bluuebunny/crossref_metadata_2025 huggingface dataset:
Ionic Stress and Osmotic Pressure Induce Different Alterations in the Lipopolysaccharide of a Rhizobium meliloti Strain
Authors: Lloret J , Bolanos L , Lucas M M , Peart J M , Brewin N J , Bonilla I , Rivilla R
Published: January 2020

A halotolerant strain of Rhizobium meliloti was isolated from nodules of a Melilotus plant growing in a salt marsh in Donana National Park (southwest Spain). This strain, EFB1, is able to grow at NaCl concentrations of up to 500 mM, and no effect on growth is produced by 300 mM NaCl. EFB1 showed alterations on its lipopolysaccharide (LPS) structure that can be related to salt stress: (i) silver-stained electrophoretic profiles showed a different mobility that was dependent on ionic stress but not on osmotic pressure, and (ii) a monoclonal antibody, JIM 40, recognized changes in LPS that were dependent on osmotic stress. Both modifications on LPS may form part of the adaptive mechanism of this bacterium for saline environments.
Seasonal variations of virus abundance and viral control of the bacterial production in a backwater system of the danube river
Authors: Mathias C B , Kirschner A , Velimirov B
Published: January 2020

The abundance of virus-like particles in a backwater system of the Danube River covered a range of 1.2 x 10(sup7) to 6.1 x 10(sup7) ml(sup-1) from 1992 to 1993. Measurements of head diameters for these particles, all of which were presumed to be viruses, led to four defined size classes, ranging from <60 nm to >150 nm. The 60- to <90-nm size class contained the largest fraction of total particles (41%), followed by the 90- to <150-nm size class (33%). The frequency of size classes was not significantly different between the two years. The frequency of bacteria with mature phages ranged from 1 to 4% over the seasons, with mean burst sizes ranging from 17 to 36 phage per host cell. Among the bacterial morphotypes, rods and vibrios were the major host systems for phages, while coccoid and filamentous cells were considered negligible. Counts from transmission electron microscopy and acridine orange direct counts confirmed that rods and vibrios accounted for 85 to 95% of the bacterial population over the seasons. Virus decay experiments showed lower decay rates for temperatures between 5 and 15(deg)C (52 to 70% of the virus population remained) relative to 18 and 25(deg)C (31 to 51% of the virus remained). Bacterial production measurements, performed at the same time and under the same conditions as decay experiments, allowed us to estimate virus-induced death rates, which ranged from 15.8 to 30.1% over the year, with an average of 20% viral control of the bacterial production. Considering that mature phage particles are visible only in the last phase of the latent period and using a mean conversion factor of 5.4 from the literature, based on descriptions of various phage host systems to relate the percentage of visibly infected cells to the total percentage of the bacterial community that is phage infected, we estimate that some 5.4 to 21.6% of the bacterial population is infected with viruses. This would imply that virus-induced death rates of bacteria range from 10.8 to 43.2%. The data on virus-induced bacterial mortality obtained by both the viral decay method and the determination of the frequency of infected cells are compared and discussed.
Optimizing conditions for the growth of Lactobacillus casei YIT 9018 in tryptone-yeast extract-glucose medium by using response surface methodology
Authors: Oh S , Rheem S , Sim J , Kim S , Baek Y
Published: January 2020

This study was undertaken to find optimum conditions of tryptone, yeast extract, glucose, Tween 80, and incubation temperature for the growth of Lactobacillus casei YIT 9018 and to assess the effects of these factors by use of response surface methodology. A central composite design was used as an experimental design for allocation of treatment combinations. A second-order polynomial regression model, which was used at first for analysis of the experiment, had a significant lack of fit. Therefore, cubic and quartic terms were incorporated into the regression model through variable selection procedures. Effects involving incubation temperature, yeast extract, glucose, and tryptone were significant, whereas the only significant effect involving Tween 80 was the interaction effect between temperature and Tween 80. It turned out that growth of L. casei YIT 9018 was most strongly affected by the incubation temperature. Estimated optimum conditions of the factors for growth of L. casei YIT 9018 are as follows: tryptone, 3.04%; yeast extract, 0.892%; glucose, 1.58%; Tween 80, 0%; incubation temperature, 35 degrees C.
Tn5-directed cloning of pqq genes from Pseudomonas fluorescens CHA0: mutational inactivation of the genes results in overproduction of the antibiotic pyoluteorin
Authors: Schnider U , Keel C , Voisard C , Défago G , Haas D
Published: January 2020

Pseudomonas fluorescens CHA0 produces several secondary metabolites, e.g., the antibiotics pyoluteorin (Plt) and 2,4-diacetylphloroglucinol (Phl), which are important for the suppression of root diseases caused by soil-borne fungal pathogens. A Tn5 insertion mutant of strain CHA0, CHA625, does not produce Phl, shows enhanced Plt production on malt agar, and has lost part of the ability to suppress black root rot in tobacco plants and take-all in wheat. We used a rapid, two-step cloning-out procedure for isolating the wild-type genes corresponding to those inactivated by the Tn5 insertion in strain CHA625. This cloning method should be widely applicable to bacterial genes tagged with Tn5. The region cloned from P. fluorescens contained three complete open reading frames. The deduced gene products, designated PqqFAB, showed extensive similarities to proteins involved in the biosynthesis of pyrroloquinoline quinone (PQQ) in Klebsiella pneumoniae, Acinetobacter calcoaceticus, and Methylobacterium extorquens. PQQ-negative mutants of strain CHA0 were constructed by gene replacement. They lacked glucose dehydrogenase activity, could not utilize ethanol as a carbon source, and showed a strongly enhanced production of Plt on malt agar. These effects were all reversed by complementation with pqq+ recombinant plasmids. The growth of a pqqF mutant on ethanol and normal Plt production were restored by the addition of 16 nM PQQ. However, the Phl- phenotype of strain CHA625 was due not to the pqq defect but presumably to a secondary mutation. In conclusion, a lack of PQQ markedly stimulates the production of Plt in P. fluorescens.
Division of Listeria monocytogenes serovar 4b strains into two groups by PCR and restriction enzyme analysis
Authors: Ericsson H , Stålhandske P , Danielsson-Tham M L , Bannerman E , Bille J , Jacquet C , Rocourt J , Tham W
Published: January 2020

