Optimization of xylanase production by Pichia kudriavzevii and Candida tropicalis isolated from the wood product workshop

Enzymatic compounds can be found abundantly and provide numerous advantages in microbial organisms. Xylanases are used in various pharmaceutical, food, livestock, poultry, and paper industries. This study aimed to investigate xylanase-producing yeasts, xylose concentration curve and their enzymatic activity under various factors including carbon and nitrogen sources, temperature, and pH. Enzyme activity was evaluated under different conditions before, during, and after purification. The yeast strains were obtained from the wood product workshop and were subsequently cultivated on YPD (yeast extract peptone dextrose) medium. Additionally, the growth curve of the yeast and its molecular identification were conducted. The optimization and design process of xylan isolated from corn wood involved the use of Taguchi software to test different parameters like carbon and nitrogen sources, temperature, and pH, with the goal of determining the most optimal conditions for enzyme production. In addition, the Taguchi method was utilized to conduct a multifactorial optimization of xylanase enzyme activity. The isolated species were partially purified using ammonium sulfate precipitation and dialysis bag techniques. The results indicated that 3 species (8S, 18S, and 16W) after molecular identification based on 18S rRNA gene sequencing were identified as Candida tropicalis SBN-IAUF-1, Candida tropicalis SBN-IAUF-3, and Pichia kudriavzevii SBN-IAUF-2, respectively. The optimal parameters for wheat carbon source and peptone nitrogen source were found at 50 °C and pH 9.0 through single-factor optimization. By using the Taguchi approach, the best combination for highest activity was rice-derived carbon source and peptone nitrogen source at 50 °C and pH 6.0. The best conditions for xylanase enzyme production in single-factor optimization of wheat bran were 2135.6 U/mL, peptone 4475.25 U/mL, temperature 50 °C 1868 U/mL, and pH 9.0 2002.4 U/mL. Among the tested yeast, Candida tropicalis strain SBN-IAUF-1 to the access number MZ816946.1 in NCBI was found to be the best xylanase product. The highest ratio of enzyme production at the end of the delayed phase and the beginning of the logarithmic phase was concluded by comparing the growth ratio of 8S, 16W, and 18S yeasts with the level of enzymatic activity. This is the first report on the production of xylan polymer with a relative purity of 80% in Iran. The extracellular xylanases purified from the yeast species of C. tropicalis were introduced as a desirable biocatalyst due to their high enzymatic activity for the degradation of xylan polymers.

Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost

We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8^T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37-60 °C (optimum, 55 °C) and pH 4.0-11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8^T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8^T was most closely related to Paenibacillus cisolokensis LC2-13A^T (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8^T belonged to the same lineage as Xylanibacillus composti K13^T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA-DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8^T and P. cisolokensis LC2-13A^T were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8^T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8^T was 52.3 mol%. The major cellular fatty acids were C_16 : 0 (42.9 %), anteiso-C_15 : 0 (20.0 %) and anteiso-C_17 : 0 (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed-Insulambacter gen. nov.-for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8^T (=JCM 34211^T=DSM 111723^T).

Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis

A Gram-stain-positive, rod-shaped, strictly aerobic, endospore-forming and motile bacterium with peritrichous flagella was isolated from a gut sample of the larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Growth was observed at 15-50 °C (optimum, 28-37 °C), pH 6.0-8.0 (pH 7.0) and only without NaCl. 16S rRNA gene sequence comparisons indicated that strain FW100M-2^T had the highest similarity to type strains of Paenibacillus thailandensis S3-4A^T (96.8 %) and Paenibacillus agaridevorans DSM 1355^T (96.3 %), and had sequence similarity values less than 96.0 % to all other taxa. The phylogenetic tree showed that strain FW100M-2^T fell into the genus Paenibacillus, and formed a cluster with P. thailandensis S3-4A^T independent from other Paenibacillus species. Antesio-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0 were detected as the major fatty acids. The only isoprenoid quinone was MK-7. Polar lipids of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified lipid were present. The meso-diaminopimelic acid was present in the cell-wall peptidoglycan. The genomic DNA G+C content was 51.5 mol%. Hence, strain FW100M-2^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus protaetiae sp. nov. is proposed, with FW100M-2^T (=KACC 19327^T=NBRC 113071^T) as the type strain.

Xylanibacillus composti gen. nov., sp. nov., isolated from compost

A novel Gram-stain-positive bacterial strain, designated as K13^T, was isolated from compost and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain showed highest similarity (93.8 %) to Paenibacillus nanensis MX2-3^T. Cells of strain K13^T were aerobic, motile rods. The major fatty acids were anteiso C15 : 0 (34.4 %), iso C16 : 0 (17.3 %) and C16 : 0 (10.0 %). The major menaquinone was MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an aminophospholipid. The DNA G+C content was 52.3 %. Based on phenotypic, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain K13^T represents a novel genus, for which the name Xylanibacillus gen. nov., sp. nov. is proposed. The type species of the genus is Xylanibacillus composti, the type strain of which is strain K13^T (=DSM 29793^T=NCAIM B.02605^T).

