The emerging role for bacteria in lignin degradation and bio-product formation

Characterization of Ligninolytic Bacteria and Analysis of Alkali-Lignin Biodegradation Products

Ligninolytic bacteria degrading lignin were isolates and identified, and their biodegradation mechanism of alkaline-lignin was investigated. Four strains with lignin degradation capability were screened and identified from the soil, straw, and silage based on their decolorizing capacity of aniline blue and colony size on alkaline-lignin medium. The degradation ratio of Bacillus aryabhattai BY5, Acinetobacter johnsonii LN2, Acinetobacter lwoffii LN4, and Micrococcus yunnanensis CL32 have been assayed using alkaline-lignin as the unique carbon source. Further, the Lip (lignin peroxidase) and Mnp (manganese peroxidase) activities of strains were investigated. Lip activity of A. lwoffii LN4 was highest after 72 h of incubation and reached 7151.7 U · l^-1. Mnp activity of M. yunnanensis CL32 was highest after 48 h and reached 12533 U · l^-1. The analysis of alkaline-lignin degradation products by GC-MS revealed that the strains screened could utilize aromatic esters compounds such as dibutyl phthalate (DBP), and decomposite monocyclic aromatic compounds through the DBP aerobic metabolic pathway. The results indicate that B. aryabhattai BY5, A. johnsonii LN2, A. lwoffii LN4, and M. yunnanensis CL32 have high potential to degrade alkaline-lignin, and might utilize aromatic compounds by DBP aerobic metabolic pathway in the process of lignin degradation.

Cellulolytic bacterium characterization and genome functional analysis: An attempt to lay the foundation for waste management

Lignocellulosic waste has offered a cost-effective and food security-wise substrate for the generation of biofuels and value-added products. Here, whole-genome sequencing and comparative genomic analyses were performed for Serratia sp. AXJ-M. The results showed that strain AXJ-M contained a high proportion of strain-specific genes related to carbohydrate metabolism. Furthermore, the genetic basis of strain AXJ-M for efficient degradation of cellulose was identified. Cellulase activity tests revealed strong cellulose degradation ability and cellulase activities in strain AXJ-M. mRNA expression indicated that GH1, GH3 and GH8 might determine the strain's cellulose degradation ability. The SWISS-MODEL and Ramachandran Plot were used to predict and evaluate the 3D structure, respectively. High performance liquid chromatography (HPLC) and gas chromatography-mass spectrometer (GC-MS) were used to analyze the cellulose degradation products. Further research is needed to elucidate the cellulose degradation mechanism and to develop industrial applications for lignocellulosic biomass degradation and waste management.

Pickering Emulsions Based on Wax and Halloysite Nanotubes: An Ecofriendly Protocol for the Treatment of Archeological Woods

A novel green protocol for the consolidation and protection of waterlogged archeological woods with wax microparticles has been designed. First, we focused on the development of halloysite nanotubes (HNTs) based Pickering emulsions using wax as the inner phase of the oil-in-water droplets. The optimization of the preparation strategy was supported by both optical microscopy and scanning electron microscopy, which allowed us to show the morphological features of the prepared hybrid systems and their structural properties, i.e., the distribution of the clay at the interface. Also, the dependence of the overall dimensions of the prepared systems on the halloysite content was demonstrated. Microdifferential scanning calorimetry (μ-DSC) was conducted in order to assess whether the thermal properties of the wax are affected after its interaction with HNTs. Then, the Pickering emulsions were employed for the treatment of waterlogged wooden samples. Compared to the archeological woods treated with pure wax, the addition of nanotubes induced a remarkable improvement in the mechanical performance in terms of stiffness and flexural strength. The proposed protocol is environmentally friendly since water is the only solvent used throughout the entire procedure, even if wax is vehiculated into the pores at room temperature. As a consequence, the design of wax/halloysite Pickering emulsions represents a promising strategy for the preservation of wooden artworks, and it has a great potential to be scaled up, thus becoming also exploitable for the treatments of shipwrecks of large size.

Lignin valorization by bacterial genus Pseudomonas: State-of-the-art review and prospects

The most prominent aromatic feedstock on Earth is lignin, however, lignin valorization is still an underrated subject. The principal preparatory strategies for lignin valorization are fragmentation and depolymerization which help in the production of fuels and chemicals. Owing to lignin's structural heterogeneity, these strategies result in product generation which requires tedious separation and purification to extract target products. The bacterial genus Pseudomonas has been dominant for its lignin valorization potency, owing to a robust enzymatic machinery that is used to funnel variable lignin derivatives into certain target products such as polyhydroxyalkanotes (PHAs) and cis, cis-muconic acid (MA). In this review, the potential of genus Pseudomonas in lignin valorization is critically reviewed along with the advanced genetic techniques and tools to ease the use of lignin/lignin-model compounds for the synthesis of bioproducts. This review also highlights the research gaps in lignin biovalorization and discuss the challenges and possibilities for future research.

