Links among extracellular enzymes, lignin degradation and cell growth establish the models to identify marine lignin-utilizing bacteria

Insights into lignin bioconversion: lignin-derived compounds treatment of a novel marine fungus K-2

BACKGROUND

The potential for the efficient conversion of lignocellulosic biomass has been extensively explored to produce a wide range of bioproducts. Many approaches have been sought for the deep conversion of lignin to generate products that are toxin-free and beneficial for processing into high-value-added components.

RESULTS

This study reported a fungus isolated from the deep sea with strong synthesis of multiple lignocellulases, conversion of lignin and guaiacol (0.1%) by 71.6% and 86.1% within 9 days at 30 °C respectively, and outstanding environmental adaptability (20-50 °C and pH 3-8). Metabolic pathway profiling showed that this fungus utilized lignin to rapidly activate multiple ring-opening reactions including the 2,3- and 3,4-cleavage pathways, with the 2,3-cleavage pathway predominating after 5 days. Conversion of metabolic intermediates confirmed the superb potential of this strain for lignin treatment. Meanwhile, its shikimic acid pathway was metabolically active under lignin.

CONCLUSION

This further expands the potential to produce valuable bioproducts during lignin treatment, especially under ambient conditions, which can significantly enhance high-value precursor compound production. © 2024 Society of Chemical Industry.

Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery. Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge to understand such complex interactions. Here, we develop a coastal lignin-degrading bacterial consortium (LD), through "top-down" enrichment. Sequencing and physiological analyses reveal that LD is dominated by the lignin degrader Pluralibacter gergoviae (>98%), with additional rare non-degraders. Interestingly, LD, cultured in lignin-MB medium, significantly enhances cell growth and lignin degradation as compared to P. gergoviae alone, implying a role of additional outliers. Using genome-scale metabolic models, metabolic profiling and culture experiments, modeling of inter-species interactions between P. gergoviae, Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens, unravels cross-feeding of amino acids, organic acids and alcohols between the degrader and non-degraders. Furthermore, the sub-population ratio is essential to enforce the synergy. Our study highlights the unrecognized role of outliers in lignin degradation.

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.

Genomic characterization and proteomic analysis of Bacillus amyloliquefaciens in response to lignin

This study examined the lignin degradation characteristics of Bacillus amyloliquefaciens MN-13. Specifically, whole-genome sequencing and comparative proteomic analysis were performed to investigate the responses of the MN-13 strain to lignin. A maximum lignin removal of 38.0 % was achieved after 36 h of inoculation in mineral salt medium with 0.2 g/L alkaline lignin, under the following conditions: the carbon to nitrogen ratio C/N = 1/1; inoculum size 6 %; addition of glucose as an exogenous carbon source. When the MN-13 strain was inoculated into mineral salt medium with and without lignin, respectively, 831 differentially expressed proteins were identified, 404 of which were up-regulated and 427 were down-regulated. Enrichment analysis revealed that up-regulated proteins were associated with microbial metabolism in diverse environment, biosynthesis of amino acids, and pathways related to energy production, including carbon metabolism, pyruvate metabolism, the TCA cycle etc. Genomic analysis revealed that the MN-13 strain possesses many ligninolytic enzymes and aromatics degradation pathway, including benzoate degradation and aminobenzoate degradation etc. Taken together, the proteomic and genomic analyses indicated that the meta-cleavage pathway of catechol, including benzoate degradation, etc., is the main lignin degradation pathway. These findings provide new insight into lignin degradation mediated by B. amyloliquefaciens.

The Phylogeny and Metabolic Potentials of a Lignocellulosic Material-Degrading Aliiglaciecola Bacterium Isolated from Intertidal Seawater in East China Sea

