Facultative Anaerobe Caldibacillus debilis GB1: Characterization and Use in a Designed Aerotolerant,Cellulose-Degrading Coculture with Clostridium thermocellum

Development of a designed coculture that can achieve aerotolerant ethanogenic biofuel production from cellulose can reduce the costs of maintaining anaerobic conditions during industrial consolidated bioprocessing (CBP). To this end, a strain of Caldibacillus debilis isolated from an air-tolerant cellulolytic consortium which included a Clostridium thermocellum strain was characterized and compared with the C. debilis type strain. Characterization of isolate C. debilis GB1 and comparisons with the type strain of C. debilis revealed significant physiological differences, including (i) the absence of anaerobic metabolism in the type strain and (ii) different end product synthesis profiles under the experimental conditions used. The designed cocultures displayed unique responses to oxidative conditions, including an increase in lactate production. We show here that when the two species were cultured together, the noncellulolytic facultative anaerobe C. debilis GB1 provided respiratory protection for C. thermocellum, allowing the synergistic utilization of cellulose even under an aerobic atmosphere.     

Thermostable alkaline lipase from a newly isolated thermophilic Bacillus,strain A30-1 (ATCC 53841)

A thermophilic bacterium was isolated from a hot spring area of Yellowstone National Park. The organism grew optimally at 60–65°C and in the pH range of 6–9. It was characterized as Bacillus sp. In the presence of corn or olive oil (1.0%) as the growth substrate, this Bacillus produced an extracellular lipolytic activity (EC 3.1.1.3). The enzyme activity could be efficiently recovered by ultrafiltration of cell-free culture supernatant. The partially purified lipase preparation had an optimum temperature of 60°C, at an optimum pH of 9.5. It retained 100% of the original activity after being heated at 75°C for half an hour. The half life of the enzyme was 8 h at 75°C. The enzyme retained at least 90% of the original activity after it was incubated at 60°C for 15 h at pH's in the range of 5 to 10.5. The enzyme was active on triglycerides containing fatty acids having a carbon chain length of C16 : 0 to C22 : 0 as well as on natural fats and oils. The enzyme activity was stable to both hydrogen peroxide and alkaline protease which are detergent ingredients. The purified enzyme had an isoelectric point of 5.15 and an approximate molecular weight of 65,000.     

Characterization of a cryptic plasmid from Bacillus sphaericus strain LP1-G

A cryptic plasmid from Bacillus sphaericus strain LP1-G, designated as pLG, was sequenced and characterized. It was an 11,066bp circular molecule, with G+C content of 37%. The plasmid pLG was predicted to encode 23 putative ORFs, and ORF 21 shared the highest identity with Rep of pGI1 and pBMB9741, members of rolling-circle replication (RCR) pC194-family. Sequence analysis revealed a pC194-type double strand origin (dso) and a single strand origin (sso) like sequence located upstream and downstream of ORF 21, respectively. Moreover, Mung bean nuclease analysis and Southern hybridization confirmed the existence of single stranded DNA (ssDNA) intermediates, indicating that pLG belongs to the RCR pC194-family. Accumulation of multiple ssDNA intermediates in native strain LP1-G and decline of ssDNA and supercoiled DNA in rifampicin-treated strain implied that a special mechanism might be employed by pLG. Furthermore, the copy number of pLG in its original host was determined and about 58 copies of the plasmid exist in each cell. Subcloning and transformation experiments proved that the minimal replicon of pLG was within a 1.6-kb fragment, which was composed of rep gene and dso. These data are a good basis for the understanding of replication mechanisms and genetics of this B. sphaericus plasmid.     

Purification and characterization of a cellulase (CMCase) from a newly isolated thermophilic aerobic bacterium Caldibacillus cellulovorans gen. nov., sp. nov

One thermostable endoglucanase (CMCase) was purified to homogeneity from the culture supernatant of a new isolated thermophilic bacterium Caldibacillus cellulovorans. The molecular weight of the enzyme was 85.1 kDa as determined by SDS Polyacrylamide gel electrophoresis (PAGE) and 174 kDa by size-exclusion chromatography. The isoelectric point of the enzyme was at pH 4.12. The temperature for maximum activity was 80 °C, with half-lives of 32 min at 80 °C, and 2 min at 85 °C, and 83% activity remaining after 3 h at 70 °C. Thermostability of the enzyme was increased twofold by the addition of bovine serum albumin. Maximal activity was observed between pH 6.5 and 7.0. The enzyme activity was significantly inhibited by Zn²⁺, Hg²⁺, and p-chloromercuribenzenesulphonic acid. The enzyme showed high activity on carboxymethylcellulose (CMC) with much lower activity on Avicel; a low level of activity was also found against xylan. Cellobiose was the major product of hydrolysis of amorphous cellulose and CMC. Viscometric analysis indicated that the enzyme hydrolysed CMC in an exo-acting fashion. Cellotriose and cellobiose were not degraded and at least four contiguous glucosyl residues were necessary for degradation by the enzyme. The K _m and V _max of the enzyme for CMC were 3.4 mg ml^–1 and 44.7 mol min^–1 (mg protein)^–1, respectively.     