Microbial polyhydroxyalkanoate production from lignin by Pseudomonas putida NX-1

Biological approaches play an important role in lignin valorization, whereas many issues in this area remain unclear. Herein, ligninolytic enzymes in Pseudomonas putida NX-1 were systematically unraveled based on genome sequence technology. Particularly, a dye-decolorizing peroxidase was systematically studied by heterologous expression, enzyme purification, and enzymatic characterization, which suggested it possessed activities on both synthetic dyes and lignin-derived aromatics. Moreover, a complete pathway for polyhydroxyalkanoate biosynthesis was annotated, and the polyhydroxyalkanoate biosynthesis capability of P. putida NX-1 was experimentally confirmed with lignin as the sole carbon source. Furthermore, the monomer compositions, molecular weights, and thermal properties of polyhydroxyalkanoate from glucose and lignin-derived aromatics were comprehensively determined by gas chromatography-mass spectrometry, gel permeation chromatography, differential scanning calorimetry, and thermogravimetric analysis. The results indicated that physical properties of polyhydroxyalkanoate prepared from glucose and lignin-derived aromatics were similar, which suggested lignin could be an alternative feedstock for polyhydroxyalkanoate production without compromising its quality.

Metagenomic assessment of the global diversity and distribution of bacteria and fungi

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.

Ideal Feedstock and Fermentation Process Improvements for the Production of Lignocellulolytic Enzymes

The usage of lignocellulosic biomass in energy production for biofuels and other value-added products can extensively decrease the carbon footprint of current and future energy sectors. However, the infrastructure in the processing of lignocellulosic biomass is not well-established as compared to the fossil fuel industry. One of the bottlenecks is the production of the lignocellulolytic enzymes. These enzymes are produced by different fungal and bacterial species for degradation of the lignocellulosic biomass into its reactive fibers, which can then be converted to biofuel. The selection of an ideal feedstock for the lignocellulolytic enzyme production is one of the most studied aspects of lignocellulolytic enzyme production. Similarly, the fermentation enhancement strategies for different fermentation variables and modes are also the focuses of researchers. The implementation of fermentation enhancement strategies such as optimization of culture parameters (pH, temperature, agitation, incubation time, etc.) and the media nutrient amendment can increase the lignocellulolytic enzyme production significantly. Therefore, this review paper summarized these strategies and feedstock characteristics required for hydrolytic enzyme production with a special focus on the characteristics of an ideal feedstock to be utilized for the production of such enzymes on industrial scales.

Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1

Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.

Improving the Yield and Rate of Acid-Catalyzed Deconstruction of Lignin by Mechanochemical Activation

Lignin is a potential biomass feedstock from plant material, but it is particularly difficult to economically process. Inspired by recent ball-milling results, state-of-the-art quantum mechanochemistry calculations have been performed to isolate and probe the purely mechanochemical stretching effect alone upon acid-catalyzed deconstruction of lignin. Effects upon cleavage of several exemplary simple ethers are examined first, and with low stretching force they all are predicted to cleave substantially faster, allowing for use of milder acids and lower temperatures. Effects upon an experimentally known lignin fragment model (containing the ubiquitous β-O-4 linkage) are next examined; this first required a mechanism refinement (3-step indirect cleavage, 1-step side reaction) and identification of the rate-limiting step under zero-force (thermal) conditions. Mechanochemical activation using very low stretching forces improves at first only yield, by fully shutting off the ring-closure side reaction. At only somewhat larger forces, in stark contrast, a switch in mechanism is found to occur, from 3-step indirect cleavage to the direct cleavage mechanism of simple ethers, finally strongly enhancing the cleavage rate of lignin. It is concluded that mechanochemical activation of the common β-O-4 link in lignin would improve the rate of its acidolysis via a mechanism switch past a low force threshold. Relevance to ball-milling experiments is discussed.

Culturable bacteria from an Alpine coniferous forest site: biodegradation potential of organic polymers and pollutants

The potential of the culturable bacterial community from an Alpine coniferous forest site for the degradation of organic polymers and pollutants at low (5 °C) and moderate (20 °C) temperatures was evaluated. The majority of the 68 strains belonged to the phylum Proteobacteria (77%). Other strains were related to Bacteroidetes (12%), Alphaproteobacteria (4%), Actinobacteria (3%), and Firmicutes (3%). The strains were grouped into 42 different OTUs. The highest bacterial diversity was found within the phylum Bacteroidetes. All strains, except one, could grow at temperatures from 5 to 25 °C. The production of enzyme activities involved in the degradation of organic polymers present in plant litter (carboxymethyl cellulose, microgranular cellulose, xylan, polygalacturonic acid) was almost comparable at 5 °C (68%) and 20 °C (63%). Utilizers of lignin compounds (lignosulfonic acid, lignin alkali) as sole carbon source were found to a higher extent at 20 °C (57%) than at 5 °C (24%), but the relative fractions among positively tested strains utilizing these compounds were almost identical at the two temperatures. Similar results were noted for utilizers of organic pollutants (n-hexadecane, diesel oil, phenol, glyphosate) as sole carbon source. More than two-thirds showed constitutively expressed catechol-1,2-dioxygenase activity both at 5 °C (74%) and 20 °C (66%). Complete phenol (2.5 mmol/L) degradation by strain Paraburkholderia aromaticivorans AR20-38 was demonstrated at 0-30 °C, amounts up to 7.5 mmol/L phenol were fully degraded at 10-30 °C. These results are useful to better understand the effect of changing temperatures on microorganisms involved in litter degradation and nutrient turnover in Alpine forest soils.

