Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Resolving the metabolism of monolignols and other lignin-related aromatic compounds in Xanthomonas citri

Lignin, a major plant cell wall component, has an important role in plant-defense mechanisms against pathogens and is a promising renewable carbon source to produce bio-based chemicals. However, our understanding of microbial metabolism is incomplete regarding certain lignin-related compounds like p-coumaryl and sinapyl alcohols. Here, we reveal peripheral pathways for the catabolism of the three main lignin precursors (p-coumaryl, coniferyl, and sinapyl alcohols) in the plant pathogen Xanthomonas citri. Our study demonstrates all the necessary enzymatic steps for funneling these monolignols into the tricarboxylic acid cycle, concurrently uncovering aryl aldehyde reductases that likely protect the pathogen from aldehydes toxicity. It also shows that lignin-related aromatic compounds activate transcriptional responses related to chemotaxis and flagellar-dependent motility, which might play an important role during plant infection. Together our findings provide foundational knowledge to support biotechnological advances for both plant diseases treatments and conversion of lignin-derived compounds into bio-based chemicals.

Bacterial valorization of lignin for the sustainable production of value-added bioproducts

As the most abundant aromatic biopolymer in the biosphere, lignin represents a promising alternative feedstock for the industrial production of various value-added bioproducts with enhanced economical value. However, the large-scale implementation of lignin valorization remains challenging because of the heterogeneity and irregular structure of lignin. General fragmentation and depolymerization processes often yield various products, but these approaches necessitate tedious purification steps to isolate target products. Moreover, microbial biocatalytic processes, especially bacterial-based systems with high metabolic activity, can depolymerize and further utilize lignin in an eco-friendly way. Considering that wild bacterial strains have evolved several metabolic pathways and enzymatic systems for lignin degradation, substantial efforts have been made to exploit their potential for lignin valorization. This review summarizes recent advances in lignin valorization for the production of value-added bioproducts based on bacterial systems. Additionally, the remaining challenges and available strategies for lignin biodegradation processes and future trends of bacterial lignin valorization are discussed.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

Valorization of sugarcane bagasse for high-yield production of laccase through Aspergillus terreus for effective azo dye decolourization

Synthetic dyes such as azo dyes are significant pollutants in the wastewater released from various textile industries. The low biodegradability and production from synthetic sources with high shelf life make azo dyes a challenging material for degradation. This study used chemically mutated Aspergillus terrus in the laccase production under solid-state fermentation using sugarcane bagasse. Initially, the wild-type strain produced a laccase activity of 4.12 U/mL. Later, the alkaline pretreatment of sugarcane bagasse showed a significant increase in laccase activity by 38.9%. Further, random mutagenesis treatment with 100 mM EMS generated a hyper laccase-producing strain with a 2.3-fold increment in laccase activity compared to the wild-type strain. The enzyme displayed optimal activity at pH 6.5 and 35 °C. The metal ions such as Fe3+ (29.4 U/mL), Fe2+ (20.8 U/mL) and Cu2+ (18.05 U/mL) showed positive effects on laccase activity. The crude laccase was used to bioremediate Congo red, a prominent azo dye used in textile and pharmaceutical industries. The preliminary studies with a crude enzyme displayed 68.86% dye decolourization after 24 h of incubation. Additionally, with Taguchi orthogonal array optimization experiments, the maximal dye decolorization of 78.24% was achieved by maintaining crude enzyme concentration (20 U), dye concentration (25 mg/L) and pH 4.5.

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.

Bioprospecting of novel ligninolytic bacteria for effective bioremediation of agricultural by-product and synthetic pollutant dyes

Lignin is a significant renewable carbon source that needs to be exploited to manufacture bio-ethanol and chemical feedstocks. Lignin mimicking methylene blue (MB) dye is widely used in industries and causes water pollution. Using kraft lignin, methylene blue, and guaiacol as a full carbon source, 27 lignin-degrading bacteria (LDB) were isolated from 12 distinct traditional organic manures for the current investigation. The ligninolytic potential of 27 lignin-degrading bacteria was assessed by qualitative and quantitative assay. In a qualitative plate assay, the LDB-25 strain produced the largest zone, measuring 6.32 ± 0.297, on MSM-L-kraft lignin plates, while the LDB-23 strain produced the largest zone, measuring 3.44 ± 0.413, on MSM-L-Guaiacol plates. The LDB-9 strain in MSM-L-kraft lignin broth was able to decolorize lignin to a maximum of 38.327 ± 0.011% in a quantitative lignin degradation assay, which was later verified by FTIR assay. In contrast, LDB-20 produced the highest decolorization (49.633 ± 0.017%) in the MSM-L-Methylene blue broth. The highest manganese peroxidase enzyme activity, measuring 6322.314 ± 0.034 U L^-1, was found in the LDB-25 strain, while the highest laccase enzyme activity, measuring 1.5105 ± 0.017 U L^-1, was found in the LDB-23 strain. A preliminary examination into the biodegradation of rice straw using effective LDB was carried out, and efficient lignin-degrading bacteria were identified using 16SrDNA sequencing. SEM investigations also supported lignin degradation. LDB-8 strain had the highest percentage of lignin degradation (52.86%), followed by LDB-25, LDB-20, and LDB-9. These lignin-degrading bacteria have the ability to significantly reduce lignin and lignin-analog environmental contaminants, therefore they can be further researched for effective bio-waste management mediated breakdown.

