bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid method for direct extraction of DNA from soil and sediments
Authors: Tsai Y L , Olson B H
Published: January 2020

A rapid method for the direct extraction of DNA from soil and sediments was developed. The indigenous microorganisms in the soil and sediments were lysed by using lysozyme and a freeze-thaw procedure. The lysate was extracted with sodium dodecyl sulfate and phenol-chloroform. In addition to a high recovery efficiency (greater than 90%), the yields of DNA were high (38 and 12 micrograms/g [wet weight] from sediments and soil, respectively). This method generated minimal shearing of the extracted DNA. The crude DNA could be further purified with an Elutip-d column if necessary. An additional advantage of this method is that only 1 g of sample is required, which allows for the analysis of small samples and the processing of many samples in a relatively short (7 h) period.
Oxidation of Aromatic Aldehydes by
Serratia marcescens
Authors: de la Fuente G. , Perestelo F. , Rodríguez-Pérez A. , Falcón M. A.
Published: January 2020

Cell suspensions of
Serratia marcescens
catalyzed the oxidation of aromatic aldehydes into the corresponding acids in high yield under mild conditions.
The Fe
2+
Chelator Proferrorosamine A Is Essential for the Siderophore-Mediated Uptake of Iron by
Pseudomonas roseus fluorescens
Authors: Vande Woestyne Marleen , Bruyneel Bart , Mergeay Max , Verstraete Willy
Published: January 2020

Pseudomonas roseus fluorescens
produces, besides the Fe
2+
chelator proferrorosamine A, Fe
3+
-chelating compounds, called siderophores. The production of proferrorosamine A and siderophores by
P. roseus fluorescens
appears to be controlled in a similar way by the concentration of available iron and by the concentration of dissolved oxygen. The higher the concentration of iron available for the microorganism, the lower the production of both chelating compounds. However, the production of siderophores was much more sensitive to iron availability than was proferrorosamine A production. Proferrorosamine A and siderophores were only produced in minimal medium C if the concentration of dissolved oxygen ranged from 4.5 to 2.0 ppm. At higher or lower concentrations, none of the iron-chelating compounds were produced. Furthermore, it has been shown that proferrorosamine-negative Tn
5
mutants of
P. roseus fluorescens
were able to form siderophores only under iron-limiting conditions when proferrorosamine A was added to the medium. Our data suggest that proferrorosamine A production is essential for siderophore synthesis by
P. roseus fluorescens
; the production of siderophores occurred only when proferrorosamine A was present.
Detection of luciferase gene sequence in nonluminescent Vibrio cholerae by colony hybridization and polymerase chain reaction
Authors: Palmer L M , Colwell R R
Published: January 2020

Bioluminescence is a trait observed among approximately 10% of Vibrio cholerae isolates. We have demonstrated that not only do some strains of V. cholerae produce low levels of light, undetectable by the human eye, but the luciferase gene sequence is present in strains of V. cholerae which emit no detectable light, evidenced by hybridization with a luciferase DNA probe. Comparisons of the amino acid sequences of luciferase enzymes of marine species have shown that these proteins have diverged to the point where they have only short regions of amino acid identity. The polymerase chain reaction method of DNA amplification with oligonucleotide primers based on these regions was used to isolate a region of the luxA gene from both luminescent and nonluminescent V. cholerae strains. The nucleotide sequence of this region was determined and reveals that nonluminescent V. cholerae have 99.7% nucleotide sequence similarity in this region with the luminescent biovar V. cholerae bv. albensis as well as significant similarity to other species of bioluminescent bacteria, a finding that is in accord with the hypothesis that these species have a common luminescent ancestor, most probably from the marine environment.
Immunofluorescence and morphology of Giardia lamblia cysts exposed to chlorine
Authors: Sauch J F , Berman D
Published: January 2020

Giardia cyst-like objects detected by immunofluorescence in chlorinated water samples often cannot be positively identified by their morphological appearance. To determine the effect of chlorine on cyst immunofluorescence and morphology, Giardia lamblia cysts were exposed to chlorine for 48 h. The majority of cysts exposed to chlorine concentrations of 1 to 11 mg/liter at 5 and 15 degrees C lost their internal morphological characteristics necessary for identification, but most of them were still detectable by immunofluorescence.
A Bacteroides ovatus chromosomal locus which contains an alpha-galactosidase gene may be important for colonization of the gastrointestinal tract
Authors: Valentine P J , Gherardini F C , Salyers A A
Published: January 2020

An alpha-galactosidase gene has been cloned from the human colonic Bacteroides species Bacteroides ovatus 0038. This alpha-galactosidase appears to be distinct from two previously characterized alpha-galactosidases, I and II, from the same strain and has been designated alpha-galactosidase III. Partially purified alpha-galactosidase III from Escherichia coli EM24 containing pFG61 delta SE had a pI of 7.6, as compared with the reported pI values for the known alpha-galactosidases of 5.6 for I and 6.9 for II. Its molecular weight as estimated on sodium dodecyl sulfate-polyacrylamide gels was 78,000, whereas the molecular weights of alpha-galactosidases I and II were 85,000 and 80,500, respectively. The only substrate hydrolyzed by alpha-galactosidase III was melibiose, whereas the other two alpha-galactosidases were able to degrade melibiose, raffinose, and stachyose and partially degraded guar gum. alpha-Galactosidase III had a pH optimum of 6.7 to 7.2. Finally, a single crossover insertion which disrupted the gene in the B. ovatus chromosome had no effect on expression of alpha-galactosidases I and II. Although this insertion had no effect on the ability of B. ovatus to grow in laboratory medium on any of the galactoside-containing carbohydrates tested, the insertion mutant was outcompeted by wild type when a combination of mutant and wild type was used to colonize germfree mice. Insertions on either side of the gene had the same effect. Thus, the locus which contains alpha-galactosidase III may be important for colonization in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)
Anaerobic biodegradation of cyanide under methanogenic conditions
Authors: Fallon R D , Cooper D A , Speece R , Henson M
Published: January 2020

