Screening of a microbial consortium for selective degradation of lignin from tree trimmings

Aromatics valorization to polyhydroxyalkanoate by the ligninolytic bacteria isolated from soil sample

Polyhydroxyalkanoates (PHA) are ecofriendly alternatives to conventional plastics due to their biodegradable nature. However, the high production cost limits their applications. Exploring novel bacteria with ligninolytic potential would be crucial to advance cost-effective PHA synthesis. The current study aims to unveil soil bacteria capable of aromatics valorization to PHA. Considering this, six aromatics resistance bacteria from a soil sample were isolated through culture acclimatization strategy and their growth was analyzed in various lignin model compounds. Ralstonia sp. BPSS-1 and Arthrobacter sp. BPSS-3 presented high-cell-densities in 4-hydroxybenzoic acid (4-HBA) and benzoate, respectively. Fluorescence microscopy confirmed the strains to be PHA positive and were subsequently evaluated for PHA synthesis from 4-HBA and benzoate at a concentration of 2 g L-1 in a nitrogen-limited M9 medium. However, applying a co-feeding strategy by the integration of 4-HBA and benzoate further increased the substrates consumption efficiency, biomass and PHA titer compared to single carbon sources. The maximum dry cell weight (DCW) and PHA yield by Ralstonia sp. BPSS-1 through the substrate co-feeding under optimized fermentation conditions was 0.69 ± 0.03, and 0.4 ± 0.02 g L-1, respectively. The draft genome analysis confirmed the genes involved in aromatic degradation. Besides, the proposed metabolic pathway was validated by studying the expression level of key genes, analyzing key intermediates and associated enzymes activities. The FTIR, 1H NMR and GC-MS determined the PHA functional group, chemical structure and monomers analysis, respectively. Overall, the current study highlighted the aromatic valorization potential of newly isolated PHA producing bacteria for sustainable biomanufacturing.

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.

Synergistic analysis of lignin degrading bacterial consortium and its application in rice straw fiber film

Fiber film have received widespread attention due to its green friendliness. We can use microorganisms to degrade lignin in straw to obtain cellulose and make fiber films. Herein, a group of high-temperature (50 °C) lignin degrading bacterial consortium (LDH) was enriched and culture conditions for lignin degradation were optimized. Combined with high-throughput sequencing technology, the synergistic effect of LDH-composited bacteria was analyzed. Then LDH was used to treat rice straw for the bio-pulping experiment. The results showed that the lignin of rice straw was degraded 32.4 % by LDH at 50 °C for 10 d, and after the optimization of culture conditions, lignin degradation rate increased by 9.05 % (P < 0.001). The bacteria that compose in LDH can synergistically degrade lignin. Paenibacillus can encode all lignin-degrading enzymes present in the LDH. Preliminary tests of LDH in the pulping industry have been completed. This study is the first to use high temperature lignin degrading bacteria to fabricate fiber film.

Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates

Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.

A high throughput screening process and quick isolation of novel lignin-degrading microbes from large number of natural biomasses

High throughput screening approaches can significantly speed up the identification of novel enzymes from natural microbial consortiums. A two-step high throughput screening process was proposed and explored to screen lignin-degrading microorganisms. By employing this modified culture enrichment method and screening based on enzyme activity, a total of 82 bacterial and 46 fungal strains were isolated from fifty decayed wood samples (100 liquid cultures) collected from the banks of the Ottawa River in Canada. Among them, ten bacterial and five fungal strains were selected and identified based on their high laccase activities by 16S rDNA and ITS gene sequencing, respectively. The study identified bacterial strains from various genera including Serratia, Enterobacter, Raoultella, and Bacillus, along with fungal counterparts including Mucor, Trametes, Conifera and Aspergillus. Moreover, Aspergillus sydowii (AORF21), Mucor sp. (AORF43), Trametes versicolor (AORF3) and Enterobacter sp. (AORB55) exhibited xylanase and β- glucanase activities in addition to laccase production. The proposed approach allowed for the quick identification of promising consortia and enhanced the chance of isolating desired strains based on desired enzyme activities. This method is not limited to lignocellulose and lignin-degrading microorganisms but can be applied to identify novel microbial strains and enzymes from different natural samples.

