Paenibacillus campinasensis BL11: a wood material-utilizing bacterial strain isolated from black liquor

Paecilomyces variotii xylanase production, purification and characterization with antioxidant xylo-oligosaccharides production

Paecilomyces variotii xylanase was, produced in stirred tank bioreactor with yield of 760 U/mL and purified using 70% ammonium sulfate precipitation and ultra-filtration causing 3.29-fold purification with 34.47% activity recovery. The enzyme purity was analyzed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) confirming its monomeric nature as single band at 32 KDa. Zymography showed xylan hydrolysis activity at the same band. The purified enzyme had optimum activity at 60 °C and pH 5.0. The pH stability range was 5-9 and the temperature stability was up 70 °C. Fe²⁺and Fe³⁺ exhibited inhibition of xylanase enzyme while Cu²⁺, Ca²⁺, Mg²⁺ and Mn²⁺ stimulated its activity. Mercaptoethanol stimulated its activity; however, Na₂-EDTA and SDS inhibited its activity. The purified xylanase could hydrolyze beechwood xylan but not carboxymethyl cellulose (CMC), avicel or soluble starch. Paecilomyces variotii xylanase K_m and V_max for beechwood were determined to be 3.33 mg/mL and 5555 U/mg, respectively. The produced xylanase enzyme applied on beech xylan resulted in different types of XOS. The antioxidant activity of xylo-oligosaccharides increased from 15.22 to 70.57% when the extract concentration was increased from 0.1 to 1.5 mg/mL. The enzyme characteristics and kinetic parameters indicated its high efficiency in the hydrolysis of xylan and its potential effectiveness in lignocellulosic hydrolysis and other industrial application. It also suggests the potential of xylanase enzyme for production of XOS from biomass which are useful in food and pharmaceutical industries.

Bacterial valorization of pulp and paper industry process streams and waste

The pulp and paper industry is a major source of lignocellulose-containing streams. The components of lignocellulose material are lignin, hemicellulose, and cellulose that may be hydrolyzed into their smaller components and used as feedstocks for valorization efforts. Much of this material is contained in underutilized streams and waste products, such as black liquor, pulp and paper sludge, and wastewater. Bacterial fermentation strategies have suitable potential to upgrade lignocellulosic biomass contained in these streams to value-added chemicals. Bacterial conversion allows for a sustainable and economically feasible approach to valorizing these streams, which can bolster and expand applications of the pulp and paper industry. This review discusses the composition of pulp and paper streams, bacterial isolates from process streams that can be used for lignocellulose biotransformations, and technological approaches for improving valorization efforts. KEY POINTS: • Reviews the conversion of pulp and paper industry waste by bacterial isolates. • Metabolic pathways for the breakdown of lignocellulose components. • Methods for isolating bacteria, determining value-added products, and increasing product yields.

The Complete Genome Sequence of a Bacterial Strain with High Alkalic Xylanase Activity Isolated from the Sludge Near a Papermill

Many organisms secrete xylanase, an import group of proteins hydrolyzing xylan, and thus are able to use xylan as their carbon source. In this study, we sequenced the whole genome of a bacterial strain, YD01, which was isolated from the sludge near the sewage discharge outlet of a papermill and showed high alkalic xylanase activity. Its genome consists of a chromosome and two plasmids. Six rRNA genes, 46 tRNA genes, 3136 CDSs as well as 955 repetitive sequences were predicted. 3046 CDSs were functionally annotated. Phylogenetic analysis on 16S rRNA shows that YD01 is a new species in Microbacterium genus and is taxonomically close to M. jejuense THG-C31^T and M. kyungheense THG-C26^T. A comparative study on phylogenetic trees of 16S rRNA and xylanase genes suggests that xylanase genes in YD01 may originate from horizontal gene transfer instead of ancestral gene duplication.

Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence

The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.

