Xylanolytic Bacterium Research Articles

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-C8T. 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-C8T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8T was most closely related to Paenibacillus cisolokensis LC2-13AT (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8T belonged to the same lineage as Xylanibacillus composti K13T (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-C8T and P. cisolokensis LC2-13AT were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8T was 52.3 mol%. The major cellular fatty acids were C16 : 0 (42.9 %), anteiso-C15 : 0 (20.0 %) and anteiso-C17 : 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-C8T (=JCM 34211T=DSM 111723T).

Co-cultivation of microalga and xylanolytic bacterium by a continuous two-step strategy to enhance algal lipid production

To enhance microalgal lipid production, canonical two-step cultivation strategy that by transferring the microalgal cells grown in nutrient-replete medium to nutrient-depleted medium is widely used. However, the harvesting step during the transfer raises the production cost. To avoid the harvesting step, this study developed a continuous two-step (CTS) cultivation strategy. In the strategy, Chlorella sacchrarophila was grown in bioreactor while a xylanolytic bacterium Cellvibrio pealriver grown in an inner bag that embedded in the bioreactor; after the first-step co-cultivation, the inner bag is removed which then start the second-step cultivation of C. sacchrarophila. Based on the strategy, the lipid production was determined as 825.34–929.79 mg·L−1, which were 1.7–1.9 times higher than that of cultivation in canonical two-step strategy using glucose as feedstock. During the CTS strategy, the co-cultivation using xylan as feedstock promotes the microalgal growth and the removal of inner bag produces nutrient-depleted condition for enhancing microalgal lipid production.

Optimization of xylanase from Pseudomonas mohnii isolated from Simlipal Biosphere Reserve, Odisha, using response surface methodology

BackgroundXylanase has long been recognized as a widely used industrially important enzyme. There are some bacterial species already reported to produce xylanase which have potent xylanolytic activity towards the use of this enzyme in the production of bioethanol from lignocellulosic biomass. In this view, an efficient xylanolytic bacterial strain was isolated and screened from the soil sample of Simlipal Biosphere Reserve. Enzymatic assay for the xylanase activity was evidenced from the most potent bacterial strain, and the culture condition was optimized for obtaining the maximum enzyme activity. The most potent xylanolytic strain was also identified using biochemical and molecular methods. ResultsNineteen xylanolytic bacteria (SXB1-SXB19) were isolated from Simlipal forest soil samples following dilution plate technique using corn cob xylan-enriched nutrient agar medium and screened for their xylanase-producing ability. Among these isolates, SXB19 showed maximum xylanolytic potential with a halozone size of 2.5 cm as evident in the formation of prominent yellow patches surrounding its growth in xylan-enriched nutrient agar plate. In unoptimized condition, SXB19 showed the highest enzymatic activity of 22.5 IU/ml among the 19 bacterial strains. In order to optimize the culture conditions for maximizing the xylanase production, Box-Behnken design of response surface methodology (RSM) was used. Four variables such as incubation time, pH, substrate (corn cob xylan) concentration, and temperature were considered for the RSM optimization study. From the results, it is evident that in an optimized condition of incubation time 36 h, pH 6.0, xylan concentration 0.5%, and temperature 42.5 °C, the enzyme activity reached a maximum of 152 IU/ml with nearly 6.75 times increase from the unoptimised condition. Besides, xylanase production from SXB19 was considerable in the presence of xylan followed by starch, nitrogen source such as urea followed by yeast extract, and mineral ion sources such as KCl followed by MgSO4 and ZnSO4. From different biochemical tests, 16S rRNA gene sequencing, and phylogenetic analysis, the bacterial strain SXB19 was identified as Pseudomonas mohnii. ConclusionThe isolation of Pseudomonas mohnii, a potent xylanolytic bacterium from Simlipal, is a new report which opens up an opportunity for industrial production of xylanase for bioethanol production and other applications. Graphical abstract▪

Differential antioxidant activity of glucuronoxylooligosaccharides (UXOS) and arabinoxylooligosaccharides (AXOS) produced by two novel xylanases