Altogether, 133 strains of Listeria monocytogenes serovar 4b were investigated. A segment of 2,916 bp containing parts of the two genes inlA and inlB in L. monocytogenes was amplified by the PCR technique. The PCR product obtained was cleaved with the restriction enzyme AluI, and the fragments generated were separated by gel electrophoresis, leading to two distinct groups: PCR-restriction enzyme analysis groups I and II, containing 37 and 96 strains, respectively. The PCR-restriction enzyme analysis method described in this paper could be a useful tool for the subtyping of L. monocytogenes serovar 4b strains.
Degradation of 1,4-dichlorobenzene by Xanthobacter flavus 14p1
Authors: Spiess E , Sommer C , Görisch H
Published: January 2020

Xanthobacter flavus 14p1 was isolated from sludge of the river Mulde by selective enrichment with 1,4-dichlorobenzene as the sole source of carbon and energy. The bacterium did not use other aromatic or chloroaromatic compounds as growth substrates. During growth on 1,4-dichlorobenzene, stoichiometric amounts of chloride ions were released. Degradation products of 1,4-dichlorobenzene were identified by gas chromatography-mass spectrometry analysis. 3,6-Dichloro-cis-1,2-dihydroxycyclohexa-3,5-diene and 3,6-dichlorocatechol were isolated from culture fluid. 2,5-Dichloromuconic acid and 2-chloromaleylacetic acid as well as the decarboxylation product 2-chloroacetoacrylic acid were identified after enzymatic conversion of 3,6-dichlorocatechol by cell extract. 1,4-Dichlorobenzene dioxygenase, dihydrodiol dehydrogenase, and catechol 1,2-dioxygenase activity were induced in cells grown on 1,4-dichlorobenzene. The results demonstrate that 1,4-dichlorobenzene degradation is initiated by dioxygenation and that ring opening proceeds via ortho cleavage.
Characterization of an H2-utilizing enrichment culture that reductively dechlorinates tetrachloroethene to vinyl chloride and ethene in the absence of methanogenesis and acetogenesis
Authors: Maymó-Gatell X , Tandoi V , Gossett J M , Zinder S H
Published: January 2020

We have been studying an anaerobic enrichment culture which, by using methanol as an electron donor, dechlorinates tetrachloroethene (PCE) to vinyl chloride and ethene. Our previous results indicated that H2 was the direct electron donor for rductive dechlorination of PCE by the methanol-PCE culture. Most-probable-number counts performed on this culture indicated low numbers (< or equal to 10(4)/ml)) of methanogens and PCE dechlorinators using methanol and high numbers (> or equal to 10(6)/ml)) of sulfidogens, methanol-utilizing acetogens, fermentative heterotrophs, and PCE dechlorinators using H2. An anaerobic H2-PCE enrichment culture was derived from a 10(-6) dilution of the methanol-PCE culture. This H2-PCE culture used PCE at increasing rates over time when transferred to fresh medium and could be transferred indefinitely with H2 as the electron donor for the PCE dechlorination, indicating that H2-PCE can serve as an electron donor-acceptor pair for energy conservation and growth. Sustained PCE dechlorination by this culture was supported by supplementation with 0.05 mg of vitamin B12 per liter, 25% (vol/vol) anaerobic digestor sludge supernatant, and 2 mM acetate, which presumably served as a carbon source. Neither methanol nor acetate could serve as an electron donor for dechlorination by the H2-PCE culture, and it did not produce CH4 or acetate from H2-CO2 or methanol, indicating the absence of methanogenic and acetogenic bacteria. Microscopic observatios of the pruified H2-PCE culture showed only two major morphotypes: irregular cocci and small rods.
A microsatellite marker for studying the ecology and diversity of fungal endophytes (Epichloë spp.) in grasses
Authors: Groppe K , Sanders I , Wiemken A , Boller T
Published: January 2020

Randomly amplified polymorphic DNA fingerprinting, which is based on PCR with arbitrary 10-nucleotide primers, were used to analyze genetic diversity among isolates of the endophytic ascomycete Epichloë typhina, which were collected at a single field site from a population of one of its hosts, the grass Bromus erectus. One of the polymorphic randomly amplified polymorphic DNA PCR products occurred in all isolates as single bands with different but closely related sizes. Two of the size variants of this product were cloned and sequenced, and they were found to represent the same DNA sequence, except for a stretch of tandem repeats of the trinucleotide AAG.TTC, which differed in size, consisting of 8 and 18 repeats, respectively. Tandem repeats of this type are called microsatellites. Oligonucleotides were synthesized corresponding to portions of the sequence flanking the microsatellite and were used for PCR amplification of the loci from the genomic DNAs of different Epichloë isolates. A single PCR product was found for most isolates, indicating that the sequence represented a single genetic locus. Five alleles that could clearly be distinguished in size were found in a population of 91 field isolates. PCR with (AAC)8 and (AAG)8 as primers yielded a number of amplified bands from genomic DNA of Epichloë isolates, indicating that these types of microsatellites occur frequently in the genome of this fungus. A survey of all fungal DNA sequences currently deposited in the DNA sequence databases of EMBL and GenBank revealed that microsatellites of different repeating units are widespread in fungi.(ABSTRACT TRUNCATED AT 250 WORDS)
Direct DNA extraction for PCR-mediated assays of soil organisms
Authors: Volossiouk T , Robb E J , Nazar R N
Published: January 2020

