bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Investigations of
Vibrio parahaemolyticus
in Oysters after Outbreaks in Washington, Texas, and New York (1997 and 1998)
Authors: DePaola Angelo , Kaysner Charles A. , Bowers John , Cook David W. 
Published: July 2002

ABSTRACT

Total
Vibrio parahaemolyticus
densities and the occurrence of pathogenic strains in shellfish were determined following outbreaks in Washington, Texas, and New York. Recently developed nonradioactive DNA probes were utilized for the first time for direct enumeration of
V. parahaemolyticus
in environmental shellfish samples.
V. parahaemolyticus
was prevalent in oysters from Puget Sound, Wash.; Galveston Bay, Tex.; and Long Island Sound, N.Y., in the weeks following shellfish-associated outbreaks linked to these areas. However, only two samples (one each from Washington and Texas) were found to harbor total
V. parahaemolyticus
densities exceeding the level of concern of 10,000 g
−1
. Pathogenic strains, defined as those hybridizing with
tdh
and/or
trh
probes, were detected in a few samples, mostly Puget Sound oysters, and at low densities (usually <10 g
−1
). Intensive sampling in Galveston Bay demonstrated relatively constant water temperature (27.8 to 31.7°C) and
V. parahaemolyticus
levels (100 to 1,000 g
−1
) during the summer. Salinity varied from 14.9 to 29.3 ppt. A slight but significant (
P
< 0.05) negative correlation (−0.25) was observed between
V. parahaemolyticus
density and salinity. Based on our data, findings of more than 10,000 g
−1
total
V. parahaemolyticus
or >10 g
−1
tdh
- and/or
trh
-positive
V. parahaemolyticus
in environmental oysters should be considered extraordinary.
Molecular Epidemiological Survey of
Listeria monocytogenes
in Seafoods and Seafood-Processing Plants
Authors: Rørvik Liv Marit , Aase Brit , Alvestad Torill , Caugant Dominique A. 
Published: July 2002

ABSTRACT

To evaluate the role of seafoods in the epidemiology of human listeriosis and the role of the processing environment as a source of
Listeria monocytogenes
in seafood products, 305
L. monocytogenes
isolates were characterized by multilocus enzyme electrophoresis using 21 genetic loci and restriction enzyme analysis of total DNA. Forty-four isolates were recovered from patients in Norway; 93 were isolated from seafoods, seafood-processing environments, and seawater from 55 different producers; and the remaining 168 isolates originated from six seafood-processing plants and one transport terminal examined in detail for
L. monocytogenes
. The patient isolates fell into 11 electrophoretic types, with four of them being responsible for 77% of the listeriosis cases in 1992 to 1996. Isolates from Norwegian seafoods and processing environments showed great genetic diversity, indicating that seafoods and seafood-processing environments do not offer a niche for specific
L. monocytogenes
strains. On the other hand, isolates from individual processing plants were genetically more homogenous, showing that plants are likely to be colonized with specific subclones of
L. monocytogenes
. The isolation of identical subclones of
L. monocytogenes
from both human patients and seafoods, including ready-to-eat products, suggests that such products may have been possible sources for listeriosis cases in Norway.
Effect of Temperature on Carbon and Electron Flow and on the Archaeal Community in Methanogenic Rice Field Soil
Authors: Fey Axel , Conrad Ralf 
Published: July 2002

ABSTRACT

Temperature is an important factor controlling CH
4
production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37°C or in a temperature gradient block covering the same temperature range at intervals of 1°C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH
4
production rates increased with temperature, with an apparent activation energy of 61 kJ mol
−1
. Steady-state partial pressures of the methanogenic precursor H
2
also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H
2
plus CO
2
-dependent methanogenesis was kept at −20 to −25 kJ mol of CH
4
−1
over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 μM. Simultaneously, the relative contribution of H
2
as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to
14
CH
4
, so that the carbon and electron flow to CH
4
was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal
Methanobacteriaceae
,
Methanomicrobiaceae
,
Methanosaetaceae
,
Methanosarcinaceae
, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and
Methanosaetaceae
were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring
Methanosarcinaceae
decreased and the more modest
Methanosaetaceae
increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.
Effects of Glucosinolates and Flavonoids on Colonization of the Roots of
Brassica napus
by
Azorhizobium caulinodans
ORS571
Authors: O'Callaghan Kenneth J. , Stone Philip J. , Hu Xiaojia , Griffiths D. Wynne , Davey Michael R. , Cocking Edward C. 
Published: July 2002