XOS are particularly interesting bioactive molecules. Bacillus safensis CBLMA18, a xylanolytic bacterium has been isolated and two of its xylanases have been identified and fully characterized. Xyn11A is an extracellular 22.5-kDa GH11 xylanase while a second xylanase, Xyn10B, corresponds to an intracellular 48-kDa GH10 enzyme. Both unimodular xylanases showed activity only on xylan substrates with important differences in their catalytic pattern. Xyn11A displays higher activity on glucuronoxylans, with an optimum at pH 8 and 50 °C, and a Vmax of 5281 U/mg on beechwood xylan, meanwhile Xyn10B prefers arabinoxylans, with an optimum of pH 7 and 60 °C, and a Vmax of 50.29 U/mg on rye arabinoxylan. The antioxidant activity of xylanase-generated XOS obtained from glucuronoxylans (UXOS) and arabinoxylans (AXOS) was tested with the ABTS (2, 2′-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)) method. UXOS showed higher antioxidant activity than AXOS (>80% of antioxidant capacity). Thin layer chromatography and MALDI-TOF MS analysis showed that UXOS comprise neutral and acidic XOS with methylglucuronic acid (MeGlcA) ramifications, while AXOS contain only neutral molecules with arabinose decorations. The MeGlcA ramifications seem to have an important role in the antioxidant capacity of oligosaccharides. Besides, the increase of UXOS size correlates with an increase in their activity.

Ruminiclostridium herbifermentans sp. nov., a mesophilic and moderately thermophilic cellulolytic and xylanolytic bacterium isolated from a lab-scale biogas fermenter fed with maize silage.

An anaerobic bacterial strain, designated MA18T, was isolated from a laboratory-scale biogas fermenter fed with maize silage. Cells stained Gram-negative and performed Gram-negative in the KOH test. The peptidoglycan type was found to be A1y-meso-Dpm direct. The major cellular fatty acids were C14 : 0 iso, C15 : 0 iso, anteiso and iso DMA as well as a C16 unidentified fatty acid. Oxidase and catalase activities were absent. Cells were slightly curved rods, motile, formed spores and measured approximately 0.35 µm in diameter and 3.0-5.0 µm in length. When cultivated on GS2 agar with cellobiose, round, arched, shiny and slightly yellow-pigmented colonies were formed. The isolate was mesophilic to moderately thermophilic with a growth optimum between 40 and 48 °C. Furthermore, neutral pH values were preferred and up to 1.2 % (w/v) NaCl supplemented to the GS2 medium was tolerated. Producing mainly acetate and ethanol, MA18T fermented arabinose, cellobiose, crystalline and amorphous cellulose, ribose, and xylan. The genome of MA18T consists of 4 817 678 bp with a G+C content of 33.16 mol%. In the annotated protein sequences, cellulosomal components were detected. Phylogenetically, MA18T is most closely related to Ruminiclostridium sufflavum DSM 19573T (76.88 % average nucleotide identity of the whole genome sequence; 97.23 % 16S rRNA gene sequence similarity) and can be clustered into one clade with other species of the genus Ruminiclostridium, family Oscillospiraceae, class Clostridia. Based on morphological, physiological and genetic characteristics, this strain represents a novel species in the genus Ruminiclostridium. Therefore, the name Ruminiclostridium herbifermentans sp. nov. is proposed. The type strain is MA18T (=DSM 109966T=JCM 39124T).

Bacterial Expression and Characterization of Recombinant β-Xylosidase from the Thermophilic Xylanolytic Bacterium Bacillus sp.

With the passage of time, energy sources are decreasing day by day. In order to meet the world's demand, much attention is being paid to the study of enzymes with xylanolytic activity as a potential means of generating energy. A thermophilic xylanolytic bacterium, Bacillus sp., was isolated from naturally decaying material by enrichment culture and serial dilution methods. The bacterium was grown in MH medium at 50°C and pH 7 for 10 h. The xylanolytic Bacillus sp. produced clear yellow haloes around the colonies in the presence of p-nitrophenyl beta-D-xylopyranoside (pNPX) as a substrate. After condition optimization, it was found that the organism produced the higher level of xylosidase activity after 14 h in the presence of arabinose as a carbon source and ammonium sulfate as a nitrogen source in the pH 7 medium of at 55°C. The maximum β-xylosidase activity after optimizing the culture condition was 5.0 U/mL. Later this thermophilic Bacillus sp. was used as a donor in cloning of the β-xylosidase gene. A genomic library of Bacillus sp. was prepared by digesting the genomic DNA of the Bacillus with the restriction endonuclease BamHI, ligating the fragments in the pUC18 cloning vector and then transforming the competent E. coli DH5α cells with the resultant chimeric plasmid. The β-xylosidase gene was identified by screening the transformants in duplicates on LB agar plates overlaid with pNPX as a substrate. Commercial production of β-xylosidase to be used as a methanol-producing enzyme can help to overcome fuel shortages.

Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium

An anaerobic, cellulolytic-xylanolytic bacterium, designated strain A7, was isolated from a cellulose-degrading bacterial community inhabiting bovine manure compost on Ishigaki Island, Japan, by enrichment culture using unpretreated corn stover as the sole carbon source. The strain was Gram-positive, non-endospore forming, non-motile, and formed orange colonies on solid medium. Strain A7 was identified as Herbivorax saccincola by DNA-DNA hybridization, and phylogenetic analysis based on 16S rRNA gene sequences showed that it was closely related to H. saccincola GGR1 (= DSM 101079T). H. saccincola A7 (= JCM 31827=DSM 104321) had quite similar phenotypic characteristics to those of strain GGR1. However, the optimum growth of A7 was at alkaline pH (9.0) and 55°C, compared to pH 7.0 at 60°C for GGR1, and the fatty acid profile of A7 contained 1.7-times more C17:0 iso than GGR1. The draft genome sequence revealed that H. saccincola A7 possessed a cellulosome-like extracellular macromolecular complex, which has also been found for Clostridium thermocellum and C. clariflavum. H. saccincola A7 contained more glycoside hydrolases (GHs) belonging to GH families-11 and -2, and more diversity of xylanolytic enzymes, than C. thermocellum and C. clariflavum. H. saccincola A7 could grow on xylan because it encoded essential genes for xylose metabolism, such as a xylose transporter, xylose isomerase, xylulokinase, and ribulose-phosphate 3-epimerase, which are absent from C. thermocellum. These results indicated that H. saccincola A7 has great potential as a microorganism that can effectively degrade lignocellulosic biomass.

Biodegradation of fibrillated oil palm trunk fiber by a novel thermophilic, anaerobic, xylanolytic bacterium Caldicoprobacter sp. CL-2 isolated from compost.

Oil palm trunk (OPT) is one of the most promising lignocellulosic bioresources. To develop effective biodegradation, thermophilic, anaerobic microorganisms were screened from bovine manure compost using fibrillated OPT (f-OPT) pretreated by wet disk milling as the substrate. One thermophilic, anaerobic bacterium, strain CL-2, whose 16S rDNA gene has 98.6% sequence identity with that of Caldicoprobacter faecale DSM 20678T, exhibited high degradation activity (32.7% reduction in total dry solids of f-OPT). Strain CL-2 did not use cellulose as a carbon source, but used hemicelluloses such as xylan, arabinoxylan, starch and pectin at 70 °C. Phylogenetic and morphologic analyses and the polysaccharide use suggest that CL-2 may be classified as a novel species of Caldicoprobacter, named Caldicoprobacter sp. CL-2. To characterize enzymatic activities of CL-2, extracellular enzymes were prepared from culture broth using beechwood xylan as the carbon source. The extracellular enzymes showed high xylanase activity, but low cellulase activity, suggesting that f-OPT degradation may depend on xylanase activity. To understand the xylanase system of CL-2, a major xylanase was cloned and characterized. The xylanase (CalXyn11A) had a modular structure consisting of a glycoside hydrolase (GH) family-11 domain and a family 36 carbohydrate-binding module. CalXyn11A did not show f-OPT degradation activity, but a strong synergistic effect was observed when CalXyn11A was added to the extracellular enzyme preparation. These results indicate that, rather than working alone, CalXyn11A has an important role in enhancing total lignocellulose degradation activity by cooperation with other GHs.

Molecular Cloning and Sequencing of AlkalophilicCellulosimicrobium cellulans CKMX1 Xylanase Gene Isolated from Mushroom Compost and Characterization of the Gene Product

A xylanolytic bacterium was isolated from mushroom compost by using enrichment technique. Results from the metabolic fingerprinting, whole-cell fatty acids methyl ester analysis and 16S rDNA sequencing suggested the bacterium to be Cellulosimicrobium cellulans CKMX1. Due to the xylanolytic activity of this bacterium, isolation and characterization of the xylanase gene were attempted. A distinct fragment of about 1671 bp was successfully amplified using PCR and cloned into Escherichia coli DH5α. A BLAST search confirmed that the DNA sequence from the amplified fragment was endo-1, 4-beta-xylanase, which was a member of glycoside hydrolase family 11. It showed 98% homology withCellulosimicrobium sp. xylanase gene (Accession no. FJ859907.1) reported from the gut of Eisenia fetida in Korea. In silicophysico-chemical characterization of amino acid sequence of xylanase showed an open reading frame encoding a 556 amino acid sequence with a molecular weight of 58 kDa and theoretical isolectric point (pI) of 4.46 was computed using Expasy's ProtParam server. Secondary and homology based 3D structure of xylanase was analysed using SOPMA and Swiss-Prot software.

