Lignin Biodegradation Research Articles

Enhanced biodegradation of lignin and lignocellulose constituents in the pulp and paper industry black liquor using integrated magnetite nanoparticles/bacterial assemblage

The study was designed to explore the efficiency of magnetite nanoparticles (Fe3O4 NPs)/bacterial cell assembly to biodegrade lignin and lignocellulose, decontaminate pulp and paper-contaminated wastewater and optimize lignin adsorption by Fe3O4 NPs. Water samples were collected from three paper and carton manufacturing companies, Alexandria Governorate, Egypt. Pseudomonas otitidis MCC10330, the most active and promising strain among 10 previously screened indigenous and exogenous isolates, was selected and decorated with magnetic Fe3O4 Nanoparticles, that were prepared by the co-precipitation method, characterized and used to decontaminate paper and pulp effluent in a batch mode bioassay for 4 h. Fe3O4 NPs/bacterial cell assembly achieved the highest removals (64.1, 52.0, 54.3 and 66.6%) of TSS, COD, BOD, and Total Tannin and Lignin after 1, 4 and 4 h, reaching residual concentrations (RCs) of 322, 216, 112 and 7 mg/L, which are still slightly higher (5.35, 2.7 and 1.86-fold) than their maximum permissible limits (MPLs), respectively. RCs of pH, DO and TDS in the treated effluent are accepted for safe discharging. Maximum lignin adsorption and removal (82.14%) using Fe3O4 NPs was achieved at the optimized conditions (pH 6, Fe3O4 NPs dosage of 100 mg and 10 min contact time). Results confirmed that the proposed magnetite-coated Pseudomonas otitidis treatment system is highly efficient and recommended to treat the highly contaminated pulp and paper wastewater. Also, as far as we know, this integrated assemblage is the first time to be used as a novel, very promising, eco-friendly, renewable and economical biotechnological approach to minimize/eliminate the involved pollutants with the least running time.

The white rot basidiomycete Gelatoporia subvermispora produces fatty aldehydes that enable fungal manganese peroxidases to degrade recalcitrant lignin structures.

The ability of some white rot basidiomycetes to remove lignin selectively from wood indicates that low molecular weight oxidants have a role in ligninolysis. These oxidants are likely free radicals generated by fungal peroxidases from compounds in the biodegrading wood. Past work supports a role for manganese peroxidases (MnPs) in the production of ligninolytic oxidants from fungal membrane lipids. However, the fatty acid alkylperoxyl radicals initially formed during this process are not reactive enough to attack the major structures in lignin. Here, we evaluate the hypothesis that the peroxidation of fatty aldehydes might provide a source of more reactive acylperoxyl radicals. We found that Gelatoporia subvermispora produced trans-2-nonenal, trans-2-octenal, and n-hexanal (a likely metabolite of trans-2,4-decadienal) during the incipient decay of aspen wood. Fungal fatty aldehydes supported the in vitro oxidation by MnPs of a nonphenolic lignin model dimer, and also of the monomeric model veratryl alcohol. Experiments with the latter compound showed that the reactions were partially inhibited by oxalate, the chelator that white rot fungi employ to detach Mn3+ from the MnP active site, but nevertheless proceeded at its physiological concentration of 1 mM. The addition of catalase was inhibitory, which suggests that the standard MnP catalytic cycle is involved in the oxidation of aldehydes. MnP oxidized trans-2-nonenal quantitatively to trans-2-nonenoic acid with the consumption of one O2 equivalent. The data suggest that when Mn3+ remains associated with MnP, it can oxidize aldehydes to their acyl radicals, and the latter subsequently add O2 to become ligninolytic acylperoxyl radicals.IMPORTANCEThe biodegradation of lignin by white rot fungi is essential for the natural recycling of plant biomass and has useful applications in lignocellulose bioprocessing. Although fungal peroxidases have a key role in ligninolysis, past work indicates that biodegradation is initiated by smaller, as yet unidentified oxidants that can infiltrate the substrate. Here, we present evidence that the peroxidase-catalyzed oxidation of naturally occurring fungal aldehydes may provide a source of ligninolytic free radical oxidants.

Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3

BackgroundBioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation.ResultsOur previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47–69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography–mass spectrometry (LC–MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization.ConclusionsOur findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.