Molecular insights into the chemodiversity of dissolved organic matter and its interactions with the microbial community in eco-engineered bauxite residue

Dissolved organic matter (DOM) plays an important role in the biogeochemical function development of bauxite residue. Nevertheless, the DOM composition at the molecular level and its interaction with microbial community during soil formation of bauxite residue driven by eco-engineering strategies are still relatively unknown. In the present study, the DOM composition at the molecular level and its interactions with the microbial community in amended and revegetated bauxite residue were explored. The results showed that the amendment applications and revegetation enhanced the accumulation of unsaturated molecules with high values of double bond equivalent (DBE) and nominal oxidation of carbon (NOSC) and aromatic compounds with high values of modified aromaticity index (AI_mod) as well as the reduction of average weighted molecular mass of DOM molecules. Significant correlations between DOM molecules and the microbial community and Fe/Al oxides were found. DOM molecules were decomposed by the microbial community and sequestered onto Fe/Al oxides, which were the main driving factors that changed DOM chemodiversity in the amended and revegetated bauxite residue. These findings are beneficial for understanding the biogeochemical behaviours of DOM and providing a critical basis for the development of eco-engineering strategies towards soil formation and the sustainable revegetation of bauxite residue.

Draft Genome Assembly of Stutzerimonas sp. Strain S1 and Achromobacter spanius Strain S4, Two Syringol-Metabolizing Bacteria Isolated from Compost Soil

Two bacterial strains able to use syringol as a sole carbon source were isolated from compost. The isolates, named S1 and S4, were sequenced using the Illumina platform. The final assemblies contained 4.2 Mbp, 63% GC, and 3,912 genes for S1 and 6.2 Mbp, 64% GC, and 5,503 genes for S4.

Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics

The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.

Prospects for utilizing microbial consortia for lignin conversion

Naturally occurring microbial communities are able to decompose lignocellulosic biomass through the concerted production of a myriad of enzymes that degrade its polymeric components and assimilate the resulting breakdown compounds by members of the community. This process includes the conversion of lignin, the most recalcitrant component of lignocellulosic biomass and historically the most difficult to valorize in the context of a biorefinery. Although several fundamental questions on microbial conversion of lignin remain unanswered, it is known that some fungi and bacteria produce enzymes to break, internalize, and assimilate lignin-derived molecules. The interest in developing efficient biological lignin conversion approaches has led to a better understanding of the types of enzymes and organisms that can act on different types of lignin structures, the depolymerized compounds that can be released, and the products that can be generated through microbial biosynthetic pathways. It has become clear that the discovery and implementation of native or engineered microbial consortia could be a powerful tool to facilitate conversion and valorization of this underutilized polymer. Here we review recent approaches that employ isolated or synthetic microbial communities for lignin conversion to bioproducts, including the development of methods for tracking and predicting the behavior of these consortia, the most significant challenges that have been identified, and the possibilities that remain to be explored in this field.

Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production

BACKGROUND

Lignin is an attractive alternative for producing biobased chemicals. It is the second major component of the plant cell wall and is an abundant natural source of aromatic compounds. Lignin degradation using microbial oxidative enzymes that depolymerize lignin and catabolize aromatic compounds into central metabolic intermediates is a promising strategy for lignin valorization. However, the intrinsic heterogeneity and recalcitrance of lignin severely hinder its biocatalytic conversion. In this context, examining microbial degradation systems can provide a fundamental understanding of the pathways and enzymes that are useful for lignin conversion into biotechnologically relevant compounds.

RESULTS

Lignin-degrading catabolism of a novel Rhodosporidium fluviale strain LM-2 was characterized using multi-omic strategies. This strain was previously isolated from a ligninolytic microbial consortium and presents a set of enzymes related to lignin depolymerization and aromatic compound catabolism. Furthermore, two catabolic routes for producing 4-vinyl guaiacol and vanillin were identified in R. fluviale LM-2.

CONCLUSIONS

The multi-omic analysis of R. fluviale LM-2, the first for this species, elucidated a repertoire of genes, transcripts, and secreted proteins involved in lignin degradation. This study expands the understanding of ligninolytic metabolism in a non-conventional yeast, which has the potential for future genetic manipulation. Moreover, this work unveiled critical pathways and enzymes that can be exported to other systems, including model organisms, for lignin valorization.

Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives

Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.

Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics

Lignin displays a highly challenging renewable. To date, massive amounts of lignin, generated in lignocellulosic processing facilities, are for the most part merely burned due to lacking value-added alternatives. Aromatic lignin monomers of recognized relevance are in particular vanillin, and to a lesser extent vanillate, because they are accessible at high yield from softwood-lignin using industrially operated alkaline oxidative depolymerization. Here, we metabolically engineered C. glutamicum towards cis, cis-muconate (MA) production from these key aromatics. Starting from the previously created catechol-based producer C. glutamicum MA-2, systems metabolic engineering first discovered an unspecific aromatic aldehyde reductase that formed aromatic alcohols from vanillin, protocatechualdehyde, and p- hydroxybenzaldehyde, and was responsible for the conversion up to 57% of vanillin into vanillyl alcohol. The alcohol was not re-consumed by the microbe later, posing a strong drawback on the producer. The identification and subsequent elimination of the encoding fudC gene completely abolished vanillyl alcohol formation. Second, the initially weak flux through the native vanillin and vanillate metabolism was enhanced up to 2.9-fold by implementing synthetic pathway modules. Third, the most efficient protocatechuate decarboxylase AroY for conversion of the midstream pathway intermediate protocatechuate into catechol was identified out of several variants in native and codon optimized form and expressed together with the respective helper proteins. Fourth, the streamlined modules were all genomically combined which yielded the final strain MA-9. MA-9 produced bio-based MA from vanillin, vanillate, and seven structurally related aromatics at maximum selectivity. In addition, MA production from softwood-based vanillin, obtained through alkaline depolymerization, was demonstrated.

