Unleashing the potential of ligninolytic bacterial contributions towards pulp and paper industry: key challenges and new insights

Enterobacter spp. isolates from an underground coal mine reveal ligninolytic activity

Lignin, the second most abundant renewable carbon source on earth, holds significant potential for producing biobased specialty chemicals. However, its complex, highly branched structure, consisting of phenylpropanoic units and strong carbon-carbon and ether bonds, makes it highly resistant to depolymerisation. This recalcitrancy highlights the need to search for robust lignin-degrading microorganisms with potential for use as industrial strains. Bioprospecting for microorganisms from lignin-rich niches is an attractive approach among others. Here, we explored the ligninolytic potential of bacteria isolated from a lignin-rich underground coalmine, the Morupule Coal Mine, in Botswana. Using a culture-dependent approach, we screened for the presence of bacteria that could grow on 2.5% kraft lignin-supplemented media and identified them using 16 S rRNA sequencing. The potential ligninolytic isolates were evaluated for their ability to tolerate industry-associated stressors. We report the isolation of twelve isolates with ligninolytic abilities. Of these, 25% (3) isolates exhibited varying robust ligninolytic ability and tolerance to various industrial stressors. The molecular identification revealed that the isolates belonged to the Enterobacter genus. Two of three isolates had a 16 S rRNA sequence lower than the identity threshold indicating potentially novel species pending further taxonomic review. ATR-FTIR analysis revealed the ligninolytic properties of the isolates by demonstrating structural alterations in lignin, indicating potential KL degradation, while Py-GC/MS identified the resulting biochemicals. These isolates produced chemicals of diverse functional groups and monomers as revealed by both methods. The use of coalmine-associated ligninolytic bacteria in biorefineries has potential.

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.

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

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

Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills

In the wood-free paper industry, whitewater is usually a mixture of additives for paper production. We are currently lacking an efficient, cost-effective purification technology for their removal. In closed whitewater cycles the additives accumulate, causing adverse production problems, such as the formation of slime and pitch. The aim of our study was to find an effective bio-based strategy for whitewater treatment using a selection of indigenous bacterial isolates. We first obtained a large collection of bacterial isolates and then tested them individually by simple plate and spectrophotometric methods for their ability to degrade the papermaking additives, i.e., carbohydrates, resin acids, alkyl ketene dimers, polyvinyl alcohol, latex, and azo and fluorescent dyes. We examined correlation between carbon source use, genera, and inoculum source of isolates using two multivariate methods: principal component analysis and FreeViz projection. Of the 318 bacterial isolates, we selected a consortium of four strains (Xanthomonadales bacterium sp. CST37-CF, Sphingomonas sp. BLA14-CF, Cellulosimicrobium sp. AKD4-BF and Aeromonas sp. RES19-BTP) that degrade the entire spectrum of tested additives by means of dissolved organic carbon measurements. A proof-of-concept study on a pilot scale was then performed by immobilizing the artificial consortium of the four strains and inserting them into a 33-liter, tubular flow-through reactor with a retention time of < 15 h. The consortium caused an 88% reduction in the COD of the whitewater, even after 21 days.

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

BACKGROUND

Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization.

RESULTS

Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA.

CONCLUSIONS

The unusual aerobic '-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.

Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea

Bacterial strains were isolated from the sediments of the Baltic Sea using ferulic acid, guaiacol or a lignin-rich softwood waste stream as substrate. In total nine isolates were obtained, five on ferulic acid, two on guaiacol and two on a lignin-rich softwood stream as a carbon source. Three of the isolates were found to be Pseudomonas sp. based on 16S rRNA sequencing. Among them, isolate 9.1, which showed the fastest growth in defined M9 medium, was tentatively identified as a Pseudomonas deceptionensis strain based on the gyrB sequencing. The growth of isolate 9.1 was further examined on six selected lignin model compounds (ferulate, p-coumarate, benzoate, syringate, vanillin and guaiacol) from different upper funneling aromatic pathways and was found able to grow on four out of these six compounds. No growth was detected on syringate and guaiacol. The highest specific growth and uptake rates were observed for benzoate (0.3 h-1 and 4.2 mmol g CDW-1  h-1) whereas the lowest were for the compounds from the coniferyl branch. Interestingly, several pathway intermediates were excreted during batch growth. Vanillyl alcohol was found to be excreted during growth on vanillin. Several other intermediates like cis,cis-muconate, catechol, vanillate and 4-hydroxybenzoate from the known bacterial catabolic pathways were excreted during growth on the model compounds.