Efficient lignin biodegradation triggered by alkali-tolerant ligninolytic bacteria through improving lignin solubility in alkaline solution

Low lignin solubility in aqueous solution is one of the major bottlenecks for lignin biodegradation and bioconversion. Alkaline solution contributes to improving lignin solubility, whereas most microbes can not survive in alkaline conditions. Herein, lignin dissolution behaviors in different pH solutions were systematically investigated, which indicated that solution pH above 10.5 contributed to high solubility of alkali lignin. To match with alkaline lignin aqueous system, several alkali-tolerant ligninolytic bacteria were isolated, most of which are distinct to previously reported ones. Then, the ligninolytic capabilities of these isolates were assessed in different pH conditions by determining their assimilation on alkali lignin, lignin-derived monomers and dimers, their decolorization capabilities, and their lignin peroxidase activities. Thereafter, the underlying ligninolytic and alkali-tolerant mechanisms of Sutcliffiella sp. NC1, an alkalophilic bacterium, was analyzed on the basis of its genome information. The results not only provide valuable information for lignin biodegradation and lignin valorization, but also expand knowledge on alkali-tolerant bacteria.

Moisture-Induced Effects on Lignocellulosic and Humification Fractions in Aerobically Composted Straw and Manure

Humic substances affect compost stability and maturation. However, the intricate structure of lignocellulosic materials hinders the biodegradation of cellulose, hemicellulose, and lignin, often promoting the use of synthetic additives which results in microbial inactivation and death. Therefore, this study examined the effects of optimal moisture levels (MC1 = 45%, MC2 = 55%, and MC3 = 65%) on lignocellulosic and humification fractions in aerobically composted straw and manure. The study showed that 65% moisture content was more efficient in decomposing cellulose, hemicellulose, and lignin, with hemicellulose (115.3% w/w ≈ 47.1%) degrading more than cellulose (76.0% w/w ≈ 39.5%) and lignin (39.9% w/w ≈ 25.9%). However, in compost heaps with 45% moisture, the humic acid concentration increased significantly by 12.4% (3.1% w/w) and 17.3% (4.3% w/w) compared with 55% and 65% moisture, respectively. All moisture levels increased the mineralization of humic substances, but the index measured was highest at 65% MC (23.8% w/w) and lowest at 45% MC (18% w/w). In addition, the humification rate showed the trend: 0.083% w/w > 0.087% w/w > 0.100% w/w for MC1, MC2, and MC3, respectively. Overall, the results indicate that an initial moisture content of 65% is aerobically efficient for the conversion of corn straw and cow manure into stable and mature compost.

Isolation and Characterization of Potential Lignin Peroxidase-Producing Bacteria from Compost Samples at Richards Bay (South Africa).

Lignin recalcitrance is a key issue in producing value-added products from lignocellulose biomass. In situ biodegradable lignin-modifying enzymes-producing bacteria are considered a suitable solution to lignin biodegradation problems, but exploitation of ligninolytic bacteria is still limited to date. Hence, this study aimed to isolate and characterize potential lignin peroxidase ligninolytic bacteria from decomposing soil, sawdust, and cow dung at Richard Bay, South Africa. The samples were collected and cultured in the lignin-enriched medium. Pure isolated colonies were characterized through 16S rRNA gene sequencing. The ability of the isolates to grow and utilize aromatic monomers (veratryl and guaiacol alcohol) and decolorize lignin-like dyes (Azure B, Congo Red, Remazol Brilliant Blue R) was evaluated. Of the twenty-six (26) bacteria isolates 10 isolates, including Pseudomonas spp. (88%), Enterobacter spp. (8%), and Escherichia coli (4%) were identified as true lignin peroxidase producers. Pseudomonas aeruginosa (CP031449.2) and E. coli (LR025096.1) exhibited the highest ligninolytic activities. These isolates could potentially be exploited in the industry and wastewater treatment as effective lignin degrading agents.