The dominant role of cooperation in fungal community drives the humification process of chicken manure composting under addition of regulatory factors

This study aimed to explore the action mechanism of fungal community on the enhancement of humification during chicken manure composting by regulating the core pathway of carbon metabolism - the tricarboxylic acid cycle. Regulators adenosine triphosphate (ATP) and malonic acid were added at the beginning of composting. The analysis of changes in humification parameters showed that the humification degree and stability of compost products were improved by adding regulators. Compared with CK, the humification parameters of adding regulators group increased by 10.98% on average. Meanwhile, adding regulators not only increased key nodes, but also strengthened the positive correlation between fungi, and network relationship was closer. Moreover, core fungi associated with humification parameters were identified by constructing OTU networks, and the division and cooperation mechanism of fungi were confirmed. Ultimately, the functional role of the fungal community acting on humification was confirmed by statistical means, that was, the fungal community promoting humification was the main group of composting process. And the contribution was more obvious in ATP treatment. This study was helpful to gain insight into the mechanism of regulators addition to advance the humification process, and provided new ideas for the safe, efficient and harmless disposal of organic solid waste.

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.

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

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

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.

Challenges in developing strategies for the valorization of lignin-a major pollutant of the paper mill industry

Apart from protecting the environment from undesired waste impacts, wastewater treatment is a crucial platform for recovery. The exploitation of suitable technology to transform the wastes from pulp and paper industries (PPI) to value-added products is vital from an environmental and socio-economic point of view that will impact everyday life. As the volume and complexity of wastewater increase in a rapidly urbanizing world, the challenge of maintaining efficient wastewater treatment in a cost-effective and environmentally friendly manner must be met. In addition to producing treated water, the wastewater treatment plant (WWTP) has a large amount of paper mill sludge (PMS) daily. Sludge management and disposal are significant problems associated with wastewater treatment plants. Applying the biorefinery concept is necessary for PPI from an environmental point of view and because of the piles of valuables contained therein in the form of waste. This will provide a renewable source for producing valuables and bio-energy and aid in making the overall process more economical and environmentally sustainable. Therefore, it is compulsory to continue inquiry on different applications of wastes, with proper justification of the environmental and economic factors. This review discusses current trends and challenges in wastewater management and the bio-valorization of paper mills. Lignin has been highlighted as a critical component for generating valuables, and its recovery prospects from solid and liquid PPI waste have been suggested.

Effect of moisture content on the evolution of bacterial communities and organic matter degradation during bioaugmented biogas residues composting

Composting is an excellent way to recycle biogas residues into a stable, non-toxic agricultural end product. In this study, the dynamic changes of physical-chemical parameters and bacterial community in three groups of bioaugmentation composting systems at different moisture contents (MC) of 50% (MC50), 60% (MC60) and 70% (MC70) were monitored. The differences of bacterial communities in composts with different initial MC were compared, and the interaction between biological and non-biological parameters was also explored. The results revealed that after 30 days of composting, the biogas residues compost in MC60 reached highest temperature of 64 °C, total Kjeldahl nitrogen (TKN) of 2%, seed germination index (GI) of 110%, and the longest thermophilic period duration of 5 days (55 °C). Additionally, the result of high-throughput sequencing showed that the diversity of bacterial communities in MC60 was the highest, and the abundance of Actinobacteria (16.93-52.63%), Firmicutes (8.71-56.75%), and Proteobacteria (16.88-46.95%) in all groups were the highest at phylum level. The LEfSe analysis indicated that the abundance of Ochrobactrum and Cellulomonadaceae in MC60 was significantly (p < 0.05) higher than with other treatments. Moreover, canonical correspondence analysis (CCA) indicated thermophilic period duration is significantly (p < 0.05) positively correlated with Paenibacillus. Besides, it was found the relative abundance of Nocardiopsis and Georgenia has a significant (p < 0.01) correlation with the fertilizer efficiency of compost. These results showed that controlling the initial moisture content at 60% can improve the maturity and fertilizer efficiency of compost, and enable the bacteria beneficial to composting to gain the advantage of proliferation.

