bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quorum-Sensing System and Stationary-Phase Sigma Factor (
rpoS
) of the Onion Pathogen
Burkholderia cepacia
Genomovar I Type Strain, ATCC 25416
Authors: Aguilar Claudio , Bertani Iris , Venturi Vittorio 
Published: March 2003

ABSTRACT

Bacterial strains belonging to
Burkholderia cepacia
can be human opportunistic pathogens, plant pathogens, and plant growth promoting and have remarkable catabolic activity.
B. cepacia
consists of several genomovars comprising what is now known as the
B. cepacia
complex. Here we report the quorum-sensing system of a genomovar I onion rot type strain ATCC 25416. Quorum sensing is a cell-density-dependent regulatory response which involves the production of
N
-acyl homoserine lactone (HSL) signal molecules. The
cep
locus has been inactivated in the chromosome, and it has been shown that CepI is responsible for the biosynthesis of an
N
-hexanoyl HSL (C
6
-HSL) and an
N
-octanoyl HSL (C
8
-HSL) and that the
cep
locus regulates protease production as well as onion pathogenicity via the expression of a secreted polygalacturonase. A
cep
-
lacZ
-based sensor plasmid has been constructed and used to demonstrate that CepR responded to C
6
-HSL with only 15% of the molar efficiency of C
8
-HSL, that a
cepR
knockout mutant synthesized 70% less HSLs, and that CepR responded best towards long-chain HSLs. In addition, we also report the cloning and characterization of the stationary-phase sigma factor gene
rpoS
of
B. cepacia
ATCC 25416. It was established that quorum sensing in
B. cepacia
has a negative effect on
rpoS
expression as determined by using an
rpoS
-
lacZ
transcriptional fusion; on the other hand,
rpoS
-null mutants displayed no difference in the accumulation of HSL signal molecules.
In Situ Accessibility of Small-Subunit rRNA of Members of the Domains
Bacteria
,
Archaea
, and
Eucarya
to Cy3-Labeled Oligonucleotide Probes
Authors: Behrens Sebastian , Rühland Caroline , Inácio João , Huber Harald , Fonseca Á. , Spencer-Martins I. , Fuchs Bernhard M. , Amann Rudolf 
Published: March 2003

ABSTRACT

Low accessibility of the rRNA is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. In this study we compare accessibility data for the 16S rRNA of
Escherichia coli
(gamma
Proteobacteria
,
Bacteria
) with the phylogenetically distantly related organisms
Pirellula
sp. strain 1 (
Planctomycetes
,
Bacteria
) and
Metallosphaera sedula
(
Crenarchaeota
,
Archaea
) and the 18S rRNA accessibility of
Saccharomyces cerevisiae
(
Eucarya
). For a total of 537 Cy3-labeled probes, the signal intensities of hybridized cells were quantified under standardized conditions by flow cytometry. The relative probe-conferred fluorescence intensities are shown on color-coded small-subunit rRNA secondary-structure models. For
Pirellula
sp., most of the probes belong to class II and III (72% of the whole data set), whereas most of the probes targeting sites on
M. sedula
were grouped into class V and VI (46% of the whole data set). For
E. coli
, 45% of all probes of the data set belong to class III and IV. A consensus model for the accessibility of the small-subunit rRNA to oligonucleotide probes is proposed which uses 60 homolog target sites of the three prokaryotic 16S rRNA molecules. In general, open regions were localized around helices 13 and 14 including target positions 285 to 338, whereas helix 22 (positions 585 to 656) and the 3′ half of helix 47 (positions 1320 to 1345) were generally inaccessible. Finally, the 16S rRNA consensus model was compared to data on the in situ accessibility of the 18S rRNA of
S. cerevisiae
.
DNA Microarray Analyses of the Long-Term Adaptive Response ofEscherichia colito Acetate and Propionate
Authors: Polen T. , Rittmann D. , Wendisch V. F. , Sahm H. 
Published: March 2003

ABSTRACTIn its natural environment,Escherichia coliis exposed to short-chain fatty acids, such as acetic acid or propionic acid, which can be utilized as carbon sources but which inhibit growth at higher concentrations. DNA microarray experiments revealed expression changes during exponential growth on complex medium due to the presence of sodium acetate or sodium propionate at a neutral external pH. The adaptive responses to acetate and propionate were similar and involved genes in three categories. First, the RNA levels for chemotaxis and flagellum genes increased. Accordingly, the expression of chromosomalfliC′-′lacZandflhDC′-′lacZfusions and swimming motility increased after adaptation to acetate or propionate. Second, the expression of many genes that are involved in the uptake and utilization of carbon sources decreased, indicating some kind of catabolite repression by acetate and propionate. Third, the expression of some genes of the general stress response increased, but the increases were more pronounced after short-term exposure for this response than for the adaptive response. Adaptation to propionate but not to acetate involved increased expression of threonine and isoleucine biosynthetic genes. The gene expression changes after adaptation to acetate or propionate were not caused solely by uncoupling or osmotic effects but represented specific characteristics of the long-term response ofE. colito either compound.
Evaluation of a Rapid, Quantitative Real-Time PCR Method for Enumeration of Pathogenic
Candida
Cells in Water
Authors: Brinkman Nichole E. , Haugland Richard A. , Wymer Larry J. , Byappanahalli Muruleedhara , Whitman Richard L. , Vesper Stephen J. 
Published: March 2003

