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Lignin, the earth’s second-most abundant biopolymer after cellulose, has long been relegated to low-value byproducts in the pulp and paper industry. However, recent advancements in valorization are transforming lignin into a sustainable and versatile feedstock for producing high-value biofuels, bioplastics, and specialty chemicals. This review explores the conversion of lignin’s complex structure, composed of syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H) units, into value-added products. We critically assess various biochemical and analytical techniques employed for comprehensive lignin characterization. Additionally, we explore strategies for lignin upgrading and functionalization to enhance its suitability for advanced biomaterials. The review emphasizes key areas of lignin valorization, including catalytic depolymerization methods, along with the associated challenges and advancements. We discuss its potential as a feedstock for diverse products such as biofuels, bioplastics, carbon fibers, adhesives, and phenolic compounds. Furthermore, the review briefly explores lignin’s inherent properties as a UV protectant and antioxidant, alongside its potential for incorporation into polymer blends and composites. By presenting recent advancements and case studies from the literature, this review highlights the significant economic and environmental benefits of lignin valorization, including waste reduction, lower greenhouse gas emissions, and decreased reliance on non-renewable resources. Finally, we address future perspectives and challenges associated with achieving large-scale, techno-economically feasible, and environmentally sustainable lignin valorization.

The hunt for renewable and alternative fuels has driven research towards the biological conversion of lignocellulosic biomass (LCB) into biofuels, including bioethanol and biohydrogen. Among the natural biomass utilization systems (NBUS), termites represent a unique and easy-to-access model system to study host–microbe interactions towards lignocellulose bioconversion/valorization. Termites have gained significant interest due to their highly efficient lignocellulolytic systems. The wood-feeding termites apply a unique and stepwise process for the hydrolysis of lignin, hemicellulose, and cellulose via biocatalytic processes; therefore, mimicking their digestive metabolism and physiochemical gut environments might lay the foundation for an innovative design of nature-inspired biotechnology. This review highlights the gut system of termites, particularly the wood-feeding species, as a unique model for future biorefinery. The gut system of termites is a treasure-trove for prospecting novel microbial species, including protists, bacteria, and fungi, having higher biocatalytic efficiencies and biotechnological potentials. The significance of potential bacteria and fungi for harnessing the enzymes appropriate for lignocellulosic biorefinery is also discussed. Termite digestomes are rich sources of lignocellulases and related enzymes that could be utilized in various industrial processes and biomass-related applications. Consideration of the host and symbiont as a single functioning unit will be one of the most crucial strategies to expedite developments in termite-modeled biotechnology in the future.

There is concern over potential toxic elements (PTEs) impacting river ecosystems due to human and industrial activities. The river’s water, sediment, and aquatic life are all severely affected by the release of chemical and urban waste. PTE concentrations in sediment, water, and aquatic species from river ecosystems are reported in this review. Among the PTEs, chromium (Cr), cadmium (Cd), lead (Pb), and nickel (Ni) revealed high pollution levels in water and aquatic species (fish and shellfish) at many rivers. The Karnaphuli, Ganga, and Lee rivers have high levels of Pb and Cd contamination, while the Buriganga and Korotoa rivers’ water had notable Ni contamination. A number of rivers with PTEs showed ecological risk as a consequence of the sediment’s potential ecological risk (PER), the pollutant load index (PLI), and the geoaccumulation index (Igeo). A comprehensive study suggests elevated PLI values in river sediments, indicating significant pollution levels, particularly in the Buriganga River sediment, marked by high Igeo values. The PER of the Shitalakshya and Buriganga rivers was marked as very high risk, with an Eir > 320, while the Dhaleshwari and Khiru rivers showed ‘high risk’, with 160 = Eir < 320. It was found that fish and shellfish from the Buriganga, Turag, and Swat rivers have a high concentration of Cr. PTE pollution across several river sites could pose health toxicity risks to humans through the consumption of aquatic species. The CR value shows the carcinogenic risk to human health from eating fish and shellfish, whereas an HI value > 1 suggests no carcinogenic risk. The occurrence of other PTEs, including manganese (Mn), arsenic (As), and nickel (Ni), significantly increases the ecological risk and concerns to aquatic life and human health. This study emphasises the importance of PTE toxicity risk and continuous monitoring for the sustainability of river ecosystems.

