bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification and characterization of extremely thermostable beta-mannanase, beta-mannosidase, and alpha-galactosidase from the hyperthermophilic eubacterium Thermotoga neapolitana 5068
Authors: Duffaud G D , McCutchen C M , Leduc P , Parker K N , Kelly R M
Published: January 2020

Thermostable and thermoactive beta-mannanase (1,4-beta-D-mannan mannanohydrolase [EC 3.2.1.78]), beta-mannosidase (beta-D-mannopyranoside hydrolase [EC 3.2.1.25]) and alpha-galactosidase (alpha-D-galactoside galactohydrolase [EC 3.2.1.22]) were purified to homogeneity from cell extracts and extracellular culture supernatants of the hyperthermophilic eubacterium Thermotoga neapolitana 5068 grown on guar gum-based media. The beta-mannanase was an extracellular monomeric enzyme with a molecular mass of 65 kDa. The optimal temperature for activity was 90 to 92 degrees C, with half-lives (t1/2) of 34 h at 85 degrees C, 13 h at 90 degrees C, and 35 min at 100 degrees C. The beta-mannosidase and alpha-galactosidase were found primarily in cell extracts. The beta-mannosidase was a homodimer consisting of approximately 100-kDa molecular mass subunits. The optimal temperature for activity was 87 degrees C, with t1/2 of 18 h at 85 degrees C, 42 min at 90 degrees C, and 2 min at 98 degrees C. The alpha-galactosidase was a 61-kDa monomeric enzyme with a temperature optimum of 100 to 103 degrees C and t1/2 of 9 h at 85 degrees C, 2 h at 90 degrees C, and 3 min at 100 degrees C. These enzymes represent the most thermostable and thermoactive versions of these types yet reported and probably act synergistically to hydrolyze extracellular galactomannans to monosaccharides by T. neapolitana for nutritional purposes. The significance of such substrates in geothermal environments remains to be seen.
Genomic Variability of the Xanthomonas Pathovar mangiferaeindicae, Agent of Mango Bacterial Black Spot
Authors: Gagnevin L , Leach J E , Pruvost O
Published: January 2020

The genetic diversity of 138 strains of the Xanthomonas pathovar mangiferaeindicae, which were isolated from three different hosts (mango, ambarella, and pepper tree) in 14 different countries, was assessed with restriction fragment length polymorphism markers. An analysis of patterns obtained by hybridization with an hrp cluster probe from Xanthomonas oryzae pv. oryzae separated 11 of the strains from all of the other strains, which suggested that these 11 strains may not be Xanthomonas pv. mangiferaeindicae strains. Hybridization with an avirulence gene from X. oryzae pv. oryzae and a repetitive DNA fragment from Xanthomonas pv. mangiferaeindicae separated the remaining 127 strains into four groups that were consistent with both geographic and host origins. The group with the greatest diversity consisted of strains from Southeast Asia, where mango originated. Other groups and subgroups contained strains that were either from widely separated countries, which suggested that wide dissemination from a single site occurred, or from localized areas, which suggested that evolution of separate lineages of strains occurred. One group of strains contained only strains isolated from pepper trees in Reunion, indicating that pepper tree may not be an alternate host for Xanthomonas pv. mangiferaeindicae strains.
Rapid and Efficient Purification Method for Small, Hydrophobic, Cationic Bacteriocins: Purification of Lactococcin B and Pediocin PA-1
Authors: Venema K , Chikindas M L , Seegers J , Haandrikman A J , Leenhouts K J , Venema G , Kok J
Published: January 2020

The bacteriocins lactococcin B and pediocin PA-1 were purified by ethanol precipitation, preparative isoelectric focusing, and ultrafiltration. The procedure reproducibly leads to high final yields in comparison to the generally low yields obtained by column chromatography. Specifically, during isoelectric focusing no loss of activity occurs. The method, in general, should be applicable to small, hydrophobic, cationic bacteriocins.
Identification of the Inducing Agent of the 2,4-Dichlorophenoxyacetic Acid Pathway Encoded by Plasmid pJP4
Authors: Filer K , Harker A R
Published: January 2020

The inducing agent of the 2,4-dichlorophenoxyacetic acid (2,4-D) pathway of Alcaligenes eutrophus JMP134 (pJP4) was determined through the analysis of promoterless lacZ transcriptional fusions with tfd structural genes. (beta)-Galactosidase activity was measured in the presence and absence of 2,4-D. Fusions of the individual genes act both as reporters and disrupters of gene expression. Increases in reporter activity were expected in fusions occurring in genes which encode enzymes which function after the production of the inducing intermediate. This analysis indicates that dichloromuconate is the inducing intermediate.
Nylon biodegradation by lignin-degrading fungi
Authors: Deguchi T , Kakezawa M , Nishida T
Published: January 2020

The biodegradation of nylon by lignin-degrading fungi was investigated. The fungus IZU-154 significantly degraded nylon-66 membrane under ligninolytic conditions. Nuclear magnetic resonance analysis showed that four end groups, CHO, NHCHO, CH3, and CONH2, were formed in the biodegraded nylon-66 membranes, suggesting that nylon-66 was degraded oxidatively.
Characterization of the Agrobacterium vitis pehA gene and comparison of the encoded polygalacturonase with the homologous enzymes from Erwinia carotovora and Ralstonia solanacearum
Authors: Herlache T C , Hotchkiss A T , Burr T J , Collmer A
Published: January 2020