Application of enzymatic and bacterial biodelignification systems for enhanced breakdown of model lignocellulosic wastes

This paper explores the extent to which enzymatic and bacterial biodelignification systems can breakdown lignocellulose in model wastes to potentially enhance biogas generation. Two representative lignocellulosic wastes (newspaper and softwood) commonly found largely undegraded in old landfills were used. A fungal peroxidase (lignin peroxidase) enzyme and a recently isolated lignin-degrading bacterial strain (Agrobacterium sp.) were used. Tests were conducted in stirred bioreactors with methanogens from sewage sludge added to produce biogas from breakdown products. Addition of lignin peroxidase resulted in ~20% enhancement in cumulative methane produced in newspaper reactors. It had a negative effect on wood. Agrobacterium sp. strain enhanced biodegradation of both wood (~20% higher release of soluble organic carbon and enhanced breakdown) and newspaper (~2-fold biogas yield). The findings of this paper have important implications for enhanced breakdown in old landfills that are rich in these wastes, and anaerobic operations utilising lignocellulosic wastes for higher degradation efficiencies and biogas production.

Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica

Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m² permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH₄⁺-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.

Microbiota in Waterlogged Archaeological Wood: Use of Next-Generation Sequencing to Evaluate the Risk of Biodegradation

Waterlogged archaeological wood (WAW) is considered a precious material, first-hand account of past civilizations. Like any organic material, it is subjected to biodegradative action of microorganisms whose activity could be particularly fast and dangerous during the phases of excavation, storage and restoration. The present work aimed to characterize the microorganisms present in WAW during these tricky periods to evaluate the biological risk it is exposed to. The bacterial and fungal communities inhabiting woods coming from two archaeological sites (Pisa and Naples) were investigated through Next-Generation Sequencing (NGS). High-throughput sequencing of extracted DNA fragments was performed using the reversible terminator-based sequencing chemistry with the Illumina MiSeq platform. The analyses revealed that the two archaeological sites showed distinct richness and biodiversity, as expected. In all the WAWs, the bacterial community harbored mainly Proteobacteria, whereas Bacteroidetes was well represented only in Naples communities and taxa belonging to the phyla Chloroflexi only in the Pisa site. Concerning the fungal community, the two sites were dominated by different phyla: Ascomycota for Naples samples and Basidiomycota for Pisa. Interestingly, most of the identified bacterial and fungal taxa have cellulolytic or ligninolytic ability. These results provide new and useful background information concerning the composition of WAW microbiota and the threat it represents for this precious material.

Bacterial succession in epiphytic biofilms and deciduous layer sediments during Hydrilla verticillata decay: A field investigation

Submersed macrophytes decay is an important natural process and has important role in mass and energy flow in aquatic ecosystems. However, little is known about the dynamical changes in nutrients release and bacterial community during submersed macrophyte decay in natural environment. In this study, a field observation was conducted in a wetland dominated with Hydrilla verticillata for 36 days. Increase of H₂O₂ and malondialdehyde (MDA) content and decrease of soluble proteins concentration were detected in leaves during H. verticillata decay. Meanwhile, ammonium-N, soluble microbial products (SMP) and TOC concentration increased in overlying water. According to bacterial 16S rRNA Illumina sequencing analysis, the Shannon values were lower in epiphytic biofilms than deciduous layer sediments. The relative abundances of Proteobacteria, Cyanobacteria and Actinobacteria were higher in epiphytic biofilms than in deciduous layer sediments (P < 0.05). Co-occurrence network analyses showed that a total of 578 and 845 pairs of correlations (|r| > 0.6) were identified from 122 and 112 genera in epiphytic biofilms and deciduous layer sediments, respectively. According to co-occurrence patterns, eight hubs were mainly from phyla Proteobacteria, Acidobacteria and Parcubacteria in epiphytic biofilms; while 37 hubs from the 14 phyla (Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, et al.) were detected in deciduous layer sediments. Our results indicate that bacterial community in deciduous layer sediments was more susceptible than in epiphytic biofilms during decay process. These data highlight the role of microbial community in deciduous layer sediments on nutrients removal during H. verticillata decay and will provide useful information for wetland management.

Lignin lags, leads, or limits the decomposition of litter and soil organic carbon

Lignin's role in litter and soil organic carbon (SOC) decomposition remains contentious. Lignin decomposition was traditionally thought to increase during midstage litter decomposition, when cellulose occlusion by lignin began to limit mass loss. Alternatively, lignin decomposition could be greatest in fresh litter as a consequence of co-metabolism, and lignin might decompose faster than bulk SOC. To test these competing hypotheses, we incubated 10 forest soils with C₄ grass litter (amended with ¹³ C-labeled or unlabeled lignin) over 2 yr and measured soil respiration and its isotope composition. Early lignin decomposition was greatest in 5 of 10 soils, consistent with the co-metabolism hypothesis. However, lignin decomposition peaked 6-24 months later in the other five soils, consistent with the substrate-limitation hypothesis; these soils were highly acidic. Rates of lignin, litter, and SOC decomposition tended to converge over time. Cumulative lignin decomposition was never greater than SOC decomposition; lignin decomposition was significantly lower than SOC decomposition in six soils. Net nitrogen mineralization predicted lignin decomposition ratios relative to litter and SOC. Although the onset of lignin decomposition can indeed be rapid, lignin still presents a likely bottleneck in litter and SOC decomposition, meriting a reconsideration of lignin's role in modern decomposition paradigms.

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

BACKGROUND

In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.

RESULTS

The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.

CONCLUSIONS

Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.

Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes

Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli,  Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.

