of lignocellulosic biomass.

Author Contributions

Conceptualization, Formal analysis, Roles/Writing—original draft, M.C.; Investigation, Supervision, Project administration, Q.L.; Methodology, Software, C.L. and E.M.; Funding acquisition, Validation, Writing—review and editing, B.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Natural Science Foundation for Youths of Hunan Province of China (No. 2025JJ60150), the Development and Expression Optimisation of Manganese-containing Peroxidase (No. E22323) and the Screening and Identification of Heterotrophic Nitrifying-aerobic Denitrifying Bacteria and Applied Research (No. E523A0).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare that they have no conflicts of interest.

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Figure 1. Pretreatment of lignocellulosic biomass [6].
Figure 1. Pretreatment of lignocellulosic biomass [6].
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Figure 2. Degradation of lignocellulose by lignocellulases [88,90,91].
Figure 2. Degradation of lignocellulose by lignocellulases [88,90,91].
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Figure 3. Degradation of cellulases and hemicelluloses by anaerobic cellulolytic bacteria and filamentous fungi [100,101,102].
Figure 3. Degradation of cellulases and hemicelluloses by anaerobic cellulolytic bacteria and filamentous fungi [100,101,102].
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Table 1. Process characteristics and enzyme cost composition of selected techno-economic analyses of industrial enzyme production.
Table 1. Process characteristics and enzyme cost composition of selected techno-economic analyses of industrial enzyme production.
Reference[11][12][13][14][15][16]
Process characteristics
Enzyme productCellulase mixCellulase mixCellulase mixCellulase mixβ-glucosidaseMultienzyme
Microbial platformTrichoderma reeseiTrichoderma reeseiTrichoderma reeseiTrichoderma reeseiEscherichia coli (recombinant)Aspergillus awamori
Cultivation modeSmCSmCSmCSmCSmCSSC
Production titer (g/L)505011–35?5?
Productivity (g∙L−1∙h−1)0.260.420.10–0.32?0.21?
Product yield (g protein/g carbon source)20%24%26%21%2.5%2.4%
Enzyme cost composition
Facility-dependent/capital-related48%21%+++20%45%43%
Raw materials/
nutrients		28%62%++60%25%31%
Utilities/
electricity		10%13%+15%2%4%
Consumables4%0% 0%23%5%
Labor/fixed cost7%4%+5%4%18%
Other costs3%0% 0%1%0%
Enzyme cost (US$ kg−1)1054531659
Table 2. Examples of fungi producing lignocellulolytic enzymes.
Table 2. Examples of fungi producing lignocellulolytic enzymes.
EnzymeMicroorganismOptimal pHOptimal Temperature
(°C)		References
EndoglucanasesCladosporium cladosporioides430[29]
Fusarium sp.5.530[30]
Aspergillus niger5.530[31]
ExoglucanasesFusarium sp.5.530[30]
Aspergillus niger5.530[31]
Phaeolus spadiceus4.525–30[32]
β-glycosidasesCladosporium cladosporioides430[29]
Aspergillus niger5–925–45[33]
Fusarium sp.5.530[30]
Trichoderma sp.528[34]
Trichoderma harzianum670[35]
XylanasesAspergillus tubingensis3–830–60[36]
Talaromyces amestolkiae730[37]
PeroxidasesPleurotus ostreatus3.325[38]
Hypsizygus ulmarius728[39]
Pleurostuus florida728[39]
LaccasesTrametes polyzona4.555[40]
Trametes versicolor4–540–50[41]
Coriolopsis gallica6–840–60[42]
Pycnoporus sp.60[43]
Table 3. Examples of bacteria producing lignocellulolytic enzymes.
Table 3. Examples of bacteria producing lignocellulolytic enzymes.
EnzymeMicroorganismOptimal pHOptimal Temperature
(°C)		Reference
EndoglucanasesBacillus subtilis560[50]
Neobacillus sedimentimangrovi760[51]
Arthrobacter woluwensis850[52]
Thermotoga naphtophila690[53]
ExoglucanasesClostridium thermocellum5.770[54]
XylanasesThermotoga marítima TmxB5100[55]
Acinetobacter johnsonii655[56]
Bacillus haynesii740[57]
Caldicoprobacter algeriensis6.580[58]
LaccasesPseudomonas spp.3–820–80[59]
Bacillus ayderensis SK3-4775[60]
EndoglucanasesLysinibacillus macroides730[61]
Pseudomonas parafulva850[62]
Table 4. Effectiveness of fungal and bacterial degradation of lignocellulose.
Table 4. Effectiveness of fungal and bacterial degradation of lignocellulose.
Compare ItemsFungiBacteriaReference
Degrading enzyme speciesExtracellular enzymes such as cellulase, hemicellulase, and ligninase are secreted to enzymatically hydrolyze lignocelluloseExtracellular enzymes such as cellulase and hemicellulase are secreted, and some bacteria can produce ligninase[77]
Degradation productsMainly carbon dioxide, water and some small molecule organic compoundsMainly simple sugars, organic acids and a small amount of carbon dioxide[78,79,80]
Degradation efficiencyIt is usually slower, but it can degrade lignocellulose more thoroughly, especially for ligninIt is relatively fast, but the overall degree of degradation of lignocellulose is not as good as that of fungi, and it is difficult to completely degrade lignin[81]
Application scenariosIt has a wide range of applications in the fields of chemicals, pulp, bioenergy production, composting, etc., and can be used to produce high-quality biofuels and bio-based productsIt is widely used in wastewater treatment, silage, composting, bioenergy development, etc., and can be used to remove organic pollutants in wastewater and produce a variety of organic acids and clean energy such as methane[45,82]
Environmental adaptabilityIt has strict requirements for environmental conditions, such as temperature, humidity and pH, etc., and the growth rate is relatively slowIt has strong adaptability to the environment, can grow in a wide range of temperature, humidity and pH value, and has a fast growth rate[83,84]
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Chen, M.; Li, Q.; Liu, C.; Meng, E.; Zhang, B. Microbial Degradation of Lignocellulose for Sustainable Biomass Utilization and Future Research Perspectives. Sustainability 2025, 17, 4223. https://doi.org/10.3390/su17094223

AMA Style

Chen M, Li Q, Liu C, Meng E, Zhang B. Microbial Degradation of Lignocellulose for Sustainable Biomass Utilization and Future Research Perspectives. Sustainability. 2025; 17(9):4223. https://doi.org/10.3390/su17094223

Chicago/Turabian Style

Chen, Mengke, Qinyu Li, Changjun Liu, Er Meng, and Baoguo Zhang. 2025. "Microbial Degradation of Lignocellulose for Sustainable Biomass Utilization and Future Research Perspectives" Sustainability 17, no. 9: 4223. https://doi.org/10.3390/su17094223

APA Style

Chen, M., Li, Q., Liu, C., Meng, E., & Zhang, B. (2025). Microbial Degradation of Lignocellulose for Sustainable Biomass Utilization and Future Research Perspectives. Sustainability, 17(9), 4223. https://doi.org/10.3390/su17094223

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