DNA sequencing of the Agrobacterium vitis pehA gene revealed a predicted protein with an M(r) of 58,000 and significant similarity to the polygalacturonases of two other plant pathogens, Erwinia carotovora and Ralstonia (= Pseudomonas or Burkholderia) solanacearum. Sequencing of the N terminus of the PehA protein demonstrated cleavage of a 34-amino-acid signal peptide from pre-PehA. Mature PehA accumulated primarily in the periplasm of A. vitis and pehA+ Escherichia coli cells during exponential growth. A. vitis PehA released dimers, trimers, and monomers from polygalacturonic acid and caused less electrolyte leakage from potato tuber tissue than did the E. carotovora and R. solanacearum polygalacturonases.
A model for the combined effects of temperature and salt concentration on growth rate of food spoilage molds
Authors: Cuppers H G , Oomes S , Brul S
Published: January 2020

We modeled mold growth on a solid culture medium at various temperatures and NaCl concentrations by using five common food spoilage molds (Penicillium roqueforti, Trichoderma harzianum, Paecilomyces variotii, Aspergillus niger, and Emericella nidulans). For the description of the growth rate (expressed as the increase in colony diameter per unit of time) as a function of temperature and NaCl concentration, a six-parameter model has been developed. The model combines either the Rosso-type or the Ratkowsky-type temperature dependence with the NaCl concentration dependence derived from the relationship between the growth rate and square root of (1 - water activity), as proposed by Gibson and coworkers (A. M. Gibson, J. Baranyi, J. I. Pitt, M. J. Eyles, and T. A. Roberts, Int. J. Food Microbiol. 23:419-431, 1994). The model will be of use to food microbiologists whose aim is to predict the likelihood of fungal spoilage.
The freeze-thaw stress response of the yeast Saccharomyces cerevisiae is growth phase specific and is controlled by nutritional state via the RAS-cyclic AMP signal transduction pathway
Authors: Park J I , Grant C M , Attfield P V , Dawes I W
Published: January 2020

The ability of cells to survive freezing and thawing is expected to depend on the physiological conditions experienced prior to freezing. We examined factors affecting yeast cell survival during freeze-thaw stress, including those associated with growth phase, requirement for mitochondrial functions, and prior stress treatment(s), and the role played by relevant signal transduction pathways. The yeast Saccharomyces cerevisiae was frozen at -20 degrees C for 2 h (cooling rate, less than 4 degrees C min-1) and thawed on ice for 40 min. Supercooling occurred without reducing cell survival and was followed by freezing. Loss of viability was proportional to the freezing duration, indicating that freezing is the main determinant of freeze-thaw damage. Regardless of the carbon source used, the wild-type strain and an isogenic petite mutant ([rho 0]) showed the same pattern of freeze-thaw tolerance throughout growth, i.e., high resistance during lag phase and low resistance during log phase, indicating that the response to freeze-thaw stress is growth phase specific and not controlled by glucose repression. In addition, respiratory ability and functional mitochondria are necessary to confer full resistance to freeze-thaw stress. Both nitrogen and carbon source starvation led to freeze-thaw tolerance. The use of strains affected in the RAS-cyclic AMP (RAS-cAMP) pathway or supplementation of an rca1 mutant (defective in the cAMP phosphodiesterase gene) with cAMP showed that the freeze-thaw response of yeast is under the control of the RAS-cAMP pathway. Yeast did not adapt to freeze-thaw stress following repeated freeze-thaw treatment with or without a recovery period between freeze-thaw cycles, nor could it adapt following pretreatment by cold shock. However, freeze-thaw tolerance of yeast cells was induced during fermentative and respiratory growth by pretreatment with H2O2, cycloheximide, mild heat shock, or NaCl, indicating that cross protection between freeze-thaw stress and a limited number of other types of stress exists.
Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18s rDNA
Authors: Kowalchuk G A , Gerards S , Woldendorp J W
Published: January 2020

Marram grass (Ammophila arenaria L.), a sand-stabilizing plant species in coastal dune areas, is affected by a specific pathosystem thought to include both plant-pathogenic fungi and nematodes. To study the fungal component of this pathosystem, we developed a method for the cultivation-independent detection and characterization of fungi infecting plant roots based on denaturing gradient gel electrophoresis (DGGE) of specifically amplified DNA fragments coding for 18S rRNA (rDNA). A nested PCR strategy was employed to amplify a 569-bp region of the 18S rRNA gene, with the addition of a 36-bp GC clamp, from fungal isolates, from roots of test plants infected in the laboratory, and from field samples of marram grass roots from both healthy and degenerating stands from coastal dunes in The Netherlands. PCR products from fungal isolates were subjected to DGGE to examine the variation seen both between different fungal taxa and within a single species. DGGE of the 18S rDNA fragments could resolve species differences from fungi used in this study yet was unable to discriminate between strains of a single species. The 18S rRNA genes from 20 isolates of fungal species previously recovered from A. arenaria roots were cloned and partially sequenced to aid in the interpretation of DGGE data. DGGE patterns recovered from laboratory plants showed that this technique could reliably identify known plant-infecting fungi. Amplification products from field A. arenaria roots also were analyzed by DGGE, and the major bands were excised, reamplified, sequenced, and subjected to phylogenetic analysis. Some recovered 18S rDNA sequences allowed for phylogenetic placement to the genus level, whereas other sequences were not closely related to known fungal 18S rDNA sequences. The molecular data presented here reveal fungal diversity not detected in previous culture-based surveys.
Rapid Recovery of Marine Bacterioplankton Activity after Inhibition by UV Radiation in Coastal Waters
Authors: Kaiser E , Herndl G J
Published: January 2020