흰 코뿔소 배설물로부터 분리한 Bacillus pumilus H10-1의 Xylanase 활성

Xylanase have been used to convert the polymetric xylan into fermentable sugars from the production of ethanol and xylitol from plant biomass. The aim of this study was to isolate and identify xylanolytic bacterium from herbivore feces and was to used the xylanase for enzymatic hydrolysis of biomass. Xylanolytic strains were isolated from 59 different feces of herbivores from Seoul Grand Park located in Gwacheon Gyeonggi-do. The xylanolytic strains were selected by congo red staining and DNS method. Total 67 strains isolated from the herbivores feces were tested for xylanase activity. Among the strains, H10-1, which has the highest xylanase activity, was isolated from feces of Ceratotherium simum. The H10-1 strain was identified as Bacillus pumilus based on its morphological/biochemical characteristics and partial 16S rDNA gene sequences. Culture conditions of B. pumilus H10-1 such as initial medium pH, incubation temperature and incubation time were optimized for maximum xylanase production. And also xylanase produced by B. pumilus H10-1 was applied for the saccharification of Miscanthus sacchariflorus cv. 'Geodae 1', which was pretreated with 1.5M NaOH. The optimized culture conditions of B. pumilus H10-1 were pH 9, <TEX>$30^{\circ}C$</TEX> incubation temperature, and 7 day incubation time, respectively. This xylanase activity under the optimized conditions was <TEX>$20.4{\pm}3.3IU$</TEX>. The crude xylanase produced by B. pumilus H10-1 was used for the saccharification of xylan derived from pretreated 'Geodae 1'. The saccharification conditions were <TEX>$50^{\circ}C$</TEX>, 200 rpm, and 5 days. Saccharification efficiency of pretreated 'Geodae 1' by B. pumilus H10-1 was 8.2%.

GH51 arabinofuranosidase and its role in the methylglucuronoarabinoxylan utilization system in Paenibacillus sp. strain JDR-2.

Methylglucuronoarabinoxylan (MeGAXn) from agricultural residues and energy crops is a significant yet underutilized biomass resource for production of biofuels and chemicals. Mild thermochemical pretreatment of bagasse yields MeGAXn requiring saccharifying enzymes for conversion to fermentable sugars. A xylanolytic bacterium, Paenibacillus sp. strain JDR-2, produces an extracellular cell-associated GH10 endoxylanse (XynA1) which efficiently depolymerizes methylglucuronoxylan (MeGXn) from hardwoods coupled with assimilation of oligosaccharides for further processing by intracellular GH67 α-glucuronidase, GH10 endoxylanase, and GH43 β-xylosidase. This process has been ascribed to genes that comprise a xylan utilization regulon that encodes XynA1 and includes a gene cluster encoding transcriptional regulators, ABC transporters, and intracellular enzymes that convert assimilated oligosaccharides to fermentable sugars. Here we show that Paenibacillus sp. JDR-2 utilized MeGAXn without accumulation of oligosaccharides in the medium. The Paenibacillus sp. JDR-2 growth rate on MeGAXn was 3.1-fold greater than that on oligosaccharides generated from MeGAXn by XynA1. Candidate genes encoding GH51 arabinofuranosidases with potential roles were identified. Following growth on MeGAXn, quantitative reverse transcription-PCR identified a cluster of genes encoding a GH51 arabinofuranosidase (AbfB) and transcriptional regulators which were coordinately expressed along with the genes comprising the xylan utilization regulon. The action of XynA1 on MeGAXn generated arabinoxylobiose, arabinoxylotriose, xylobiose, xylotriose, and methylglucuronoxylotriose. Recombinant AbfB processed arabinoxylooligosaccharides to xylooligosaccharides and arabinose. MeGAXn processing by Paenibacillus sp. JDR-2 may be achieved by extracellular depolymerization by XynA1 coupled to assimilation of oligosaccharides and further processing by intracellular enzymes, including AbfB. Paenibacillus sp. JDR-2 provides a GH10/GH67 system complemented with genes encoding intracellular GH51 arabinofuranosidases for efficient utilization of MeGAXn.