By using the rDNA of a plant wilt pathogen (Verticillium dahliae) as the target sequence, a direct method for the extraction of DNA from soil samples which can be used for PCR-mediated diagnostics without a need for further DNA purification has been developed. The soil organisms are disrupted by grinding in liquid nitrogen with the natural abrasives in soil, and losses due to degradation and adsorption are largely eliminated by the addition of skim milk powder. The DNA from disrupted cells is extracted with sodium dodecyl sulfate-phenol and collected by ethanol precipitation. After suitable dilution, this DNA extract can be assayed directly by PCR amplification technologies. The method is rapid, cost efficient, and when combined with suitable internal controls can be applied to the detection and quantification of specific soil organisms or pathogens on a large-scale basis.
Direct sequencing of hepatitis A virus strains isolated during an epidemic in France
Authors: Apaire-Marchais V , Robertson B H , Aubineau-Ferre V , Le Roux M G , Leveque F , Schwartzbrod L , Billaudel S
Published: January 2020

Direct sequencing of PCR products was used to study the VP1 region of the hepatitis A virus (HAV) genome (position 2199 to 2356) of nine strains isolated from human stools collected during a hepatitis A epidemic (western France, 1992), three strains from environmental samples (1990, 1991, and 1992), and two HAV cell culture isolates (the French strain CF53/Lyon and strain CLF). These viruses differed from CF53/Lyon (genotype I) by between 1 and 10.3%, and results indicated the existence of two groups of strains belonging to two different subgenotypes (IA and IB). With this sequencing technique it was possible to monitor the epidemiology of HAV and study its relations.
Greenhouse and Field Evaluations of an Autoselective System Based on an Essential Thymidylate Synthase Gene for Improved Maintenance of Plasmid Vectors in Modified Rhizobium meliloti
Authors: O'flaherty S , Moenne-Loccoz Y , Boesten B , Higgins P , Dowling D N , Condon S , O'gara F
Published: January 2020

The stability of the thy autoselective system, based on an essential thymidylate synthase gene, for enhanced maintenance of plasmid vectors in Rhizobium meliloti was evaluated in the greenhouse and with field-grown alfalfa. The thy autoselective system consists of a free-replicating, broad-host-range plasmid vector containing a copy of the thyA gene from Lactococcus lactis subsp. lactis and a spontaneous mutant of R. meliloti deficient in thymidylate synthase (Thy(sup-)). Under greenhouse conditions, Thy(sup-) rhizobia did not persist in rooting solution alone unless supplemented with thymidine but survived in the presence of the host plant. Nodules formed on alfalfa plants grown in thymidine-free rooting solution and inoculated with Thy(sup-) rhizobia contained only Thy(sup+) revertants. In soil, Thy(sup-) rhizobia were compromised and failed to nodulate alfalfa. Thy(sup-) mutants containing a thy plasmid survived in the rhizosphere and nodulated alfalfa like the wild-type strain. The thy autoselective system was tested in the field with Thy(sup-) strain Rm24T and pPR602, a thy plasmid vector devoid of antibiotic resistance genes and marked with constitutively expressed lacZY. At 80 days after sowing, most rhizobia isolated from the nodules of field-grown alfalfa inoculated with Rm42T(pPR602) contained pPR602. The thy autoselective system proved useful to ensure maintenance of the plasmid vector under greenhouse and field conditions in R. meliloti.
Sequence and expression of a xylanase gene from the hyperthermophile Thermotoga sp. strain FjSS3-B.1 and characterization of the recombinant enzyme and its activity on kraft pulp
Authors: Saul D J , Williams L C , Reeves R A , Gibbs M D , Bergquist P L
Published: January 2020

A gene expressing xylanase activity was isolated from a genomic library of Thermotoga sp. strain FjSS3-B.1. The sequence of the gene shows that it encodes a single domain, family 10 xylanase. The recombinant enzyme has extremely high thermal stability, activity over a relatively broad pH range, and activity on Pinus radiata kraft pulp.
Utilization of Halogenated Benzenes, Phenols, and Benzoates by Rhodococcus opacus GM-14
Authors: Zaitsev G M , Uotila J S , Tsitko I V , Lobanok A G , Salkinoja-Salonen M S
Published: January 2020

Strain GM-14 was isolated by selective enrichment from contaminated soil with chlorobenzene as the sole source of carbon and energy. It utilizes an exceptionally wide spectrum of haloaromatic substrates. It is a gram-positive, weakly acid-fast actinomycete, with a morphological cycle from cocci and short rods to long rods and branched filaments; it grew optimally at 28(deg)C; and it tolerated 5% NaCl in rich medium. The chemotaxonomic characteristics, the diagnostic biochemical tests, the whole-cell fatty acid composition, and 16S rDNA analysis were consistent with Rhodococcus opacus. R. opacus GM-14 grew on 48 of 117 different aromatic and haloaromatic compounds. It utilized phenol at concentrations up to 1.2 g/liter, 3- and 4-methylphenols up to 0.5 g/liter, 2- and 4-chlorophenols up to 0.25 g/liter, and 3-chlorophenol up to 0.1 g/liter. It grew in saturated aqueous solutions of benzene, chlorobenzene, and 1,3- and 1,4-dichlorobenzene (up to 13, 3, 0.5, and 0.5 g/liter, respectively). The specific growth rate of strain GM-14 on phenol and 3- and 4-chlorophenols in batch culture was 0.27 to 0.29 h(sup-1), and that on benzene and chlorobenzene was similar to the rate on fructose, i.e., 0.2 h(sup-1). The growth yield on benzene and on chlorobenzene (<=0.4 g liter(sup-1)) was 40 to 50 g (dry weight) per mol of substrate consumed, equalling 8 g of dry weight biomass per mol of substrate carbon, similar to that obtained on acetate. During growth of strain GM-14 on chlorobenzene, 1,3-dichlorobenzene, and all isomers of monochlorophenol, stoichiometric amounts of chloride were released, and 50% of the stoichiometric amount was released from 1,4-dichlorobenzene.
UV B-Induced Vertical Migrations of Cyanobacteria in a Microbial Mat
Authors: Bebout B M , Garcia-Pichel F
Published: January 2020