Exploring the compatibility between hydrothermal depolymerization of alkaline lignin from sugarcane bagasse and metabolization of the aromatics by bacteria

Although hydrothermal treatments for biomass fractionation have been vastly studied, their effect on the depolymerization of isolated lignins in terms of yield, composition, and compatibility of the produced lignin bio-oils with bioconversion is still poorly investigated. In this study, we evaluated the hydrothermal depolymerization of an β-O-4'-rich lignin extracted from sugarcane bagasse by alkaline fractionation, investigating the influence of temperature (200-350 °C), time (30-90 min), and solid-liquid ratio (1:10-1:50 m.v^-1) on yield of bio-oils (up to 31 wt%) rich in monomers (light bio-oils). Principal Components Analysis showed that the defunctionalization of the aromatic monomers was more pronounced in the most severe reaction conditions and that the abundance of more hydrophobic monomers increased in more diluted reactions. While the high-molecular-weight (heavy) bio-oil generated at 350 °C, 90 min, and 1:50 m.v^-1 failed to support bacterial growth, the corresponding light bio-oil rich in aromatic monomers promoted the growth of bacteria from 9 distinct species. The isolates Pseudomonas sp. LIM05 and Burkholderia sp. LIM09 showed the best growth performance and tolerance to lignin-derived aromatics, being the most promising for the future development of biological upgrading strategies tailored for this lignin stream.

Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes

BACKGROUND

The Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will contribute to an intensification of terrestrial organic matter release to the Arctic Ocean. Although considered recalcitrant to degradation due to complex aromatic structures, humic substances can serve as substrate for microbial growth in terrestrial environments. However, the capacity of marine microbiomes to process aromatic-rich humic substances, and how this processing may contribute to carbon and nutrient cycling in a changing Arctic Ocean, is relatively unexplored. Here, we used a combination of metagenomics and metatranscriptomics to assess the prevalence and diversity of metabolic pathways and bacterial taxa involved in aromatic compound degradation in the salinity-stratified summer waters of the Canada Basin in the western Arctic Ocean.

RESULTS

Community-scale meta-omics profiling revealed that 22 complete pathways for processing aromatic compounds were present and expressed in the Canada Basin, including those for aromatic ring fission and upstream funneling pathways to access diverse aromatic compounds of terrestrial origin. A phylogenetically diverse set of functional marker genes and transcripts were associated with fluorescent dissolved organic matter, a component of which is of terrestrial origin. Pathways were common throughout global ocean microbiomes but were more abundant in the Canada Basin. Genome-resolved analyses identified 12 clades of Alphaproteobacteria, including Rhodospirillales, as central contributors to aromatic compound processing. These genomes were mostly restricted in their biogeographical distribution to the Arctic Ocean and were enriched in aromatic compound processing genes compared to their closest relatives from other oceans.

CONCLUSION

Overall, the detection of a phylogenetically diverse set of genes and transcripts implicated in aromatic compound processing supports the view that Arctic Ocean microbiomes have the capacity to metabolize humic substances of terrestrial origin. In addition, the demonstration that bacterial genomes replete with aromatic compound degradation genes exhibit a limited distribution outside of the Arctic Ocean suggests that processing humic substances is an adaptive trait of the Arctic Ocean microbiome. Future increases in terrestrial organic matter input to the Arctic Ocean may increase the prominence of aromatic compound processing bacteria and their contribution to Arctic carbon and nutrient cycles. Video Abstract.

Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630

Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate "biological funneling" pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the β-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin.

Keystone microbial taxa drive the accelerated decompositions of cellulose and lignin by long-term resource enrichments

Lignin and cellulose are the most important component of crop straw entering arable soil. The decomposition of lignin and cellulose are related to carbon sequestration and soil fertility. The keystone microbes decomposing lignin and cellulose in cropland and their impact on agricultural management, however, remains largely unclear. In this study, we traced the carbon (C) from highly enriched ¹³C-labeled (atom% ¹³C = 99 %) lignin and cellulose to functional keystone microbes in soils of a 26-year fertilization field experiment with stable isotope probing (SIP). ¹³C-cellulose and ¹³C-lignin decomposition were significantly accelerated with the long-term application of fertilization, especially with the combination of organic and chemical fertilization (NPKM). The ¹³C was mainly assimilated by bacteria Acidobacteria (i.e. GP1, GP3, GP6), Proteobacteria (i.e. unidentified gamaproteobactiera, Bradyrhizobium), and fungi Ascomycota (i.e. Talaromyces and Fusarium, etc.). The keystone bacteria taxa decomposing cellulose and lignin were large overlapped, but substantially shaped by fertilization. For instance, GP3 was the dominant bacterium that decomposed both cellulose and lignin in no fertilizer control (CK), while GP1 and GP6 were the ones in chemical fertilization (NPK) and NPKM, respectively. The decomposition rates of cellulose in different fertilizations were majorly predicted by soil total phosphorus (TP), functional fungi abundance, total nitrogen (TN), whereas functional bacterial and fungal abundance, TP, and community structure of functional fungi manipulated the decomposing rate of lignin. Together, we demonstrate that keystone functional microbes decomposing cellulose and lignin were largely concurring and significantly altered by long-term resources enrichment, which drives the similar patterns of decomposition rates of these two substrates along the resource enrichment gradient.

Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation

The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.

Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts

The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.

Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.

Potential of Using Dual-Media Biofilm Reactors as a Real Coffee Industrial Effluent Pre-Treatment

The coffee processing industry produces toxic and low biodegradable effluent, which can pollute water bodies. A pre-treatment study on coffee effluent using a dual-media biofilm reactor (DM-BR) containing sand and Hexafilter (HEX) was conducted alongside a control biofilm reactor (C-BR) containing sand media. The novelty of this study lies in the use of dual media in biofilm reactor (DM-BR) for real coffee effluent treatment, where these processes were used individually in previous studies. The performance of DM-BR and C-BR in treating coffee effluent were investigated at different hydraulic retention times (HRTs), 24, 48 and 72 h, and the degrading bacteria were identified. Both biofilm reactors were inoculated with a recycled paper mill-activated sludge and acclimatised for 97 days. The DM-BR displayed the highest removal of chemical oxygen demand (COD) and NH4+-N at 47% and 38%, respectively, within 48 h of HRT, whereas colour and tannin–lignin reached maximum average removal of 21% and 29%, respectively, at 24 h of HRT. The combination of sand and HEX media in a system showed COD and NH4+-N removal improvement at 48 h of HRT and encouraged a variety of bacterial species growth. Bacterial characterisation analysis revealed Proteobacteria to be dominant.

Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review

Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.

Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments

Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P. R. China. By combining analytical chemistry, metagenomics, and bioinformatics methods, we analyzed composition, source and degradation pathways of lignin/lignin-derived aromatic fragments and their potential decomposers in these samples. A diversity of bacterial and archaeal taxa, mostly those from Proteobacteria (Deltaproteobacteria, Gammaproteobacteria etc.), including some lineages (e.g., Nitrospria, Polyangia, Tectomicrobia_uc) not previously implicated in lignin degradation, were identified as potential polymeric lignin or its aromatic fragments degraders. The abundance of lignin degradation pathways genes exhibited distinct spatial distribution patterns with the area adjacent to the outlet of Modaomen as a potential degradation hot zone and the Syringyl lignin fragments, 3,4-PDOG, and 4,5-PDOG pathways as the primary potential lignin aromatic fragments degradation processes. Notably, the abundance of ferulic acid metabolic pathway genes exhibited significant correlations with degree of lignin oxidation and demethylation/demethoxylization and vegetation source. Additionally, the abundance of 2,3-PDOG degradation pathways genes also showed a positive significant correlation with degree of lignin oxidation. Our study provides a meaningful insight into the microbial ecology of TerrOC degradation in the estuary.

Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review

Biodiesel is a renewable fuel that can be produced from a range of organic and renewable feedstock including fresh or vegetable oils, animal fats, and oilseed plants. In recent years, the lignin-based aromatic wastes, such as various aromatic waste polymers from agriculture, or organic dye wastewater from textile industry, have attracted much attention in academia, which can be uniquely selected as a potential renewable feedstock for biodiesel product converted by yeast cell factory technology. This current investigation indicated that the highest percentage of lipid accumulation can be achieved as high as 47.25% by an oleaginous yeast strain, Meyerozyma caribbica SSA1654, isolated from a wood-feeding termite gut system, where its synthetic oil conversion ability can reach up to 0.08 (g/l/h) and the fatty acid composition in yeast cells represents over 95% of total fatty acids that are similar to that of vegetable oils. Clearly, the use of oleaginous yeasts, isolated from wood-feeding termites, for synthesizing lipids from aromatics is a clean, efficient, and competitive path to achieve "a sustainable development" towards biodiesel production. However, the lacking of potent oleaginous yeasts to transform lipids from various aromatics, and an unknown metabolic regulation mechanism presented in the natural oleaginous yeast cells are the fundamental challenge we have to face for a potential cell factory development. Under this scope, this review has proposed a novel concept and approach strategy in utilization of oleaginous yeasts as the cell factory to convert aromatic wastes to lipids as the substrate for biodiesel transformation. Therefore, screening robust oleaginous yeast strain(s) from wood-feeding termite gut system with a set of the desirable specific tolerance characteristics is essential. In addition, to reconstruct a desirable metabolic pathway/network to maximize the lipid transformation and accumulation rate from the aromatic wastes with the applications of various "omics" technologies or a synthetic biology approach, where the work agenda will also include to analyze the genome characteristics, to develop a new base mutation gene editing technology, as well as to clarify the influence of the insertion position of aromatic compounds and other biosynthetic pathways in the industrial chassis genome on the expressional level and genome stability. With these unique designs running with a set of the advanced biotech approaches, a novel metabolic pathway using robust oleaginous yeast developed as a cell factory concept can be potentially constructed, integrated and optimized, suggesting that the hypothesis we proposed in utilizing aromatic wastes as a feedstock towards biodiesel product is technically promising and potentially applicable in the near future.