This study reports the green synthesis of silver nanoparticles (AgNPs) using the fruit extract of Withania somnifera and their application as a colorimetric sensor for selective manganese (Mn2+) ion detection. The synthesis of AgNPs was optimized by varying pH, reaction time, and concentrations of fruit extract and AgNO3. UV–visible spectroscopy revealed that the highest absorbance of AgNPs occurred at pH 11, indicating optimal conditions for NPs formation. The absorbance behavior over time demonstrated the nucleation and stabilization processes, with optimal stability achieved after 1800 min. Increasing concentrations of fruit extract and AgNO3 enhanced NPs synthesis, reaching a plateau at 1.0 mL of extract and 1.0 mM AgNO3, respectively. Transmission electron microscopy (TEM) confirmed the formation of spherical AgNPs of 43–85 nm. Fourier-transform infrared spectroscopy (FTIR) indicated the involvement of functional groups such as O-H and C=O in the reduction and stabilization of AgNPs. The green-synthesized AgNPs exhibited notable antioxidant activity, with moderate free radical scavenging abilities compared to ascorbic acid. The colorimetric detection of Mn2+ was achieved through the aggregation of AgNPs, leading to a visible color change. UV–vis absorption spectra showed a prominent peak at 412 nm, with a linear relationship between absorbance change and Mn2+ concentration, demonstrating high sensitivity and selectivity. Comparative studies with other metal ions (Co2+, Cr3+, Ni2+) confirmed the specificity of AgNPs towards Mn2+. In conclusion, the green-synthesized AgNPs from W. somnifera offer a cost-effective and environmentally friendly approach for Mn2+ detection, with significant potential for environmental monitoring and biomedical applications.

The presence of diverse carbohydrate-active enzymes (CAZymes) is crucial for the direct bioconversion of lignocellulose. In this study, various anaerobic microbial consortia were employed for the degradation of 10 g/L of minimally pretreated corncob. The involvement of lactic acid bacteria (LAB) and a CAZyme-rich bacterium (Bacteroides cellulosilyticus or Paenibacillus lautus) significantly enhanced the lactic acid production by Ruminiclostridium cellulolyticum from 0.74 to 2.67 g/L (p < 0.01), with a polysaccharide conversion of 67.6%. The supplement of a commercial cellulase cocktail, CTec 2, into the microbial consortia continuously promoted the lactic acid production to up to 3.35 g/L, with a polysaccharide conversion of 80.6%. Enzymatic assays, scanning electron microscopy, and Fourier transform infrared spectroscopy revealed the substantial functions of these CAZyme-rich consortia in partially increasing enzyme activities, altering the surface structure of biomass, and facilitating substrate decomposition. These results suggested that CAZyme-intensified consortia could significantly improve the levels of bioconversion of lignocellulose. Our work might shed new light on the construction of intensified microbial consortia for direct conversion of lignocellulose.

In this article, Persea americana aqueous peels extract was used to synthesize silver nanoparticles in a simple and environmentally friendly manner. The properties of synthesized silver nanoparticles (AV-AgNPs) were studied via several techniques, including UV–vis spectroscopy, DLS, TEM, EDX, and FTIR. The UV–Vis spectra analysis revealed that the highest absorption peak occurred at 428 nm, providing strong evidence for forming AV-AgNPs. The TEM results indicate that the synthesized AV-AgNPs were uniformly dispersed, exhibiting a spherical shape with an average size of 24 nm. EDX imaging also confirmed the presence of AgNPs. FTIR analysis shows P. americana's phenolic compounds and proteins significantly contribute to AV-AgNP synthesis and stabilization. In addition, the antimicrobial activity of AV-AgNPs was assessed against pathogenic bacteria commonly found in humans, exhibiting a moderate zone of inhibition against the selected pathogens. Additionally, AV-AgNPs were used in antioxidant studies with the robust antioxidant properties 2, 2 diphenyl-1-picrylhydrazyl (DPPH). In vitro studies have shown that AV-AgNPs can remarkably inhibit α-amylase in a dose-dependent manner, indicating their potential as antidiabetic agents. In silico research, it was revealed that naringenin derived from P. americana exhibited a strong binding to S. typhi and B. cereus (−8.7 and −7.5 kcal/mol, respectively). At the same time, quercetin demonstrated a high binding affinity and energy to α-Amylase (−8.9 kcal/mol). This study presents the first investigation into the biosynthesis of AgNPs utilizing the aqueous peel extract derived from P. americana with multiple uses, including antioxidant, antimicrobial, and antidiabetic activity.