ABSTRACT

Plants of
Brassica napus
were assessed quantitatively for their susceptibility to lateral root crack colonization by
Azorhizobium caulinodans
ORS571(pXLGD4) (a rhizobial strain carrying the
lacZ
reporter gene) and for the concentration of glucosinolates in their roots by high-pressure liquid chromatography (HPLC). High- and low-glucosinolate-seed (HGS and LGS) varieties exhibited a relatively low and high percentage of colonized lateral roots, respectively. HPLC showed that roots of HGS plants contained a higher concentration of glucosinolates than roots of LGS plants. One LGS variety showing fewer colonized lateral roots than other LGS varieties contained a higher concentration of glucosinolates than other LGS plants. Inoculated HGS plants treated with the flavonoid naringenin showed significantly more colonization than untreated HGS plants. This increase was not mediated by a naringenin-induced lowering of the glucosinolate content of HGS plant roots, nor did naringenin induce bacterial resistance to glucosinolates or increase the growth of bacteria. The erucic acid content of seed did not appear to influence colonization by azorhizobia. Frequently, leaf assays are used to study glucosinolates and plant defense; this study provides data on glucosinolates and bacterial colonization in roots and describes a bacterial reporter gene assay tailored easily to the study of ecologically important phytochemicals that influence bacterial colonization. These data also form a basis for future assessments of the benefits to oilseed rape plants of interaction with plant growth-promoting bacteria, especially diazotrophic bacteria potentially able to extend the benefits of nitrogen fixation to nonlegumes.
Identification of thepgmGGene, Encoding a Bifunctional Protein with Phosphoglucomutase and Phosphomannomutase Activities, in the Gellan Gum-Producing StrainSphingomonas paucimobilisATCC 31461
Authors: Videira Paula A. , Cortes Luísa L. , Fialho Arsénio M. , Sá-Correia Isabel 
Published: July 2002

ABSTRACTThepgmGgene ofSphingomonas paucimobilisATCC 31461, the industrial gellan gum-producing strain, was cloned and sequenced. It encodes a 50,059-Da polypeptide that has phosphoglucomutase (PGM) and phosphomannomutase (PMM) activities and is 37 to 59% identical to other bifunctional proteins with PGM and PMM activities from gram-negative species, includingPseudomonas aeruginosaAlgC. Purified PgmG protein showed a marked preference for glucose-1-phosphate (G1P); the catalytic efficiency was about 50-fold higher for G1P than it was for mannose-1-phosphate (M1P). The estimated apparentKmvalues for G1P and M1P were high, 0.33 and 1.27 mM, respectively. ThepgmGgene allowed the recovery of alginate biosynthetic ability in aP. aeruginosamutant with a defectivealgCgene. This result indicates that PgmG protein can convert mannose-6-phosphate into M1P in the initial steps of alginate biosynthesis and, together with other results, suggests that PgmG may convert glucose-6-phosphate into G1P in the gellan pathway.
Isolation and Characterization of
Desulfovibrio dechloracetivorans
sp. nov., a Marine Dechlorinating Bacterium Growing by Coupling the Oxidation of Acetate to the Reductive Dechlorination of 2-Chlorophenol
Authors: Sun Baolin , Cole James R. , Sanford Robert A. , Tiedje James M. 
Published: July 2002