Laboratory and in situ experiments were performed in order to evaluate the role of UV radiation on bacterial activity. Particular attention was given to the determination of the role of UV-A and photosynthetic active radiation (PAR) and different nutrient conditions on the recovery of bacterial activity. Laboratory experiments with nearly natural radiation intensities indicated a 20 to 40% reduction from the initial level of bacterial activity after UV-B exposure for 2 to 4 h. Bacterial activity in freshly collected seawater showed a more pronounced inhibition and faster recovery than bacterial activity in aged, nutrient-depleted seawater. The results of in situ experiments with filtered water (0.8-(mu)m-pore-size filter) and natural surface solar radiation levels agreed with those of the laboratory experiments and revealed that UV-A and PAR are important for the recovery of bacterial activity and result in levels of bacterial activity that are higher than those prior to exposure to full solar radiation. Bacterioplankton exposed to full solar radiation for 3 h and subsequently incubated at different depths within the upper mixed water column showed an increase in bacterial activity with increased depth; the highest bacterial activity was detected at depths of 5.5 to 10.5 m, where the short-wavelength UV-B was already largely attenuated, but enough long wavelength UV-A and short PAR were available to allow recovery. This elevated bacterial activity following exposure to UV-B was attributed to the photolysis of dissolved organic matter (DOM) exposed to near-surface radiation and to the rapid recovery of bacteria from UV stress once they were mixed into deeper layers of the upper mixed water column, where they efficiently utilize the photolytically cleaved DOM. It is concluded that studies on the role of UV on the carbon and energy flux through the upper layer of the ocean should take into account the highly dynamic radiation conditions.
Effects of Osmolyte Precursors on the Distribution of Compatible Solutes in Methanohalophilus portucalensis
Authors: Robinson P M , Roberts M F
Published: January 2020

The halophilic methanogen Methanohalophilus portucalensis synthesizes three distinct zwitterions, (beta)-glutamine, N(sup(epsilon))-acetyl-(beta)-lysine (NA(beta)Lys), and glycine betaine, as osmolytes when it is grown at high concentrations of external NaCl. The selective distribution of these three species was determined by growing cells in the presence of osmolyte biosynthetic precursors. Glycine betaine is formed by the stepwise methylation of glycine. Exogenous glycine (10 mM) and sarcosine (10 mM), although internalized, do not bias the cells to accumulate any more betaine. However, exogenous N,N-dimethylglycine (10 mM) is available to the appropriate methyltransferase and the betaine generated from it suppresses the synthesis of other osmolytes. Precursors of the two zwitterionic (beta)-amino acids ((beta)-glutamate for (beta)-glutamine and (alpha)-lysine and diaminopimelate for NA(beta)Lys) have only small effects on (beta)-amino acid accumulation. The largest effect is provided by L-(alpha)-glutamine, suggesting that nitrogen assimilation is a key factor in osmolyte distribution.
Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples
Authors: Sticher P , Jaspers M C , Stemmler K , Harms H , Zehnder A J , van der Meer J R
Published: January 2020

A microbial whole-cell biosensor was developed, and its potential to measure water-dissolved concentrations of middle-chain-length alkanes and some related compounds by bioluminescence was characterized. The biosensor strain Escherichia coli DH5 alpha(pGEc74, pJAMA7) carried the regulatory gene alkS from Pseudomonas oleovorans and a transcriptional fusion of PalkB from the same strain with the promoterless luciferase luxAB genes from Vibrio harveyi on two separately introduced plasmids. In standardized assays, the biosensor cells were readily inducible with octane, a typical inducer of the alk system. Light emission after induction periods of more than 15 min correlated well with octane concentration. In well-defined aqueous samples, there was a linear relationship between light output and octane concentrations between 24 and 100 nM. The biosensor responded to middle-chain-length alkanes but not to alicyclic or aromatic compounds. In order to test its applicability for analyzing environmentally relevant samples, the biosensor was used to detect the bioavailable concentration of alkanes in heating oil-contaminated groundwater samples. By the extrapolation of calibrated light output data to low octane concentrations with a hyperbolic function, a total inducer concentration of about 3 nM in octane equivalents was estimated. The whole-cell biosensor tended to underestimate the alkane concentration in the groundwater samples by about 25%, possibly because of the presence of unknown inhibitors. This was corrected for by spiking the samples with a known amount of an octane standard. Biosensor measurements of alkane concentrations were further verified by comparing them with the results of chemical analyses.
Phenotypic and genotypic biotyping of environmental strains of Vibrio cholerae non-O1 isolated in Italy
Authors: Filetici E , Bonadonna L , Ciccozzi M , Anastasio M P , Fantasia M , Shimada T
Published: January 2020

The purpose of this study was to characterize strains of Vibrio cholerae non-O1 isolated in Italy from different sources by biochemical and serological assays, antibiotic susceptibility testing, and molecular biotyping. Serotyping and genomic analysis by pulsed-field gel electrophoresis proved to be useful in discriminating the isolates. The data obtained show a wide heterogeneity at the genomic level, and in keeping with this, the serogrouping classification provided evidence of a high variability of the investigated strains. In addition, none of the strains tested produced cholera-like toxins.
Detection of Mycobacterium ulcerans in environmental samples during an outbreak of ulcerative disease
Authors: Ross B C , Johnson P D , Oppedisano F , Marino L , Sievers A , Stinear T , Hayman J A , Veitch M G , Robins-Browne R M
Published: January 2020