Dye-polluted wastewater poses a serious threat to humans’, animals’ and plants’ health, and to avoid these health risks in the future, the treatment of wastewater containing dyes is necessary before its release to environment. Herein, a biological approach is used; the textile azo dye brown 703 is degraded utilizing Pseudomonas aeruginosa. The bacterial strain was isolated from textile wastewater dumping sites in Mingora, Swat. The optimization for bacterial degradation was carried out on the nutrient broth medium, which was then subjected to a variety of environmental physicochemical conditions and nutritional source supplementation before being tested. Under micro-aerophilic circumstances, the maximum decolorization and degradation of dye occurred at a 20 ppm dye concentration within 3 days of incubation at a neutral pH and 38 °C. The decrease in the intensity of the absorbance peak in the UV–Vis spectrum was used to measure the extent of decolorization. Initially, 15 bacterial strains were isolated from the textile effluent. Out of these strains, Pseudomonas aeruginosa was found to be the most potent degrading bacteria, with a degradation extent of around 71.36% at optimum conditions. The appearance and disappearance of some new peaks in the FT-IR analysis after the degradation of brown 703 showed that the dye was degraded by Pseudomonas aeruginosa. The GC–MS analysis performed helped in identifying the degraded compounds of azo dye that were utilized in illustrating the under-study process of brown 703 degradation. The biodegradation brought about by Pseudomonas aeruginosa can be employed successfully in the future as an eco-friendly approach with far reaching results.

The sustainable extraction of natural compounds has recently attracted significant attention. The extraction of high-quality natural vanillin in active form is crucial for its efficient use in various industries, but conventional solvents are not suitable for this purpose. The flammability, volatility, and toxicity of organic solvents can harm extraction personnel, and their waste liquid can cause environmental pollution. Natural deep eutectic solvents (NADES) are cost-effective, environmentally friendly, biodegradable, and non-toxic organic alternative to conventional solvents. In this study, 20 different NADES were tested for the sustainable extraction of natural vanillin. Among these, a DES system composed of choline chloride: 1,4-butanediol: lactic acid exhibited the highest extraction rate (15.9 mg/g). Employing response surface methodology (RSM), optimal extraction conditions were determined, yielding a vanillin content 18.5 mg/g with water content of 33.9%, extraction temperature of 64.6°C, extraction time of 32.3 min, and a solid-liquid ratio of 44.9 mg/mL. Subsequently, the optimized NADES system was then assessed for reusability in extracting vanillin from vanilla pods and kraft lignin over three cycles, retaining 43% of its extraction efficiency and demonstrating potential for waste reduction. Purification of vanillin was achieved through chromatography using a non-polar resin SP700, with ethanol as a desorption eluent and a feed solution pH of 4.0, resulting in the highest vanillin purity. HPLC and GC-MS analyses confirmed purity, while antioxidant activity assays (DPPH and ABTS) showcased significant antioxidant activity of the purified vanillin. Moreover, vanillin exhibited notable antimicrobial activity against a panel of food-borne bacteria. This study introduces an environmentally friendly approach to vanillin extraction highlights using NADES, emphasizing the potential for producing high-quality bioactive vanillin with reduced environmental impact. The applicability of NADES systems extends beyond vanillin, offering a versatile method for extracting diverse natural compounds.

Lignin valorization to produce functionalized materials is challenging. This study harnessed the versatile properties of lignin through a grafting reaction involving the aryl hydroxyl group of alkali lignin (AL) and enzymatically modified-alkali lignin (EMAL) using Bacillus ligninphilus-derived laccase (Lacc) L1 and C. seriivinvornas-derived dye-decolorizing peroxidase (DyP) with keratin (K) amide group. This reaction was executed utilizing an eco-friendly solvent with the aim of generating thin films. A thorough investigation was conducted, focusing on grafting AL and EMAL onto K. The incorporation of EMAL into the films enhanced tensile strength (TS) (14.8±1.8 MPa) and elongation at break (EAB) (23.7±0.3 %). Additionally, it enhanced thermal stability, suppressed the proliferation of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), and mitigated oxidative stress. This study introduces a novel approach for lignin valorization, offering the potential to tailor mechanical properties, antibacterial and antioxidant properties of the final material, making it sustainable substitute for petroleum-based products.