Upflow, anaerobic, fixed-bed, activated charcoal biotreatment columns capable of operating at free cyanide concentrations of greater than 100 mg liter-1 with a hydraulic retention time of less than 48 h were developed. Methanogenesis was maintained under a variety of feed medium conditions which included ethanol, phenol, or methanol as the primary reduced carbon source. Under optimal conditions, greater than 70% of the inflow free cyanide was removed in the first 30% of the column height. Strongly complexed cyanides were resistant to removal. Ammonia was the nitrogen end product of cyanide transformation. In cell material removed from the charcoal columns, [14C]bicarbonate was the major carbon end product of [14C]cyanide transformation.
Bacteriocin-Producing Strain of
Lactococcus lactis
subsp.
diacitilactis
S50
Authors: Kojic M. , Svircevic J. , Banina A. , Topisirovic L.
Published: January 2020

Lactococcus lactis
subsp.
diacitilactis
S50 produces a bacteriocin, designated bacteriocin S50, which has a narrow antibacterial spectrum. It was active only against
Lactococcus
species, including a nisin producer exhibiting a bactericidal effect. The activity of bacteriocin S50 was sensitive to proteases. It retained antimicrobial activity after being heated to 100°C for up to 60 min and in the pH range 2 to 11.
Dye to use with virus challenge for testing barrier materials
Authors: Lytle C D , Felten R P , Truscott W
Published: January 2020

Can FD&C Blue no. 1 dye photoinactivate bacteriophages phi X174, T7, PRD1, and phi 6 under laboratory lighting conditions? At high levels of light, the dye (500 microM) photoinactivated only phi 6. Thus, this dye can be used at concentrations up to 500 microM with bacteriophages phi X174, T7, and PRD1 to test barrier material integrity.
Bacteriological composition and structure of granular sludge adapted to different substrates
Authors: Grotenhuis J T , Smit M , Plugge C M , Xu Y S , van Lammeren A A , Stams A J , Zehnder A J
Published: January 2020

The bacteriological composition and ultrastructure of mesophilic granular methanogenic sludge from a large-scale Upflow Anaerobic Sludge Blanket reactor treating wastewater from a sugar plant and of sludge granules adapted to ethanol and propionate were studied by counting different bacterial groups and by immunocytochemical methods. Propionate-grown granular sludge consisted of two types of clusters, those of a rod-shaped bacterium immunologically related to Methanothrix soehngenii and those consisting of two different types of bacteria with a specific spatial orientation. One of these bacteria reacted with antiserum against Methanobrevibacter arboriphilus AZ, whereas the other is most likely a propionate-oxidizing bacterium immunologically unrelated to Syntrophobacter wolinii. Sludge granules obtained from the large-scale Upflow Anaerobic Sludge Blanket reactor and granules cultivated on ethanol did not show the typical spatial orientation of bacteria. Examination of the bacterial composition of the three types of granules by light and electron microscopy, the most-probable-number method, and by isolations showed that M. arboriphilus and M. soehngenii were the most abundant hydrogenotrophic and acetoclastic methanogens in propionate-grown sludge. Methanospirillum hungatei and Methanosarcina barkeri predominated in ethanol-grown granules, whereas many morphotypes of methanogens were abundant in granules from the full-scale reactor.
Anaerobic Growth and Fermentation Characteristics of
Paecilomyces lilacinus
Isolated from Mullet Gut
Authors: Mountfort Douglas O. , Rhodes Lesley L.
Published: January 2020

The anaerobic growth and fermentation of a marine isolate of
Paecilomyces lilacinus
is described. The fungus was isolated from mullet gut and grew optimally at 30°C and at a salinity of ≥10%. The best growth was obtained with glucose or laminarin as substrate, and the growth yield was 5.0 g (dry weight of fungus) per mol of hexose fermented. Moles of products as a percentage of moles of hexose fermented were acetate, 29.0%; ethanol, 156.6%; CO
2
, 108.0%; and lactate, 4.3%. Together these products accounted for >80% of hexose carbon. Hydrogen and formate were not detectable as fermentation end products (<0.5%). Other substrates utilized for growth, although less effectively than laminarin or glucose, included the monosaccharides galactose, fructose, arabinose, and xylose and the disaccharides maltose and cellobiose. No growth of the fungus occurred on cellulose, and of a variety of other polysaccharides tested only xylan supported growth.
Comparison of cold enrichment and U.S. Department of Agriculture methods for isolating Listeria monocytogenes from naturally contaminated foods. The Listeria Study Group
Authors: Hayes P S , Graves L M , Ajello G W , Swaminathan B , Weaver R E , Wenger J D , Schuchat A , Broome C V
Published: January 2020

We compared the cold enrichment (CE) and U.S. Department of Agriculture (USDA) methods for isolating Listeria monocytogenes by examining 402 food samples. The food samples were collected from refrigerators of listeriosis patients as part of a multistate active surveillance project to determine the role of foods in sporadic listeriosis in the United States. L. monocytogenes was isolated from 51 food samples (13%). The USDA method was significantly better (P less than 0.001) than the CE method. The isolation efficiencies of the USDA and CE methods were 96 and 59%, respectively. Quantitation of L. monocytogenes in the food samples revealed that many food samples containing less than 0.3 CFU/g were negative as determined by the CE method but positive as determined by the USDA method.
Cholera enterotoxin production in Vibrio cholerae O1 strains isolated from the environment and from humans in Japan
Authors: Minami A , Hashimoto S , Abe H , Arita M , Taniguchi T , Honda T , Miwatani T , Nishibuchi M
Published: January 2020