Discovery and characterization of endo-xylanase and β-xylosidase from a highly xylanolytic bacterium in the hindgut of Holotrichia parallela larvae

A highly xylanolytic bacterium, Sphingobacterium sp. HP455, was isolated from the hindgut of soil-dwelling Holotrichia parallela larvae. The endo-xylanase (Xyn455) gene of the glycoside hydrolase (GH) family 10 and β-xylosidase (Xyl455) gene of the GH43 family were cloned and expressed in vitro from this highly xylanolytic bacterium. Both the Xyn455 and Xyl455 enzymes acted on a broad range of hemicelluloses. Xyn455 cleaved xylan to liberate xylooligosaccharides (XOS), and the XOS were subsequently cleaved into xylose through the action of Xyl455. This synergistic action significantly increased the xylan hydrolysis to 62.8%, which is higher than the sum of hydrolysis achieved by the enzymes individually (26.65%). Furthermore, Xyl455 is a bifunctional enzyme with both β-d-xylosidase and α-l-arabinofuranosidase activities. Xyl455 also exhibits high xylose tolerance and a broad pH stability. The pH-dependent half-lives of Xyl455 range from 8.77 h to 43.52 h after pre-incubation for 1 h at 4 °C in buffers ranging from pH 3.0 to 9.0. These results suggest that both recombinant Xyn455 and Xyl455 and the bacterium are potential candidates to be used in commercial biomass conversion.

Bacteroides luti sp. nov., an anaerobic, cellulolytic and xylanolytic bacterium isolated from methanogenic sludge

A mesophilic, anaerobic, cellulolytic and xylanolytic strain, UasXn-3T, was isolated from anaerobic granular sludge in a mesophilic upflow anaerobic sludge blanket reactor, which was used to treat municipal sewage. The cells were Gram-stain-negative, non-motile, and non-spore-forming rods. The optimal temperature for growth was 37-40 °C and the optimal pH for growth was pH 6.5-7.0. Strain UasXn-3T could grow on several polysaccharides and sugars, including cellulose, cellobiose, xylan, xylose, glucose, fructose, arabinose, mannose, raffinose, trehalose and starch. The DNA G+C content was 44.4 mol%. On the basis of comparative 16S rRNA gene sequence analysis, strain UasXn-3T was identified as a member of the genus Bacteroides and most closely related to Bacteroides oleiciplenus, B. intestinalis, B. cellulosilyticus and B. graminisolvens (sequence similarities of 91.3-91.6%). Since the genetic and phenotypic properties suggest that strain UasXn-3T represents a novel species, we propose the name Bacteroides luti sp. nov. The type strain is UasXn-3T (=JCM 19020T=DSM 26991T).

Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512 T , Isolated from the Gut of a Termite

Here we report the draft genome sequence of Bacteroides reticulotermitis strain JCM 10512T, a xylanolytic and cellulolytic bacterium isolated from the gut of a wood-feeding termite. The genome information will facilitate the study of this strain for biomass degradation and adaptation to the gut environment.

Paenibacillus marinumsp. nov., a thermophilic xylanolytic bacterium isolated from a marine hot spring in Tunisia

Among a large collection of Tunisian hot springs bacterial isolates a bacterial strain, THE22(T) , with xylanolytic properties was identified. The bacterium was isolated from a natural hot spring "Ain Echefa" at Mediteranean sea (Korbous, North-Eastern Tunisia). The novel strain was Gram positive, spore-forming, rod-shaped, facultatively anaerobic and grew optimally under conditions of 55 °C, 1% (w/v) NaCl and pH 7-8. The 16S rRNA gene sequence analysis showed that strain THE22(T) fell within the radiation of the cluster comprising Paenibacillus species with Paenibacillus phyllosphaerae PALXIL04(T) as the closest phylogenetic neighbour (95.8%). The predominant components in the fatty methyl ester profile were iso-C16:0 (34.46%), C16:0 (19.64%), anteiso-C15:0 (19.18%) and anteiso-C17:0 (18.11%). The major respiratory quinone was menaquinone-7 (MK-7). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The base composition of DNA was 56 mol%. Based on the polyphasic taxonomic data, strain THE-22(T) (=DSM 18499(T) = LMG 23758(T) ) was recognized as a novel species within the genus Paenibacillus. The name Paenibacillus marinum sp. nov. is proposed.