Construction and Identification of a Food-Grade Recombinant Cyberlindnera jadinii Strain Expressing Lignin Peroxidase

Lignin peroxidase is one of a series of enzymes involved in lignin degradation and is secreted by white-rot fungi. However, white-rot fungi have a long growth cycle and low enzyme activity, which limits their application. An efficient and stable heterologous expression system might be the solution to overcome these critical limitations. In this study, the lignin peroxidase gene of white-rot fungus (Phanerodontia chrysosporium) was cloned and heterologously expressed in the food-grade yeast Cyberlindnera jadinii for the first time. The strain ZHMX4 expressing lignin peroxidase was constructed, and its genetic stability, enzyme activity and phenotypic analysis were evaluated. ZHMX4 retained and maintained genetic stability for up to 100 generations. Its lignin peroxidase activity reached a maximum at 96 h with 68.52 U/L. Phenotypic analysis (Biolog) showed obvious changes in the substrate metabolism of the engineered strain compared to Cyberlindnera jadinii. Thus, ZHMX4 is a food-grade genetically engineered strain with great potential for lignin degradation. This study successfully expressed lignin peroxidase in Cyberlindnera jadinii as a new approach for the biodegradation of lignin. These findings should be useful for further academic studies, industrial applications of lignin peroxidase and construction of artificial white-rot fungi.

Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions.

Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.

Degradation of lignin in different lignocellulosic biomass by steam explosion combined with microbial consortium treatment

The difficulty of degrading lignin is the main factor limiting the high-value conversion process of lignocellulosic biomass. The biodegradation of lignin has attracted much attention because of its strong environmental friendliness, but it still faces some dilemmas such as slow degradation rate and poor adaptability. The microbial consortia with high lignin degradation efficiency and strong environmental adaptability were obtained in our previous research. To further increase the lignin degradation efficiency, this paper proposes a composite treatment technology of steam explosion combined with microbial consortium degradation to treat three kinds of biomass. We measured the lignin degradation efficiency, selectivity value (SV) and enzymatic saccharification efficiency. The structural changes of the biomass materials and microbial consortium structure were also investigated. The experimental results showed that after 1.6 MPa steam explosion treatment, the lignin degradation efficiency of the eucalyptus root reached 35.35% on the 7th days by microbial consortium. At the same time, the lignin degradation efficiency of the bagasse and corn straw treated by steam explosion followed by microbial biotreatment was 37.61–44.24%, respectively, after only 7 days of biotreatment. The microbial consortium also showed strong selectivity degradation to lignin. The composite treatment technology can significantly improve the enzymatic saccharification efficiency. Saccharomycetales, Ralstonia and Pseudomonadaceae were the dominant microorganisms in the biomass degradation systems. It was proved that the combined treatment technology of steam explosion and microbial consortium degradation could overcome the drawbacks of traditional microbial pretreatment technology, and can facilitate the subsequent high-value conversion of lignocellulose.

Biodegradation characteristics of lignin in pulping wastewater by the thermophilic Serratia sp. AXJ-M: Performance, genetic background, metabolic pathway and toxicity assessment

The key to the efficient removal of pulping wastewater lies in the effective degradation of lignin at high temperature. There is thus an urgent need to seek effective eco-environmental techniques to overcome this environmental limit for lignin degradation. The soil isolate thermophilic Serratia sp. AXJ-M efficiently metabolizes lignin. Nevertheless, the underlying comprehensive molecular mechanism of lignin degradation by thermophilic AXJ-M is poorly understood. Here, strain AXJ-M showed excellent degradation ability toward diverse lignin-related aromatic compounds. Functional genome analysis and RNA-Seq disclosed several traits which in joint consideration suggest a high efficiency of AXJ-M representative to the lignin degradation and environmental adaptation. Multiomics analyses combined with GC–MS revealed seven potential lignin biodegradation pathways. DyP was predicted to be involved in the breakdown of the β-O-4 ether bond, Cα-Cβ bond and Cα oxidation of lignin by prokaryotic expression and gene knockout and complementation. Molecular docking deepens the understanding of the interaction between DyP and lignin. Toxicity assessment experiments clearly indicated that AXJ-M significantly reduced the toxicity of the metabolites. This work expands the knowledge about the degradation mechanism of thermophilic lignin-degrading bacteria, most importantly, offers a new perspective on potential applications in utilizing this strain in pulping wastewater bioremediation.

Description of Dissolved Organic Matter Transformational Networks at the Molecular Level.