Lignocellulosic materials are composed of cellulose, hemicellulose and lignin and are one of the most abundant biopolymers in marine environments. The extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, a novel lignin-degrading bacterial strain, LCG003, was isolated from intertidal seawater in Lu Chao Harbor, East China Sea. Phylogenetically, strain LCG003 was affiliated with the genus Aliiglaciecola within the family Alteromonadaceae. Metabolically, strain LCG003 contains various extracellular (signal-fused) glycoside hydrolase genes and carbohydrate transporter genes and can grow with various carbohydrates as the sole carbon source, including glucose, fructose, sucrose, rhamnose, maltose, stachyose and cellulose. Moreover, strain LCG003 contains many genes of amino acid and oligopeptide transporters and extracellular peptidases and can grow with peptone as the sole carbon and nitrogen source, indicating a proteolytic lifestyle. Notably, strain LCG003 contains a gene of dyp-type peroxidase and strain-specific genes involved in the degradation of 4-hydroxy-benzoate and vanillate. We further confirmed that it can decolorize aniline blue and grow with lignin as the sole carbon source. Our results indicate that the Aliiglaciecola species can depolymerize and mineralize lignocellulosic materials and potentially play an important role in the marine carbon cycle.

Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column

Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.

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.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope

A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.

Factors Influencing the Bioavailability of Organic Molecules to Bacterial Cells-A Mini-Review

The bioavailability of organic compounds to bacterial cells is crucial for their vital activities. This includes both compounds that are desirable to the cells (e.g., sources of energy, carbon, nitrogen, and other nutrients) and undesirable compounds that are toxic to the cells. For this reason, bioavailability is an issue of great importance in many areas of human activity that are related to bacteria, e.g., biotechnological production, bioremediation of organic pollutants, and the use of antibiotics. This article proposes a classification of factors determining bioavailability, dividing them into factors at the physicochemical level (i.e., those related to the solubility of a chemical compound and its transport in aqueous solution) and factors at the microbiological level (i.e., those related to adsorption on the cell surface and those related to transport into the cell). Awareness of the importance of and the mechanisms governing each of the factors described allows their use to change bioavailability in the desired direction.

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

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

Identification and Characterization of a New Serratia proteamaculans Strain That Naturally Produces Significant Amount of Extracellular Laccase

Natural biodegradation processes hold promises for the conversion of agro-industrial lignocellulosic biomaterials into biofuels and fine chemicals through lignin-degrading enzymes. The high cost and low stability of these enzymes remain a significant challenge to economic lignocellulosic biomass conversion. Wood-degrading microorganisms are a great source for novel enzyme discoveries. In this study, the decomposed wood samples were screened, and a promising γ-proteobacterial strain that naturally secreted a significant amount of laccase enzyme was isolated and identified as Serratia proteamaculans AORB19 based on its phenotypic and genotypic characteristics. The laccase activities in culture medium of strain AORB19 were confirmed both qualitatively and quantitatively. Significant cultural parameters for laccase production under submerged conditions were identified following a one-factor-at-a-time (OFAT) methodology: temperature 30°C, pH 9, yeast extract (2 g/l), Li+, Cu2+, Ca2+, and Mn2+ (0.5 mM), and acetone (5%). Under the selected conditions, a 6-fold increase (73.3 U/L) in laccase production was achieved when compared with the initial culturing conditions (12.18 U/L). Furthermore, laccase production was enhanced under alkaline and mesophilic growth conditions in the presence of metal ions and organic solvents. The results of the study suggest the promising potential of the identified strain and its enzymes in the valorization of lignocellulosic wastes. Further optimization of culturing conditions to enhance the AORB19 strain laccase secretion, identification and characterization of the purified enzyme, and heterologous expression of the specific enzyme may lead to practical industrial and environmental applications.

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

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

Effective bioremediation of pulp and paper mill wastewater using Bacillus cereus as a possible kraft lignin-degrading bacterium

The effective degradation of KL from paper mill effluent is an important for environmental safety. This research is primarily concerned with the identification of KL-degrading Bacillus cereus from activated sludge and their possible use for the degradation of Kraft lignin (KL). This strain was involved in the production of lignin peroxidase-LiP (3.20 U/mL), manganese peroxidase-MnP (20.36 U/mL), and laccase (21.35 U/mL) enzymes, which were responsible for high KL degradation (89%) and decolorization (40%) at 1000 mg/L KL in 3 days. The SEM-EDS, UV-Vis, FTIR, and GC-MS analysis were used to analyze the bacterial cell and KL interactions to trace the KL degradation process. The significant reduction of pollutants (KL-72.5%, color-62.0%, COD-45.05%) and reduction in toxicity (80%) of bacterial-treated effluent indicated that B. cereus has the potential to be used in the degradation of pollutants from paper mill effluents.

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.