ABSTRACT

Quantitative PCR (QPCR) technology, incorporating fluorigenic 5′ nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of
Candida
(
C. albicans
,
C. tropicalis
,
C. krusei
,
C. parapsilosis
,
C. glabrata
and
C. lusitaniae
) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target
Candida
species detected in these analyses and colony counts of
Enterococcus
organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic
Candida
species from drinking and recreational waters and may have applications in the detection of fecal pollution.
Kinetics and Strain Specificity of Rhizosphere and Endophytic Colonization by Enteric Bacteria on Seedlings of
Medicago sativa
and
Medicago truncatula
Authors: Dong Yuemei , Iniguez A. Leonardo , Ahmer Brian M. M. , Triplett Eric W. 
Published: March 2003

ABSTRACT

The presence of human-pathogenic, enteric bacteria on the surface and in the interior of raw produce is a significant health concern. Several aspects of the biology of the interaction between these bacteria and alfalfa (
Medicago sativa
) seedlings are addressed here. A collection of enteric bacteria associated with alfalfa sprout contaminations, along with
Escherichia coli
K-12,
Salmonella enterica
serotype Typhimurium strain ATCC 14028, and an endophyte of maize,
Klebsiella pneumoniae
342, were labeled with green fluorescent protein, and their abilities to colonize the rhizosphere and the interior of the plant were compared. These strains differed widely in their endophytic colonization abilities, with
K. pneumoniae
342 and
E. coli
K-12 being the best and worst colonizers, respectively. The abilities of the pathogens were between those of
K. pneumoniae
342 and
E. coli
K-12. All
Salmonella
bacteria colonized the interiors of the seedlings in high numbers with an inoculum of 10
2
CFU, although infection characteristics were different for each strain. For most strains, a strong correlation between endophytic colonization and rhizosphere colonization was observed. These results show significant strain specificity for plant entry by these strains. Significant colonization of lateral root cracks was observed, suggesting that this may be the site of entry into the plant for these bacteria. At low inoculum levels, a symbiosis mutant of
Medicago truncatula
,
dmi1
, was colonized in higher numbers on the rhizosphere and in the interior by a
Salmonella
endophyte than was the wild-type host. Endophytic entry of
M. truncatula
appears to occur by a mechanism independent of the symbiotic infections by
Sinorhizobium meliloti
or mycorrhizal fungi.
Enhanced Accumulation of Cd
2+
by a
Mesorhizobium
sp. Transformed with a Gene from
Arabidopsis thaliana
Coding for Phytochelatin Synthase
Authors: Sriprang Rutchadaporn , Hayashi Makoto , Ono Hisayo , Takagi Masahiro , Hirata Kazumasa , Murooka Yoshikatsu 
Published: March 2003

ABSTRACT

We expressed the
Arabidopsis thaliana
gene for phytochelatin synthase (

PCS
At

) in
Mesorhizobium huakuii
subsp.
rengei
B3, a microsymbiont of
Astragalus sinicus
, a legume used as manure. The

PCS
At

gene was expressed under the control of the
nifH
promoter, which regulates the nodule-specific expression of the
nifH
gene. The expression of the

PCS
At

gene was demonstrated in free-living cells under low-oxygen conditions. Phytochelatin synthase (PCS) was expressed and catalyzed the synthesis of phytochelatins [(γ-Glu-Cys)

n

-Gly; PCs] in strain B3. A range of PCs, with values of
n
from 2 to 7, was synthesized by cells that expressed the

PCS
At

gene, whereas no PCs were found in control cells that harbored the empty plasmid. The presence of CdCl
2
activated PCS and induced the synthesis of substantial amounts of PCs. Cells that contained PCs accumulated 36 nmol of Cd
2+
/mg (dry weight) of cells. The expression of the

PCS
At

gene in
M. huakuii
subsp.
rengei
B3 increased the ability of cells to bind Cd
2+
approximately 9- to 19-fold. The PCS protein was detected by immunostaining bacteroids of mature nodules of
A. sinicus
containing the