Enzymatic and genetic characterization of lignin depolymerization by Streptomyces sp. S6 isolated from a tropical environment

The conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure. This research focuses on the isolation and characterization of a lignin-degrading bacterial strain from a decaying oil palm empty fruit bunch (OPEFB). The isolated strain, identified as Streptomyces sp. S6, grew in a minimal medium with Kraft lignin (KL) as the sole carbon source. Several known ligninolytic enzyme assays were performed, and lignin peroxidase (LiP), laccase (Lac), dye-decolorizing peroxidase (DyP) and aryl-alcohol oxidase (AAO) activities were detected. A 55.3% reduction in the molecular weight (Mw) of KL was observed after 7 days of incubation with Streptomyces sp. S6 based on gel-permeation chromatography (GPC). Gas chromatography-mass spectrometry (GC-MS) also successfully highlighted the production of lignin-derived aromatic compounds, such as 3-methyl-butanoic acid, guaiacol derivatives, and 4,6-dimethyl-dodecane, after treatment of KL with strain S6. Finally, draft genome analysis of Streptomyces sp. S6 also revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin depolymerization, as well as for the mineralization of the lower molecular weight compounds, confirming the lignin degradation capability of the bacterial strain.

Oxidative Catabolism of (+)-Pinoresinol Is Initiated by an Unusual Flavocytochrome Encoded by Translationally Coupled Genes within a Cluster of (+)-Pinoresinol-Coinduced Genes in Pseudomonas sp. Strain SG-MS2

Burkholderia sp. strain SG-MS1 and Pseudomonas sp. strain SG-MS2 have previously been found to mineralize (+)-pinoresinol through a common catabolic pathway. Here, we used comparative genomics, proteomics, protein semipurification, and heterologous expression to identify a flavoprotein from the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family in SG-MS2 that carries out the initial hydroxylation of (+)-pinoresinol at the benzylic carbon. The cognate gene is translationally coupled with a downstream cytochrome gene, and the cytochrome is required for activity. The flavoprotein has a unique combination of cofactor binding and cytochrome requirements for the VAO/PCMH family. The heterologously expressed enzyme has a K_m of 1.17 μM for (+)-pinoresinol. The enzyme is overexpressed in strain SG-MS2 upon exposure to (+)-pinoresinol, along with 45 other proteins, 22 of which were found to be encoded by genes in an approximately 35.1-kb cluster also containing the flavoprotein and cytochrome genes. Homologs of 18 of these 22 genes, plus the flavoprotein and cytochrome genes, were also found in a 38.7-kb cluster in SG-MS1. The amino acid identities of four of the other proteins within the SG-MS2 cluster suggest they catalyze conversion of hydroxylated pinoresinol to protocatechuate and 2-methoxyhydroquinone. Nine other proteins upregulated in SG-MS2 on exposure to (+)-pinoresinol appear to be homologs of proteins known to comprise the protocatechuate and 2-methoxyhydroquinone catabolic pathways, but only three of the cognate genes lie within the cluster containing the flavoprotein and cytochrome genes.IMPORTANCE (+)-Pinoresinol is an important plant defense compound, a major food lignan for humans and some other animals, and the model compound used to study degradation of the β-β' linkages in lignin. We report a gene cluster, in one strain each of Pseudomonas and Burkholderia, that is involved in the oxidative catabolism of (+)-pinoresinol. The flavoprotein component of the α-hydroxylase which heads the pathway belongs to the 4-phenol oxidizing (4PO) subgroup of the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family but constitutes a novel combination of cofactor and electron acceptor properties for the family. It is translationally coupled with a cytochrome gene whose product is also required for activity. The work casts new light on the biology of (+)-pinoresinol and its transformation to other bioactive molecules. Potential applications of the findings include new options for deconstructing lignin into useful chemicals and the generation of new phytoestrogenic enterolactones from lignans.

Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation

Rumen fermentation is known to be effective for lignocellulosic-wastes biodegradation to certain extent but it is still unclear if there exists a termination of the microorganisms' action to further degrade the bio-refractory fractions. In order to illuminate the related microbiological characteristics, experiments were conducted in a prolonged duration of rumen fermentation of mechanically ruptured wheat straw, with inoculation of cow rumen microorganisms in vitro. Although the organic wastes could not be biodegraded quickly, continuous conversion of the lignocellulosic contents to volatile fatty acids and biogas proceeded in the duration of more than three months, resulting in 96-97% cellulose and hemicellulose decomposition, and 42% lignin decomposition. X-ray diffraction and Fourier transform infrared spectroscopy further demonstrated the characteristics of lignocellulosic structure decomposition. Under the actions of cow rumen microorganisms, stable pH was maintained in the fermentation liquid, along with a steady NH₄⁺-N, volatile fatty acids accumulation, and a large buffering ability. It was identified by enzyme analysis and Illumina MiSeq sequencing that the rich core lignocellulolytic enzymes secreted by the abundant and diverse rumen bacteria and fungi contributed to the persistent degradation of lignocellulosic wastes. Members of the Clostridiales order and Basidiomycota phylum were found to be the dominant lignocellulolytic bacteria and fungi, respectively. It could thus be inferred that the main lignocellulose degradation processes were a series of catalytic reactions under the actions of lignocellulolytic enzymes secreted from bacteria and fungi. The dominant hydrogenotrophic methanogens (Methanomassiliicoccus, Methanobrevibacter, Methanosphaera, and Methanoculleus) in the rumen could also assist CH₄ production if the rumen fermentation was followed with anaerobic digestion.