Aminopeptidase from a thermophilic strain of Bacillus licheniformis

Aminopeptidase is isolated and purified from the culture liquid of the thermophilic strain of Bacillus licheniformis. The aminopeptidase predominantly splits off N-terminal leucin in short peptides and hydrolyzes leucinamide as well. The molecular weight of the enzyme is about 60 kDa. The enzyme is able to form aggregates. Optimum of aminopeptidase activity was demonstrated at pH 8.0-8.3 and temperature of 85 degrees C. The enzyme is inactivated by metal-binding reagents and reducing substances, and is activated by cobalt and PCMB ions. The EDTA-inactivated enzyme activity is reduced by cobalt and zinc ions, however the latter has no activating action. The enzyme under study is characterized by high thermostability: in the presence of the substrate at the temperature of 90 degrees C the reaction linearity is retained for not less than 2 h and without the substrate the half-life of the aminopeptidase at 90 degrees C is 145 min. Extracellular aminopeptidase of the thermophilic strain of B. licheniformis is a new enzyme differing from the aminopeptidases described by the present in high thermostability, induced, evidently, by the presence of one or several disulphide bonds in the enzyme molecule.     

Characterization of cyanobacteriochrome TePixJ from a thermophilic cyanobacterium Thermosynechococcus elongatus strain BP-1

A putative photoreceptor gene, TepixJ, of a thermophilic cyanobacterium is homologous to SypixJ1 that mediates positive phototaxis in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. The putative chromophore-binding GAF domain of TePixJ protein was overexpressed as a fusion with a polyhistidine tag (His-TePixJ_GAF) in Synechocystis cells and isolated to homogeneity. The photoreversible conversion of His-TePixJ_GAF showed peaks at 531, 341 and 266 nm for the green light-absorbing form (Pg form), and peaks at 433 and 287 nm for the blue light-absorbing form (Pb form). At 77K, the Pg form fluoresced at 580 nm, while the Pb form did not emit any fluorescence. Mass spectrometry of the tryptic chromopeptide demonstrated that a phycocyanobilin isomer binds to the conserved cysteine at ring A via a thioether bond. It is established that TePixJ and SyPixJ1 are novel photoreceptors in cyanobacteria ('cyanobacteriochromes') that are similar, but distinct from the phytochromes and bacteriophytochromes.     

Description of a mirror-image doublet from a Brazilian strain of Gastrostyla setifera (Engelmann, 1862) Kent, 1882 (Ciliophora: Stichotrichia)

The present work describes a mirror-image doublet morph found in a Brazilian strain of the stichotrich ciliate Gastrostyla setifera (Engelmann, 1862) Kent, 1882, obtained from a sample of water and sediment from an urban freshwater stream in the city of Juiz de Fora (Minas Gerais, Brazil). The doublet measured 63 x 49 microm, and had two components where the right one has upside-down arranged adoral membranelles with a set of small oblique membranelles at its proximal (posterior) end. The fronto-ventral-transverse ciliature comprised 34 cirri, mostly related to the left component, as well as two marginal rows. On the dorsal surface there were eight dorsal kineties and six caudal cirri. Dorsomarginal kineties were lacking. The macronucleus comprised one irregular-shaped transverse nodule and two smaller roughly ellipsoid longitudinal nodules.     

柔弱下盾螨雌螨形态补充及后若螨描述(蜱螨亚纲:革螨股:厉螨科)

本文补充柔弱下盾螨 Hypoaspis debilis Ma, 1996 雌螨形态特征,并描述其后若螨.     

Description of a methanotrophic strain BOH1, isolated from Al-Bohyriya well,Al-Ahsa City,Saudi Arabia