Dissolved Organic Matter (DOM) is an important component of the global carbon cycle. Unscrambling the structural footprint of DOM is key to understand its biogeochemical transformations at the mechanistic level. Although numerous studies have improved our knowledge of DOM chemical makeup, its three-dimensional picture remains largely unrevealed. In this work, we compare four solid phase extracted (SPE) DOM samples from three different freshwater ecosystems using high resolution mobility and ultrahigh-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FT-ICR MS/MS). Structural families were identified based on neutral losses at the level of nominal mass using continuous accumulation of selected ions-collision induced dissociation (CASI-CID)FT-ICR MS/MS. Comparison of the structural families indicated dissimilarities in the structural footprint of this sample set. The structural family representation using Cytoscape software revealed characteristic clustering patterns among the DOM samples, thus confirming clear differences at the structural level (Only 10% is common across the four samples.). The analysis at the level of neutral loss-based functionalities suggests that hydration and carboxylation are ubiquitous transformational processes across the three ecosystems. In contrast, transformation mechanisms involving methoxy moieties may be constrained in estuarine systems due to extensive upstream lignin biodegradation. The inclusion of the isomeric content (mobility measurements at the level of chemical formula) in the structural family description suggests that additional transformation pathways and/or source variations are possible and account for the dissimilarities observed. While the structural character of more and diverse types of DOM samples needs to be assessed and added to this database, the results presented here demonstrate that Graph-DOM is a powerful tool capable of providing novel information on the DOM chemical footprint, based on structural interconnections of precursor molecules generated by fragmentation pathways and collisional cross sections.

Biotechnological methods in pulp and paper production from an alternative source of raw materials - the savior of the ecosystem

The pulp and paper industry is at its peak due to the annual growth in demand for paper products which includes packaging board, hygienic paper products, printing papers and the list is endless. To date, the main source of raw materials for pulp and paper production is wood. However, its use and the use of standard flow charts in pulp and paper production creates environmental problems. For example, deforestation to obtain raw materials leads to a disruption of biogeocenoses, and technology using alkalis and acids are sources of toxic wastewater that pollute the hydrosphere and lithosphere. In order to avoid the above environmental problems, other options for sustainable sources of raw materials can be considered, such as agricultural waste - straw. By its natural origin, straw is a non-woody plant, which will significantly simplify the flow chart of pulp and paper production, on the one hand, and on the other hand, the use of straw in production will help to reduce the risks of early global warming, since most of the straw is burned in the fields. As far as toxic wastewater emissions are concerned, they can be drastically reduced through the biological degradation of straw lignin to produce pure pulp. Biodegradation of lignin can be produced by widespread wood-destroying fungi due to their ability to synthesize lignin-degrading enzymes. Thus, the use of biological agents in pulp and paper production will make it possible to eliminate the use of caustic acids and alkalis.

Biological degradation of lignin: A critical review on progress and perspectives

As the second most abundant biopolymer on earth after cellulose, lignin is considered to be an alternative source of various polymers and biomaterials since it can be cleaved into a large number of phenolic compounds . Due to its complex structure and low reactivity, depolymerization of lignin is the premise and rate-limiting step of its valorization. In nature, lignin can be degraded by microorganisms and their secreted enzymes into building blocks that can potentially be converted into high-value chemicals. In this review, the research progress on lignin biodegradation is discussed, focusing on the key enzymes and reaction mechanisms of lignin degradation, which provides a molecular basis for lignin bio-depolymerization. In addition, the metabolic pathways of different lignin derivatives in microorganisms are summarized, and value-added compounds derived from lignin are reviewed. Finally, the challenges and prospects of lignin biorefinery concepts are discussed. • Lignin is a potential feedstock for production of aromatic chemicals. • Lignin-degrading microorganisms degrade lignin by secreting extracellular enzymes. • Microorganisms metabolize lignin derivatives through the biological funnel mechanism. • Transformation of lignin into various biochemicals by several microorganisms are discussed.

Optimizing biocatalytic potential of Dipodascus australiensis M-2 for degrading lignin under laboratory conditions