Global meta-analysis on the responses of soil extracellular enzyme activities to warming

Soil enzymes play critical roles in the decomposition of organic matter and determine the availability of soil nutrients, however, there are significant uncertainties in regard to how enzymatic responses to global warming. To reveal the general response patterns and controlling factors of various extracellular enzyme activities (EEA), we collected data from 78 peer-reviewed papers to investigate the responses of extracellular enzyme activities (EEA), including β-1,4-glucosidase (BG), β-d-cellobiosidase (CBH), β-1,4-xylosidase (XYL), leucine amino peptidase (LAP), N-acetyl-glucosaminidase (NAG), urease (URE), phosphatase (PHO), peroxidase (PER), phenol oxidase (POX), and polyphenol oxidase (PPO), to experimental warming. Our results showed that warming treatments increased soil temperature by 1.9 °C on average. The oxidative EEA, calculated as the sum of PER, POX and PPO, was on average stimulated by 9.4% under warming. However, the responses of C acquisition EEA (the sum of BG, CBH and XYL), N acquisition EEA (the sum of LAP, NAG and URE), and P acquisition EEA to warming had large variations across studies. The warming effects on C, N, P acquisition EEA and oxidative EEA tended to increase with soil warming magnitude and duration as well as the mean annual temperature. The response of C acquisition EEA to warming was positively correlated with fungal biomass, while that of P acquisition EEA had positive relationships with fungi: bacteria ratios. The response of oxidative EEA was negatively correlated with the abundance of gram-positive bacterial biomass. Our results suggested that warming consistently stimulated oxidative EEA, but had diverse effects on hydrolytic EEA, which were dependent on the warming magnitude or duration, or environmental factors. The observed relationships between changes in microbial traits and extracellular enzymes suggested that microbial compositions drive changes in enzyme decomposition under warming. Thus, incorporation of microbial modification in biogeochemistry models is essential to better predict ecosystem carbon and nutrient dynamics.

Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism

Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.

A Natural High-Sugar Diet Has Different Effects on the Prokaryotic Community Structures of Lower and Higher Termites (Blattaria)

The lignocellulosic digestive symbiosis in termites is a dynamic survival adaptation system. While the contribution of hereditary and habitat factors to the development of the symbiotic bacterial community of termites had been confirmed, the manner in which these factors affect functional synergism among different bacterial lineages has still not been fully elucidated. Therefore, the 16S rRNA gene libraries of Odontotermes formosanus Shiraki (Blattodea: Termitidae) and Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) sampled from sugarcane fields (high sugar) or pine tree forests (no free sugar) were sequenced. The results verify that the prokaryotic community structures of termites could be significantly reshaped by native dietary isolation within a species. Although the most dominant phyla are convergent in all samples, their relative abundances in these two termite species exhibited a reverse variation pattern when the termite hosts were fed on the high-sugar diet. Furthermore, we showed that the taxonomic composition of the dominant phyla at the family or genus level differentiate depending on the diet and the host phylogeny. We hypothesize that the flexible bacterial assemblages at low taxonomic level might exert variable functional collaboration to accommodate to high-sugar diet. In addition, the functional predictions of Tax4Fun suggest a stable metabolic functional structure of the microbial communities of the termites in both different diet habitats and taxonomy. We propose that the symbiotic bacterial community in different host termites developed a different functional synergistic pattern, which may be essential to maintain the stability of the overall metabolic function for the survival of termites.

Genome Sequence of Lignin-Degrading Arthrobacter sp. Strain RT-1, Isolated from Termite Gut and Rumen Fluid

Here, we report the genome sequence of Arthrobacter sp. strain RT-1, isolated from a cocktail of termite gut and rumen fluid. Strain RT-1 degrades a variety of lignin monomers and dimers as the growth substrates. The genome annotation predicted the genes necessary for the catabolism of lignin-derived aromatic compounds.

Here, we report the genome sequence of Arthrobacter sp. strain RT-1, isolated from a cocktail of termite gut and rumen fluid. Strain RT-1 degrades a variety of lignin monomers and dimers as the growth substrates. The genome annotation predicted the genes necessary for the catabolism of lignin-derived aromatic compounds.

The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870

BACKGROUND

Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst.

RESULTS

The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci.

CONCLUSIONS

The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

Studies on peroxidase production and detection of Sporotrichum thermophile-like catalase-peroxidase gene in a B acillus species isolated from Hogsback forest reserve, South Africa

This study sought to determine the process conditions for optimum peroxidase production by a Bacillus species (Bacillus sp. FALADE-1-KX640922) isolated from Hogsback forest reserve in South Africa and characterize the peroxidase gene in the bacteria. We optimized peroxidase production by manipulating the environmental and nutritional parameters under submerged fermentation. Subsequently, the gene encoding heme-peroxidase was determined through nested polymerase chain reaction and Sanger DNA sequencing. The studied bacteria had maximum peroxidase production at pH 8, 30 °C and 150 rpm. The addition of guaiacol to lignin fermentation medium enhanced peroxidase production by over 100 % in the studied bacteria. However, the other lignin monomers (veratryl alcohol, vanillin, vanillic acid and ferulic acid) repressed the enzyme activity. Modification of the fermentation medium with ammonium sulphate gave the maximum peroxidase yield (8.87 U mL⁻¹). Under the predetermined culture conditions, Bacillus sp. FALADE-1 expressed maximum specific peroxidase activity at 48 h (8.32 U mg⁻¹). Interestingly, a search of the sequenced gene in PeroxiBase showed 100% similarity to Sporotrichum thermophile catalase-peroxidase gene (katG), as well, the deduced protein sequence clustered with bacterial catalase-peroxidases and had a molecular weight of about 11.45 kDa with 7.01 as the estimated isoelectric point. Subsequently, the nucleotide sequence was deposited in the National Center for Biotechnology Information (NCBI) repository with the accession number MF407314. In conclusion, Bacillus sp. FALADE-1 is a promising candidate for improved peroxidase production.