Identifying ligninolytic bacteria for lignin valorization to bioplastics

Biological valorization of lignin to bioplastics is a promising route to improve biorefinery efficiency and address environmental challenges. A two-stage screening procedure had been designed to successfully identify four ligninolytic bacteria from soil samples. The isolated bacteria displayed substrate preference of guaiacyl- and hydroxyphenyl-based aromatics, but they effectively synthesized polyhydroxyalkanoates (PHAs). B. cepacia B1-2 and P. putida KT3-1 accumulated 27.3% and 20.9% PHA in cells and achieved a titer of 280.9 and 204.1 mg/L, respectively, from p-hydroxybenzoic acid. The isolated bacteria exhibited good ligninolytic performance indicated by the degradation of β-O-4 linkage and small molecules. B. cepacia B1-2 grew well on actual lignin substrate and yielded a PHA titer of 87.2 mg/L. With the design of fed-batch mode, B. cepacia B1-2 produced the highest PHA titer of 1420 mg/L from lignin-derived aromatics. Overall, isolated ligninolytic bacteria show good PHA accumulation capacity, which are the promising host strains for lignin valorization.

Augmentation characteristics and microbial community dynamics of low temperature resistant composite strains LTF-27

Biogas production in the cold regions of China is hindered by low temperatures, which led to slow lignocellulose biotransformation. Cold-adapted lignocellulose degrading microbial complex community LTF-27 was used to investigate the influence of hydrolysis on biogas production. After 5 days of hydrolysis at 15 ± 1 °C, the hydrolysis conversion rate of the corn straw went up to 22.64%, and the concentration of acetic acid increased to 2596.56 mg/L. The methane production rates of total solids (TS) inoculated by LTF-27 reached 204.72 mL/g, which was higher than the biogas (161.34 mL/g), and the control group (CK) inoculated with cultural solution (121.19 mL/g), the methane production rate of volatile solids (VS) increased by 26.88% and 68.92%, respectively. Parabacteroides, Lysinibacillus, and Citrobacter were the main organisms that were responsible for hydrolysis. While numerous other bacteria genera in the gas-producing phase, Macellibacteroides were the most commonly occurring one. Methanosarcina and Methanobacteriaceae contributed 86.25% and 11.80% of the total Archaea abundance during this phase. This study proves the psychrotrophic LTF-27's applicability in hydrolysis and biomass gas production in low temperatures.

Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion

Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.

Screening and Application of Ligninolytic Microbial Consortia to Enhance Aerobic Degradation of Solid Digestate

Recirculation of solid digestate through digesters has been demonstrated to be a potential simple strategy to increase continuous stirred-tank reactor biogas plant efficiency. This study extended this earlier work and investigated solid digestate post-treatment using liquid isolated ligninolytic aerobic consortia in order to increase methane recovery during the recirculation. Based on sampling in several natural environments, an enrichment and selection method was implemented using a Lab-scale Automated and Multiplexed (an)Aerobic Chemostat system to generate ligninolytic aerobic consortia. Then, obtained consortia were further cultivated under liquid form in bottles. Chitinophagia bacteria and Sordariomycetes fungi were the two dominant classes of microorganisms enriched through these steps. Finally, these consortia where mixed with the solid digestate before a short-term aerobic post-treatment. However, consortia addition did not increase the efficiency of aerobic post-treatment of solid digestate and lower methane yields were obtained in comparison to the untreated control. The main reason identified is the respiration of easily degradable fractions (e.g., sugars, proteins, amorphous cellulose) by the selected consortia. Thus, this paper highlights the difficulties of constraining microbial consortia to sole ligninolytic activities on complex feedstock, such as solid digestate, that does not only contain lignocellulosic structures.