ABSTRACT

Strain SF3, a gram-negative, anaerobic, motile, short curved rod that grows by coupling the reductive dechlorination of 2-chlorophenol (2-CP) to the oxidation of acetate, was isolated from San Francisco Bay sediment. Strain SF3 grew at concentrations of NaCl ranging from 0.16 to 2.5%, but concentrations of KCl above 0.32% inhibited growth. The isolate used acetate, fumarate, lactate, propionate, pyruvate, alanine, and ethanol as electron donors for growth coupled to reductive dechlorination. Among the halogenated aromatic compounds tested, only the
ortho
position of chlorophenols was reductively dechlorinated, and additional chlorines at other positions blocked
ortho
dechlorination. Sulfate, sulfite, thiosulfate, and nitrate were also used as electron acceptors for growth. The optimal temperature for growth was 30°C, and no growth or dechlorination activity was observed at 37°C. Growth by reductive dechlorination was revealed by a growth yield of about 1 g of protein per mol of 2-CP dechlorinated, and about 2.7 g of protein per mole of 2,6-dichlorophenol dechlorinated. The physiological features and 16S ribosomal DNA sequence suggest that the organism is a novel species of the genus
Desulfovibrio
and which we have designated
Desulfovibrio dechloracetivorans
. The unusual physiological feature of this strain is that it uses acetate as an electron donor and carbon source for growth with 2-CP but not with sulfate.
Rapid Virus Production and Removal as Measured with Fluorescently Labeled Viruses as Tracers
Authors: Noble Rachel T. , Fuhrman Jed A. 
Published: July 2002

ABSTRACT

Pelagic marine viruses have been shown to cause significant mortality of heterotrophic bacteria, cyanobacteria, and phytoplankton. It was previously demonstrated, in nearshore California waters, that viruses contributed to up to 50% of bacterial mortality, comparable to protists. However, in less productive waters, rates of virus production and removal and estimates of virus-mediated bacterial mortality have been difficult to determine. We have measured rates of virus production and removal, in nearshore and offshore California waters, by using fluorescently labeled viruses (FLV) as tracers. Our approach is mathematically similar to the isotope dilution technique, employed in the past to simultaneously measure the release and uptake of ammonia and amino acids. The results indicated overall virus removal rates in the dark ranging from 1.8 to 6.2% h
−1
and production rates in the dark ranging from 1.9 to 6.1% h
−1
, corresponding to turnover times of virus populations of 1 to 2 days, even in oligotrophic offshore waters. Virus removal rates determined by the FLV tracer method were compared to rates of virus degradation, determined at the same locations by radiolabeling methods, and were similar even though the current FLV method is suitable for only dark incubations. Our results support previous findings that virus impacts on bacterial populations may be more important in some environments and less so in others. This new method can be used to determine rates of virus degradation, production, and turnover in eutrophic, mesotrophic, and oligotrophic waters and will provide important inputs for future investigations of microbial food webs.
Identification of
Bacillus thuringiensis
subsp.
kurstaki
Strain HD1-Like Bacteria from Environmental and Human Samples after Aerial Spraying of Victoria, British Columbia, Canada, with Foray 48B
Authors: Valadares de Amorim Giovana , Whittome Beatrixe , Shore Benjamin , Levin David B. 
Published: July 2002

ABSTRACT

Aerial applications of Foray 48B, which contains
Bacillus thuringiensis
strain HD1, were carried out on 9 to 10 May, 19 to 21 May, and 8 to 9 June 1999 to control European gypsy moth (
Lymantria dispar
) populations in Victoria, British Columbia, Canada. A major assessment of the health impact of
B. thuringiensis
subsp.
kurstaki
was conducted by the Office of the Medical Health Officer of the Capital Health Region during this period. Environmental (air and water) and human (nasal swab) samples, collected before and after aerial applications of Foray 48B, both in the spray zone and outside of the spray zone, were analyzed for the presence of strain HD1-like bacteria. Random amplified polymorphic DNA analysis,
cry
gene-specific PCR, and dot blot DNA hybridization techniques were used to screen over 11,000 isolates of bacteria. We identified bacteria with genetic patterns consistent with those of
B. thuringiensis
subsp.
kurstaki
HD1 in 9,102 of 10,659 (85.4%) isolates obtained from the air samples, 13 of 440 (2.9%) isolates obtained from the water samples, and 131 of 171 (76.6%) isolates from the nasal swab samples. These analyses suggest that
B. thuringiensis
subsp.
kurstaki
HD1-like bacteria were present both in the environment and in the human population of Victoria prior to aerial applications of Foray 48B. The presence of
B. thuringiensis
subsp.
kurstaki
HD1-like bacteria in human nasal passages increased significantly after the application of Foray 48B, both inside and outside the spray zone.
Identification of Methyl Halide-Utilizing Genes in the Methyl Bromide-Utilizing Bacterial Strain IMB-1 Suggests a High Degree of Conservation of Methyl Halide-Specific Genes in Gram-Negative Bacteria
Authors: Woodall Claire A. , Warner Karen L. , Oremland Ronald S. , Murrell J. Colin , McDonald Ian R. 
Published: July 2002