Lignin, the largest non-carbohydrate component of lignocellulosic biomass, is also a recalcitrant component of the plant cell wall. While the aerobic degradation mechanism of lignin has been well-documented, the anaerobic degradation mechanism is still largely elusive. In this work, a versatile facultative anaerobic lignin-degrading bacterium, Klebsiella aerogenes TL3, was isolated from a termite gut, and was found to metabolize a variety of carbon sources and produce a single kind or multiple kinds of acids. The percent degradation of alkali lignin reached 14.8% under anaerobic conditions, and could reach 17.4% in the presence of glucose within 72 h. Based on the results of infrared spectroscopy and 2D nuclear magnetic resonance analysis, it can be inferred that the anaerobic degradation of lignin may undergo the cleavage of the C-O bond (β-O-4), as well as the C-C bond (β-5 and β-β), and involve the oxidation of the side chain, demethylation, and the destruction of the aromatic ring skeleton. Although the anaerobic degradation of lignin by TL3 was slightly weaker than that under aerobic conditions, it could be further enhanced by adding glucose as an electron donor. These results may shed new light on the mechanisms of anaerobic lignin degradation.

The current transition to sustainability and the circular economy can be viewed as a socio-technical response to environmental impacts and the need to enhance the overall performance of the linear production and consumption paradigm. The concept of biowaste refineries as a feasible alternative to petroleum refineries has gained popularity. Biowaste has become an important raw material source for developing bioproducts and biofuels. Therefore, effective environmental biowaste management systems for the production of bioproducts and biofuels are crucial and can be employed as pillars of a circular economy. Bioplastics, typically plastics manufactured from bio-based polymers, stand to contribute to more sustainable commercial plastic life cycles as part of a circular economy in which virgin polymers are made from renewable or recycled raw materials. Various frameworks and strategies are utilized to model and illustrate additional patterns in fossil fuel and bioplastic feedstock prices for various governments' long-term policies. This review paper highlights the harmful impacts of fossil-based plastic on the environment and human health, as well as the mass need for eco-friendly alternatives such as biodegradable bioplastics. Utilizing new types of bioplastics derived from renewable resources (e.g., biowastes, agricultural wastes, or microalgae) and choosing the appropriate end-of-life option (e.g., anaerobic digestion) may be the right direction to ensure the sustainability of bioplastic production. Clear regulation and financial incentives are still required to scale from niche polymers to large-scale bioplastic market applications with a truly sustainable impact.

This review delves into the mesmerizing technology of nano-agrochemicals, specifically pesticides and herbicides, and their potential to aid in the achievement of UN SDG 17, which aims to reduce hunger and poverty globally. The global market for conventional pesticides and herbicides is expected to reach USD 82.9 billion by 2027, growing 2.7% annually, with North America, Europe, and the Asia–Pacific region being the biggest markets. However, the extensive use of chemical pesticides has proven adverse effects on human health as well as the ecosystem. Therefore, the efficacy, mechanisms, and environmental impacts of conventional pesticides require sustainable alternatives for effective pest management. Undoubtedly, nano-agrochemicals have the potential to completely transform agriculture by increasing crop yields with reduced environmental contamination. The present review discusses the effectiveness and environmental impact of nanopesticides as promising strategies for sustainable agriculture. It provides a concise overview of green nano-agrochemical synthesis and agricultural applications, and the efficacy of nano-agrochemicals against pests including insects and weeds. Nano-agrochemical pesticides are investigated due to their unique size and exceptional performance advantages over conventional ones. Here, we have focused on the environmental risks and current state of nano-agrochemicals, emphasizing the need for further investigations. The review also draws the attention of agriculturists and stakeholders to the current trends of nanomaterial use in agriculture especially for reducing plant diseases and pests. A discussion of the pros and cons of nano-agrochemicals is paramount for their application in sustainable agriculture.

Abstract Identification of novel enzymes from lignin degrading microorganisms will help to develop biotechnologies for biomass valorization and aromatic hydrocarbons degradation. Bacillus ligniniphilus L1 grows with alkaline lignin as the single carbon source and is a great candidate for ligninolytic enzyme identification. The first dioxygenase from strain L1 was heterologously expressed, purified, and characterized with an optimal temperature and pH of 32.5 °C and 7.4, respectively. It showed the highest activity with 3-ethylcatechol and significant activities with other substrates in the decreasing order of 3-ethylcatechol > 3-methylcatechol > 3-isopropyl catechol > 2, 3-dihydroxybiphenyl > 4-methylcatechol > catechol. It did not show activities against other tested substrates with similar structures. Most reported catechol 2,3-dioxygenases (C23Os) are Fe2+-dependent whereas Bacillus ligniniphilus catechol 2,3-dioxygenase (BLC23O) is more Mn2+- dependent. At 1 mM, Mn2+ led to 230-fold activity increase and Fe2+ led to 22-fold increase. Sequence comparison and phylogenetic analyses suggested that BL23O is different from other Mn-dependent enzymes and uniquely grouped with an uncharacterized vicinal oxygen chelate (VOC) family protein from Paenibacillus apiaries. Gel filtration analysis showed that BLC23O is a monomer under native condition. This is the first report of a C23O from Bacillus ligniniphilus L1 with unique substrate preference, metal-dependency, and monomeric structure.