Vibrio cholerae O1 strains isolated from various sources in Japan over the years 1977 through 1987 were examined to confirm the presence or absence of the cholera enterotoxin (CT) gene and production of CT and to determine the kappa-phage type. The CT gene was detected in none of 225 isolates from natural waters but was present in all of the 10 isolates from environmental waters implicated in domestic cholera cases, in 64 strains (26.6%) of the 241 isolates from imported seafoods, in 43 strains (95.6%) of the 45 isolates from domestic cholera cases, and in 119 strains (93.7%) of the 127 isolates from imported cholera cases. The results suggest that the CT gene-positive strains of V. cholerae O1 have been imported into Japan through seafoods and/or by travelers. Sporadic cholera cases have resulted in contamination of the surrounding environment, but the CT gene-positive strains may not have persisted in natural waters to serve as a reservoir for epidemic cholera. The commercially available VET-RPLA kit (a latex agglutination kit for immunological detection of CT) detected production of CT in all of the CT gene-positive strains, indicating that there was no silent CT gene in the test strains. There was a strong correlation between the kappa-phage type and the presence or absence of the CT gene, suggesting a significant clonal difference between CT gene-positive and -negative strains. Five CT gene-negative strains isolated from imported cholera cases (travelers with mild diarrhea) induced a considerable amount of fluid accumulation in rabbit and/or suckling mouse intestines, indicating production of an enterotoxic factor(s) other than CT.(ABSTRACT TRUNCATED AT 250 WORDS)
Chromosomal stabilization of the proteinase genes in Lactococcus lactis
Authors: Leenhouts K J , Gietema J , Kok J , Venema G
Published: January 2020

The plasmid-encoded proteinase genes prtP and prtM of Lactococcus lactis subsp. cremoris Wg2 were integrated by a Campbell-like mechanism into the L. lactis subsp. lactis MG1363 chromosome by using the insertion vector pKLG610. Two transformants were obtained that differed in the number of amplified pKLG610 copies in head-to-tail arrangements on their chromosomes; MG610 contained approximately two copies, and MG611 contained about eight copies. The amplifications were stably maintained during growth in milk in the absence of antibiotics. The proteolytic activity of strain MG611 was approximately 11-fold higher than that of strain MG610 and about 1.5 times higher than that of strain MG1363(pGKV552), which carried the proteinase genes on an autonomously replicating plasmid with a copy number of approximately 5. All three strains showed rapid growth in milk with concomitant rapid production of acid. The results suggest that a limited number of copies of the proteinase genes prtP and prtM per genome is sufficient for good growth in milk.
Degradation of substituted indoles by an indole-degrading methanogenic consortium
Authors: Gu J D , Berry D F
Published: January 2020

Degradation of indole by an indole-degrading methanogenic consortium enriched from sewage sludge proceeded through a two-step hydroxylation pathway yielding oxindole and isatin. The ability of this consortium to hydroxylate and subsequently degrade substituted indoles was investigated. Of the substituted indoles tested, the consortium was able to transform or degrade 3-methylindole and 3-indolyl acetate. Oxindole, 3-methyloxindole, and indoxyl were identified as metabolites of indole, 3-methylindole, and 3-indolyl acetate degradation, respectively. Isatin (indole-2,3-dione) was produced as an intermediate when the consortium was amended with oxindole, providing evidence that degradation of indole proceeded through successive hydroxylation of the 2- and 3-positions prior to ring cleavage between the C-2 and C-3 atoms on the pyrrole ring of indole. The presence of a methyl group (-CH3) at either the 1- or 2-position of indole inhibited the initial hydroxylation reaction. The substituted indole, 3-methylindole, was hydroxylated in the 2-position but not in the 3-position and could not be further metabolized through the oxindole-isatin pathway. Indoxyl (indole-3-one), the deacetylated product of 3-indolyl acetate, was not hydroxylated in the 2-position and thus was not further metabolized by the consortium. When an H atom or electron-donating group (i.e., -CH3) was present at the 3-position, hydroxylation proceeded at the 2-position, but the presence of electron-withdrawing substituent groups (i.e., -OH or -COOH) at the 3-position inhibited hydroxylation.
Production of an Amylase-Sensitive Bacteriocin by an Atypical
Leuconostoc paramesenteroides
Strain
Authors: Lewus Catherine B. , Sun Stephen , Montville Thomas J.
Published: January 2020

An atypical
Leuconostoc paramesenteroides
strain isolated from retail lamb produced a bacteriocin, leuconocin S, that was inactivated by α-amylase, trypsin, α-chymotrypsin, protease, and proteinase K but not by lipase or heat treatment at 60°C for 30 min. Supernatants from culture broths produced two glycoprotein bands on sodium dodecyl sulfate-polyacrylamide gels; these had molecular weights of 2,000 and 10,000 and activity against
Lactobacillus sake
ATCC 15521. The crude bacteriocin preparation was bacteriostatic and dissipated proton motive force. Bacteriocin activity was produced over a wide pH range (5.2 to 7.9) on buffered agar medium, with an optimum pH of pH 6.15. The optimum pH for production in broth was 6.5 to 7.0.
Purification, characterization, and mode of action of endoxylanases 1 and 2 from Fibrobacter succinogenes S85
Authors: Matte A , Forsberg C W
Published: January 2020