Exposure to moderate doses of UV B (0.35 to 0.79 W m(sup-2) s(sup-1) or 0.98 to 2.2 (mu)mol of photons m(sup-2) s(sup-1) at 310 nm) caused the surface layers of microbial mats from Solar Lake, Sinai, Egypt, to become visibly lighter green. Concurrent with the color change were rapid and dramatic reductions in gross photosynthesis and in the resultant high porewater oxygen concentrations in the surface layers of the mats. The depths at which both maximum gross photosynthesis and maximum oxygen concentrations occurred were displaced downward. In contrast, gross photosynthesis in the deeper layers of the mats increased in response to UV B incident upon the surface. The cessation of exposure to UV B partially reversed all of these changes. Taken together, these responses suggest that photoautotrophic members of the mat community, most likely the dominant cyanobacterium Microcoleus chthonoplastes, were migrating in response to the added UV B. The migration phenomenon was also observed in response to increases in visible radiation and UV A, but UV B was ca. 100-fold more effective than visible radiation and ca. 20-fold more effective than UV A in provoking the response. Migrating microorganisms within this mat are apparently able to sense UV B directly and respond behaviorally to limit their exposure to UV. Because of strong vertical gradients of light and dissolved substances in microbial mats, the migration and the resultant vertical redistribution of photosynthetic activity have important consequences for both the photobiology of the cyanobacteria and the net primary productivity of the mat ecosystem.
Factors affecting the determination of respiratory activity on the basis of cyanoditolyl tetrazolium chloride reduction with membrane filtration
Authors: Pyle B H , Broadaway S C , McFeters G A
Published: January 2020

Deficiencies in traditional bacterial enumeration techniques which rely on colony formation have led to the use of total direct counting methods, such as the acridine orange direct count technique for the enumeration of planktonic bacteria. As total direct counts provide no information on the viability or activity of the organisms, demonstration of respiratory activity with the fluorochrome cyanoditolyl tetrazolium chloride (CTC) has been employed. We have modified this technique by performing filtration prior to CTC incubation. Cells captured on a polycarbonate membrane were incubated on absorbent pads saturated with medium containing CTC. Following counterstaining with DAPI (4(prm1),6-diamidino-2-phenylindole) total and respiring cells were enumerated by epifluorescence microscopy. Factors affecting CTC reduction by Klebsiella pneumoniae, Salmonella typhimurium, and Escherichia coli K-12 were investigated. With K. pneumoniae, nutrient additions to the CTC medium did not increase the number of respiring cells detected. CTC reduction by all three organisms decreased in response to an increase of the pH of the CTC medium above pH 6.5. Increasing phosphate concentrations contributed to this inhibitory effect. CTC-membrane filter counts of K. pneumoniae, S. typhimurium, and E. coli K-12 and of bacteria in well water corresponded closely with plate counts (r = 0.987). The results show that careful attention should be given to the composition of CTC-containing media which are used to enumerate respiring bacteria. With an appropriate medium, reliable enumeration of respiring bacteria can be achieved within a few hours.
Phenolic Azo Dye Oxidation by Laccase from Pyricularia oryzae
Authors: Chivukula M , Renganathan V
Published: January 2020

Laccase oxidation of phenolic azo dyes was examined with a commercially available laccase from Pyricularia oryzae as the model. Methyl-, methoxy-, chloro-, and nitro-substituted derivatives of 4-(4(prm1)-sulfophenylazo)-phenol were examined as substrates for this laccase. Only the substituents on the phenolic ring were changed. Among the dyes examined, only 2-methyl-, 2-methoxy-, 2,3-dimethyl-, 2,6-dimethyl-, 2,3-dimethoxy-, and 2,6-dimethoxy-substituted 4-(4(prm1)-sulfophenylazo)-phenol served as substrates. Preliminary kinetic studies suggest that 2,6-dimethoxy-substituted 4-(4(prm1)-sulfophenylazo)-phenol is the best substrate. Laccase oxidized the 2,6-dimethyl derivative of 4-(4(prm1)-sulfophenylazo)-phenol to 4-sulfophenylhydroperoxide (SPH) and 2,6-dimethyl-1,4-benzoquinone. The 2-methyl- and 2-methoxy-substituted dyes were oxidized to SPH and either 2-methyl- or 2-methoxy-benzoquinone. Six products were formed from laccase oxidation of the 2,6-dimethoxy-substituted dye. Three of them were identified as SPH, 4-hydroxybenzenesulfonic acid, and 2,6-dimethoxybenzoquinone. A mechanism for the formation of benzoquinone and SPH from laccase oxidation of phenolic azo dyes is proposed. This study suggests that laccase oxidation can result in the detoxification of azo dyes.
Natural assemblages of marine bacteria exhibiting high-speed motility and large accelerations
Authors: Mitchell J G , Pearson L , Dillon S , Kantalis K
Published: January 2020