In present research, a potent fungal strain was isolated from paper mill effluent (black liquor) in order to investigate its potential for the biodegradation of lignin. Two step strategy was used to screen most efficient fungal strain having ability to growin MSM-black liquor medium and to degrade alkali lignin.The results of initial screening indicated that the strain M-2 produced comparatively higher ligninolytic zone on MSN agar plates supplemented with black liquor (BL) and alkali ligninase compared to the other isolates.The results of 18S rRNA gene sequencing revealed that strain M-2 showed ≥ 99% sequence homology with Dipodasceus australiansis.The process for the biodegradation of lignin was optimized using Taguchi Orthogonal Array design. Under optimized conditions of pH 9, 40 °C and 4% inoculum, a maximum of 89% lignin was degraded with 41% color reduction after 8 days of incubation period by Dipodasceus australiansis M-2. The pH and temperature were found to be significant terms with the p-values of 0.002 and 0.001 respectively. The laccase activity of the Dipodascus australiensis was found to be maximum of 1.511 U/mL. The HPLC analysis of lignin biodegradation indicated sharp transformation of peaks as compared to the control. Our results suggested that the strain Dipodascus australiensis M-2 possess excellent lignin degradation and color reduction capability and can be applied in waste treatment systems for pulp and paper mill effluent. In present work we are reporting first hand information regarding biodegradation of lignin by a potent strain of Dipodascus australiensis and statistical optimization of the bioprocess.

Impact of composting factors on the biodegradation of lignin in Eichhornia crassipes (water hyacinth): A response surface methodological (RSM) investigation

Water hyacinth (Eichhornia crassipes) is a hydrophyte weed that causes havoc in the aquatic ecosystem as an invasive plant that can obstruct waterways and bring about nutrient imbalance. This study aims to address how this invasive hydrophyte can be physically harvested and biochemically transformed into a bioproduct that can enhance the restoration of damaged soil. Biocomposting, a low-cost biotechnological technique, was designed to degrade the lignocellulosic Eichhornia crassipes biomass and transform it into a valuable bioproduct. The process used response surface methodology (RSM) to investigate the aggregate effect of moisture content, turning frequency, and microbial isolate (Chitinophaga terrae) inoculum size on the breakdown of lignin over 21 days. The moisture content (A), (45, 55, 65) % v/w, inoculum size (B), (5, 7.5, 10)% v/v, and turning frequency (C), (1, 3, 5) days were considered independent variables, while percentage lignin degradation was considered a response variable. The optimal conditions for lignin breakdown were 65.7 percent (v/w) moisture, 7.5 percent (v/v) inoculum concentration, and 5-day interval turning. The R2 score of 0.9733 demonstrates the model's integrity and reliability. Thus, the RSM approach resulted in a fine grain dark brown Nutri-compost that proved effective in enhancing soil fertility. This procedure is recommended for a scale-up process where large quantities of the hydrophyte could be treated for conversion into Nutri compost.

New approach of bioprocessing towards lignin biodegradation

Bio-utilization of lignocellulosic biomass is of huge significance as it can directly replace petroleum resources by producing liquid fuels and organic chemical products in a more sustainable way. However, studies on developing lignin-degrading microbial resources are still very few, which affects on establishing a consolidated bioprocessing of lignocellulosic resource. The main aim of this work is to discover thermostable laccases for lignin thermo-biodegradation by metagenome-mining and biochemical characterization. Results indicate that 124 putative thermostable laccase genes were identified from generated metagenomes. Significantly, 3 rationally selected proteins showed actual activity and structural stability at temperatures up to 60 °C and pH values as low as 4.87. These active recombinant enzymes verify a practical advance in the functional prediction of target proteins, and simultaneous sequence-to-function relationships in this metagenome. In short, the identified thermostable laccase genes in this work could expand range of lignin biocatalysts and contribute to build an efficient lignin biorefinery.

Analysis of decomposing wood wastes in the Lagos Lagoon using terminal-restriction fragment length polymorphism and illumina sequencing platform

Indiscriminate disposal of wood shavings and sawdust into the Lagos lagoon usually constitute environmental hazard and varying degree of threats to marine biotic communities. In this study we applied terminal-restriction fragment length polymorphism (T-RFLP) and illumina sequencing of 16S ribosomal RNA gene, to describe the microbial ecology of decomposing wood wastes in the Lagos lagoon, Nigeria. The terminal restriction fragments (TRFs) generated corresponds to over 100 bacterial genera and numerous uncultured bacterial clones. Phylogenetic analysis of the TRFs of 16S rRNA gene sequences and cultured bacterial sequences established genetic relatedness and divergent relationships. T-RFLP in combination with illumina sequencing platform identified bacterial species (Acinetobacter sp., Clostridium sp., Planctomyces sp., Escherichia coli, Pantoea agglomerans, Dyella japonica, Ochrobactrum sp., Prevotella sp., Runella slithyformis, Enterobacter aerogenes, Gordonia amicalis, Klebsiella sp., Thalassospira sp. and Serratia sp.) not previously accounted for in culture-dependent analysis. Bacterial strains such as Ruminococcus flavefaciens, Fibrobacter succinogenes, Simiduia agarivorans, Microbulbifer sp. and Cellulomonas fimi further identified in illumina sequences were found to be involved in the biodegradation of lignin and lignin derivatives. Hence, understanding of the diverse autochthonous microbiota of decomposing wood wastes in the Lagos lagoon is essential in the development of effective biotechnology programme, to tackling the menace of sawdust pollution.