Construction of a fungal consortium for effective degradation of rice straw lignin and potential application in bio-pulping

To improve the lignin degradation efficiency, we established a co-culture consortium (LDFC) consisting of Trametes hirsuta BYL-3, Trametes versicolor BYL-7 and Trametes hirsuta BYL-8. The testing results showed that the constructed consortium showed improved the lignin degradation rate by fungi. The optimal cultivation conditions were mixture at 1:1:1 vol ratio of each fungus, 7% (w/v) of inoculum amount, culture temperature at 26 °C, pH was 6.9 and 10 days of culturing time. Under these conditions, the degradation rate of lignin was 39.7%, which was 9.3% higher than those before optimization (30.4%). Using rice straw for treatment by LDFC to papermaking, the paper tensile strength was 8 N, and the ring pressure index was 2.46 N·m/g, which meets the standards for the production of corrugated paper for packaging. These results indicate that LDFC has potential application value to convert rice straw resources for bio-pulping to make papers.

Degradation of lignin by Bacillus altitudinis SL7 isolated from pulp and paper mill effluent

Lignin is a major by-product of pulp and paper industries, and is resistant to depolymerization due to its heterogeneous structure. Degradation of lignin can be achieved by the use of potential lignin-degrading bacteria. The current study was designed to evaluate the degradation efficiency of newly isolated Bacillus altitudinis SL7 from pulp and paper mill effluent. The degradation efficiency of B. altitudinis SL7 was determined by color reduction, lignin content, and ligninolytic activity from degradation medium supplemented with alkali lignin (3 g/L). B. altitudinis SL7 reduced color and lignin content by 26 and 44%, respectively, on the 5th day of incubation, as evident from the maximum laccase activity. Optimum degradation was observed at 40 °C and pH 8.0. FT-IR spectroscopy and GC-MS analysis confirmed lignin degradation by emergence of the new peaks and identification of low-molecular-weight compounds in treated samples. The identified compounds such as vanillin, 2-methyoxyhenol, 3-methyl phenol, oxalic acid and ferulic acid suggested the degradation of coniferyl and sinapyl groups of lignin. Degradation efficiency of B. altitudinis SL7 towards high lignin concentration under alkaline pH indicated the potential application of this isolate in biological treatment of the lignin-containing effluents.

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Lignin is nature's largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

Enhanced lignin biodegradation by consortium of white rot fungi: microbial synergistic effects and product mapping

BACKGROUND

As one of the major components of lignocellulosic biomass, lignin has been considered as the most abundant renewable aromatic feedstock in the world. Comparing with thermal or catalytic strategies for lignin degradation, biological conversion is a promising approach featuring with mild conditions and diversity, and has received great attention nowadays.

RESULTS

In this study, a consortium of white rot fungi composed of Lenzites betulina and Trametes versicolor was employed to enhance the ligninolytic enzyme activity of laccase (Lac) and manganese peroxidase (MnP) under microbial synergism. The maximum enzymatic activity of Lac and MnP was individually 18.06 U mL^-1 and 13.58 U mL^-1 along with a lignin degradation rate of 50% (wt/wt), which were achieved from batch cultivation of the consortium. The activities of Lac and MnP obtained from the consortium were both improved more than 40%, as compared with monocultures of L. betulina or T. versicolor under the same culture condition. The enhanced biodegradation performance was in accordance with the results observed from scanning electron microscope (SEM) of lignin samples before and after biodegradation, and secondary-ion mass spectrometry (SIMS). Finally, the analysis of heteronuclear single quantum coherence (HSQC) NMR and gas chromatography-mass spectrometry (GC-MS) provided a comprehensive product mapping of the lignin biodegradation, suggesting that the lignin has undergone depolymerization of the macromolecules, side-chain cleavage, and aromatic ring-opening reactions.

CONCLUSIONS

Our results revealed a considerable escalation on the enzymatic activity obtained in a short period from the cultivation of the L. betulina or T. versicolor due to the enhanced microbial synergistic effects, providing a potential bioconversion route for lignin utilization.

Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production

Cellulosimicrobium strain SE3^T was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3^T was shown to belong to a novel species within the genus, together with five other strains. The name Cellulosimicrobium fucosivorans sp. nov. is proposed, with strain SE3^T as the type strain. The strain encodes a unique alpha-L-fucosidase and the L-fucose metabolic pathway is homologous to the one recently described in Campylobacter jejuni. C. fucosivorans is able to grow on L-fucose, and interestingly, the biosynthesis of the yellow carotenoid is dependent on the presence of L-fucose in the media. The ability to metabolize fucose and the linked production of carotenoids are expected to provide C. fucosivorans with a competitive advantage in the sunny coastal lagoon area.