Natural communities of marine bacteria, an isolate (FMB-Bf3) from one marine community, and Escherichia coli were examined by video microscopy for the magnitude and uniformity of their speed. Natural communities formed tight microswarms that showed higher speeds (mean = 230 microns s-1) than did E. coli (15 microns s-1) or FMB-Bf3 (mean = 62 microns s-1). Outside the microswarms, the marine bacteria slowed to 45 microns s-1. Between turns, in mid run, and while travelling in straight lines, the natural-community bacteria accelerated up to 1,450 microns s-2 while the cultured bacteria showed maximum accelerations of 70 and 166 microns s-2. The frequency distribution of speed change for the marine bacteria was skewed towards a few large negative accelerations and a range of positive accelerations. The general pattern was one of relatively slow increases in speed followed by abrupt declines. The results indicate that the mechanical generation and energetic maintenance, as well as the environmental function, of bacterial motility need reappraisal. We conclude that the standard bacterial motility parameters of low and uniform speed, derived from culture-based studies, are not necessarily applicable to marine bacterial communities.
Distribution and properties of fructosyl amino acid oxidase in fungi
Authors: Yoshida N , Sakai Y , Serata M , Tani Y , Kato N
Published: January 2020

Fructosyl amino acid oxidase, and enzyme that can be used for the determination of glycated proteins in blood samples from diabetic patients, was used to screen cultures in our microorganism culture collection. Fructosyl amino acid oxidase was found only in the strains of four genera of fungi, Aspergillus, Fusarium, Gibberella, and Penicillium and exhibited different substrate specificities against fructosyl valine and N epsilon-fructosyl N alpha-Z-lysine. A fructosyl valine-specific enzyme from Penicillium janthinellum AKU3413 was monomeric (M(r), 49,000), was most active at 35 degrees C and pH 8.0, and had a covalently bound flavin adenine dinucleotide as a prosthetic group.
Alkalophilic Bacillus sp. strain LG12 has a series of serine protease genes
Authors: Schmidt B F , Woodhouse L , Adams R M , Ward T , Mainzer S E , Lad P J
Published: January 2020

Four tandem subtilisin-like protease genes were found on a 6,854-bp DNA fragment cloned from the alkalophilic Bacillus sp. strain LG12. The two downstream genes (sprC and sprD) appear to be transcribed independently, while the two upstream genes (sprA and sprB) seem to be part of the same transcript.
Substrate diversity and expression of the 2,4,5-trichlorophenoxyacetic acid oxygenase from Burkholderia cepacia AC1100
Authors: Danganan C E , Shankar S , Ye R W , Chakrabarty A M
Published: January 2020

Burkholderia cepacia AC1100 uses the chlorinated aromatic compound 2,4,5-trichlorophenoxyacetic acid as a sole source of carbon and energy. The genes encoding the proteins involved in the first step (tftA and tftB [previously designated tftA1 and tftA2, respectively]) have been cloned and sequenced. The oxygenase, TftAB, is capable of converting not only 2,4,5-trichlorophenoxyacetic acid to 2,4,5-trichlorophenol but also a wide range of chlorinated aromatic phenoxyacetates to their corresponding phenolic derivatives, as shown by whole-cell and cell-free assays. The rate of substrate utilization by TftAB depends upon the extent of chlorination of the substrate, the positions of the chlorines, and the phenoxy group. These results indicate a mechanistic similarity between TftAB and the 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate-dependent dioxygenase, TfdA, from Alcaligenes eutrophus JMP134. The promoter of the oxygenase genes was localized by promoter-probe analysis, and the transcriptional start site was identified by primer extension. The beta-galactosidase activity of the construct containing the promoter region cloned upstream of the beta-galactosidase gene in the promoter-probe vector pKRZ-1 showed that this construct is constitutively expressed in Escherichia coli and in AC1100. The -35 and -10 regions of the oxygenase genes show significant sequence identity to typical Escherichia coli sigma 70 promoters.
Concentration and purification of beef extract mock eluates from water samples for the detection of enteroviruses, hepatitis A virus, and Norwalk virus by reverse transcription-PCR
Authors: Schwab K J , De Leon R , Sobsey M D
Published: January 2020

In this study we developed a concentration and purification procedure to facilitate reverse transcription (RT)-PCR detection of enteric viruses in water sample concentrates obtained by conventional filter adsorption-elution methods. One liter of beef extract-glycine eluate with or without humic acid and seeded with poliovirus type 1, hepatitis A virus, and Norwalk virus was used as a model system, and the eluent was further processed for RT-PCR compatibility. The sample concentration and purification procedures which we used included polyethylene glycol precipitation, Pro-Cipitate precipitation, a second polyethylene glycol precipitation, spin column chromatography, and ultrafiltration. The sample volumes were reduced from 1 liter to 20 to 50 microliters, and the samples were purified enough so that viruses could be detected by the RT-PCR. The ability to detect low levels of enteric viruses by molecular techniques was compared directly with the ability to detect enteric viruses by cell culture infectivity procedures. As little as 3 PFU of poliovirus type 1 in an initial 1 liter of mock eluate was detected by the RT-PCR.
Convenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth
Authors: Rosso L , Lobry J R , Bajard S , Flandrois J P
Published: January 2020