Methanotrophic bacteria have a unique ability to utilize methane as their carbon and energy sources. Therefore, methanotrophs play a key role in suppressing methane emissions from different ecosystems and hence in alleviating the global climate change. Despite methanotrophs having many ecological, economical and biotechnological applications, little is known about this group of bacteria in Al-Ahsa. Therefore, the main objective of the current work was to expand our understanding of methane oxidizing bacteria in Al-Ahsa region. The specific aim was to describe a methanotrophic strain isolated from Al-Bohyriya well, Al-Ahsa using phenotypic, genotypic (such as 16S rRNA and pmoA gene sequencing) and phylogenetic characterization. The results indicated that the strain belongs to the genus Methylomonas that belongs to Gammaproteobacteria as revealed by the comparative sequence analysis of the 16S rRNA and pmoA genes. There is a general agreement in the profile of the phylogenetic trees based on the sequences of 16srRNA and pmoA genes of the strain BOH1 indicating that both genes are efficient taxonomic marker in methanotrophic phylogeny. The strain possesses the particulate but not the soluble methane monooxygenase as a key enzyme for methane metabolism. Further investigation such as DNA:DNA hybridization is needed to assign the strain as a novel species of the genus Methyomonas and this will open the door to explore the talents of the strain for its potential role in alleviating global warming and biotechnological applications in Saudi Arabia such as bioremediation of toxic by-products released in oil industry. In addition, the strain enhances our knowledge of methanotrophic bacteria and their adaptation to desert ecosystems.     

Description and validation of a rapid (1 h) flow cytometry test for enumerating thermophilic bacteria in milk powders

AIMS: The aim of this study was to develop a rapid assay for enumerating thermophilic bacteria in milk powder. METHODS AND RESULTS: The BactiFlow flow cytometer was used to count bacteria based on esterase activity in viable bacterial cells. A protocol for total viable bacteria was modified by heat-treating the sample to selectively label thermophilic bacteria. Samples of milk powder dissolved in 0.1% peptone were treated with 0.8% ethylenediaminetetraacetic acid to reduce background interference because of denatured milk proteins. Either thermophilic bacteria were added to the dissolved milk powder or milk powder solutions were incubated at 55 degrees C for 2-3 h to enrich the natural thermophile population for testing. Results from the BactiFlow were compared with traditional plate count results. CONCLUSIONS: Thermophilic bacteria in milk powder can be enumerated within 1 h using the BactiFlow flow cytometer. SIGNIFICANCE AND IMPACT OF THE STUDY: Microbiological test results obtained within 1 h can potentially be used to monitor manufacturing processes, effectively trace problems and provide confidence in the manufacture of product.     

Structure of ATPase (coupling factor TF1) from a thermophilic bacterium.

Sheets of soluble ATPase from a thermophilic bacterium, identified with coupling factor TF₁, were shown to be two-dimensional crystals. Computer filtering of an electron micrograph showed that the shape of ATPase (TF₁) is hexagonal and has pseudo 6-fold and 3-fold symmetry. The length of each side of a hexagon is about 38 Å.These observations suggest that there are six rather than four large subunits in ATPase.     

Description of a new cryptic,shallow‐water tonguefish (Pleuronectiformes: Cynoglossidae: Symphurus) from the western North Pacific Ocean

Combined results based on morphological characters and analyses of partial sequences of the 16s rRNA and coI genes confirm the validity of a new, cryptic, symphurine tonguefish from the western North Pacific Ocean. Symphurus leucochilus n. sp., a diminutive species reaching sizes to c. 67 mm standard length, is described from nine specimens that were collected from fish‐landing ports and from trawls made at c. 150 m off Taiwan and Japan. Symphurus leucochilus shares many similar features with those of Symphurus microrhynchus and that of several undescribed species that are morphologically similar to S. microrhynchus. Symphurus leucochilus has also been misidentified as Symphurus orientalis in fish collections because of shared similarities in some aspects of their morphology. The new species differs from all congeners by the following combination of meristic, morphological and pigmentation features: a predominant 1–2–2–2–2 pattern of interdigitation of proximal dorsal‐fin pterygiophores and neural spines; 12 caudal‐fin rays; 89–92 dorsal‐fin rays; 76–80 anal‐fin rays; 49–51 total vertebrae; four hypurals; 75–83 longitudinal scale rows; 32–35 transverse scales; 15–17 scale rows on the head posterior to the lower orbit; absence of a fleshy ridge on the ocular‐side lower jaw and a membranous connection between the anterior nostril and lower part of the eye; a narrow interorbital space and dorsal‐fin origin anterior to the vertical through the anterior margin of the upper eye; absence of both dermal spots at bases of anterior dorsal‐fin rays and melanophores on the isthmus; uniformly yellow to light‐brown ocular‐side colouration without bands; dorsal and anal fins with alternating series of dark rectangular blotches and unpigmented areas; a uniform white blind side and a bluish‐black peritoneum. Despite overall similarities in morphology between S. leucochilus and S. orientalis, as well as between two of the nominal species morphologically similar to S. microrhynchus, analyses of partial 16s rRNA and coI gene sequences show that S. leucochilus, S. orientalis and the two other nominal species represent three distinct lineages within the genus Symphurus.     