Low-Temperature Biodegradation of Lignin-Derived Aromatic Model Monomers by the Cold-Adapted Yeast Rhodosporidiobolus colostri Isolated from Alpine Forest Soil

The contribution of cold-adapted yeasts to the emerging field of lignin biovalorization has not yet been studied. The red-pigmented basidiomycetous yeast strain Rhodosporidiobolus colostri DBVPG 10655 was examined for its potential to degrade five selected lignin-derived aromatic monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, and vanillic acid). The strain utilized p-coumaric acid, 4-hydroxybenzoic acid, and ferulic acid not only as the sole carbon source; full biodegradation occurred also in mixtures of multiple monomers. Vanillic acid was not utilized as the sole carbon source, but was degraded in the presence of p-coumaric acid, 4-hydroxybenzoic acid, and ferulic acid. Syringic acid was utilized neither as the sole carbon source nor in mixtures of compounds. Biodegradation of lignin-derived aromatic monomers was detected over a broad temperature range (1–25 °C), which is of ecological significance and of biotechnological relevance.

Culturable and metagenomic approaches of wheat bran and wheat straw phyllosphere's highlight new lignocellulolytic microorganisms

The phyllosphere, defined as the aerial parts of plants, is one of the most prevalent microbial habitats on earth. The microorganisms present on the phyllosphere can have several interactions with the plant. The phyllosphere represents then a unique niche where microorganisms have evolved through time in that stressful environment and may have acquired the ability to degrade lignocellulosic plant cell walls in order to survive to oligotrophic conditions. The dynamic lignocellulolytic potential of two phyllospheric microbial consortia (wheat straw and wheat bran) has been studied. The microbial diversity rapidly changed between the native phyllospheres and the final degrading microbial consortia after 48 hours of culture. Indeed, the initial microbial consortia was dominated by the Ralstonia (35.8%) and Micrococcus (75.2%) genera for the wheat bran and wheat straw whereas they were dominated by Candidatus phytoplasma (59%) and Acinetobacter (31.8%) in the final degrading microbial consortia respectively. Culturable experiments leading to the isolation of several new lignocellulolytic isolates (belonging to Moraxella and Atlantibacter genera) and metagenomic reconstruction of the microbial consortia highlighted the existence of an unpredicted microbial diversity involved in lignocellulose fractionation but also the existence of new pathways in known genera (presence of CE2 for Acinetobacter,several AAs for Pseudomonas and several GHs for Bacillus in different Metagenomes Assembled Genomes). The phyllosphere from agricultural co-products represents then a new niche as a lignocellulolytic degrading ecosystem.

Efficient O-demethylation of lignin monoaromatics using the peroxygenase activity of cytochrome P450 enzymes

Selective O-demethylation of the lignin monoaromatics, syringol and guaiacol, using the peroxygenase activity of two distinct cytochrome P450 enzymes.

Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry

Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.

Lignin degradation by microorganisms: A review

Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.

Chemodiversity of Soil Dissolved Organic Matter and Its Association With Soil Microbial Communities Along a Chronosequence of Chinese Fir Monoculture Plantations

The total dissolved organic matter (DOM) content of soil changes after vegetation transformation, but the diversity of the underlying chemical composition has not been explored in detail. Characterizing the molecular diversity of DOM and its fate enables a better understanding of the soil quality of monoculture forest plantations. This study characterized the chemodiversity of soil DOM, assessed the variation of the soil microbial community composition, and identified specific linkages between DOM molecules and microbial community composition in soil samples from a 100-year chronosequence of Chinese fir monoculture plantations. With increasing plantation age, soil total carbon and dissolved organic carbon first decreased and then increased, while soil nutrients, such as available potassium and phosphorus and total nitrogen, potassium, and phosphorus, increased significantly. Lignin/carboxylic-rich alicyclic molecule (CRAM)-like structures accounted for the largest proportion of DOM, while aliphatic/proteins and carbohydrates showed a decreasing trend along the chronosequence. DOM high in H/C (such as lipids and aliphatic/proteins) degraded preferentially, while low-H/C DOM (such as lignin/CRAM-like structures and tannins) showed recalcitrance during stand development. Soil bacterial richness and diversity increased significantly as stand age increased, while soil fungal diversity tended to increase during early stand development and then decrease. The soil microbial community had a complex connectivity and strong interaction with DOM during stand development. Most bacterial phyla, such as Acidobacteria, Chloroflexi, and Firmicutes, were very significantly and positively correlated with DOM molecules. However, Verrucomicrobia and almost all fungi, such as Basidiomycota and Ascomycota, were significantly negatively correlated with DOM molecules. Overall, the community of soil microorganisms interacted closely with the compositional variability of DOM in the monoculture plantations investigated, both by producing and consuming DOM. This suggests that DOM is not intrinsically recalcitrant but instead persists in soils as a result of simultaneous consumption, transformation, and formation by soil microorganisms with extended stand ages of Chinese fir plantations.

Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates

Whole-cell bioconversion of technical lignins using Pseudomonas putida strains overexpressing amine transaminases (ATAs) has the potential to become an eco-efficient route to produce phenolic amines. Here, a novel cell growth-based screening method to evaluate the in vivo activity of recombinant ATAs towards vanillylamine in P. putida KT2440 was developed. It allowed the identification of the native enzyme Pp-SpuC-II and ATA from Chromobacterium violaceum (Cv-ATA) as highly active towards vanillylamine in vivo. Overexpression of Pp-SpuC-II and Cv-ATA in the strain GN442ΔPP_2426, previously engineered for reduced vanillin assimilation, resulted in 94- and 92-fold increased specific transaminase activity, respectively. Whole-cell bioconversion of vanillin yielded 0.70 ± 0.20 mM and 0.92 ± 0.30 mM vanillylamine, for Pp-SpuC-II and Cv-ATA, respectively. Still, amine production was limited by a substantial re-assimilation of the product and formation of the by-products vanillic acid and vanillyl alcohol. Concomitant overexpression of Cv-ATA and alanine dehydrogenase from Bacillus subtilis increased the production of vanillylamine with ammonium as the only nitrogen source and a reduction in the amount of amine product re-assimilation. Identification and deletion of additional native genes encoding oxidoreductases acting on vanillin are crucial engineering targets for further improvement.

One-pot microbial bioconversion of wheat bran ferulic acid to biovanillin

Due to growing consumer preference towards natural ingredients in food products, the production of flavors by microbial biotransformation of agrowastes provides an eco-friendly, cost-effective and sustainable pathway for biovanillin production. In the present study, biovanillin was produced by microbial biotransformation of ferulic acid (FA) using Streptomyces sp. ssr-198. The strain was able to grow in glucose medium supplemented with 1 g/L FA and produce 20.91 ± 1.11 mg/L vanillin within 96 h, along with 5.78 ± 0.13 mg/L vanillic acid in 144 h. Estimation of enzymes involved in FA degradation detected maximum feruloyl-CoA synthetase activity (1.21 ± 0.03 U/mg protein) at 96 h and maximum vanillin dehydrogenase activity (0.31 ± 0.008 U/mg protein) at 168 h, with small amounts of ferulic acid esterase activity (0.13 ± 0.002 U/mg protein) in the fermentation medium. Further, the glucose deficient production medium supplemented with 3 g/L of ferulic acid when inoculated with Streptomyces sp. ssr-198 (6% wet weight) produced maximum vanillin (685 ± 20.11 mg/L) within 72 h at 37 °C under agitation (150 rpm) and declined thereafter. Furthermore, in a one-pot experiment, wherein crude ferulic acid esterase (700 IU/g of substrate) from Enterococcus lactis SR1 was added into 10% w/v wheat bran (natural source of ferulic acid) based medium and was inoculated with 1% w/v of Streptomyces sp. ssr-198 resulted in maximum vanillin production (1.02 ± 0.02 mg/g of substrate) within 60 h of incubation. The study provides an insight into synergistic effect of using FAE of E. lactis SR1 and Streptomyces sp. ssr-198 for bioproduction of biovanillin using agro residues.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03006-0.

Identification of novel membrane proteins for improved lignocellulose conversion

Lignocellulose processing yields a heterogeneous mixture of substances, which are poorly utilized by current industrial strains. For efficient valorization of recalcitrant biomass, it is critical to identify and engineer new membrane proteins that enable the broad uptake of hydrolyzed substrates. Whereas glucose consumption rarely presents a bottleneck for cell factories, there is also a lack of transporters that allow co-consumption of glucose with other abundant biomass sugars such as xylose. This review discusses recent efforts to bioinformatically identify membrane proteins of high biotech potential for lignocellulose conversion and metabolic engineering in both model and nonconventional organisms. Of particular interest are transporters sourced from anaerobic gut fungi resident to large herbivores, which produce Sugars Will Eventually be Exported Transporters (SWEETs) that enhance xylose transport in the yeast Saccharomyces cerevisiae and enable glucose and xylose co-utilization. Additionally, recently identified fungal cellodextrin transporters are valuable alternatives to mitigate glucose repression and transporter inhibition.

Using MALDI-FTICR-MS Imaging to Track Low-Molecular-Weight Aromatic Derivatives of Fungal Decayed Wood

Low-molecular-weight (LMW) aromatics are crucial in meditating fungal processes for plant biomass decomposition. Some LMW compounds are employed as electron donors for oxidative degradation in brown rot (BR), an efficient wood-degrading strategy in fungi that selectively degrades carbohydrates but leaves modified lignins. Previous understandings of LMW aromatics were primarily based on “bulk extraction”, an approach that cannot fully reflect their real-time functions during BR. Here, we applied an optimized molecular imaging method that combines matrix-assisted laser desorption ionization (MALDI) with Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to directly measure the temporal profiles of BR aromatics as Rhodonia placenta decayed a wood wafer. We found that some phenolics were pre-existing in wood, while some (e.g., catechin-methyl ether and dihydroxy-dimethoxyflavan) were generated immediately after fungal activity. These pinpointed aromatics might be recruited to drive early BR oxidative mechanisms by generating Fenton reagents, Fe²⁺ and H₂O₂. As BR progressed, ligninolytic products were accumulated and then modified into various aromatic derivatives, confirming that R. placenta depolymerizes lignin. Together, this work confirms aromatic patterns that have been implicated in BR fungi, and it demonstrates the use of MALDI-FTICR-MS imaging as a new approach to monitor the temporal changes of LMW aromatics during wood degradation.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832^T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836^T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837^T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