Studies on properties of the xylan-binding domain and linker sequence of xylanase XynG1-1 from Paenibacillus campinasensis G1-1

Xylanase XynG1-1 from Paenibacillus campinasensis G1-1 consists of a catalytic domain (CD), a family 6_36 carbohydrate-binding module which is a xylan-binding domain (XBD), and a linker sequence (LS) between them. The structure of XynG1-3 from Bacillus pumilus G1-3 consists only of a CD. To investigate the functions and properties of the XBD and LS of XynG1-1, two truncated forms (XynG1-1CDL, XynG1-1CD) and three fusion derivatives (XynG1-3CDL, XynG1-3CDX and XynG1-3CDLX) were constructed and biochemically characterized. The optimum conditions for the catalytic activity of mutants of XynG1-1 and XynG1-3 were 60 °C and pH 7.0, and 55 °C and pH 8.0, respectively, the same as for the corresponding wild-type enzymes. XynGs with an XBD were stable over a broad temperature (30–80 °C) and pH range (4.0–11.0), respectively, on incubation for 3 h. Kinetic parameters (K  m, k  cat, k  cat/K  m) of XynGs were determined with soluble birchwood xylan and insoluble oat spelt xylan as substrates. XynGs with the XBD showed better affinities toward, and more efficient catalysis of hydrolysis of the insoluble substrate. The XBD had positive effects on thermostability and pH stability and a crucial function in the ability of the enzyme to bind and hydrolyze insoluble substrate. The LS had little effect on the overall stability of the xylanase and no relationship with affinities for soluble and insoluble substrates or catalytic efficiency.

Bacterial biodegradation and bioconversion of industrial lignocellulosic streams

Lignocellulose is a term for plant materials that are composed of matrices of cellulose, hemicellulose, and lignin. Lignocellulose is a renewable feedstock for many industries. Lignocellulosic materials are used for the production of paper, fuels, and chemicals. Typically, industry focuses on transforming the polysaccharides present in lignocellulose into products resulting in the incomplete use of this resource. The materials that are not completely used make up the underutilized streams of materials that contain cellulose, hemicellulose, and lignin. These underutilized streams have potential for conversion into valuable products. Treatment of these lignocellulosic streams with bacteria, which specifically degrade lignocellulose through the action of enzymes, offers a low-energy and low-cost method for biodegradation and bioconversion. This review describes lignocellulosic streams and summarizes different aspects of biological treatments including the bacteria isolated from lignocellulose-containing environments and enzymes which may be used for bioconversion. The chemicals produced during bioconversion can be used for a variety of products including adhesives, plastics, resins, food additives, and petrochemical replacements.

¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of a family 36 carbohydrate binding module of xylanase from Paenibacillus campinasensis

Paenibacillus campinasensis BL11 isolated from black liquor secretes multiple glycoside hydrolases (GHs) against all kinds of polysaccharides. GH consists of a catalytic module and non-catalytic carbohydrate-binding modules (CBMs), in which CBMs append to the catalytic module, mediating specific interactions with insoluble carbohydrates to promote the hydrolysis efficiency of the cognate enzyme. Endo-β-1,4-xylanase (XylX) is one of the GHs reveals high enzymatic activity in a wide range of pH and thermal endurance, suitable for bioconversion and bio-refinement applications. In this work, we report the resonance assignments of a family 36 CBM (characterized as CBM36) derived from XylX. Our investigations will facilitate molecular structure determination and molecular dynamics analysis of CBMs.

Isolation of Paenibacillus glucanolyticus from pulp mill sources with potential to deconstruct pulping waste

Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. A microorganism was isolated from a black liquor sample collected from the Department of Forest Biomaterials at North Carolina State University. The organism was identified as Paenibacillus glucanolyticus using 16S rRNA sequence analysis and was shown to be capable of growth on black liquor as the sole carbon source based on minimal media growth studies. Minimal media growth curves demonstrated that this facultative anaerobic microorganism can degrade black liquor as well as cellulose, hemicellulose, and lignin. Gas chromatography-mass spectrometry was used to identify products generated by P. glucanolyticus when it was grown anaerobically on black liquor. Fermentation products which could be converted into high-value chemicals such as succinic, propanoic, lactic, and malonic acids were detected.

Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1

From different natural reserves in the subtropical region of China, a total of 245 aerobic bacterial strains were isolated on agar plates containing sugarcane bagasse pulp as the sole carbon source. Of the 245 strains, 22 showed hydrolyzing zones on agar plates containing carboxymethyl cellulose after Congo-red staining. Molecular identification showed that the 22 strains belonged to 10 different genera, with the Burkholderia genus exhibiting the highest strain diversity and accounting for 36.36% of all the 22 strains. Three isolates among the 22 strains showed higher carboxymethyl cellulase (CMCase) activity, and isolate ME27-1 exhibited the highest CMCase activity in liquid culture. The strain ME27-1 was identified as Paenibacillus terrae on the basis of 16S rRNA gene sequence analysis as well as physiological and biochemical properties. The optimum pH and temperature for CMCase activity produced by the strain ME27-1 were 5.5 and 50°C, respectively, and the enzyme was stable at a wide pH range of 5.0–9.5. A 12-fold improvement in the CMCase activity (2.08 U/mL) of ME27-1 was obtained under optimal conditions for CMCase production. Thus, this study provided further information about the diversity of cellulose-degrading bacteria in the subtropical region of China and found P. terrae ME27-1 to be highly cellulolytic.

Halo-alkalitolerant and thermostable cellulases with improved tolerance to ionic liquids and organic solvents from Paenibacillus tarimensis isolated from the Chott El Fejej, Sahara desert, Tunisia

The wide number of industrial processes applying cellulases highlights the importance of discovering robust enzymes able to work under harsh conditions. In this study, carboxymethyl cellulase (CMCase) activity of Paenibacillus tarimensis was characterized. A high activity was observed in pH range 3.0-10.5 and 9 mM-5 M NaCl. In high salt buffer at 80°C, >80% and >76% of relative activity was retained at 20% of the ionic liquids (ILs) [EMIM]Ac and [BMIM]Cl; while >40% was detected with 40% [BMIM]Cl. Five CMCases were detected by renaturing SDS-PAGE. Their activity was retained in presence of 1.7 up to 5 M NaCl (for CMC1) or 4.6 M KCl; 5% organic solvents or 10 mM bivalent ions, EDTA and heavy metals; under neutral and halo-alkaline conditions. These cellulases stabile and highly functional under harsh conditions are promising candidates for application in detergents, textiles, paper/pulp industry; and simultaneous ILs treatment-saccharification of lignocellulose.

Indigenous cellulolytic and hemicellulolytic bacteria enhanced rapid co-composting of lignocellulose oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge

The composting of lignocellulosic oil palm empty fruit bunch (OPEFB) with continuous addition of palm oil mill (POME) anaerobic sludge which contained nutrients and indigenous microbes was studied. In comparison to the conventional OPEFB composting which took 60-90 days, the rapid composting in this study can be completed in 40 days with final C/N ratio of 12.4 and nitrogen (2.5%), phosphorus (1.4%), and potassium (2.8%), respectively. Twenty-seven cellulolytic bacterial strains of which 23 strains were closely related to Bacillus subtilis, Bacillus firmus, Thermobifida fusca, Thermomonospora spp., Cellulomonas sp., Ureibacillus thermosphaericus, Paenibacillus barengoltzii, Paenibacillus campinasensis, Geobacillus thermodenitrificans, Pseudoxanthomonas byssovorax which were known as lignocellulose degrading bacteria and commonly involved in lignocellulose degradation. Four isolated strains related to Exiguobacterium acetylicum and Rhizobium sp., with cellulolytic and hemicellulolytic activities. The rapid composting period achieved in this study can thus be attributed to the naturally occurring cellulolytic and hemicellulolytic strains identified.

Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut

A cellulolytic bacterial strain, designated P118, isolated from the gut of the tropical fish Parotocinclus maculicauda was identified as belonging to the genus Paenibacillus based on phenotypic and chemotaxonomic characteristics and the 16S rRNA gene sequence. The novel strain was Gram-positive, spore-forming and rod-shaped. Catalase but not oxidase was produced. Carboxymethylcellulose was hydrolyzed but starch or gelatin was not. Acetoin production was negative whereas nitrate reduction and urease production were positive. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant isoprenoid quinone. Anteiso-C15:0 (38.73%) and C16:0 (20.85%) were the dominant cellular fatty acids. Strain P118 was closely related to Paenibacillus amylolyticus NRRL NRS-290, P. pabuli HSCC 492, P. tundrae Ab10b, P. xylanexedens B22a, and P. tylopili MK2 with 98.3-98.8% 16S rRNA gene sequence similarity. The results presented here suggest that strain P118 represents a novel species of the genus Paenibacillus and it is a potential strain for further studies concerning its role in the production of industrially important products from cellulosic biomass.

Characterization and pulp refining activity of a Paenibacillus campinasensis cellulase expressed in Escherichia coli

The Cel-BL11 gene from Paenibacillus campinasensis BL11 was cloned and expressed in Escherichia coli as a His-tag fusion protein. Zymographic analysis of the recombinant protein revealed cellulase activity corresponding to a protein with a 38-kDa molecular weight. The optimum temperature and pH for purified cellulase were 60 °C and pH 7.0, respectively. The enzyme retained more than 80% activity after 8h at 60 °C at pH 6 and 7. The cellulase has a Km of 11.25 mg/ml and a Vmax of 1250 μmol/min/mg with carboxylmethyl cellulose (CMC). Then enzyme was active on Avicel, swollen Avicel, CMC, barley β-glucan, laminarin in the presence of 100 mM acetate buffer. It was inhibited by Hg²⁺, Cu²⁺ and Zn²⁺. Significant kraft pulp refining energy saving, 10%, was exhibited by the pretreatment of this cellulase applied at 2 IU per gram of oven-dried pulp. Broad pH and temperature stability render this cellulase a convenient applicability toward current mainstream biomass conversion and other industrial processes.

Biosynthesis of selenium nanoparticles using Klebsiella pneumoniae and their recovery by a simple sterilization process

The use of biologically derived metal nanoparticles for various proposes is going to be an issue of considerable importance; thus, appropriate methods should be developed and tested for the biological synthesis and recovery of these nanoparticles from bacterial cells. In this research study, a strain of Klebsiella pneumoniae was tested for its ability to synthesize elemental selenium nanoparticles from selenium chloride. A broth of Klebsiella pneumoniae culture containing selenium nanoparticles was subjected to sterilization at 121(o)C and 17 psi for 20 minutes. Released selenium nanoparticles ranged in size from 100 to 550 nm, with an average size of 245 nm. Our study also showed that no chemical changes occurred in selenium nanoparticles during the wet heat sterilization process. Therefore, the wet heat sterilization process can be used successfully to recover elemental selenium from bacterial cells.

One-step purification and characterization of cellulase-free xylanase produced by alkalophilic Bacillus subtilis ash

The present study describes the one-step purification and characterization of an extracellular cellulase-free xylanase from a newly isolated alkalophilic and moderately thermophilic strain of Bacillus subtilis ASH. Xylanase was purified to homogeneity by 10.5-fold with ~43% recovery using ion-exchange chromatography through CM-Sephadex C-50. The purified enzyme revealed a single band on SDS-PAGE gel with a molecular mass of 23 kDa. It showed an optimum pH at 7.0 and was stable over the pH range 6.0-9.0. The optimum temperature for enzyme activity was 55 °C. The purified xylanase did not lose any activity up to 45 ºC, however, it retained 80% and 51% of its activity after pre-incubation at 55 ºC and 60 ºC, respectively. The enzyme obeyed Michaelis-Menton kinetics towards birch wood xylan with apparent K_m 3.33 mg/ml and V_max 100 IU/ml. The enzyme was strongly inhibited by Hg²⁺and Cu²⁺while enhanced by Co²⁺ and Mn²⁺. The purified enzyme could be stored at 4 ºC for six weeks without any loss of catalytic activity. The faster and economical purification of the cellulase-free xylanase from B. subtilis ASH by one-step procedure together with its appreciable stability at high temperature and alkaline pH makes it potentially effective for industrial applications.