ABSTRACT

Strain IMB-1, an aerobic methylotrophic member of the alpha subgroup of the
Proteobacteria
, can grow with methyl bromide as a sole carbon and energy source. A single c
mu
gene cluster was identified in IMB-1 that contained six open reading frames:
cmuC, cmuA, orf146, paaE, hutI
, and partial
metF
. CmuA from IMB-1 has high sequence homology to the methyltransferase CmuA from
Methylobacterium chloromethanicum
and
Hyphomicrobium chloromethanicum
and contains a C-terminal corrinoid-binding motif and an N-terminal methyltransferase motif. However,
cmuB
, identified in
M. chloromethanicum
and
H. chloromethanicum,
was not detected in IMB-1.
Biogenic Magnetite Formation through Anaerobic Biooxidation of Fe(II)
Authors: Chaudhuri Swades K. , Lack Joseph G. , Coates John D. 
Published: July 2002

ABSTRACT
The presence of isotopically light carbonates in association with fine-grained magnetite is considered to be primarily due to the reduction of Fe(III) by Fe(III)-reducing bacteria in the environment. Here, we report on magnetite formation by biooxidation of Fe(II) coupled to denitrification. This metabolism offers an alternative environmental source of biogenic magnetite.
Survival of
Escherichia coli
O157:H7 ATCC 43895 in a Model Apple Juice Medium with Different Concentrations of Proline and Caffeic Acid
Authors: Reinders Robert D. , Biesterveld Steef , Bijker Peter G. H. 
Published: July 2002

ABSTRACT

The effects of proline and caffeic acid on the survival of Shiga toxin-producing
Escherichia coli
(STEC) O157:H7 strain ATCC 43895 in a model apple juice medium were studied. It is hypothesized that the inhibitory effect of caffeic acid may explain why almost all outbreaks of STEC O157:H7 infections linked to apple juice or cider have occurred in October or November.
Energy Yield of Respiration on Chloroaromatic Compounds in
Desulfitobacterium dehalogenans
Authors: van de Pas Bram A. , Jansen Stefan , Dijkema Cor , Schraa Gosse , de Vos Willem M. , Stams Alfons J. M. 
Published: July 2002

ABSTRACT

The amount of energy that can be conserved via halorespiration by
Desulfitobacterium dehalogenans
JW/IU-DC1 was determined by comparison of the growth yields of cells grown with 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) and different electron donors. Cultures that were grown with lactate, pyruvate, formate, or hydrogen as an electron donor and Cl-OHPA as an electron acceptor yielded 3.1, 6.6, 1.6, and 1.6 g (dry weight) per mol of reduction equivalents, respectively. Fermentative growth on pyruvate yielded 14 g (dry weight) per mol of pyruvate oxidized. Pyruvate was not fermented stoichiometrically to acetate and lactate, but an excess of acetate was produced. Experiments with
13
C-labeled bicarbonate showed that during pyruvate fermentation, approximately 9% of the acetate was formed from the reduction of CO
2
. Comparison of the growth yields suggests that 1 mol of ATP is produced per mol of acetate produced by substrate-level phosphorylation and that there is no contribution of electron transport phosphorylation when
D. dehalogenans
grows on lactate plus Cl-OHPA or pyruvate plus Cl-OHPA. Furthermore, the growth yields indicate that approximately 1/3 mol of ATP is conserved per mol of Cl-OHPA reduced in cultures grown in formate plus Cl-OHPA and hydrogen plus Cl-OHPA. Because neither formate nor hydrogen nor Cl-OHPA supports substrate-level phosphorylation, energy must be conserved through the establishment of a proton motive force. Pyruvate ferredoxin oxidoreductase, lactate dehydrogenase, formate dehydrogenase, and hydrogenase were localized by in vitro assays with membrane-impermeable electron acceptors and donors. The orientation of chlorophenol-reductive dehalogenase in the cytoplasmic membrane, however, could not be determined. A model is proposed, which may explain the topology analyses as well as the results obtained in the yield study.
Heteroduplex Panel Analysis, a Novel Method for Genetic Identification of
Aspergillus
Section
Flavi
Strains
Authors: Kumeda Yuko , Asao Tsutomu 
Published: July 2002