Microbial bioprospecting for lignocellulose degradation at a unique Greek environment

Bacterial systems have gained wide attention for depolymerization of lignocellulosic biomass, due to their high functional diversity and adaptability. To achieve the full microbial exploitation of lignocellulosic residues and the cost-effective production of bioproducts within a biorefinery, multiple metabolic pathways and enzymes of various specificities are required. In this work, highly diverse aerobic, mesophilic bacteria enriched from Keri Lake, a pristine marsh of increased biomass degradation and natural underground oil leaks, were explored for their metabolic versatility and enzymatic potential towards lignocellulosic substrates. A high number of Pseudomonas species, obtained from enrichment cultures where organosolv lignin served as the sole carbon and energy source, were able to assimilate a range of lignin-associated aromatic compounds. Comparatively more complex bacterial consortia, including members of Actinobacteria, Proteobacteria, Bacilli, Sphingobacteria, and Flavobacteria, were also enriched from cultures with xylan or carboxymethyl cellulose as sole carbon sources. Numerous individual isolates could target diverse structural lignocellulose polysaccharides by expressing hydrolytic activities on crystalline or amorphous cellulose and xylan. Specific isolates showed increased potential for growth in lignin hydrolysates prepared from alkali pretreated agricultural wastes. The results suggest that Keri isolates represent a pool of effective lignocellulose degraders with significant potential for industrial applications in a lignocellulose biorefinery.

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli

Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.

A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2

A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.

Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil

Abstract

Lignin bio-valorization is an emerging field of applied biotechnology and has not yet been studied at low temperatures. Paraburkholderia aromaticivorans AR20-38 was examined for its potential to degrade six selected lignin monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, vanillic acid, benzoic acid) from different upper funneling aromatic pathways. The strain degraded four of these compounds at 10°C, 20°C, and 30°C; syringic acid and vanillic acid were not utilized as sole carbon source. The degradation of 5 mM and 10 mM ferulic acid was accompanied by the stable accumulation of high amounts of the value-added product vanillic acid (85–89% molar yield; 760 and 1540 mg l⁻¹, respectively) over the whole temperature range tested. The presence of essential genes required for reactions in the upper funneling pathways was confirmed in the genome. This is the first report on biodegradation of lignin monomers and the stable vanillic acid production at low and moderate temperatures by P. aromaticivorans.

Key points

• Paraburkholderia aromaticivorans AR20-38 successfully degrades four lignin monomers.

• Successful degradation study at low (10°C) and moderate temperatures (20–30°C).

• Biotechnological value: high yield of vanillic acid produced from ferulic acid.

Natural diversity of FAD-dependent 4-hydroxybenzoate hydroxylases

4-Hydroxybenzoate 3-hydroxylase (PHBH) is the most extensively studied group A flavoprotein monooxygenase (FPMO). PHBH is almost exclusively found in prokaryotes, where its induction, usually as a consequence of lignin degradation, results in the regioselective formation of protocatechuate, one of the central intermediates in the global carbon cycle. In this contribution we introduce several less known FAD-dependent 4-hydroxybenzoate hydroxylases. Phylogenetic analysis showed that the enzymes discussed here reside in distinct clades of the group A FPMO family, indicating their separate divergence from a common ancestor. Protein homology modelling revealed that the fungal 4-hydroxybenzoate 3-hydroxylase PhhA is structurally related to phenol hydroxylase (PHHY) and 3-hydroxybenzoate 4-hydroxylase (3HB4H). 4-Hydroxybenzoate 1-hydroxylase (4HB1H) from yeast catalyzes an oxidative decarboxylation reaction and is structurally similar to 3-hydroxybenzoate 6-hydroxylase (3HB6H), salicylate hydroxylase (SALH) and 6-hydroxynicotinate 3-monooxygenase (6HNMO). Genome mining suggests that the 4HB1H activity is widespread in the fungal kingdom and might be responsible for the oxidative decarboxylation of vanillate, an import intermediate in lignin degradation. 4-Hydroxybenzoyl-CoA 1-hydroxylase (PhgA) catalyzes an intramolecular migration reaction (NIH shift) during the three-step conversion of 4-hydroxybenzoate to gentisate in certain Bacillus species. PhgA is phylogenetically related to 4-hydroxyphenylacetate 1-hydroxylase (4HPA1H). In summary, this paper shines light on the natural diversity of group A FPMOs that are involved in the aerobic microbial catabolism of 4-hydroxybenzoate.

Effective pretreatment of lignocellulosic co-substrates using barley straw-adapted microbial consortia to enhanced biomethanation by anaerobic digestion

Microbial pretreatments have been identified as a compatible and sustainable process with anaerobic digestion compared to energy-intensive physicochemical pretreatments. In this study, barley straw and hay co-substrate was pretreated with a microaerobic barley straw-adapted microbial (BSAM) consortium prior to anaerobic digestion. The improved digestibility was investigated through 16S rRNA gene sequencing, microbial counts and C:N ratios. BSAM pretreatment resulted in 15.2 L kg^-1 TS of methane yield after 35 days, almost 40 times more than the control. The methane content in total biogas produced were 58% (v/v) and 10% (v/v) in BSAM and control, respectively. This research demonstrated that BSAM-based pretreatment significantly increased the digestibility and surface area of the lignocellulosic material and considerably enhanced biomethanation. This study generates new potential bio-research opportunities in the emerging field of lignocellulosic anaerobic digestion-biorefineries.