A new model in which the maximum microbial specific growth rate ((mu)(infmax)) is described as a function of pH and temperature is presented. The seven parameters of this model are the three cardinal pH parameters (the pH below which no growth occurs, the pH above which no growth occurs, and the pH at which the (mu)(infmax) is optimal), the three cardinal temperature parameters (the temperature below which no growth occurs, the temperature above which no growth occurs, and the temperature at which the (mu)(infmax) is optimal), and the specific growth rate at the optimum temperature and optimum pH. The model is a combination of the cardinal temperature model with inflection and the cardinal pH model (CPM). The CPM was compared with the models of Wijtzes et al. and Zwietering et al. by using previously published data sets. The models were compared on the basis of the usual criteria (simplicity, biological significance and minimum number of parameters, applicability, quality of fit, minimum structural correlations, and ease of initial parameter estimation), and our results justified the choice of the CPM. Our combined model was constructed by using the hypothesis that the temperature and pH effects on the (mu)(infmax) are independent. An analysis of this new model with an Escherichia coli O157:H7 data set showed that there was a good correspondence between observed and calculated (mu)(infmax) values. The potential and convenience of the model are discussed.
Effect of pH on Bacillus thermoamylovorans Growth and Glucose Fermentation
Authors: Combet-Blanc Y , Kalamba K K , Kergoat P Y
Published: January 2020

The effect of pH on the growth and physiology of Bacillus thermoamylovorans, a new moderately thermophilic and non-spore-forming bacterium isolated from palm wine, was studied. Growth occurred from pH 5.4 to 8.5, with optimum growth at 7.0. During the exponential growth phase at optimum pH, glucose was consumed at the maximum rate (qs), 17.87 mmol g(sup-1) h(sup-1), and was mainly fermented into acetate, ethanol, and formate (76.5% of metabolites produced). In acidic or alkaline conditions, glucose specific consumption rates were considerably reduced (qs = 8.06 mmol g(sup-1) h(sup-1) at pH 5.6 and 2.85 mmol g(sup-1) h(sup-1) at pH 8.4), and a switch in glucose metabolism toward lactate production (62.6% of metabolites produced at pH 5.6 and 41.2% of those produced at pH 8.4) was observed. Moreover, optimum cellular yield (Y(infx/ATP)), 14.8 g mol(sup-1), and optimum energy yield (Y(infATP/s)), 2.65 mol mol(sup-1), were observed at neutrality. The results of this study were compared with published data about lactic acid bacteria; this comparison allowed us to complement our previous taxonomic study of B. thermoamylovorans and to identify additional phenotypic differences between B. thermoamylovorans and lactobacilli.
Purification and characterization of two thermostable acetyl xylan esterases from Thermoanaerobacterium sp. strain JW/SL-YS485
Authors: Shao W , Wiegel J
Published: January 2020

Two acetyl esterases (EC 3.1.1.6) were purified to gel electrophoretic homogeneity from Thermoanaerobacterium sp. strain JW/SL-YS485, an anaerobic, thermophilic endospore former which is able to utilize various substituted xylans for growth. Both enzymes released acetic acid from chemically acetylated larch xylan. Acetyl xylan esterases I and II had molecular masses of 195 and 106 kDa, respectively, with subunits of 32 kDa (esterase I) and 26 kDa (esterase II). The isoelectric points were 4.2 and 4.3, respectively. As determined by a 2-min assay with 4-methylumbelliferyl acetate as the substrate, the optimal activity of acetyl xylan esterases I and II occurred at pH 7.0 and 80 degrees C and at pH 7.5 and 84 degrees C, respectively. Km values of 0.45 and 0.52 mM 4-methylumbelliferyl acetate were observed for acetyl xylan esterases I and II, respectively. At pH 7.0, the temperatures for the 1-h half-lives for acetyl xylan esterases I and II were 75 degrees and slightly above 100 degrees C, respectively.
Use of suppressor analysis to find genes involved in the colonization deficiency of a Bacteroides thetaiotaomicron mutant unable to grow on the host-derived mucopolysaccharides chondroitin sulfate and heparin
Authors: Cheng Q , Salyers A A
Published: January 2020

Bacteroides thetaiotaomicron, one of the numerically predominant species of human colonic bacteria, can ferment two types of host-derived mucopolysaccharides, chondroitin sulfate (CS) and heparin (HP). Originally, the pathways for utilization of CS and HP appeared to be completely independent of each other, but we have recently identified a gene, chuR, that links the two utilization systems. chuR is probably a regulatory gene, but it controls only a small subset of genes involved in CS and HP utilization. Some of the genes controlled by chuR are important for survival of B. thetaiotaomicron in the colon because a mutant that no longer produced ChuR was unable to compete with the wild type for colonization of the intestinal tract of germfree mice. In an attempt to identify genes that either were controlled by ChuR or encoded proteins that interacted with ChuR, we used transposon mutagenesis to generate suppressor mutations that restored the ability of a chuR disruption mutant to grow on CS and HP. Two classes of suppressors were isolated. One class grew as well as the wild type on CS and HP and had recovered the ability to compete with the wild type for colonization of the germfree mouse intestinal tract. A second class grew more slowly on CS and HP and reached only a half-maximum level on CS. This mutant still had a colonization defect. Representatives of both classes of suppressor mutants have been characterized, and the results of this analysis suggest that the transposon insertions in the suppressor mutants probably affected regulatory genes whose products interact with ChuR.
Purification and characterization of a dipeptidase from Lactobacillus sake
Authors: Montel M C , Seronie M P , Talon R , Hébraud M
Published: January 2020

A dipeptidase was purified from cell extracts of Lactobacillus sake. This compound was a monomer having a molecular weight of 50,000 and a pI of 4.7 and exhibited broad specificity against all dipeptides except those with proline or glycine at the N terminus. The enzyme was inhibited by EDTA or 1,10-phenanthroline but could be reactivated with CoCl2 and MnCl2.
Genetic Diversity among Xanthomonas campestris Strains Pathogenic for Small Grains
Authors: Bragard C , Verdier V , Maraite H
Published: January 2020