Mycobacterium ulcerans is an environmental bacterium which causes chronic skin ulcers. Despite significant epidemiological evidence to suggest that water is the source of infection, the organism has never been identified in the environment. Environmental water samples were collected from a small town in which an outbreak of 29 cases had occurred in a 3-year period. These were examined by mycobacterial culture and PCR amplification. Similar to previous studies, M. ulcerans was not cultured from the water samples. However, five samples were positive for M. ulcerans by PCR. These samples were collected from a swamp and a golf course irrigation system within the outbreak area. This is the first time that M. ulcerans has been demonstrated to be present in the environment and supports the postulated epidemiology of disease due to this organism.
Nucleoside Oxidase, a Hydrogen Peroxide-Forming Oxidase, from Flavobacterium meningosepticum
Authors: Koga S , Ogawa J , Cheng L , Choi Y , Yamada H , Shimizu S
Published: January 2020

A novel enzyme which catalyzes the oxidation of nucleosides to nucleoside-5(prm1)-carboxylic acids, forming hydrogen peroxide, was purified to homogeneity from Flavobacterium meningosepticum T-2799. The enzyme has a molecular weight of about 500,000, and four nonidentical subunits (molecular weights of 81,000, 69,000, 33,000, and 16,000) were detected on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. On the basis of visible absorption spectra of the purified enzyme, the enzyme is concluded to be a hemoprotein. It also contains covalently bound flavin adenine dinucleotide. The various nucleosides, such as adenosine (K(infm) = 48 (mu)M), inosine (K(infm) = 66 (mu)M), guanosine (K(infm) = 21 (mu)M), thymidine (K(infm) = 50 (mu)M), uridine (K(infm) = 80 (mu)M), and cytidine (K(infm) = 50 (mu)M), were oxidized by the enzyme, but nucleotides, bases, and ribose were not.
cis-trans isomerization of unsaturated fatty acids: cloning and sequencing of the cti gene from Pseudomonas putida P8
Authors: Holtwick R , Meinhardt F , Keweloh H
Published: January 2020

Transposon mutants of Pseudomonas putida P8 were generated by applying a mini-Tn5 mutagenesis system. The mutants obtained were checked for their ability to tolerate increased temperatures and elevated phenol concentrations. Approximately 5,800 transposon mutants were used to generate a pool of 600 temperature-sensitive strains; one of these strains was identified as being damaged in its ability to perform cis-trans isomerization of fatty acids. A gene library of P. putida P8 was constructed and screened by using as a probe sequences immediately adjacent to the mini-Tn5 insertion. A DNA fragment that complemented the mutation was isolated and cloned. The corresponding gene, termed cti, is located close to the methionine synthase locus (metH) in P. putida P8. A cti-carrying fragment integrated into a plasmid also conferred the ability for cis-trans isomerization to Escherichia coli; the cti gene was completely sequenced, and the amino acid sequence was deduced.
A biosensor for environmental genotoxin screening based on an SOS lux assay in recombinant Escherichia coli cells
Authors: Ptitsyn L R , Horneck G , Komova O , Kozubek S , Krasavin E A , Bonev M , Rettberg P
Published: January 2020

A genetically controlled luminescent bacterial reporter assay, the SOS lux test, was developed for rapid detection of environmental genotoxins. The bioassay is based on the recombinant plasmid pPLS-1, which was constructed as a derivative of pBR322, carrying the promoterless luxCDABFE genes of Photobacterium leiognathi downstream of a truncated cda gene from ColD with a strong SOS promoter. E. coli recA+ strains containing this construction are inducible to high levels of light production in the presence of substances or agents that cause damage to the DNA of the cells. The light signal, reflecting the SOS-inducing potency, is recorded from the growing culture within 1 s, and the test results are available within 1 to 2 h. Induction of bioluminescence was demonstrated by treatment of E. coli C600(pPLS-1) with 6 genotoxic chemicals (mitomycin C, N-methyl-N'-nitro-N-nitrosoguanidine, nalidixic acid, dimethylsulfate, hydrogen peroxide, and formaldehyde) and with UV and gamma radiation. A clear dose-response relationship was established for all eight genotoxins. The sensitivity of the SOS lux test is similar to that of other bioassays for genotoxicity or mutagenicity, such as the SOS chromotest, umu test, and Ames mutatest. These results indicate that the SOS lux test is potentially useful for the in situ and continuous detection of genotoxins.
Imaging of Lactobacillus brevis single cells and microcolonies without a microscope by an ultrasensitive chemiluminescent enzyme immunoassay with a photon-counting television camera
Authors: Yasui T , Yoda K
Published: January 2020

An ultrasensitive chemiluminescent enzyme immunoassay (CLEIA) was developed for the rapid detection and quantification of Lactobacillus brevis contaminants in beer and pitching yeast (Saccharomyces cerevisiae slurry collected for reinoculation). L. brevis cells trapped on a 47-mm nucleopore membrane (0.4-micron pore size) were reacted with a peroxidase-labelled Lactobacillus group E antibody and then subjected to an enhanced CLEIA analysis with 4-iodophenol as the enhancer. The combination of a nucleopore membrane with low background characteristics that enables the antigen-antibody reaction to proceed through the pores of the membrane and a labelled antibody prepared by the maleimide hinge method with minimal nonspecific binding characteristics was essential to minimize background in the detection of single cells. An ultrahigh sensitive charge-coupled device (CCD) camera equipped with a fiber optics image intensifier permitted the imaging of single cells. A clear correlation existed between the number of luminescent spots observed and the plate count [y (CLEIA) = 0.990x (plate count) + 15.9, where n = 7, r = 0.993, and P < 0.001]. Microscopic observation confirmed that the luminescent spots were produced by single cells. This assay could be used to detect approximately 20 L. brevis cells in 633 ml of beer within 4 h. Our ultrasensitive CLEIA could also be used to detect microcolonies approximately 20 microns in diameter which had formed on a membrane after 15 to 18 h of incubation. This method, which we called the microcolony immunoluminescence (MIL) method, increased the signal-to-noise ratio dramatically. The MIL method could be used to detect a 10(0) level of L. brevis contamination in 633 ml of beer and a 1/10(8) level of L. brevis contamination in pitching yeast within 1 day (15 to 18 h to form microcolonies and 2 h for CLEIA).
Degradation of 4-Chlorophenol via the meta Cleavage Pathway by Comamonas testosteroni JH5
Authors: Hollender J , Hopp J , Dott W
Published: January 2020