Decoding lignin valorization pathways in the extremophilicBacillus ligniniphilusL1 for vanillin biosynthesis

An efficient bioconversion procedure for the accumulation of vanillin from lignin by pathway engineering and milking fermentation has been developed.

Inhibition of Phenolics Uptake by Ligninolytic Fungal Cells and Its Potential as a Tool for the Production of Lignin-Derived Aromatic Building Blocks

Lignin is the principal natural source of phenolics but its structural complexity and variability make it difficult to valorize through chemical depolymerization approaches. White rots are one of the rare groups of organisms that are able to degrade lignin in ecosystems. This biodegradation starts through extracellular enzymes producing oxidizing agents to depolymerize lignin and continue with the uptake of the generated oligomers by fungal cells for further degradation. Phanerochaete chrysosporium is one of the most studied species for the elucidation of these biodegradation mechanisms. Although the extracellular depolymerization step appears interesting for phenolics production from lignin, the uptake and intracellular degradation of oligomers occurring in the course of the depolymerization limits its potential. In this study, we aimed at inhibiting the phenolics uptake mechanism through metabolic inhibitors to favor extracellular oligomers accumulation without preventing the ligninases production that is necessary for extracellular depolymerization. The use of sodium azide confirmed that an active transportation phenomenon is involved in the phenolics uptake in P. chrysosporium. A protocol based on carbonyl cyanide m-chlorophenyl hydrazone enabled reaching 85% inhibition for vanillin uptake. This protocol was shown not to inhibit, but on the contrary, to stimulate the depolymerization of both dehydrogenation polymers (DHPs) and industrial purified lignins.

Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1

Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD⁺-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain.

Effects of Bacterial Supplementation on Black Soldier Fly Growth and Development at Benchtop and Industrial Scale

Historically, research examining the use of microbes as a means to optimize black soldier fly (BSF) growth has explored few taxa. Furthermore, previous research has been done at the benchtop scale, and extrapolating these numbers to industrial scale is questionable. The objectives of this study were to explore the impact of microbes as supplements in larval diets on growth and production of the BSF. Three experiments were conducted to measure the impact of the following on BSF life-history traits on (1) Arthrobacter AK19 supplementation at benchtop scale, (2) Bifidobacterium breve supplementation at benchtop scale, and (3) Arthrobacter AK19 and Rhodococcus rhodochrous 21198 as separate supplements at an industrial scale. Maximum weight, time to maximum weight, growth rate, conversion level of diet to insect biomass, and associated microbial community structure and function were assessed for treatments in comparison to a control. Supplementation with Arthrobacter AK19 at benchtop scale enhanced growth rate by double at select time points and waste conversion by approximately 25–30% with no impact on the microbial community. Predicted gene expression in microbes from Arthrobacter AK19 treatment was enriched for functions involved in protein digestion and absorption. Bifidobacterium breve, on the other hand, had the inverse effect with larvae being 50% less in final weight, experiencing 20% less conversion, and experienced suppression of microbial community diversity. For those tested at the industrial scale, Arthrobacter AK19 and R. rhodochrous 21198 did not impact larval growth differently as both resulted in approximately 22% or more greater growth than those in the control. Waste conversion with the bacteria was similar to that recorded for the control. Diets treated with the supplemental bacteria showed increased percent difference in predicted genes compared to control samples for functions involved in nutritional assimilation (e.g., protein digestion and absorption, energy metabolism, lipid metabolism). Through these studies, it was demonstrated that benchtop and industrial scale results can differ. Furthermore, select microbes can be used at an industrial scale for optimizing BSF larval production and waste conversion, while others cannot. Thus, targeted microbes for such practices should be evaluated prior to implementation.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach

An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of de-lignification, with a growing interest in the use of microbes. Here we investigate the physiology and molecular response of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, to lignin under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 accumulates higher biomass and has a shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in late logarithmic phase. Ferrozine assays of the supernatant confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

Cultivation of Mushrooms and Their Lignocellulolytic Enzyme Production Through the Utilization of Agro-Industrial Waste

A large amount of agro-industrial waste is produced worldwide in various agricultural sectors and by different food industries. The disposal and burning of this waste have created major global environmental problems. Agro-industrial waste mainly consists of cellulose, hemicellulose and lignin, all of which are collectively defined as lignocellulosic materials. This waste can serve as a suitable substrate in the solid-state fermentation process involving mushrooms. Mushrooms degrade lignocellulosic substrates through lignocellulosic enzyme production and utilize the degraded products to produce their fruiting bodies. Therefore, mushroom cultivation can be considered a prominent biotechnological process for the reduction and valorization of agro-industrial waste. Such waste is generated as a result of the eco-friendly conversion of low-value by-products into new resources that can be used to produce value-added products. Here, we have produced a brief review of the current findings through an overview of recently published literature. This overview has focused on the use of agro-industrial waste as a growth substrate for mushroom cultivation and lignocellulolytic enzyme production.

Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods

Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.