Two different endoxylanases (1,4-beta-D-xylan xylanohydrolases, EC 3.2.1.8), designated 1 and 2, have been purified by column chromatography to apparent homogeneity from the nonsedimentable extracellular culture fluid of the strictly anaerobic, ruminal bacterium Fibrobacter succinogenes S85 grown on crystalline cellulose. Endoxylanases 1 and 2 were shown to be basic proteins of 53.7 and 66.0 kDa, respectively, with different pH and temperature optima, as well as different substrate hydrolysis characteristics. The Km and Vmax values with water-soluble oat spelts xylan as substrate were 2.6 mg ml-1 and 33.6 mumol min-1 mg-1 for endoxylanase 1 and 1.3 mg ml-1 and 118 mumol min-1 mg-1 for endoxylanase 2. Endoxylanase 1, but not endoxylanase 2, released arabinose from water-soluble oat spelts xylan and rye flour arabinoxylan, but not from arabinan, arabinogalactan, or aryl-alpha-L-arabinofuranosides. With an extended hydrolysis time, endoxylanase 1 released 62.5 and 50% of the available arabinose from water-soluble oat spelts xylan and rye flour arabinoxylan, respectively. Endoxylanase 1 released arabinose directly from the xylan backbone, and this preceded hydrolysis of the xylan to xylooligosaccharides. Endoxylanase 2 showed significant activity against carboxymethyl cellulose but was unable to substantially hydrolyze acid-swollen cellulose. Both enzymes were endo-acting, as revealed by their hydrolysis product profiles on water-soluble xylan and xylooligosaccharides. Because of their unique hydrolytic properties, endoxylanases 1 and 2 appear to have strategic roles in plant cell wall digestion by F. succinogenes in vivo.
Denitrification, Dissimilatory Reduction of Nitrate to Ammonium, and Nitrification in a Bioturbated Estuarine Sediment as Measured with
15
N and Microsensor Techniques
Authors: Binnerup Svend Jørgen , Jensen Kim , Revsbech Niels Peter , Jensen Mikael Hjorth , Sørensen Jan
Published: January 2020

Nitrogen and oxygen transformations were studied in a bioturbated (reworked by animals) estuarine sediment (Norsminde Fjord, Denmark) by using a combination of
15
N isotope (NO
3
-
), specific inhibitor (C
2
H
2
), and microsensor (N
2
O and O
2
) techniques in a continuous-flow core system. The estuarine water was NO
3
-
rich (125 to 600 μM), and NO
3
-
was consistently taken up by the sediment on the four occasions studied. Total NO
3
-
uptake (3.6 to 34.0 mmol of N m
-2
day
-1
) corresponded closely to N
2
production (denitrification) during the experimental steady state, which indicated that dissimilatory, as well as assimilatory, NO
3
-
reduction to NH
4
+
was insignificant. When C
2
H
2
was applied in the flow system, denitrification measured as N
2
O production was often less (58 to 100%) than the NO
3
-
uptake because of incomplete inhibition of N
2
O reduction. The NO
3
-
formed by nitrification and not immediately denitrified but released to the overlying water, uncoupled nitrification, was calculated both from
15
NO
3
-
dilution and from changes in NO
3
-
uptake before and after C
2
H
2
addition. These two approaches gave similar results, with rates ranging between 0 and 8.1 mmol of N m
-2
day
-1
on the four occasions. Attempts to measure total nitrification activity by the difference between NH
4
+
fluxes before and after C
2
H
2
addition failed because of non-steady-state NH
4
+
fluxes. The vertical distribution of denitrification and oxygen consumption was studied by use of N
2
O and O
2
microelectrodes. The N
2
O profiles measured during the experimental steady state were often irregularly shaped, and the buildup of N
2
O after C
2
H
2
was added was much too fast to be described by a simple diffusion model. Only bioturbation by a dense population of infauna could explain these observations. This was corroborated by the relationship between diffusive and total fluxes, which showed that only 19 to 36 and 29 to 62% of the total O
2
uptake and denitrification, respectively, were due to diffusion-reaction processes at the regular sediment surface, excluding animal burrows.
Involvement of a chlorobenzoate-catabolic transposon, Tn5271, in community adaptation to chlorobiphenyl, chloroaniline, and 2,4-dichlorophenoxyacetic acid in a freshwater ecosystem
Authors: Fulthorpe R R , Wyndham R C
Published: January 2020

A chlorobenzoate-catabolic transposon (Tn5271) was introduced on a conjugative plasmid (pBRC60) in the natural host, Alcaligenes sp. strain BR60, into lake water and sediment flowthrough microcosms. Experimental microcosms were exposed to micromolar levels of 3-chlorobenzoate, 4-chloroaniline, 2,4-dichlorophenoxyacetate, or 3-chlorobiphenyl. The populations of the host, BR60, and organisms carrying Tn5271 were monitored over a 100-day period by use of selective plate counts and the most-probable-number-DNA hybridization method. Populations of Tn5271-carrying bacteria were significantly higher in microcosms dosed with 3-chlorobenzoate, 4-chloroaniline, and 3-chlorobiphenyl than in the control microcosms, indicating that each of these chemicals exerts a selective force on this particular genotype in natural systems. The rates of 3-chlorobenzoate uptake and respiration correlated with Tn5271-carrying populations, as did the rates of 4-chloroaniline uptake and respiration. Plasmid transfer in the 3-chlorobenzoate- and 3-chlorobiphenyl-dosed microcosms resulted in the selection of three phenotypic clusters of chlorobenzoate degraders, only one of which was closely related to the original pBRC60 (Tn5271) donor, Alcaligenes sp. strain BR60. Bacteria dominating 4-chloroaniline-dosed microcosms carried IS1071, the class II insertion sequence that brackets Tn5271, on a plasmid unrelated to pBRC60. The importance of plasmid transfer and transposition during chemical adaptation is discussed.
Enrichment of Thermophilic Propionate-Oxidizing Bacteria in Syntrophy with
Methanobacterium thermoautotrophicum
or
Methanobacterium thermoformicicum
Authors: Stams Alfons J. M. , Grolle Katja C. F. , Frijters Carla T. M. , Van Lier Jules B.
Published: January 2020