A collection of 51 Xanthomonas campestris strains from throughout the world was studied to detect and assess genetic diversity among pathogens of small grains. Isolates from barley, bread wheat, bromegrass, canary grass, cassava, maize, orchard grass, rice, rough-stalked meadow grass, rye, timothy, and triticale were analyzed by pathogenicity tests on bread wheat cv. Alondra and barley cv. Corona, indirect immunofluorescence, and restriction fragment length polymorphism (RFLP). Three probes were used for the RFLP analysis. They were an acetylaminofluorene-labelled 16S+23S rRNA probe from Escherichia coli and two (sup32)P-labelled restriction fragments from either plasmidic (pBSF2) or chromosomal (pBS8) DNA of X. campestris pv. manihotis. Strains clustered in 9 and 20 groups with the rRNA probe and the pBSF2 DNA probe, respectively. Strains of X. campestris pv. graminis, X. campestris pv. phleipratensis, and X. campestris pv. poae are shown to be related but are also distinguishable by RFLP patterns, serology, and pathogenicity on bread wheat. Strains pathogenic only for barley and not for wheat grouped together. Another group is temporarily designated deviant X. campestris pv. undulosa. These South American isolates from bread wheat did not react by indirect immunofluorescence and produced atypical lesions in pathogenicity tests. The results stress the need to perform pathogenicity tests before strains are named at the pathovar level. The importance of the different probes used for epidemiological studies or phylogenetic studies of closely related strains is underlined.
Insoluble Glucan Formation by Leuconostoc mesenteroides B-1355
Authors: Zahnley J C , Smith M R
Published: January 2020

Leuconostoc mesenteroides B-1355 produced at least three glucosyltransferases (GTFs). We previously identified GTF-2 as alternansucrase and GTF-3 as fraction L dextransucrase. We here show that GTF-1 is a previously unreported sucrase that synthesized water-insoluble dextran. Our evidence consisted of the following. (i) GTF-1 was a major component and GTF-2 was a minor component of culture supernatant fractions, but supernatant fractions actively synthesized water-insoluble glucan. (ii) GTF-1 and culture supernatants produced an unusual high-pressure liquid chromatography pattern of malto-oligosaccharides that was not reproduced by GTF-2-GTF-3 mixtures. (iii) GTF-2, GTF-3, and GTF-2-GTF-3 mixtures did not synthesize insoluble glucan from sucrose. Nearly all of the alternansucrase in young (less than 17-h) cultures was associated with the cells.
Quantification and Characterization of Phagocytosis in the Soil Amoeba Acanthamoeba castellanii by Flow Cytometry
Authors: Avery S V , Harwood J L , Lloyd D
Published: January 2020

Phagocytosis in the common grazing soil amoeba Acanthamoeba castellanii was characterized by flow cytometry. Uptake of fluorescently labelled latex microbeads by cells was quantified by appropriate setting of thresholds on light scatter channels and, subsequently, on fluorescence histograms. Confocal laser scanning microscopy was used to verify the effectiveness of sodium azide as a control for distinguishing between cell surface binding and internalization of beads. It was found that binding of beads at the cell surface was complete within 5 min and 80% of cells had beads associated with them after 10 min. However, the total number of phagocytosed beads continued to rise up to 2 h. The prolonged increase in numbers of beads phagocytosed was due to cell populations containing increasing numbers of beads peaking at increasing time intervals from the onset of phagocytosis. Fine adjustment of thresholds on light scatter channels was used to fractionate cells according to cell volume (cell cycle stage). Phagocytotic activity was approximately threefold higher in the largest (oldest) than in the smallest (newly divided) cells of A. castellanii and showed some evidence of periodicity. At no stage in the cell cycle did phagocytosis cease. Binding and phagocytosis of beads were also markedly influenced by culture age and rate of rotary agitation of cell suspensions. Saturation of phagocytosis (per cell) at increasing bead or decreasing cell concentrations occurred at bead/cell ratios exceeding 10:1. This was probably a result of a limitation of the vacuolar uptake system of A. castellanii, as no saturation of bead binding was evident. The advantages of flow cytometry for characterization of phagocytosis at the single-cell level in heterogeneous protozoal populations and the significance of the present results are discussed.
Comparison of Lactobacillus strains with respect to bile salt hydrolase activity, colonization of the gastrointestinal tract, and growth rate of the murine host
Authors: Bateup J M , McConnell M A , Jenkinson H F , Tannock G W
Published: January 2020

The significance of bile salt hydrolase production by lactobacilli in the microecology of the murine intestinal tract has not been extensively studied previously. Assays of bile salt hydrolase (sodium taurocholate as substrate) associated with cell extracts of five Lactobacillus strains of murine origin gave a range of activities (from 915 nmol of cholate released per mg of protein per 30 min to none detected). All of the strains tested colonized the murine gastrointestinal tract equally well. The growth rates of mice were not affected by colonization of their intestinal tracts by lactobacilli whether or not the bacteria produced bile salt hydrolase.
Clostridium cellulolyticum Viability and Sporulation under Cellobiose Starvation Conditions
Authors: Gehin A , Gelhaye E , Raval G , Petitdemange H
Published: January 2020