Epigenetic modifications, mainly aberrant DNA methylation, have been shown to silence the expression of genes involved in epigenetic diseases, including cancer suppression genes. Almost all conventional cancer therapeutic agents, such as the DNA hypomethylation drug 5-aza-2-deoxycytidine, have insurmountable side effects. To investigate the role of the well-known DNA protectant (ectoine) in skin cell DNA methylation and cancer cell proliferation, comprehensive methylome sequence analysis, 5-methyl cytosine (5mC) analysis, proliferation and tumorigenicity assays, and DNA epigenetic modifications-related gene analysis were performed. The results showed that extended ectoine treatment globally hypomethylated DNA in skin cells, especially in the CpG island (CGIs) element, and 5mC percentage was significantly reduced. Moreover, ectoine mildly inhibited skin cell proliferation and did not induce tumorigenicity in HaCaT cells injected into athymic nude mice. HaCaT cells treated with ectoine for 24 weeks modulated the mRNA expression levels of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Hdac1, Hdac2, Kdm3a, Mettl3, Mettl14, Snrpn, and Mest. Overall, ectoine mildly demethylates DNA in skin cells, modulates the expression of epigenetic modification-related genes, and reduces cell proliferation. This evidence suggests that ectoine is a potential anti-aging agent that prevents DNA hypermethylation and subsequently activates cancer-suppressing genes.

Abstract The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.

Fungus-growing termites are eusocial insects that represent one of the most efficient and unique systems for lignocellulose bioconversion, evolved from a sophisticated symbiosis with lignocellulolytic fungi and gut bacterial communities. Despite a plethora of information generated during the last century, some essential information on gut bacterial profiles and their unique contributions to wood digestion in some fungus-growing termites is still inadequate. Hence, using the culture-dependent approach, the present study aims to assess and compare the diversity of lignocellulose-degrading bacterial symbionts within the gut systems of three fungus-growing termites: Ancistrotermes pakistanicus, Odontotermes longignathus, and Macrotermes sp. A total of 32 bacterial species, belonging to 18 genera and 10 different families, were successfully isolated and identified from three fungus-growing termites using Avicel or xylan as the sole source of carbon. Enterobacteriaceae was the most dominant family represented by 68.1% of the total bacteria, followed by Yersiniaceae (10.6%) and Moraxellaceae (9%). Interestingly, five bacterial genera such as Enterobacter, Citrobacter, Acinetobacter, Trabulsiella, and Kluyvera were common among the tested termites, while the other bacteria demonstrated a termite-specific distribution. Further, the lignocellulolytic potential of selected bacterial strains was tested on agricultural waste to evaluate their capability for lignocellulose bioconversion. The highest substrate degradation was achieved with E. chengduensis MA11 which degraded 45.52% of rice straw. All of the potential strains showed endoglucanase, exoglucanase, and xylanase activities depicting a symbiotic role towards the lignocellulose digestion within the termite gut. The above results indicated that fungus-growing termites harbor a diverse array of bacterial symbionts that differ from species to species, which may play an inevitable role to enhance the degradation efficacy in lignocellulose decomposition. The present study further elaborates our knowledge about the termite-bacteria symbiosis for lignocellulose bioconversion which could be helpful to design a future biorefinery.