Foliar Cellulose and Lignin Degradation of Two Dominant Tree Species in a Riparian Zone of the Three Gorges Dam Reservoir, China

The riparian zone can affect the degradation of foliar cellulose and lignin by changing the hydrological gradient of the foliage decomposition environment. However, their degradation dynamics during the process of foliage decomposition remain unclear in mixed plantation forests in a riparian zone. Herein, we explored degradation of cellulose and lignin for two dominant riparian species, bald cypress [Taxodium distichum (L.) Rich.] and Chinese willow (Salix matsudana Koidz.), and a combined treatment with equal proportions of foliar mass of these species, involving three water treatments [no submergence (CK), shallow submergence (SS), and deep submergence (DS)] in a riparian zone of the Three Gorges Dam Reservoir (TGDR), China. Throughout an entire year's incubation, the degradation of cellulose and lignin was 55.57-97.76% and 79.87-93.82%, respectively. In the early stage of decomposition (i.e., the first 30 days), cellulose and lignin were rapidly degraded, and the mass loss of cellulose and lignin in water environments (SS and DS) was greater than that in a non-flooded environment (CK) regardless of the foliage type. The degradation of cellulose and lignin was mainly related to the quality of the leaf litter (as indicated by the concentrations of cellulose and lignin, and the contents of C, N, and P), decomposition period, and local environmental factors (temperature, water gradients, and dissolved oxygen). Our results will provide a clear insight into the material cycling process in a riparian zone of the TGDR and similar ecosystems in other regions.

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (-31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin-derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin-derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin-derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus

Wood is consistently found in high levels in the gastrointestinal tract of the Amazonian catfish Panaque nigrolineatus, which, depending on environmental conditions, can switch between xylivorous and detritivorous dietary strategies. This is highly unusual among primary wood consumers and provides a unique system to examine the effect of dietary change in a xylivorous system. In this study, microbiome and predictive metagenomic analyses were performed for P. nigrolineatus fed either wood alone or a less refractory mixed diet containing wood and plant nutrition. While diet had an impact on enteric bacterial community composition, there was a high degree of interindividual variability. Members of the Proteobacteria and Planctomycetes were ubiquitous and dominated most communities; Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia also contributed in a tissue and diet-specific manner. Although predictive metagenomics revealed functional differences between communities, the relative abundance of predicted lignocellulose-active enzymes remained similar across diets. The microbiomes from both diets appeared highly adapted for hemicellulose hydrolysis as the predicted metagenomes contained several classes of hemicellulases and lignin-modifying enzymes. Enteric communities from both diets appeared to lack the necessary cellobiohydrolases for efficient cellulose hydrolysis, suggesting that cellobiose is not the primary source of dietary carbon for the fish. Our findings suggest that the P. nigrolineatus gut environment selects for an enteric community based on function, rather than a vertically transferred symbiotic relationship. This functional selection strategy may provide an advantage to an organism that switches between dietary strategies to survive a highly variable environment.

Genomic analysis of Burkholderia sp. ISTR5 for biofunneling of lignin-derived compounds

BACKGROUND

Lignin is the second most abundant natural polymer on earth. Industries using lignocellulosic biomass as feedstock generate a considerable amount of lignin as a byproduct with minimal usage. For a sustainable biorefinery, the lignin must be utilized in improved ways. Lignin is recalcitrant to degradation due to the complex and heterogeneous structure. The depolymerization of lignin and its conversion into specific product stream are the major challenges associated with lignin valorization. The blend of oligomeric, dimeric and monomeric lignin-derived compounds (LDCs) generated during depolymerization can be utilized by microbes for production of bioproducts.

RESULTS

In the present study, a novel bacterium Burkholderia sp. strain ISTR5 (R5), a proteobacteria belonging to class betaproteobacteria, order Burkholderiales and family Burkholderiaceae, was isolated and characterized for the degradation of LDCs. R5 strain was cultured on 12 LDCs in mineral salt medium (MSM) supplemented with individual compounds such as syringic acid, p-coumaric acid, ferulic acid, vanillin, vanillic acid, guaiacol, 4-hydroxybenzoic acid, gallic acid, benzoic acid, syringaldehyde, veratryl alcohol and catechol. R5 was able to grow and utilize all the selected LDCs. The degradation of selected LDCs was monitored by bacterial growth, total organic carbon (TOC) removal and UV-Vis absorption spectra in scan mode. TOC reduction shown in the sample contains syringic acid 80.7%, ferulic acid 84.1%, p-coumaric acid 85.9% and benzoic acid 83.2%. In UV-Vis absorption spectral scan, most of the lignin-associated peaks were found at or near 280 nm wavelength in the obtained absorption spectra. Enzyme assay for the ligninolytic enzymes was also performed, and it was observed that lignin peroxidase and laccase were predominantly expressed. Furthermore, the GC-MS analysis of LDCs was performed to identify the degradation intermediates from these compounds. The genomic analysis showed the robustness of this strain and identified various candidate genes responsible for the degradation of aromatic or lignin derivatives, detoxification mechanism, oxidative stress response and fatty acid synthesis. The presence of peroxidases (13%), laccases (4%), monooxygenases (23%), dioxygenase (44%), NADPH: quinone oxidoreductases (16%) and many other related enzymes supported the degradation of LDCs.