Raw sugarcane bagasse as carbon source for xylanase production by Paenibacillus species: a potential degrader of agricultural wastes

Paenibacillus species isolated from a variety of natural sources have shown to be important glycoside hydrolases producers. These enzymes play a key role in bio-refining applications, as they are central biocatalysts for the processing of different types of polymers from vegetal biomass. Xylanase production by three native isolates belonging to the genus Paenibacillus was approached by utilizing mineral-based medium and agricultural by-products as a convenient source to produce biocatalysts suitable for their degradation. While varieties of alkali pretreated sugarcane bagasse were useful substrates for the strains from Paenibacillus genus evaluated, raw sugarcane bagasse was the most effective substrate for endoxylanase production by Paenibacillus sp. AR247. This strain was then selected to further improvement of its enzyme production by means of a two-step statistical approach. It was determined that the carbon source, provided as an inexpensive agro-waste, as well as phosphate and magnesium were the culture media components that most influenced the enzyme production, which was improved three times compared to the screening results.

Conversion of ammonia-pretreated switchgrass to biofuel precursors by bacterial-fungal consortia under solid-state and submerged-state cultivation

AIM

The aim of this study was to develop and evaluate bacterial-fungal communities to deconstruct switchgrass to biofuel precursors.

METHODS AND RESULTS

Bacterial-fungal consortia, mesophilic (25°C) and thermophilic (50°C), were enriched from switchgrass bales from which enzyme mixtures were used to deconstruct delignified switchgrass (DSG). The bacterial-fungal consortia were able to produce enzymes including endoglucanase, exoglucanase, β-glucosidase, xylanase, xylosidase and pectinase to convert DSG to soluble carbohydrates. 454 pyrosequencing revealed that Paenibacillus and Streptomyces were the dominant bacteria in the mesophilic and thermophilic consortia respectively. Penicillium and Acremonium were the dominant fungi in the mesophilic consortia, whereas Aspergillus and Penicillium were the dominant fungi present in the thermophilic consortia.

CONCLUSIONS

The results show that the state of cultivation, solid-state or submerged-state, affects the community structure as well as enzyme activities produced by these bacterial-fungal consortia. The enzyme mixture produced by the bacterial-fungal consortia released a higher amount of xylose than glucose during saccharification of DSG.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides a novel approach to produce enzymes for conversion of lignocellulolytic feedstocks to soluble sugars which can be used to produce biofuel precursors.

Paenibacillus lentus sp. nov., a β-mannanolytic bacterium isolated from mixed soil samples in a selective enrichment using guar gum as the sole carbon source

A novel bacterial strain, CMG1240T, was isolated in 1988 from mixed soil samples collected from the United States and South America in a selective enrichment medium with guar gum as the sole carbon source. This microbial isolate showed β-mannanolytic activity to hydrolyse the galactomannans present in guar gum. Strain CMG1240T was aerobic, Gram-stain-variable, non-motile, rod-shaped and endospore-forming. It was further examined based on a combination of phenotypic, physiological and genetic characterization. On the basis of 16S rRNA gene sequence similarity, cellular lipid profile and fatty acid composition, strain CMG1240T was shown to belong unequivocally to the genus Paenibacillus . Quinone analysis showed that MK-7 was the only menaquinone detected. The main cell-wall sugar was xylose with trace amounts of mannose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unknown glycolipids, phospholipids, phosphoglycolipids and other lipids. The peptidoglycan structure was A1γ (meso-diaminopimelic acid-direct). The major fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content was 46 mol% as determined experimentally and by analysis of the genomic sequence. The 16S rRNA gene sequence of strain CMG1240T shared highest similarity with that of Paenibacillus fonticola ZLT (97.6 %) while all other tested Paenibacillus strains showed lower sequence similarities (≤95.3 %). The results of DNA–DNA hybridization and chemotaxonomic tests enabled the genotypic and phenotypic differentiation of strain CMG1240T from P. fonticola . Based on these results, strain CMG1240T ( = ATCC BAA-2594T = DSM 25539T) should be designated the type strain of a novel species within the genus Paenibacillus , for which the name Paenibacillus lentus sp. nov. is proposed.

Isolation of Paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-Do, Korea

Using a new culture method for unculturable soil bacteria, strain NB5(T) was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0-9.5 (optimum, 6.5-9.5) and at temperatures between 15°C and 45°C (optimum, 25-40°C). Growth was possible at 0-5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3(T) and P. agaridevorans DSM 1355(T), respectively. The predominant menaquinone in NB5(T) was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472(T)=KEMB 9005-025(T)=JCM 19203(T)).