Lignin Biodegradation and Its Valorization

Lignin, a rigid polymer composed of phenolic subunits with high molecular weight and complex structure, ranks behind only cellulose in the contribution to the biomass of plants. Therefore, lignin can be used as a new environmentally friendly resource for the industrial production of a variety of polymers, dyes and adhesives. Since laccase was found to be able to degrade lignin, increasing attention had been paid to the valorization of lignin. Research has mainly focused on the identification of lignin-degrading enzymes, which play a key role in lignin biodegradation, and the potential application of lignin degradation products. In this review, we describe the source, catalytic specificity and enzyme reaction mechanism of the four classes of the lignin-degrading enzymes so far discovered. In addition, the major pathways of lignin biodegradation and the applications of the degradative products are also discussed. Lignin-degrading bacteria or enzymes can be used in combination with chemical pretreatment for the production of value-added chemicals from lignin, providing a promising strategy for lignin valorization.

Enzymatic hydrolysis of corn stover lignin by laccase, lignin peroxidase, and manganese peroxidase

Lignin of high purity and structural integrity was isolated from the enzymatic residue of corn stover. Degradation of the lignin by laccase, lignin peroxidase, and manganese peroxidase was investigated. Structural changes in the lignin after degradation were characterized by scanning electron microscopy, nitrogen adsorption and Fourier transform infrared spectroscopy, and the enzymatic products were systematically analyzed by gas chromatography mass spectrometry. The highest percentage of lignin degradation was obtained with a mixture of three enzymes (25.79%): laccase (Lac), the starting enzyme of the mixed enzyme reaction, worked with lignin peroxidase (LiP), and manganese peroxidase (MnP) to further degrade lignin. This degradation destroyed the macromolecular structure of lignin, broke its key chemical bonds, and opened benzene rings, thus producing more acidic compounds. This study elucidated the concept of degrading lignin from corn stover using the Lac, LiP and MnP enzymes synergistically, thus providing a theoretical basis for the biodegradation of lignin.

In silico homology modeling, docking and sequence analysis of some bacterial laccases to unravel enzymatic specificity towards lignin biodegradation

Laccase is a delignifying enzyme that belongs to the oxidoreductase family, and it has long been investigated as a pretreatment agent in biofuel production. In this study, amino acid sequences of five bacterial laccases from Bifidobacterium breve, Klebsiella pneumonia, Pseudodesulfovibrio hydrargyri, Pseudomonas aeruginosa and Veillonella rodentium have been retrieved from UniProtKB for sequence alignment, phylogenetic analysis using MEGA 7.0 and 3 D structure prediction by homology modeling in SWISS-MODEL. Multiple sequence alignment between all the bacterial laccase sequences revealed a similar structural fold, although the overall protein sequence varied greatly with the substrate binding sites. Further molecular docking in AutoDock Vina and MD stimulation (MDS) in GROMACS for those modelled enzymes were performed considering both apo and ligand bound structures considering both apo and its ligand bound form. Investigation of molecular interaction utilizing docking of five bacterial laccases with three substrates (ABTS, DMP and Guaiacol) revealed that ABTS with K. pneumoniae laccase had the highest binding energy of −7.00 kcal/mol. In the current MDS investigation, bacterial laccases demonstrated greater binding and substrate energy in the ligand bound complex than in the apo form for ABTS, DMP and Guaiacol. In most cases of bacterial laccase, MDS revealed that DMP bound complex was more stable within an average RMSD value lower than 0.5 nm throughout 100 ns time scale. Thus, in silico studies undertaken in this work will be useful in determining the stable enzyme-substrate complex which further might improve the enzymatic catalysis of bacterial laccases for lignin breakdown and biofuel generation.