Enhanced Biogas Production by Ligninolytic Strain Enterobacter hormaechei KA3 for Anaerobic Digestion of Corn Straw

Lignin-feeding insect gut is a natural ligninolytic microbial bank for the sustainable conversion of crop straw to biogas. However, limited studies have been done on highly efficient microbes. Here, an efficient ligninolytic strain Enterobacter hormaechei KA3 was isolated from the gut microbiomes of lignin-feeding Hypomeces squamosus Fabricius, and its effects on lignin degradation and anaerobic digestion were investigated. No research has been reported. Results showed that strain KA3 had better lignin-degrading ability for corn straw with a higher lignin-degrading rate (32.05%) and lignin peroxidase activity (585.2 U/L). Furthermore, the highest cumulative biogas yield (59.19 L/kg-VS) and methane yield (14.76 L/kg-VS) were obtained for KA3 inoculation, which increased by 20% and 31%, respectively, compared to CK. Higher removal rates of COD, TS, and vs. of 41.6%, 43.11%, and 66.59% were also found. Moreover, microbial community diversity increased as digestion time prolonged in TG, and bacteria were more diverse than archaea. The dominant genus taxon, for methanogens, was Methanosate in TG, while in CK was Methanosarcina. For bacteria, dominant taxa were similar for all groups, which were Solibacillus and Clostridium. Therefore, strain KA3 improved the methane conversion of the substrate. This study could provide a new microbial resource and practical application base for lignin degradation.

Screening and Comparison of Lignin Degradation Microbial Consortia from Wooden Antiques

Lignin, which is a component of wood, is difficult to degrade in nature. However, serious decay caused by microbial consortia can happen to wooden antiques during the preservation process. This study successfully screened four microbial consortia with lignin degradation capabilities (J-1, J-6, J-8 and J-15) from decayed wooden antiques. Their compositions were identified by genomic sequencing, while the degradation products were analyzed by GC-MS. The lignin degradation efficiency of J-6 reached 54% after 48 h with an initial lignin concentration of 0.5 g/L at pH 4 and rotation speed of 200 rpm. The fungal consortium of J-6 contained Saccharomycetales (98.92%) and Ascomycota (0.56%), which accounted for 31% of the total biomass. The main bacteria in J-6 were Shinella sp. (47.38%), Cupriavidus sp. (29.84%), and Bosea sp. (7.96%). The strongest degradation performance of J-6 corresponded to its composition, where Saccharomycetales likely adapted to the system and improved lignin degradation enzymes activities, and the abundant bacterial consortium accelerated lignin decomposition. Our work demonstrated the potential utilization of microbial consortia via the synergy of microbial consortia, which may overcome the shortcomings of traditional lignin biodegradation when using a single strain, and the potential use of J-6 for lignin degradation/removal applications.

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.

Degradation of rice straw at low temperature using a novel microbial consortium LTF-27 with efficient ability

In this study, a novel psychrotrophic lignocelluloses degrading microbial consortium LTF-27 was successfully obtained from cold perennial forest soil by successive enrichment culture under facultative anaerobic static conditions. The microbial consortium showed efficient degradation of rice straw, which cellulose, hemicelluloses and lignin lost 71.7%, 65.6% and 12.5% of its weigh, respectively, in 20 days at 15 °C. The predominant liquid products were acetic acid and butyric acid during degrading lignocellulose in anaerobic digestion (AD) process inoculated with the LTF-27. The consortium mainly composed of Parabacteroides, Alcaligenes, Lysinibacillus, Sphingobacterium, and Clostridium, along with some unclassified uncultured bacteria, indicating powerful synergistic interaction in AD process. A multi-species lignocellulolytic enzyme system working cooperatingly on lignocelluolse degradation was revealed by proteomics analysis of cellulose bound fraction of the crude extracellular enzyme, which provides key theoretical base for further exploration and application of LTF-27.

Bioethanol production from waste lignocelluloses: A review on microbial degradation potential

Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.

Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline

Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.