Thermophilic propionate-oxidizing, proton-reducing bacteria were enriched from the granular methanogenic sludge of a bench-scale upflow anaerobic sludge bed reactor operated at 55°C with a mixture of volatile fatty acids as feed. Thermophilic hydrogenotrophic methanogens had a high decay rate. Therefore, stable, thermophilic propionate-oxidizing cultures could not be obtained by using the usual enrichment procedures. Stable and reproducible cultivation was possible by enrichment in hydrogen-pregrown cultures of
Methanobacterium thermoautotrophicum
ΔH which were embedded in precipitates of FeS, achieved by addition of FeCl
2
to the media. The propionate-oxidizing bacteria formed spores which resisted pasteurization for 30 min at 90°C or 10 min at 100°C. Highly purified cultures were obtained with either
M. thermoautotrophicum
ΔH or
Methanobacterium thermoformicicum
Z245 as the syntrophic partner organism. The optimum temperature for the two cultures was 55°C. Maximum specific growth rates of cultures with
M. thermoautotrophicum
ΔH were somewhat lower than those of cultures with
M. thermoformicicum
Z245 (0.15 and 0.19 day
-1
, respectively). Growth rates were even higher (0.32 day
-1
) when aceticlastic methanogens were present as well.
M. thermoautotrophicum
ΔH is an obligately hydrogen-utilizing methanogen, showing that interspecies hydrogen transfer is the mechanism by which reducing equivalents are channelled from the acetogens to this methanogen. Boundaries of hydrogen partial pressures at which propionate oxidation occurred were between 6 and 34 Pa. Formate had a strong inhibitory effect on propionate oxidation in cultures with
M. thermoautotrophicum.
Inhibition by formate was neutralized by addition of the formate-utilizing methanogen or by addition of fumarate. Results indicate that formate inhibited succinate oxidation to fumarate, an intermediate step in the biochemical pathway of propionate oxidation.
Specific detection of Clostridium botulinum type B by using the polymerase chain reaction
Authors: Szabo E A , Pemberton J M , Desmarchelier P M
Published: January 2020

The polymerase chain reaction (PCR) and a radiolabeled oligonucleotide probe were used to specifically detect proteolytic and nonproteolytic Clostridium botulinum type B. Two synthetic primers deduced from the amino acid sequence data of type B neurotoxin were used to amplify a 1.5-kbp fragment corresponding to the light chain of the toxin. Although, nonspecific priming was observed when the PCR protocol was tested with other clostridial species, only the PCR product from C. botulinum type B isolates reacted with the radiolabeled internal probe. As little as 100 fg of DNA (approximately 35 clostridial cells) could be detected after only 25 amplification cycles.
Diurnal Cycles of Sulfate Reduction under Oxic Conditions in Cyanobacterial Mats
Authors: Fründ Claudia , Cohen Yehuda
Published: January 2020

Diurnal cycles of sulfate reduction were examined in a well-developed cyanobacterial mat which grew in an outdoor experimental hypersaline pond system at a constant salinity of 75 ± 5% for 3 years. Vertical profiles of sulfate reduction were determined for the upper 12 mm of the microbial mat. Sulfate reduction activities were compared with diurnal variations of oxygen and sulfide concentrations measured by microelectrodes. Significant activity of sulfate-reducing bacteria was detected under aerobic conditions during the daytime, with maximal activity at 2 p.m. When comparing sulfate reduction activities in sediment cores taken at 6 a.m. and 12 a.m. and incubated at a constant temperature in the light and in the dark, a distinct stimulation of the activity in the vertical profile of sulfate reduction by light was evident. It is therefore concluded that the maximal in situ activities, measured at 2 p.m. in the chemocline of the cyanobacterial mat, cannot be attributed to diurnal changes of temperature alone. The response of sulfate-reducing bacteria to the addition of specific carbon sources was significantly different in the cyanobacterial layer, the anoxygenic phototrophic bacterial layer, and the permanently reduced layer of the microbial mat. Sulfate reduction in the mat layer exposed to high oxygen concentrations as a result of cyanobacterial oxygenic photosynthesis was enhanced only by glycolate; in the microzone where the chemocline is found during the daytime, ethanol was the only carbon source to enhance sulfate reduction, while both ethanol and lactate enhanced this activity in the permanently reduced zone.
Phenotypic, antigenic, and molecular characterization of Pasteurella piscicida strains isolated from fish
Authors: Magariños B , Romalde J L , Bandín I , Fouz B , Toranzo A E
Published: January 2020