Depending on the moment of cellobiose starvation, Clostridium cellulolyticum cells behave in different ways. Cells starved during the exponential phase of growth sporulate at 30%, whereas exhaustion of the carbon substrate at the beginning of growth does not provoke cell sporulation. Growth in the presence of excess cellobiose generates 3% spores. The response of C. cellulolyticum to carbon starvation involves changes in proteolytic activities; higher activities (20% protein degradation) corresponded to a higher level of sporulation; lower proteolysis (5%) was observed in cells starved during the beginning of exponential growth, when sporulation was not observed; with an excess of cellobiose, an intermediate value (10%), accompanied by a low level of sporulation, was observed in cells taken at the end of the exponential growth phase. The basal percentage of the protein breakdown in nonstarved culture was 4%. Cells lacking proteolytic activities failed to induce sporulation. High concentrations of cellobiose repressed proteolytic activities and sporulation. The onset of carbon starvation during the growth phase affected the survival response of C. cellulolyticum via the sporulation process and also via cell-cellulose interaction. Cells from the exponential growth phase were more adhesive to filter paper than cells from the stationary growth phase but less than cells from the late stationary growth phase.
Characterization and substrate specificity of an endo-beta-1,4-D-glucanase I (Avicelase I) from an extracellular multienzyme complex of Bacillus circulans
Authors: Kim C H
Published: January 2020

An endo-1,4-beta-D-glucanase I (Avicelase I; EC 3.2.1.4) was purified to homogeneity from an extracellular celluloxylanosome of Bacillus circulans F-2. The purification in the presence of 6 M urea yielded homogeneous enzyme. The enzyme had a monomeric structure, its relative molecular mass being 75 kDa as determined by gel filtration and 82 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The pI was 5.4, and the N-terminal amino acid sequence was ASNIGGWVGGNESGFEFG. The optimal pH was 4.5, and the enzyme was stable at pH 4 to 10. The enzyme has a temperature optimum of 50 degrees C, it was stable at 55 degrees C for 46 h, and it retains approximately 20% of its activity after 30 min at 80 degrees C. It showed high-level activity towards carboxymethyl cellulose (CMC) as well as p-nitrophenyl-beta-D-cellobioside, 4-methylumbelliferyl cellobioside, xylan, Avicel, filter paper, and some cello-oligosaccharides. Km values for birch xylan, CMC, and Avicel were 4.8, 7.2, and 87.0 mg/ml, respectively, while Vmax values were 256, 210, and 8.6 mumol x min-1 x mg-1, respectively. Cellotetraose was preferentially cleaved into cellobiose (G2) plus G2, and cellopentaose was cleaved into G2 plus cellotriose (G3), while cellohexaose was cleaved into cellotetraose plus G2 and to a lesser extent G3 plus G3. G3 was not cleaved at all. G2 was the main product of Avicel hydrolysis. Xylotetraose (X4) and xylobiose (X2) were mainly produced by the enzyme hydrolysis of xylan. G2 inhibited the activity of carboxymethyl cellulase and Avicelase, whereas Mg2+ stimulated it. The enzyme was completely inactivated by Hg2+, and it was inhibited by a thiol-blocking reagent. Hydrolysis of CMC took place, with a rapid decrease in viscosity but a slow liberation of reducing sugars. On the basis of these results, it appeared that the cellulase should be regarded as endo-type cellulase, although it hydrolyzed Avicel.
Suppression of Listeria monocytogenes colonization following adsorption of nisin onto silica surfaces
Authors: Bower C K , McGuire J , Daeschel M A
Published: January 2020

Nisin is an antimicrobial peptide proven to be an effective inhibitor of gram-positive bacteria. It is known that nisin can adsorb to various surfaces and still retain much of its original activity (M. A. Daeschel, J. McGuire, and H. Al-Makhlafi, J. Food Prot. 55:731-735, 1992). In this study, nisin films were allowed to form on silanized silica surfaces and then exposed to medium containing Listeria monocytogenes. Representative areas were selected from each surface, and images of resident listeriae were obtained at 4-h intervals for 12 h. During this time, cells on surfaces that had been in contact with a high concentration of nisin (1.0 mg/ml) exhibited no signs of growth and many displayed evidence of cellular deterioration. Surfaces treated with a lower concentration of nisin (0.1 mg/ml) had a smaller degree of inhibition. In contrast, both protein-free surfaces and those with films of heat-inactivated nisin allowed attached L. monocytogenes cells to grow and reproduce. These studies, when repeated with a nisin-resistant strain of L. monocytogenes, resulted in no inhibition of growth on surfaces with adsorbed nisin. The bactericidal effect of adsorbed nisin was also studied with iodonitrotetrazolium violet, a tetrazolium salt, which is reduced to a red formazan crystal by viable bacteria. Crystals were visible in 95% of the cells adhered to control surfaces but were present in less than 20% of the cells on surfaces with adsorbed nisin. These data indicate that adsorbed nisin may have potential for use as a food grade antimicrobial agent on food contact surfaces.
Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences
Authors: Robison-Cox J F , Bateson M M , Ward D M
Published: January 2020

Detection of chimeric artifacts formed when PCR is used to retrieve naturally occurring small-subunit (SSU) rRNA sequences may rely on demonstrating that different sequence domains have different phylogenetic affiliations. We evaluated the CHECK_CHIMERA method of the Ribosomal Database Project and another method which we developed, both based on determining nearest neighbors of different sequence domains, for their ability to discern artificially generated SSU rRNA chimeras from authentic Ribosomal Database Project sequences. The reliability of both methods decreases when the parental sequences which contribute to chimera formation are more than 82 to 84% similar. Detection is also complicated by the occurrence of authentic SSU rRNA sequences that behave like chimeras. We developed a naive statistical test based on CHECK_CHIMERA output and used it to evaluate previously reported SSU rRNA chimeras. Application of this test also suggests that chimeras might be formed by retrieving SSU rRNAs as cDNA. The amount of uncertainty associated with nearest-neighbor analyses indicates that such tests alone are insufficient and that better methods are needed.