A novel microbial habitat of alkaline black liquor with very high pollution load: microbial diversity and the key members in application potentials

A microbial community which developed naturally in alkaline black liquor was investigated by culture-based and culture-independent techniques. The community was effective in lowering pH, color, and chemical oxygen demand (COD) of black liquor, and the community activities varied in different seasons. Both 16S ribosomal DNA (rDNA) clone library and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses suggested that the seasonal bacterial communities had obvious differences in diversities and compositions. Clostridium species were suggested to be the key agents in black liquor treatment. Moreover, the isolates of the genera Halomonas and Bacillus were shown to be effective in treating very heavily polluted black liquor. The strains of Halomonas, Clostridium and especially Bacillus, might be the key producers of xylanase and CMCase in the community. The worldwide problem of black liquor treatment and renewable resource utilization would benefit from these microorganisms in application potentials.

The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass

Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.

A constructed alkaline consortium and its dynamics in treating alkaline black liquor with very high pollution load

Background

Paper pulp wastewater resulting from alkaline extraction of wheat straw, known as black liquor, is very difficult to be treated and causes serious environmental problems due to its high pH value and chemical oxygen demand (COD) pollution load. Lignin, semicellulose and cellulose are the main contributors to the high COD values in black liquor. Very few microorganisms can survive in such harsh environments of the alkaline wheat straw black liquor. A naturally developed microbial community was found accidentally in a black liquor storing pool in a paper pulp mill of China. The community was effective in pH decreasing, color and COD removing from the high alkaline and high COD black liquor.

Findings

Thirty-eight strains of bacteria were isolated from the black liquor storing pool, and were grouped as eleven operational taxonomy units (OTUs) using random amplified polymorphic DNA-PCR profiles (RAPD). Eleven representative strains of each OTU, which were identified as genera of Halomonas and Bacillus, were used to construct a consortium to treat black liquor with a high pH value of 11.0 and very high COD pollution load of 142,600 mg l⁻¹. After treatment by the constructed consortium, about 35.4% of color and 39,000 mg l⁻¹ (27.3%) COD_cr were removed and the pH decreased to 7.8. 16S rRNA gene polymerase chain reaction denaturant gradient gel electrophoresis (PCR-DGGE) and gas chromatography/mass spectrometry (GC/MS) analysis suggested a two-stage treatment mechanism to elucidate the interspecies collaboration: Halomonas isolates were important in the first stage to produce organic acids that contributed to the pH decline, while Bacillus isolates were involved in the degradation of lignin derivatives in the second stage under lower pH conditions.

Conclusions/Significance

Tolerance to the high alkaline environment and good controllability of the simple consortium suggested that the constructed consortium has good potential for black liquor treatment. Facilitating the treatment process by the constructed consortium would provide a promising opportunity to reduce the pollution, as well as to save forest resources and add value to a waste product.

Characterisation of Paenibacillus jamilae strains that produce exopolysaccharide during growth on and detoxification of olive mill wastewaters

A total of 10 bacterial strains were isolated from a compost of corn treated with olive mill wastewaters (OMW) and selected by their capacity to synthesize exopolysaccharides (EPS). Morphological, physiological, biochemical and nutritional tests were used for a phenotypic study. A numerical analysis showed that all strains were 90% similar to each other. A DNA-DNA hybridization assay confirmed that all the strains belonged to Paenibacillus jamilae species. All the characterized strains were able to produce EPS growing on OMW batch cultures. The strain which was able to produce the highest EPS yield was chosen to perform an assay for testing its putative detoxifying activity, and it showed to reduce more than half the toxic capacity of the OMW. The results presented in this study, indicated the possible perspectives for using these bacterial strains to produce EPS and contribute to the bioremediation of the waste waters that are produced in the olive oil elaboration process.