Comamonas testosteroni JH5 used 4-chlorophenol (4-CP) as its sole source of energy and carbon up to a concentration of 1.8 mM, accompanied by the stoichiometric release of chloride. The degradation of 4-CP mixed with the isomeric 2-CP by resting cells led to the accumulation of 3-chlorocatechol (3-CC), which inactivated the catechol 2,3-dioxygenase. As a result, further 4-CP breakdown was inhibited and 4-CC accumulated as a metabolite. In the crude extract of 4-CP-grown cells, catechol 1,2-dioxygenase and muconate cycloisomerase activities were not detected, whereas the activities of catechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde dehydrogenase, 2-hydroxymuconic semialdehyde hydrolase, and 2-oxopent-4-enoate hydratase were detected. These enzymes of the meta cleavage pathway showed activity with 4-CC and with 5-chloro-2-hydroxymuconic semialdehyde. The activities of the dioxygenase and semialdehyde dehydrogenase were constitutive. Two key metabolites of the meta cleavage pathway, the meta cleavage product (5-chloro-2-hydroxymuconic semialdehyde) and 5-chloro-2-hydroxymuconic acid, were detected. Thus, our previous postulation that C. testosteroni JH5 uses the meta cleavage pathway for the complete mineralization of 4-CP was confirmed.
Application of the extracellular alpha-amylase gene from Streptococcus bovis 148 to construction of a secretion vector for yogurt starter strains
Authors: Satoh E , Ito Y , Sasaki Y , Sasaki T
Published: January 2020

Streptococcus thermophilus ATCC 19258, Lactobacillus delbrueckii subsp. bulgaricus T-11, and Lactococcus lactis subsp. lactis IL1403 were transformed with the alpha-amylase gene (amyA) from Streptococcus bovis 148 by using a wide host-range vector, and all the transformants secreted the alpha-amylase successfully. Since the promoter and the secretion signal of the amyA gene were functional in these strains, we constructed a secretion vector using the expression elements of amyA. Trials to secrete foreign enzymes in yogurt starter strains were performed using this novel secretion vector.
A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides
Authors: Ulrich G A , Krumholz L R , Suflita J M
Published: January 2020

Volume, 63, no. 4, p. 1627-1630. After publication of this article, it was brought to the attention of the authors that an earlier paper, similar in both methodology and salient findings to ours, was published by Y. P. Hsieh and C. H. Yang. Both papers describe a diffusion method for the extraction and recovery of reduced inorganic sulfides from sediment samples placed in sealed reaction vessels. Our paper describes the application of the method to the measurement of sulfate reduction rates. The earlier work contains important information, but unfortunately, the existence of the work was realized only after publication of our paper. We regret this omission, and the following reference should have been cited in our article. 13a.Hsieh, Y. P., and C. H. Yang. 1989. Diffusion methods for the determination of reduced inorganic sulfur species in sediments. Limnol. Oceanogr. 34: 1126-1130. [This corrects the article on p. 1627 in vol. 63.].
Reactivities of various mediators and laccases with kraft pulp and lignin model compounds
Authors: Bourbonnais R , Paice M G , Freiermuth B , Bodie E , Borneman S
Published: January 2020

Laccase-catalyzed oxygen delignification of kraft pulp offers some potential as a replacement for conventional chemical bleaching and has the advantage of requiring much lower pressure and temperature. However, chemical mediators are required for effective delignification by laccase, and their price is currently too high at the dosages required. To date, most studies have employed laccase from Trametes versicolor. We have found significant differences in reactivity between laccases from different fungi when they are tested for pulp delignification in the presence of the mediators 2,2(prm1)-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS) and 1-hydroxybenzotriazole (HBT). A more detailed study of T. versicolor laccase with ABTS and HBT showed that HBT gave the most extensive delignification over 2 h but deactivated the enzyme, and therefore a higher enzyme dosage was required. Other mediators, including 1-nitroso-2-naphthol-3,6-disulfonic acid, 4-hydroxy-3-nitroso-1-naphthalenesulfonic acid, promazine, chlorpromazine, and Remazol brilliant blue, were also tested for their ability to delignify kraft pulp. Studies with dimeric model compounds indicated that the mechanisms of oxidation by ABTS and HBT are different. In addition, oxygen uptake by laccase is much slower with HBT than with ABTS. It is proposed that the dication of ABTS and the 1-oxide radical of HBT, with redox potentials in the 0.8- to 0.9-V range, are required for pulp delignification.
The faeA genes from Aspergillus niger and Aspergillus tubingensis encode ferulic acid esterases involved in degradation of complex cell wall polysaccharides
Authors: de Vries R P , Michelsen B , Poulsen C H , Kroon P A , van den Heuvel R H , Faulds C B , Williamson G , van den Hombergh J P , Visser J
Published: January 2020