Cohnella formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L

A Gram-positive, spore-forming, aerobic, rod-shaped, xylanolytic bacterium designated strain CC-Alfalfa-35(T) was isolated from the rhizosphere of Medicago sativa L. in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CC-Alfalfa-35(T) was affiliated to the genus Cohnella. Strain CC-Alfalfa-35(T) shared 95.3 % pairwise 16S rRNA gene sequence similarity to the type strain of the type species of the genus Cohnella (Cohnella thermotolerans DSM 17683(T)) besides showing a similarity of 97.4-93.6 % with other recognized species of the genus Cohnella. The DNA-DNA hybridization value between CC-Alfalfa-35(T) and Cohnella thailandensis KCTC 22296(T) was 37.7 % ± 1.7 % (reciprocal value, 55.7 % ± 3.0 %). Predominant cellular fatty acids were iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile constituted diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. The major respiratory quinone was MK-7 and the DNA G+C content was 58.3 mol%. Strain CC-Alfalfa-35(T) contained meso-diaminopimelic acid as the major diamino acid in the cell-wall peptidoglycan. Based on the polar lipid and fatty acid profiles, which were in line with those of C. thermotolerans DSM 17683(T), coupled with additional distinguishing genotypic, phenotypic and chemotaxonomic features, strain CC-Alfalfa-35(T) is proposed to represent a novel species within the genus Cohnella, for which the name Cohnella formosensis sp. nov. is proposed. The type strain is CC-Alfalfa-35(T) ( = JCM 18405(T) = BCRC 80428(T)).

Isolation and Characterization of a Xylanolytic Bacterium, Bacillus sp. MX47

A xylanolytic bacterial strain, MX47, was isolated from rotting plant matter in soil. The strain was aerobic and gram positive, and grew between pH 6.0 and 11.0. Cells were susceptible to thiostrepton and chloramphenicol. The major fatty acids (>3%) comprised 64.55% of iso-, 22.76% of anteiso-, and 3.92% of iso-. The G/C content of the DNA was 44.15 mol%. The predominant respiratory quinone was menaquinone 7 (MK-7). Searches for 16S rRNA gene sequence similarity as well as phylogenetic analyses strongly suggested that the strain should be classified to the genus Bacillus. However, its biochemical characteristics, including acid production and enzyme activities, are different from those of other Bacillus strains in the same clade, and therefore, we propose the name Bacillus sp. MX47.

Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring

A hyperthermophilic anaerobic bacterium, designated D2C22(T), was isolated from the hydrothermal hot spring of Guelma in north-east Algeria. The isolate was a Gram-stain-positive, non-sporulating, non-motile rod, appearing singly or in pairs (0.3-0.4 × 8.0-9.0 µm). Strain D2C22(T) grew anaerobically at 45-85 °C (optimum 65 °C), at pH 5-9 (optimum pH 6.8) and with 0-20 g NaCl l(-1). Strain D2C22(T) used glucose, galactose, lactose, fructose, ribose, xylose, arabinose, maltose, cellobiose, mannose, melibiose, sucrose, xylan and pyruvate (only in the presence of yeast extract or biotrypticase) as electron donors. The end products from glucose fermentation were acetate, lactate, CO2 and H2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate and sulfite were not used as electron acceptors. The predominant cellular fatty acids were iso-C15:0 and iso-C17:0. The DNA G+C content was 41.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain D2C22(T) was most closely related to Caldicoprobacter oshimai JW/HY-331(T), Caldicoprobacter algeriensis TH7C1(T) and Acetomicrobium faecale DSM 20678(T) (95.5, 95.5 and 95.3% 16S rRNA gene sequence similarity, respectively). Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain D2C22(T) is proposed to be a representative of a novel species of the genus Caldicoprobacter within the order Clostridiales, for which the name Caldicoprobacter guelmensis sp. nov. is proposed. The type strain is D2C22(T) (=DSM 24605(T)=JCM 17646(T)).

AxyR, an AraC Family Transcriptional Activator of the Xylanase 3 Gene, Requires Xylo-Oligosaccharides as a Cofactor for DNA Binding inPaenibacillussp. Strain W-61

The xylanolytic bacterium Paenibacillus sp. strain W-61 encodes three extracellular xylanase genes, xyn1, xyn3, and xyn5. In this study, we identified a transcriptional activator required for transcription of the xyn3 gene in strain W-61. The activator, AxyR, contained the highly homologous AraC-type DNA binding domain and required xylobiose, xylotriose, or xylotetraose as cofactor for binding to the xyn3 promoter region.

Complete genome sequence of Paenibacillus sp. strain JDR-2.

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.