There is increasing interest in research on lignin biodegradation compounds as potential building blocks in applications related to renewable products. More attention is necessary to evaluate the effects of the initial pH conditions during the bacterial degradation of lignin. In this study we performed experiments on lignin biodegradation under acidic and mild alkaline conditions. For acidic biodegradation, lignin was chemically pretreated with hydrogen peroxide. Alkaline biodegradation was achieved by developing the bacterial growth on Luria and Bertani medium with alkali lignin as the sole carbon source. The mutant strain Escherichia coli BL21(Lacc) was used to carry out lignin biodegradation over 10 days of incubation. Results demonstrated that under acidic conditions there was a predominance of aliphatic compounds of the C3–C4 type. Alkaline biodegradation was produced in the context of oxidative stress, with a greater abundance of aryl compounds. The final pH values of acidic and alkaline biodegradation of lignin were 2.53 and 7.90, respectively. The results of the gas chromatography mass spectrometry analysis detected compounds such as crotonic acid, lactic acid and 3-hydroxybutanoic acid for acidic conditions, with potential applications for adhesives and polymer precursors. Under alkaline conditions, detected compounds included 2-phenylethanol and dehydroabietic acid, with potential applications for perfumery and anti tumor/anti-inflammatory medications. Size-exclusion chromatography analysis showed that the weight-average molecular weight of the alkaline biodegraded lignin increased by 6.75-fold compared to the acidic method, resulting in a repolymerization of its molecular structure. Lignin repolymerization coincided with an increase in the relative abundance of dehydroabietic acid and isovanillyl alcohol, from 2.70 and 3.96% on day zero to 13.43 and 10.26% on 10th day. The results of the Fourier-transformed Infrared spectroscopy detected the presence of C = O bond and OH functional group associated with carboxylic acids in the acidic method. In the alkaline method there was a greater preponderance of signals related to skeletal aromatic structures, the amine functional group and the C – O – bond. Lignin biodegradation products from E. coli BL21(Lacc), under different initial pH conditions, demonstrated a promising potential to enlarge the spectrum of renewable products for biorefinery activities.

The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

Abstract Background The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35. Results The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2–4 µm—when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C–C and C–O–C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modified. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC–MS analysis. Through genome sequencing and annotation, and from GC–MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria. Conclusion Elucidation of the β-aryl ether cleavage pathway in the strain SP-35 indicates that the β-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.

Abstract Background Wood-feeding termite, Coptotermes formosanus Shiraki, represents a highly efficient system for biomass deconstruction and utilization. However, the detailed mechanisms of lignin modification and carbohydrate degradation in this system are still largely elusive. Results In order to reveal the inherent mechanisms for efficient biomass degradation, four different organs (salivary glands, foregut, midgut, and hindgut) within a complete digestive system of a lower termite, C. formosanus, were dissected and collected. Comparative transcriptomics was carried out to analyze these organs using high-throughput RNA sequencing. A total of 71,117 unigenes were successfully assembled, and the comparative transcriptome analyses revealed significant differential distributions of GH (glycosyl hydrolase) genes and auxiliary redox enzyme genes in different digestive organs. Among the GH genes in the salivary glands, the most abundant were GH9, GH22, and GH1 genes. The corresponding enzymes may have secreted into the foregut and midgut to initiate the hydrolysis of biomass and to achieve a lignin-carbohydrate co-deconstruction system. As the most diverse GH families, GH7 and GH5 were primarily identified from the symbiotic protists in the hindgut. These enzymes could play a synergistic role with the endogenous enzymes from the host termite for biomass degradation. Moreover, twelve out of fourteen genes coding auxiliary redox enzymes from the host termite origin were induced by the feeding of lignin-rich diets. This indicated that these genes may be involved in lignin component deconstruction with its redox network during biomass pretreatment. Conclusion These findings demonstrate that the termite digestive system synergized the hydrolysis and redox reactions in a programmatic process, through different parts of its gut system, to achieve a maximized utilization of carbohydrates. The detailed unique mechanisms identified from the termite digestive system may provide new insights for advanced design of future biorefinery.

Glycoside hydrolase (GH) represents a crucial category of enzymes for carbohydrate utilization in most organisms. A series of glycoside hydrolase families (GHFs) have been classified, with relevant information deposited in the CAZy database. Statistical analysis indicated that most GHFs (134 out of 154) were prone to exist in bacteria rather than archaea, in terms of both occurrence frequencies and average gene numbers. Co-occurrence analysis suggested the existence of strong or moderate-strong correlations among 63 GHFs. A combination of network analysis by Gephi and functional classification among these GHFs demonstrated the presence of 12 functional categories (from group A to L), with which the corresponding microbial collections were subsequently labeled, respectively. Interestingly, a progressive enrichment of particular GHFs was found among several types of microbes, and type-L as well as type-E microbes were deemed as functional intensified species which formed during the microbial evolution process toward efficient decomposition of lignocellulose as well as pectin, respectively. Overall, integrating network analysis and enzymatic functional classification, we were able to provide a new angle of view for GHs from known prokaryotic genomes, and thus this study is likely to guide the selection of GHs and microbes for efficient biomass utilization.

BACKGROUND:Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS:Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. CONCLUSIONS:This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.