CONCLUSION

Numerous pathway intermediates were observed during experiment. Vanillin was found during growth on syringic acid, ferulic acid and p-coumaric acid. Some other intermediates like catechol, acetovanillone, syringaldehyde and 3,4-dihydroxybenzaldehyde from the recognized bacterial metabolic pathways existed during growth on the LDCs. The ortho- and meta cleavage pathway enzymes, such as the catechol-1,2-dioxygenase, protocatechuate 3,4-dioxygenase, catechol-2,3-dioxygenase and toluene-2,3-dioxygenase, were observed in the genome. In addition to the common aromatic degradation pathways, presence of the epoxyqueuosine reductase, 1,2-epoxyphenylacetyl-CoA isomerase in the genome advocates that this strain may follow the epoxy Coenzyme A thioester pathway for degradation.

Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates

Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.

Biotransformation and Cytotoxicity Evaluation of Kraft Lignin Degraded by Ligninolytic Serratia liquefaciens

Various chemical compounds emerged including kraft lignin (KL) during the processes of papermaking. These chemical compounds in effluent of the paper industry have hazardous environmental impacts. KL is liable for causing pollution of aquatic and water bodies; hence, it must be minimized in order to maintain a healthy and sustainable environment. In the present study, KL degradation was performed with ligninolytic bacterium Serratia liquefaciens and we confirmed biotransformation of KL to various less polluted or harmless compounds. KL being degraded as 1000 mg/L^–1 concentration with incubating 30°C for 72, 168, and 240 h, shaking at 120 rpm under laboratory conditions. We found 65% maximum degradation of KL and 62% decolorization by the treatment with S. liquefaciens for 240 h (10 days). After being the treatment of KL, clear changes were observed in its morphology (using scanning electron microscopy and stereo microscopy), hydrodynamic size (using dynamic light scattering), and the functional groups [using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR–FTIR)]. Biotransformation of KL monitored by Gas Chromatography–Mass Spectrometry (GC–MS) revealed formation of various metabolites. In addition to degradation of KL, detoxification (involving biotransformation into various metabolites) was assessed using cytotoxicity assays 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide [MTT and calcein-acetoxymethyl (AM) assays] using a human kidney cell line (NRK-52E), which indicated improved cell survival rates (74% for the bacteria-treated KL solution treated for 240 h) compared to the control (27%). Thus, the present study suggests that bacteria S. liquefaciens might be useful in reducing the pollution of KL by transforming it into various metabolites along with cytotoxicity reduction for environmental protection.

Degradation mechanism of lignocellulose in dairy cattle manure with the addition of calcium oxide and superphosphate

Cellulose and lignin belongs to refractory organic matters in the traditional composting. In this research, the degradation of lignocellulose in dairy cattle manure was investigated through adding calcium oxide (CaO) and superphosphate (SSP). In the presence of CaO and SSP, the degradation rate of cellulose and lignin were improved by 25.0% and 8.33%, respectively. The results indicated that the pH value in system would be slightly higher with the addition of CaO and SSP. Besides, the pH value of all cow manure piles were about 8.4 after composting rotten, which could be well neutralized by the gradually acidified soil in the southwest of China with the full effect of fertilizer released. In addition, the abundance of Bacillales, Actinomycetes, and Thermoactinomycetaceae in the experimental groups (AR) was slightly better than that in the control groups (CK) during composting, which led to a conclusion that an elaborate physical-chemical-multivariate aerobic microorganism evolution model of cellulose degradation products (PCMC) was deduced and the physical-chemical-multivariate aerobic microorganism model of lignin cycle degradation (PCML) was developed.

Activation of lignin by selective oxidation: An emerging strategy for boosting lignin depolymerization to aromatics

Lignin is the most abundant, renewable aromatic resource on earth and holds great potential for the production of value-added chemicals. The efficient valorization of lignin requires to deal with several formidable challenges, especially to prevent it from re-condensation reactions during its depolymerization. Recently, a strategy involving the activation of lignin side chains by selective oxidation of the benzylic alcohol in β-O-4 linkages to facilitate lignin degradation to aromatic monomers has become very popular. This strategy provides great advantages for lignin selective degradation to high yields of aromatics under mild conditions, but requires an additional pre-oxidation step. The purpose of this review is to provide the latest cutting-edge innovations of this novel approach. Various catalytic systems, including those using chemo-catalytic methods, physio-chemo catalytic methods, and/or bio-catalytic methods, for the oxidative activation of lignin side chains are summarized. By analyzing the current situation of lignin depolymerization, certain promising directions are emphasized.