ABSTRACT

For genetic identification of
Aspergillus
Section
Flavi
isolates and detection of intraspecific variation, we developed a novel method for heteroduplex panel analysis (HPA) utilizing fragments of the internal transcribed spacer (ITS) regions (ITS1-5.8S-ITS2) of the rRNA gene that was PCR amplified with universal primers. The method involves formation of heteroduplexes with a set of reference fragments amplified from
Aspergillus flavus, A. parasiticus, A. tamarii
, and
A. nomius
and subsequent minislab vinyl polymer gel electrophoresis. The test panel is compared with species-specific standard panels (F-1, P-1, T-1, and N-1) generated by pairwise reannealing among four reference fragments. Of 90 test panels, 89 succeeded in identifying the species and 74 were identical to one of the four standard panels. Of the 16 new panels, 11
A. flavus/A. oryzae
panels were identical and typed as F-2 and 4 of 5
A. nomius
panels were typed as N-2 or N-3. The other strain,
A. nomius
IMI 358749, was unable to identify the species because no single bands were formed with any of the four reference strains. DNA sequencing revealed that our HPA method has the highest sensitivity available and is able to detect as little as one nucleotide of diversity within the species. When
Penicillium
or non-Section
Flavi Aspergillus
was subjected to HPA, the resulting bands of heteroduplexes showed apparently lower mobility and poor heteroduplex formation. This indicates that HPA is a useful identification method without morphological observation and is suitable for rapid and inexpensive screening of large numbers of isolates. The HPA typing coincided with the taxonomy of Section
Flavi
and is therefore applicable as an alternative to the conventional methods (Samson, R. A., E. S. Hoekstra, J. C. Frisvad, and O. Filtenborg, p. 64–97,
in Introduction to Food- and Airborne Fungi
, 6th ed., 2000).
Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (
cehA
) from
Rhizobium
sp. Strain AC100
Authors: Hashimoto Masayuki , Fukui Mitsuru , Hayano Kouichi , Hayatsu Masahito 
Published: July 2002

ABSTRACT

Rhizobium
sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-
N
-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (
cehA
) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing
cehA
. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the
cehA
gene. Six open reading frames including the
cehA
gene were found in the 10-kb region, and sequencing analysis shows that the
cehA
gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.
Influence of Medium Buffering Capacity on Inhibition ofSaccharomyces cerevisiaeGrowth by Acetic and Lactic Acids
Authors: Thomas K. C. , Hynes S. H. , Ingledew W. M. 
Published: July 2002

ABSTRACTAcetic acid (167 mM) and lactic acid (548 mM) completely inhibited growth ofSaccharomyces cerevisiaeboth in minimal medium and in media which contained supplements, such as yeast extract, corn steep powder, or a mixture of amino acids. However, the yeast grew when the pH of the medium containing acetic acid or lactic acid was adjusted to 4.5, even though the medium still contained the undissociated form of either acid at a concentration of 102 mM. The results indicated that the buffer pair formed when the pH was adjusted to 4.5 stabilized the pH of the medium by sequestering protons and by lessening the negative impact of the pH drop on yeast growth, and it also decreased the difference between the extracellular and intracellular pH values (ΔpH), the driving force for the intracellular accumulation of acid. Increasing the undissociated acetic acid concentration at pH 4.5 to 163 mM by raising the concentration of the total acid to 267 mM did not increase inhibition. It is suggested that this may be the direct result of decreased acidification of the cytosol because of the intracellular buffering by the buffer pair formed from the acid already accumulated. At a concentration of 102 mM undissociated acetic acid, the yeast grew to higher cell density at pH 3.0 than at pH 4.5, suggesting that it is the total concentration of acetic acid (104 mM at pH 3.0 and 167 mM at pH 4.5) that determines the extent of growth inhibition, not the concentration of undissociated acid alone.