We report the cloning and characterization of a gene encoding a ferulic acid esterase, faeA, from Aspergillus niger and Aspergillus tubingensis. The A. niger and A. tubingensis genes have a high degree of sequence identity and contain one conserved intron. The gene product, FAEA, was overexpressed in wild-type A. tubingensis and a protease-deficient A. niger mutant. Overexpression of both genes in wild-type A. tubingensis and an A. niger protease-deficient mutant showed that the A. tubingensis gene product is more sensitive to degradation than the equivalent gene product from A. niger. FAEA from A. niger was identical to A. niger FAE-III (C. B. Faulds and G. Williamson, Microbiology 140:779-787, 1994), as assessed by molecular mass, pH and temperature optima, pI, N-terminal sequence, and activity on methyl ferulate. The faeA gene was induced by growth on wheat arabinoxylan and sugar beet pectin, and its gene product (FAEA) released ferulic acid from wheat arabinoxylan. The rate of release was enhanced by the presence of a xylanase. FAEA also hydrolyzed smaller amounts of ferulic acid from sugar beet pectin, but the rate was hardly affected by addition of an endo-pectin lyase.
Synthesis of optically active amino acids from alpha-keto acids with Escherichia coli cells expressing heterologous genes
Authors: Galkin A , Kulakova L , Yoshimura T , Soda K , Esaki N
Published: January 2020

We describe a simple method for enzymatic synthesis of L and D amino acids from alpha-keto acids with Escherichia coli cells which express heterologous genes. L-amino acids were produced with thermostable L-amino acid dehydrogenase and formate dehydrogenase (FDH) from alpha-keto acids and ammonium formate with only an intracellular pool of NAD+ for the regeneration of NADH. We constructed plasmids containing, in addition to the FDH gene, the genes for amino acid dehydrogenases, including i.e., leucine dehydrogenase, alanine dehydrogenase, and phenylalanine dehydrogenase. L-Leucine, L-valine, L-norvaline, L-methionine, L-phenylalanine, and L-tyrosine were synthesized with the recombinant E. coli cells with high chemical yields (> 80%) and high optical yields (up to 100% enantiomeric excess). Stereospecific conversion of various alpha-keto acids to D amino acids was also examined with recombinant E. coli cells containing a plasmid coding for the four heterologous genes of the thermostable enzymes D-amino acid aminotransferase, alanine racemase, L-alanine dehydrogenase, and FDH. Optically pure D enantiomers of glutamate and leucine were obtained.
Transient Accumulation of Glycine Betaine and Dynamics of Endogenous Osmolytes in Salt-Stressed Cultures of Sinorhizobium meliloti
Authors: Talibart R , Jebbar M , Gouffi K , Pichereau V , Gouesbet G , Blanco C , Bernard T , Pocard J
Published: January 2020

The fate of exogenously supplied glycine betaine and the dynamics of endogenous osmolytes were investigated throughout the growth cycle of salt-stressed cultures of strains of Sinorhizobium meliloti which differ in their ability to use glycine betaine as a growth substrate, but not as an osmoprotectant. We present (sup13)C nuclear magnetic resonance spectral and radiotracer evidence which demonstrates that glycine betaine is only transiently accumulated as a cytoplasmic osmolyte in young cultures of wild-type strains 102F34 and RCR2011. Specifically, these strains accumulate glycine betaine as a preferred osmolyte which virtually prevents the accumulation of endogenous osmolytes during the lag and early exponential phases of growth. Then, betaine levels in stressed cells decrease abruptly during the second half of the exponential phase. At this stage, the levels of glutamate and the dipeptide N-acetylglutaminylglutamine amide increase sharply so that the two endogenous solutes supplant glycine betaine in the ageing culture, in which it becomes a minor osmolyte because it is progressively catabolized. Ultimately, glycine betaine disappears when stressed cells reach the stationary phase. At this stage, wild-type strains of S. meliloti also accumulate the disaccharide trehalose as a third major endogenous osmolyte. By contrast, glycine betaine is always the dominant osmolyte and strongly suppresses the buildup of endogenous osmolytes at all stages of the growth cycle of a mutant strain, S. meliloti GMI766, which does not catabolize this exogenous osmoprotectant under any growth conditions.
Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4.1
Authors: O'Gara J P , Gomelsky M , Kaplan S
Published: January 2020

The ability of the facultative photoheterotroph Rhodobacter sphaeroides to tolerate and reduce high levels of tellurite in addition to at least 10 other rare earth metal oxides and oxyanions has considerable potential for detoxification and bioremediation of contaminated environments. We report the identification and characterization of two loci involved in high-level tellurite resistance. The first locus contains four genes, two of which, trgAB, confer increased tellurite resistance when introduced into the related bacterium Paracoccus denitrificans. The trgAB-derived products display no significant homology to known proteins, but both are likely to be membrane-associated proteins. Immediately downstream of trgB, the cysK (cysteine synthase) and orf323 genes were identified. Disruption of the cysK gene resulted in decreased tellurite resistance in R. sphaeroides, confirming earlier observations on the importance of cysteine metabolism for high-level tellurite resistance. The second locus identified is represented by the telA gene, which is separated from trgAB by 115 kb. The telA gene product is 65% similar to the product of the klaB (telA) gene from the tellurite-resistance-encoding kilA operon from plasmid RK2. The genes immediately linked to the R. sphaeroides telA gene have no similarity to other components of the kilA operon. R. sphaeroides telA could not functionally substitute for the plasmid RK2 telA gene, indicating substantial functional divergence between the two gene products. However, inactivation of R. sphaeroides telA resulted in a significant decrease in tellurite resistance compared to the wild-type strain. Both cysK and telA null mutations readily gave rise to suppressors, suggesting that the phenomenon of high-level tellurite resistance in R. sphaeroides is complex and other, as yet uncharacterized, loci may be involved.
Growth reduction of Listeria spp. caused by undefined industrial red smear cheese cultures and bacteriocin-producing Brevibacterium lines as evaluated in situ on soft cheese
Authors: Eppert I , Valdés-Stauber N , Götz H , Busse M , Scherer S
Published: January 2020