Isolation and characterization of a d-glucose/xylose isomerase from a new thermophilic strain Streptomyces sp. (PLC)

A thermostable d-xylase isomerase from a newly isolated thermophilic Streptomyces sp. (PLC) strain is described. The enzyme was purified to homogeneity. It is a homotetramer with a native molecular mass of 183 kDa and a subunit molecular mass of 46 kDa. The enzyme has a K _m of 35 mM for d-xylose and also accepts d-glucose as substrate, however, with a tenfold higher K _m (0.4 M) and half the maximum velocity. Both the activity and stability of this d-xylose isomerase depend strongly on divalent metal ions. Two metal ions bind per subunit to non-identical sites. Mg²⁺, Mn²⁺ and Co²⁺ are of comparable efficiency for the d-xylose isomerase reaction. Con²⁺ is the most efficient cofactor for d-glucose isomerization. The enzyme remains fully active up to 95°C. The activity decreases at 53°C in the presence of Co²⁺ and Mg²⁺ with a half-life of 7 and 9 days respectively. In the presence of Mn²⁺ the enzyme activity remains constant for at least 10 days and at 70°C 50% of the activity is lost after 5 days.     

A new iron oxidase from a moderately thermophilic iron oxidizing bacterium strain TI-1.

Iron oxidase was purified from plasma membranes of a moderately thermophilic iron oxidizing bacterium strain TI-1 in an electrophoretically homogeneous state. Spectrum analyses of purified enzyme showed the existence of cytochrome a, but not cytochrome b and c types. Iron oxidase was composed of five subunits with apparent molecular masses of 46 kDa (alpha), 28 kDa (beta), 24 kDa (gamma), 20 kDa (delta), and 17 kDa (epsilon). As the molecular mass of a native enzyme was estimated to be 263 kDa in the presence of 0.1% n-dodecyl-beta-D-maltopyranoside (DM), a native iron oxidase purified from strain TI-1 seems to be a homodimeric enzyme (alpha beta gamma delta epsilon)(2). Optimum pH and temperature for iron oxidation were pH 3.0 and 45 degrees C, respectively. The K(m) of iron oxidase for Fe(2+) was 1.06 mM and V(max) for O(2) uptake was 13.8 micromol x mg(-1) x min(-1). The activity was strongly inhibited by cyanide and azide. Purified enzyme from strain TI-1 is a new iron oxidase in which electrons of Fe(2+) were transferred to haem a and then to the molecular oxygen.     

Immobilization of cells with nitrilase activity from a thermophilic bacterial strain

Cells of the moderately thermophilic Bacillus sp. UG-5B strain, producing nitrilase (EC3.5.5.1), which converts nitriles directly to the corresponding acid and ammonia, were immobilized using different types of matrices and techniques. A variety of sol-gel silica hybrids were tested for entrapment and adsorption of bacterial cells as well as chemical binding on polysulphone membranes. Activation of the matrix surface with formaldehyde led to an increase in immobilization efficiency and operational stability of the biocatalysts. Among the supports screened, membranes gave the best results for enzyme activity and especially operational stability, with retention of 100% activity after eight reaction cycles.     

Purification of RuBisCO from the thermophilic cyanobacterium Synechococcus sp. strain a-1

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key enzyme of the Calvin Benson cycle, has been purified from a thermophilic cyanobacterium, Synechococcus sp. strain a-1 and characterized. The enzyme is an L₈S₈-type hexadecamer with a molecular mass of 530 kDa. The enzyme was stable against heat treatment up to 70°C, which is the highest value among the RuBisCOs so far purified. The K_m value for ribulose bisphosphate on the carboxylase activity was substantially higher than those observed for RuBisCOs obtained from mesophilic autotrophs. The N-terminal amino acid sequence for the large subunit of the enzyme was highly similar to those of the other cyanobacteria despite the significant differences in heat stability.     

Characterization of a cryptic plasmid, pSM103mini, from polyethylene-glycol degrading Sphingopyxis macrogoltabida strain 103

A cryptic plasmid, pSM103mini, was found in polyethylene-glycol degrading bacterium Sphingopyxis macrogoltabida, strain 103. The plasmid was 4,328-bp long and its GC content was 57.5%. It contained four open reading frames, but only two of them showed significant similarity to reported proteins. ORF3 and ORF4 were assumed to encode resolvase and replication protein (RepA) respectively. Downstream of ORF4 we found complex repeat sequences. These together with ORF3 and 4 were necessary and sufficient for plasmid maintenance in strain 103, as analyzed by constructing deletion plasmids. The pHSG398-fused plasmid (pHSG-SM103mini) functioned as a shuttle vector between strain 103 and Escherichia coli. The plasmid constructed was maintained in strain 103 and its close relative, S. macrogoltabida strain 203, but not efficiently in PEG-degrading S. terrae.