We compared Pasteurella piscicida strains isolated from different fish species in several European countries with strains isolated in Japan and the United States. The taxonomic analysis revealed that, regardless of the geographic origin and source of isolation, all the strains exhibited the same biochemical and physiological characteristics. Serological assays with different rabbit antisera demonstrated a high level of antigenic similarity among strains, with cross-agglutination titers of 20,480 to 40,960. This serological homogeneity was supported by the lipopolysaccharide (LPS) and membrane protein profiles. All the P. piscicida strains had the same electrophoretic LPS pattern, showing O side chains with a ladder-like structure, and shared at least four major outer membrane proteins, of 20, 30, 42, and 53 kDa. Western blot (immunoblot) analysis with LPS and protein indicated that all the P. piscicida strains are immunologically related. In addition, the chromosomal DNA fingerprint patterns obtained for the European strains with the enzymes EcoRI and BamHI were practically identical to those of the Japanese and U.S. strains. Although some differences were found in the plasmid profiles of P. piscicida, a large number of strains possessed in common plasmid bands of 20 and 7 MDa. In addition, a plasmid of 50 MDa was present in the majority of the European strains. Restriction endonuclease analysis demonstrated the genetic homology of the plasmid bands shared by most of the European strains. All the P. piscicida strains had the same drug resistance patterns, indicating that a correlation between plasmid carriage and resistance to a specific antimicrobial agent cannot be established. The high levels of phenotypic, serological, and genetic homogeneity found among the P. piscicida strains should facilitate the development of DNA probes with diagnostic purposes as well as the design of effective vaccines.
Microbial transformation of benzocyclobutene to benzocyclobutene-1-ol and benzocyclobutene-1-one
Authors: Swanson P E
Published: January 2020

Oxidation of benzocyclobutene by intact cells of Pseudomonas fluorescens 127-68 XVII, containing naphthalene dioxygenase, yielded exclusively benzylic oxidation products; benzocyclobutene-1-ol and benzocyclobutene-1-one. No evidence for incorporation of oxygen into the aromatic ring was found.
A
Lactobacillus helveticus
-Specific DNA Probe Detects Restriction Fragment Length Polymorphisms in This Species
Authors: de los Reyes-Gavilán Clara G. , Limsowtin Gaëtan K. Y. , Tailliez Patrick , Séchaud Laurent , Accolas Jean-Pierre
Published: January 2020

A cloned 2-kb
Eco
RI fragment (fragment f) from a 34-kb plasmid of
Lactobacillus helveticus
CNRZ 1094 was shown by dot blot to specifically hybridize to total DNAs of 75
L. helveticus
strains. No hybridization was found with
L. acidophilus, L. crispatus, L. delbrueckii
subsp.
bulgaricus, L. delbrueckii
subsp.
lactis, L. gasseri
, or
L. intestinalis
strains. When Southern blots of
Eco
RI digests of
L. helveticus
strains were probed with fragment f, these strains displayed restriction fragment length polymorphisms on the basis of which they could be grouped into several clusters.
Xylanase Activity of
Phanerochaete chrysosporium
Authors: Dobozi M�ria Szak�cs , Szak�cs Gy�rgy , Bruschi Carlo V.
Published: January 2020

Xylan-degrading enzymes were induced when
Phanerochaete chrysosporium
was grown at 30�C in shake flask media containing xylan, Avicel PH 102, or ground corn stalks. The highest xylanase activity was produced in the corn stalk medium, while the xylan-based fermentation resulted in the lowest induction. Analytical and preparative isoelectric focusing were used to characterize xylanase multienzyme components. Preparative focusing was performed only with the cultures grown on Avicel and corn stalk. Of over 30 protein bands separated by analytical focusing from the Avicel and corn stalk media, three main groups (I, II, and III) of about five isoenzymes each showed xylanase activity when a zymogram technique with a xylan overlay was used. Enzyme assays revealed the presence of 1,4-β-endoxylanase and arabinofuranosidase activities in all three isoenzyme groups separated by preparative isoelectric focusing. β-Xylosidase activity appeared in the first peak and also as an independent peak between peaks II and III. Denatured molecular masses for the three isoenzyme groups were found to be between 18 and 90 kDa, and pI values were in the range of 4.2 to 6.0. β-Xylosidase has an apparent molecular mass of 20, 30, and 90 kDa (peak I) and 18 and 45 kDa (independent peak), indicating a trimer and dimer structure, respectively, with pI values of 4.2 and 5.78, respectively. Three more minor xylanase groups were produced on corn stalk medium: a double peak in the acidic range (pI 6.25 to 6.65 and 6.65 to 7.12) and two minor peaks in the alkaline range (pI 8.09 to 8.29 and 9.28 to 9.48, respectively). The profile of xylanases separated by isoelectric focusing (zymogram) of culture filtrate from cells grown on corn stalk media was more complex than that of culture supernatants from cells grown on cellulose. The pH optima of the three major xylanase groups are in the range of pH 4 to 5.5.
Activity of glutaraldehyde at low concentrations against capsid proteins of poliovirus type 1 and echovirus type 25
Authors: Chambon M , Bailly J L , Peigue-Lafeuille H
Published: January 2020

The activity of glutaraldehyde (GTA) against capsid proteins of poliovirus type 1 and echovirus type 25 was studied to understand the mode of action of this reagent against enteroviruses. The viruses were treated with GTA concentrations ranging from 0.005 to 0.10%. In the poliovirus particles, high-molecular-weight products were formed by 0.05% GTA, whereas in the echovirus particles, they were formed at 0.005% GTA. These products consist of complexes composed essentially of VP1 and VP3. There seemed to be differences in the composition of the complexes in the two viruses. Cross-linkings between the two polypeptides of the poliovirus capsid may be due to the accessibility to GTA of lysine residues on the loops of VP1 and VP3, which twist out from the surface of the shell.
Purification and partial characterization of two feruloyl esterases from the anaerobic fungus Neocallimastix strain MC-2
Authors: Borneman W S , Ljungdahl L G , Hartley R D , Akin D E
Published: January 2020