Biodegradation of alkali lignin by Bacillus flexus RMWW II: analyzing performance for abatement of rice mill wastewater

A potential bacterium Bacillus flexus RMWW II has been isolated from rice mill effluent, and examined for its decolorizing potential for lignin-mimicking dyes. The biodegradation of alkali lignin by the rod-shaped, Gram-positive, oxidase and catalase-positive Bacillus flexus RMWW II bacteria is due to its uptake of lignin as the sole carbon source. The lignin degradation was 100% at a lignin concentration of 50 mg L^-1 but the degradation reduced to 20% at 400 mg L^-1. The bacterial-mediated biodegradation of alkali lignin was suitably explained by the Edward kinetics model with a maximal specific biodegradation rate (q_max) of 0.056 h^-1 and true specific biodegradation rate (q*) of 0.042 h^-1. The non-toxic nature of the metabolites of alkali lignin after bacterial degradation was illustrated by phytotoxicity studies. This bacterium was utilized to treat complex rice mill wastewater, as lignin is one of the major components of the effluent. A considerable reduction of 84% of chemical oxygen demand (COD) was observed in a batch reactor in 70 h of operation. The bacterial treatment results for the actual rice mill effluent indicate that Bacillus flexus RMWW II could be a promising agent for microbial remediation of lignin-laden raw rice mill wastewater.

Recent advancement in lignin biorefinery: With special focus on enzymatic degradation and valorization

With the intensive development of lignocellulosic biorefineries to produce fuels and chemicals from biomass-derived carbohydrates, lignin was generated at a large quantity every year. Therefore, lignin has received increasing attention as an abundant aromatics resource in terms of research and development efforts for value-added chemicals production. In this review, studies about lignin degradation especially the crucial enzymes involved and the reaction mechanism were substantially discussed, which provided the molecular basis of lignin biodegradation. Then, the latest improvements in lignin valorization by biological methods were summarized and case studies about value-added compounds from lignin were introduced. Afterwards, challenges, opportunities and prospects regarding biorefinery of lignin were presented.

Biotransformation of lignin: Mechanisms, applications and future work

As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.

Studies of advanced lignin valorization based on various types of lignolytic enzymes and microbes

Lignin is a robust material that is considered useless because it has an inhibitory effect on microbes and acts as a physical barrier for cellulose degradation. Therefore, it has been removed from cellulosic biomass to produce high-value materials. However, lignin monomers can be converted to value-added chemicals such as biodegradable plastics and food additives by appropriately engineered microbes. Lignin degradation through peroxidase, laccase and other proteins with auxiliary activity is the first step in lignin valorization. Metabolic engineering of microorganisms for increased tolerance and production yield is the second step for lignin valorization. Here, this review offers a summary of current biotechnologies using various enzymatic activities, synergistic enzyme mixtures and metabolic engineering for lignin valorization in biorefinery.

Exoproduction and Molecular Characterization of Peroxidase from Ensifer adhaerens

The increased industrial application potentials of peroxidase have led to high market demand, which has outweighed the commercially available peroxidases. Hence, the need for alternative and efficient peroxidase-producers is imperative. This study reported the process parameters for enhanced exoperoxidase production by Ensifer adhaerens NWODO-2 (accession number: KX640918) for the first time, and characterized the enzyme using molecular methods. Peroxidase production by the bacteria was optimal at 48 h, with specific productivity of 12.76 U mg−1 at pH 7, 30 °C and 100 rpm in an alkali lignin fermentation medium supplemented with guaiacol as the most effective inducer and ammonium sulphate as the best inorganic nitrogen source. Upon assessment of some agricultural residues as sources of carbon for the enzyme production, sawdust gave the highest peroxidase productivity (37.50 U mg−1) under solid-state fermentation. A search of the polymerase chain reaction (PCR)-amplified peroxidase gene in UniProtKB using blastx showed 70.5% similarity to an uncharacterized protein in Ensifer adhaerens but phylogenetic analysis suggests that the gene may encode a catalase-peroxidase with an estimated molecular weight of approximately 31 kDa and isoelectric point of about 11. The nucleotide sequence of the detected gene was deposited in the GenBank under the accession number MF374336. In conclusion, the ability of the strain to utilize lignocellulosic materials for peroxidase production augurs well for biotechnological application as this would greatly reduce cost, which is a major challenge in industrial enzyme production.

Identification and Characterization of New Laccase Biocatalysts from Pseudomonas Species Suitable for Degradation of Synthetic Textile Dyes

Laccases are multicopper-oxidases with variety of biotechnological applications. While predominantly used, fungal laccases have limitations such as narrow pH and temperature range and their production via heterologous protein expression is more complex due to posttranslational modifications. In comparison, bacterial enzymes, including laccases, usually possess higher thermal and pH stability, and are more suitable for expression and genetic manipulations in bacterial expression hosts. Therefore, the aim of this study was to identify, recombinantly express, and characterize novel laccases from Pseudomonas spp. A combination of approaches including DNA sequence analysis, N-terminal protein sequencing, and genome sequencing data analysis for laccase amplification, cloning, and overexpression have been used. Four active recombinant laccases were obtained, one each from P. putida KT2440 and P. putida CA-3, and two from P. putida F6. The new laccases exhibited broad temperature and pH range and high thermal stability, as well as the potential to degrade selection of synthetic textile dyes. The best performing laccase was CopA from P. putida F6 which degraded five out of seven tested dyes, including Amido Black 10B, Brom Cresol Purple, Evans Blue, Reactive Black 5, and Remazol Brilliant Blue. This work highlighted species of Pseudomonas genus as still being good sources of biocatalytically relevant enzymes.