The undefined microbial floras derived from the surface of ripe cheese which are used for the ripening of commercial red smear cheeses have a strong impact on the growth of Listeria spp. In some cases, these microbial consortia inhibit Listeria almost completely. From such undefined industrial cheese-ripening floras, linocin M18-producing (lin+) (N. Valdés-Stauber and S. Scherer, Appl. Environ. Microbiol. 60:3809-3814, 1994) and -nonproducing Brevibacterium linens strains were isolated and used as single-strain starter cultures on model red smear cheeses to evaluate their potential inhibitory effects on Listeria strains in situ. On cheeses ripened with lin+ strains, a growth reduction of L. ivanovii and L. monocytogenes of 1 to 2 log units was observed compared to cheeses ripened with lin strains. Linocin M18 activity was detected in cheeses ripened with lin+ strains but was not found in those ripened with lin strains. We suggest that production of linocin M18 contributes to the growth reduction of Listeria observed on model red smear cheeses but is unsufficient to explain the almost complete inhibition of Listeria caused by some undefined microbial floras derived from the surface of ripe cheeses.
Temperature determines the pattern of anaerobic microbial dechlorination of Aroclor 1260 primed by 2,3,4,6-tetrachlorobiphenyl in Woods Pond sediment
Authors: Wu Q , Bedard D L , Wiegel J
Published: January 2020

Reductive dechlorination of the Aroclor 1260 residue in Woods Pond (Lenox, Mass.) sediment samples was investigated for a year at incubation temperatures from 4 to 66 degrees C. Sediment slurries were incubated anaerobically with and without 2,3,4,6-tetrachlorobiphenyl (2346-CB; 350 microM) as a primer for dechlorination of the Aroclor 1260 residue. Dechlorination of the Aroclor residue occurred only in live samples primed with 2346-CB and only at 8 to 34 degrees C and 50 to 60 degrees C. The extent and pattern of polychlorinated biphenyl (PCB) dechlorination were temperature dependent. At 8 to 34 degrees C, the dechlorination resulted in 28 to 65% decreases of the hexathrough nonachlorobiphenyls and corresponding increases in the tri- and tetrachlorobiphenyls. At 12 to 30 degrees C, 30 to 40% of the hexa- through nonachlorobiphenyls were dechlorinated in just 3 months. The optimal temperature for overall chlorine removal was 20 to 27 degrees C. We observed four different microbial dechlorination processes with different but partially overlapping temperature ranges, i.e., Process N (flanked meta dechlorination) at 8 to 30 degrees C, Process P (flanked para dechlorination) at 12 to 34 degrees C, Process LP (unflanked para dechlorination) at 18 to 30 degrees C, and Process T (a very restricted meta dechlorination of specific hepta- and octachlorobiphenyls) at 50 to 60 degrees C. These temperature ranges should aid in the development of strategies for the enrichment and isolation of the microorganisms responsible for each dechlorination process. The incubation temperature determined the relative dominance of the four PCB dechlorination processes and the extent and products of dechlorination. Hence, understanding the effects of temperature on PCB dechlorination at contaminated sites should assist in predicting the environmental fate of PCBs or planning bioremediation strategies at those sites.
Direct detection and isolation of plasmid-bearing virulent serotypes of Yersinia enterocolitica from various foods
Authors: Bhaduri S , Cottrell B
Published: January 2020

A procedure was developed for direct detection, isolation, and maintenance of plasmid-bearing virulent serotypes of Yersinia enterocolitica from different food sources. Plasmid-bearing virulent strains of Y. enterocolitica representing five serotypes were simultaneously detected and isolated from enriched swab samples of artificially contaminated pork chops, ground pork, cheese, and zucchini, using Congo red binding and low-calcium-response tests. The method was also effective in isolating plasmid-bearing virulent strains of Y. enterocolitica from naturally contaminated porcine tongues. Virulence of the strains isolated from these foods was confirmed by PCR, the expression of plasmid-associated phenotypes, and mouse pathogenicity.
Bacteria, molds, and toxins in water-damaged building materials
Authors: Andersson M A , Nikulin M , Köljalg U , Andersson M C , Rainey F , Reijula K , Hintikka E L , Salkinoja-Salonen M
Published: January 2020