Two extracellular feruloyl esterases (FAE-I and FAE-II) produced by the anaerobic fungus Neocallimastix strain MC-2 which cleave ferulic acid from O-(5-O-[(E)-feruloyl]-alpha-L- arabinofuranosyl)-(1-->3)-O-beta-D-xylopyranosyl-(1-->4)-D-xylopyranose (FAXX) were purified. The molecular masses of FAE-I and FAE-II were 69 and 24 kDa, respectively, under both denaturing and nondenaturing conditions. Apparent Km and maximum rate of hydrolysis with FAXX were 31.9 microM and 2.9 mumol min-1 mg-1 for FAE-I and 9.6 microM and 11.4 mumol min-1 mg-1 for FAE-II. FAE-II was specific for FAXX, but FAE-I hydrolyzed FAXX and PAXX, the equivalent p-coumaroyl ester, at a maximum rate of metabolism ratio of 3:1.
Alteration of specific activity and stability of thermostable neutral protease by site-directed mutagenesis
Authors: Kubo M , Mitsuda Y , Takagi M , Imanaka T
Published: January 2020

On the basis of three-dimensional information, many amino acid substitutions were introduced in the thermostable neutral protease (NprM) of Bacillus stearothermophilus MK232 by site-directed mutagenesis. When Glu at position 143 (Glu-143), which is one of the proposed active sites, was substituted for by Gln and Asp, the proteolytic activity disappeared. F114A (Phe-114 to Ala), Y110W (Tyr-110 to Trp), and Y211W (Tyr-211 to Trp) mutant enzymes had higher activity (1.3- to 1.6-fold) than the wild-type enzyme. When an autolysis site, Tyr-93, was replaced by Gly and Ser, the remaining activities of those mutant enzymes were higher than that of the wild-type enzyme.
Biphenomycin A production by a mixed culture
Authors: Ezaki M , Iwami M , Yamashita M , Komori T , Umehara K , Imanaka H
Published: January 2020

Production of biphenomycin A by Streptomyces griseorubiginosus 43708 was stimulated by a mixed culture with a partner strain, Pseudomonas maltophilia 1928. This stimulatory effect on biphenomycin A accumulation by the mixed culture was caused by the enzyme activity which strain 1928 possessed. It is suggested that in a mixed culture strain 43708 produces a precursor of biphenomycin A in culture broth and that strain 1928 converts the precursor to biphenomycin A.
Cyclization characteristics of cyclodextrin glucanotransferase are conferred by the NH2-terminal region of the enzyme
Authors: Fujiwara S , Kakihara H , Woo K B , Lejeune A , Kanemoto M , Sakaguchi K , Imanaka T
Published: January 2020

Cyclodextrin glucanotransferase (CGTase; EC 2.4.1.19) is produced mainly by Bacillus strains. CGTase from Bacillus macerans IFO3490 produces alpha-cyclodextrin as the major hydrolysis product from starch, whereas thermostable CGTase from Bacillus stearothermophilus NO2 produces alpha- and beta-cyclodextrins. To analyze the cyclization characteristics of CGTase, we cloned different types of CGTase genes and constructed chimeric genes. CGTase genes from these two strains were cloned in Bacillus subtilis NA-1 by using pTB523 as a vector plasmid, and their nucleotide sequences were determined. Three CGTase genes (cgt-1, cgt-5, and cgt-232) were isolated from B. stearothermophilus NO2. Nucleotide sequence analysis revealed that the three CGTase genes have different nucleotide sequences encoding the same amino acid sequence. Base substitutions were found at the third letter of five codons among the three genes. Each open reading frame was composed of 2,133 bases, encoding 711 amino acids containing 31 amino acids as a signal sequence. The molecular weight of the mature enzyme was estimated to be 75,374. The CGTase gene (cgtM) of B. macerans IFO3490 was composed of 2,142 bases, encoding 714 amino acids containing 27 residues as a signal sequence. The molecular weight of the mature enzyme was estimated to be 74,008. The sequence determined in this work was quite different from that reported previously by other workers. From data on the three-dimensional structure of a CGTase, seven kinds of chimeric CGTase genes were constructed by using cgt-1 from B. stearothermophilus NO2 and cgtM from B. macerans IFO3490. We examined the characteristics of these chimeric enzymes on cyclodextrin production and thermostability. It was found that the cyclization reaction was conferred by the NH2-terminal region of CGTase and that the thermostability of some chimeric enzymes was lower than that of the parental CGTases.
Subculturing of a polychlorinated biphenyl-dechlorinating anaerobic enrichment on solid media
Authors: May H D , Boyle A W , Price W A , Blake C K
Published: January 2020

An anaerobic culture capable of dechlorinating polychlorinated biphenyls was subcultured under strict anaerobic conditions on solid media containing sterilized river sediment. The dechlorination activity was transferred as a bacterial colony on a solid medium three times. After two transfers on solid medium, the culture was no longer methanogenic but still dechlorinated a mixture of tri- and tetrachlorobiphenyls. This demonstrates that anaerobic bacteria are responsible for the polychlorinated biphenyl dechlorination and can be grown without polychlorinated biphenyl on solid media.
Production of Concentrated
Lactococcus lactis
subsp.
cremoris
Suspensions in Calcium Alginate Beads
Authors: Morin Nicole , Bernier-Cardou Michèle , Champagne Claude P.
Published: January 2020