Paenibacillus thermoaerophilus sp. nov., a moderately thermophilic bacterium isolated from compost

A rod-shaped, endospore-forming, Gram-reaction-positive bacterium, designated strain TC22-2bT, was isolated from compost in Tochigi, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to a cluster comprising species of the genus Paenibacillus and was most closely related to the type strain of Paenibacillus elgii (93.4 % similarity). The major cellular fatty acids were C16:0 (25.5 %), iso-C16:0 (23.6 %) and anteiso-C15:0 (21.5 %). The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The diamino acid found in the cell wall peptidoglycan was meso-diaminopimelic acid, and the DNA G+C content was 59.1 mol%. The results of physiological and biochemical tests enabled the phenotypic differentiation of strain TC22-2bT from the most closely related species with validly published names. Phylogenetic and phenotypic evidence reveals that strain TC22-2bT represents a novel species of the genus Paenibacillus , for which the name Paenibacillus thermoaerophilus sp. nov. is proposed. The type strain of the novel species is TC22-2bT ( = DSM 26310T  = JCM 18657T).

Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester

A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1(T), was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C(15:0), iso-C(16:0), anteiso-C(17:0), and C(16:0) were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1(T) belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1(T) were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1(T) should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1(T) (=NBRC 106381(T) =KCTC 13719(T) =TISTR 1914(T)).

Isolation of a Paenibacillus sp. strain and structural elucidation of its broad-spectrum lipopeptide antibiotic

This research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as a Paenibacillus sp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted from Paenibacillus OSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C(15) fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium. Paenibacterin is resistant to trypsin, lipase, α-glucosidase, and lysozyme. Its antimicrobial activity was lost after digestion by pronase and polymyxin acylase. Paenibacterin is readily soluble in water and fairly stable to exposure to heat and a wide range of pH values. The new isolate and its antimicrobial agent are being investigated for usefulness in food and medical applications.

Paenibacillus sacheonensis sp. nov., a xylanolytic and cellulolytic bacterium isolated from tidal flat sediment

A Gram-negative-staining, rod-shaped bacterium, designated strain SY01T, was isolated from tidal flat sediment from Sacheon Bay, South Korea. Strain SY01T was characterized with respect to its phenotypic and phylogenetic characteristics. The novel strain was spore-forming, motile, catalase-negative and oxidase-positive. Optimal growth of the strain occurred at 30 °C and pH 7.0. The DNA G+C content was 56.1 mol%. The predominant menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids were detected in the polar lipid profile. Anteiso-C15 : 0 (47.2 %), iso-C15 : 0 (18.9 %) and iso-C16 : 0 (10.5 %) were the major cellular fatty acids of strain SY01T. The highest 16S rRNA gene sequence similarities were found with Paenibacillus phyllosphaerae PALXIL04T (95.9 %), Paenibacillus tarimensis SA-7-6T (94.6 %) and Paenibacillus mendelii C/2T (94.4 %). Based on the phylogenetic, chemotaxonomic and physiological characteristics presented in this study, strain SY01T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sacheonensis sp. nov. is proposed. The type strain is SY01T ( = DSM 23054T = KACC 14895T).

Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil

A xylan-degrading bacterium, strain X11-1T, was isolated from soil collected in Nan province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain X11-1T was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7, anteiso-C15 : 0 (56.6 %) and C16 : 0 (14.0 %) were the predominant cellular fatty acids and diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol were the major phospholipids. The DNA G+C content was 51.6 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain X11-1T was affiliated to the genus Paenibacillus and was closely related to Paenibacillus naphthalenovorans KACC 11505T and Paenibacillus validus CCM 3894T, with 96.5 % sequence similarity. Therefore, the strain represents a novel species of the genus Paenibacillus, for which the name Paenibacillus xylanisolvens sp. nov. is proposed. The type strain is X11-1T (=KCTC 13042T =PCU 311T =TISTR 1829T).

Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease

Strain KIT 00200-70066-1(T) was isolated from the sputum of a patient with pulmonary disease. Cells of the strain were Gram-variable, facultatively anaerobic, motile, spore-forming rods and formed colourless to white colonies on tryptic soy agar at 30&emsp14;°C and pH&emsp14;7. The pathogenicity of the strain is not known. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, anteiso-C₁₅:₀, iso-C₁₆:₀ and C₁₆:₀ as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus nanensis MX2-3(T), Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus alkaliterrae KSL-134(T) (95.4, 95.2 and 94.8 %, respectively), and that it occupied a distinct position within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain KIT 00200-70066-1(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sputi sp. nov. is proposed; the type strain is KIT 00200-70066-1(T) (=KCTC 13252(T) =DSM 22699(T)).