Microbial toxins and eukaryotic cell toxicity from indoor building materials heavily colonized by fungi and bacteria were analyzed. The dominant colonizers at water-damaged sites of the building were Stachybotrys chartarum (10(3) to 10(5) visible conidia cm-2), Penicillium and Aspergillus species (10(4) CFU mg-1), gram-negative bacteria (10(4) CFU mg-1), and mycobacteria (10(3) CFU mg-1). The mycobacterial isolates were most similar to M. komossense, with 98% similarity of the complete 16S rDNA sequence. Limulus assay of water extracts prepared from a water-damaged gypsum liner revealed high contents of gram-negative endotoxin (17 ng mg-1 of E. coli lipopolysaccharide equivalents) and beta-D-glucan (210 ng mg-1 of curdlan equivalents). High-performance liquid chromatography analysis of the methanol extracts showed that the water-damaged gypsum liner also contained satratoxin (17 ng mg-1). This methanol-extracted substance was 200 times more toxic to rabbit skin and fetus feline lung cells than extract of gypsum liner sampled from a non-water-damaged site. The same extract contained toxin(s) that paralyzed the motility of boar spermatozoa at extremely low concentrations; the 50% effective concentration was 0.3 microgram of dry solids per ml. This toxicity was not explainable by the amount of bacterial endotoxin, beta-D-glucan, or satratoxin present in the same extract. The novel in vitro toxicity test that utilized boar spermatozoa as described in this article is convenient to perform and reproducible and was a useful tool for detecting toxins of microbial origin toward eukaryotic cells not detectable in building materials by the other methods.
Antagonistic activity exerted in vitro and in vivo by Lactobacillus casei (strain GG) against Salmonella typhimurium C5 infection
Authors: Hudault S , Liévin V , Bernet-Camard M F , Servin A L
Published: January 2020

The aim of this study was to compare the antagonistic properties of Lactobacillus casei GG exerted in vitro against Salmonella typhimurium C5 in a cellular model, cultured enterocyte-like Caco-2 cells, to those exerted in vivo in an animal model, C3H/He/Oujco mice. Our results show that a 1-h contact between the invading strain C5 and either the culture or the supernatant of L. casei GG impeded the invasion by the Salmonella strain in Caco-2 cells, without modifying the viability of the strain. After neutralization at pH 7, no inhibition of the invasion by C5 was observed. The antagonistic activity of L. casei GG was examined in C3H/He/Oujco mice orally infected with C5 as follows: (i) L. casei GG was given daily to conventional animals as a probiotic, and (ii) it was given once to germ-free animals in order to study the effect of the population of L. casei GG established in the different segments of the gut. In vivo experiments show that after a single challenge with C5, this strain survives and persists at a higher level in the feces of the untreated conventional mice than in those of the treated group. In L. casei GG germ-free mice, establishment of L. casei GG in the gut significantly delayed the occurrence of 100% mortality of the animals (15 days after C5 challenge versus 9 days in germ-free mice [P < 0.01]). Cecal colonization level and translocation rate of C5 to the mesenteric lymph nodes, spleen, and liver were significantly reduced during the first 2 days post-C5 challenge, although the L. casei GG population level in the gut dramatically decreased in these animals.
The Bacillus thuringiensis vegetative insecticidal protein Vip3A lyses midgut epithelium cells of susceptible insects
Authors: Yu C G , Mullins M A , Warren G W , Koziel M G , Estruch J J
Published: January 2020

The Vip3A protein is a member of a newly discovered class of vegetative insecticidal proteins with activity against a broad spectrum of lepidopteran insects. Histopathological observations indicate that Vip3A ingestion by susceptible insects such as the black cutworm (Agrotis ipsilon) and fall armyworm (Spodoptera frugiperda) causes gut paralysis at concentrations as low as 4 ng/cm2 of diet and complete lysis of gut epithelium cells resulting in larval death at concentrations above 40 ng/cm2. The European corn borer (Ostrinia nubilalis), a nonsusceptible insect, does not develop any pathology upon ingesting Vip3A. While proteolytic processing of the Vip3A protein by midgut fluids obtained from susceptible and nonsusceptible insects is comparable, in vivo immunolocalization studies show that Vip3a binding is restricted to gut cells of susceptible insects. Therefore, the insect host range for Vip3A seems to be determined by its ability to bind gut cells. These results indicate that midgut epithelium cells of susceptible insects are the primary target for the Vip3A insecticidal protein and that their subsequent lysis is the primary mechanism of lethality. Disruption of gut cells appears to be the strategy adopted by the most effective insecticidal proteins.
Comparison of methods for isolation of mycobacteria from water
Authors: Neumann M , Schulze-Robbecke R , Hagenau C , Behringer K
Published: January 2020

Twelve methods for the isolation of mycobacteria were compared by applying them in parallel to 26 samples of surface water and 109 samples of treated water. Each method was defined by a particular combination of decontamination method, growth medium, and incubation temperature. For the decontamination of surface water, we used cetylpyridinium chloride (CPC) (30 min, 0.05%), as well as sample preincubation in tryptic soy broth (TSB) followed by decontamination with a cocktail of NaOH, cycloheximide, and malachite green. Treated water was decontaminated with 0.005 and 0.05% CPC (30 min). After enrichment by filtration, all samples were incubated on Lowenstein-Jensen medium (LJ), Ogawa egg yolk medium (OEY), and Ogawa whole-egg medium containing ofloxacin and ethambutol (OEOE) at temperatures of 30 and 37(deg)C. The efficacy of each method was determined by calculating the positivity rate, negativity rate, contamination rate, mean number of mycobacterial colonies grown, and mean number of different mycobacterial strains isolated. The last value was determined by subjecting the isolates to PCR restriction analysis and mycolic acid thin-layer chromatography. Statistical analysis demonstrated that both the TSB method and 0.05% CPC were appropriate for the decontamination of surface water. Decontamination with 0.005% CPC was best for treated water. The results for incubation on LJ were at least equal to those for incubation on OEY and always superior to the results with OEOE. At an incubation temperature of 30(deg)C, all methods achieved higher yields than at 37(deg)C.