The effect of simultaneous modification of medium composition and growth conditions on the production of
Lactococcus lactis
subsp.
cremoris
biomass in calcium alginate beads was studied by the response surface method. Statistical methods of data analysis for unbalanced experiments are illustrated. The media tested were whey, whey supplemented with yeast extract and/or meat extract, milk, and the commercial medium Gold Complete (Nordica). Fermentations were performed at 23°C under pH control (5.6, 6.0, 6.4, or 6.8). In one complete series, 1% CaCO
3
was added to the growth media. There were strong interactions between CaCO
3
and media, CaCO
3
and pH level, and CaCO
3
, media, and pH level. In media with CaCO
3
, all first-order interactions between media, pH, and sampling time were significant. The addition of CaCO
3
increased cell counts in whey-meat extract medium, but no significant difference was found with the other media. Uncoupling between growth and acidification occurred between 16 and 22 h. Highest counts were obtained on milk and Gold Complete (6 × 10
10
/g). In CaCO
3
-containing media, pH influenced cell counts only in whey and in Gold Complete (pH 5.6 and 6.0 giving the best results); pH also influenced the bead mass obtained at the end of the fermentation. Biomass production in alginate gels is proposed as a method of obtaining concentrated cell suspensions without centrifugation or filtration.
Anaerobic transformation and toxicity of trichlorophenols in a stable enrichment culture
Authors: Madsen T , Aamand H
Published: January 2020

The transformation and toxicity of trichlorophenols (TCPs) were studied with a methanogenic enrichment culture derived from sewage sludge. Transformation of TCPs rapidly resumed after heating of the culture at *) degrees C for 1 h, suggesting that the dechlorinating bacteria are spore-forming anaerobes. 2,4,6-TCP was rapidly dechlorinated via 2,4-dichlorophenol to 4-chlorophenol. During the transformation of 2,4,6-TCP, the most probable number of dechlorinating bacteria increased by 4 orders of magnitude. The most extensive dechlorination was observed in media with complex carbon sources such as yeast extract, peptone, and Casamino Acids, but glucose, galactose, and lactose were also used by the consortium. Experiments using chloramphenicol indicated that the reductive dechlorination of 2,4,6-TCP was regulated by an inducible enzyme system. The highest initial concentration at which dechlorination of 2,4,6-TCP was observed was 400 microM. 2,4,5-TCP and 3,4,5-TCP were dechlorinated to, respectively, 3,4-dichlorophenol and 3-chlorophenol at initial concentrations of less than or equal to 40 microM. Toxicity for the acid-producing and methanogenic bacteria in the consortium was a function of chemical structure, as the inhibition of these activities increased from 2,4,6-TCP, via 2,4,5-TCP, to 3,4,5,-TCP.
Purification and Characterization of Extracellular Pectinolytic Enzymes Produced by
Sclerotinia sclerotiorum
Authors: Riou Christine , Freyssinet Georges , Fevre Michel
Published: January 2020

An exopolygalacturonase (exoPG) and an exopolymethylgalacturonase (exoPMG) produced by
Sclerotinia sclerotiorum
have been purified by ammonium sulfate precipitation, gel filtration, and ion exchange chromatography. The exoPG and the exoPMG were purified 66- and 50-fold, respectively, by using a series of separation procedures that included ammonium sulfate precipitation and gel chromatography. Molecular masses of the native proteins were 68 kDa for exoPG and 140 kDa for exoPMG. The pH optima of the enzymes were about pH 5, and their optimum temperature was 45°C. Activities of both enzymes were inhibited by Hg
2+
, Zn
2+
, Cu
2+
, and
p
-chloromercuribenzoate. ExoPMG activity, in contrast to exoPG activity, was stimulated by Mn
2+
and Co
2+
. ExoPMG hydrolyzed only citrus pectin, while exoPG degraded sodium polygalacturonate and, to a lesser extent, citrus pectin. The exo mode of action of the enzymes was revealed by thin-layer chromatography of substrate hydrolysates. Antibodies raised against each purified protein exhibited no cross-reaction, thus confirming the biochemical specificities of the enzymes.
Molecular Cloning of the Tryptophan Operon from an
Aeromonas hydrophila
Freshwater Isolate
Authors: Anguita Juan , Rivero Octavio , Naharro Germán
Published: January 2020

A genomic library of
Aeromonas hydrophila
F9 was constructed by using pBR322 as a vector. From that, two DNA fragments (5.8 and 11.6 kb) were isolated containing genetic information to complement
trpA
and
trpB
defects (5.8-kb fragment) and to complement
trpA, trpB, trpC, trpD
, and
trpE
defects (11.6-kb fragment) in
Escherichia coli
mutants. Evidence of the existence of a secondary promoter is given.
Soluble methane monooxygenase component B gene probe for identification of methanotrophs that rapidly degrade trichloroethylene
Authors: Tsien H C , Hanson R S
Published: January 2020

Restriction fragment length polymorphisms, Western blot (immunoblot) analysis, and fluorescence-labelled signature probes were used for the characterization of methanotrophic bacteria as well as for the identification of methanotrophs which contained the soluble methane monooxygenase (MMO) gene and were able to degrade trichloroethylene (TCE). The gene encoding a soluble MMO component B protein from Methylosinus trichosporium OB3b was cloned. It contained a 2.2-kb EcoRI fragment. With this cloned component B gene as probe, methanotroph types I, II, and X and environmental and bioreactor samples were screened for the presence of the gene encoding soluble MMO. Fragments produced by digestion of DNA with rare cutting restriction endonucleases were separated by pulsed-field gel electrophoresis and transferred to Zeta-Probe membrane (Bio-Rad) for Southern blot analysis. Samples were also analyzed for the presence of soluble MMO by Western blot analysis and the ability to degrade TCE. The physiological groups of methanotrophs in each sample were determined by hybridizing cells with fluorescence-labelled signature probes. Among twelve pure or mixed cultures, DNA fragments of seven methanotrophs hybridized with the soluble MMO B gene probe. When grown in media with limited copper, all of these bacteria degraded TCE. All of them are type II methanotrophs. The soluble MMO component B gene of the type X methanotroph, Methylococcus capsulatus Bath, did not hybridize to the M. trichosporium OB3b soluble MMO component B gene probe, although M. capsulatus Bath also produces a soluble MMO.