PCS
At

gene. When recombinant
M. huakuii
subsp.
rengei
B3 established the symbiotic relationship with
A. sinicus
, the symbionts increased Cd
2+
accumulation in nodules 1.5-fold.
Strong Synergy between a Eukaryotic Antimicrobial Peptide and Bacteriocins from Lactic Acid Bacteria
Authors: Lüders Torben , Birkemo Gunn Alice , Fimland Gunnar , Nissen-Meyer Jon , Nes Ingolf F. 
Published: March 2003

ABSTRACT

The antimicrobial effect obtained upon combining the prokaryotic antimicrobial peptides (AMPs; more commonly referred to as bacteriocins) pediocin PA-1, sakacin P, and curvacin A (all produced by lactic acid bacteria [LAB]) with the eukaryotic AMP pleurocidin (from fish) has been investigated. The three LAB AMPs alone were active against gram-positive
Listeria ivanovii
bacteria at nanomolar concentrations, whereas they were inactive against gram-negative
Escherichia coli
bacteria. Pleurocidin alone was active against both of these types of bacteria at micromolar concentrations. Little if any synergy between the LAB AMPs and pleurocidin against the gram-positive
L. ivanovii
strain was obtained. In contrast, the LAB AMPs and pleurocidin acted highly synergistically against the gram-negative
E. coli
strain. Nanomolar concentrations of LAB AMPs increased the growth inhibitory potency of pleurocidin by about fourfold. When micromolar concentrations of LAB AMPs were combined with 2 μg of pleurocidin/ml, 100% growth inhibition was attained, whereas pleurocidin alone at a concentration of 2 μg/ml gave no growth inhibition. Most noteworthy, when high concentrations (128 μg/ml) of pleurocidin in the absence of LAB AMPs were used over a long period of incubation (1 week), some growth of
E. coli
was observed, whereas 16 μg of pleurocidin/ml completely abolished growth in the presence of 64 to 128 ng of LAB AMPs/ml over the same period of time. The results clearly demonstrate that combining eukaryotic and prokaryotic AMPs can greatly increase the specific activity and broaden the target-cell range of these peptides.
Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils
Authors: Girvan Martina S. , Bullimore Juliet , Pretty Jules N. , Osborn A. Mark , Ball Andrew S. 
Published: March 2003

ABSTRACT
Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.
PCR Detection of Virulence Genes in
Yersinia enterocolitica
and
Yersinia pseudotuberculosis
and Investigation of Virulence Gene Distribution
Authors: Thoerner P. , Bin Kingombe C. I. , Bögli-Stuber K. , Bissig-Choisat B. , Wassenaar T. M. , Frey J. , Jemmi T. 
Published: March 2003

ABSTRACT

PCR-based assays were developed for the detection of plasmid- and chromosome-borne virulence genes in
Yersinia enterocolitica
and
Yersinia pseudotuberculosis
, to investigate the distribution of these genes in isolates from various sources. The results of PCR genotyping, based on 5 virulence-associated genes of 140 strains of
Y. enterocolitica
, were compared to phenotypic tests, such as biotyping and serotyping, and to virulence plasmid-associated properties such as calcium-dependent growth at 37°C and Congo red uptake. The specificity of the PCR results was validated by hybridization. Genotyping data correlated well with biotype data, and most biotypes resulted in (nearly) homogeneous genotypes for the chromosomal virulence genes (
ystA
,
ystB
, and
ail
); however, plasmid-borne genes (
yadA
and
virF
) were detected with variable efficiency, due to heterogeneity within the bacterial population for the presence of the virulence plasmid. Of the virulence genes, only
ystB
was present in biotype 1A; however, within this biotype, pathogenic and apathogenic isolates could not be distinguished based on the detection of virulence genes. Forty
Y. pseudotuberculosis
isolates were tested by PCR for the presence of
inv
,
yadA
, and
lcrF
. All isolates were
inv
positive, and 88% of the isolates contained the virulence plasmid genes
yadA
and
lcrF
. In conclusion, this study shows that genotyping of
Yersinia
spp., based on both chromosome- and plasmid-borne virulence genes, is feasible and informative and can provide a rapid and reliable genotypic characterization of field isolates.
Inactivation of
gacS
Does Not Affect the Competitiveness of
Pseudomonas chlororaphis
in the
Arabidopsis thaliana
Rhizosphere
Authors: Schmidt-Eisenlohr Heike , Gast Astrid , Baron Christian 
Published: March 2003

ABSTRACT

Quorum-sensing-controlled processes are considered to be important for the competitiveness of microorganisms in the rhizosphere. They affect cell-cell communication, biofilm formation, and antibiotic production, and the GacS-GacA two-component system plays a role as a key regulator. In spite of the importance of this system for the regulation of various processes, strains with a Gac
−
phenotype are readily recovered from natural habitats. To analyze the influence of quorum sensing and the influence of the production of the antibiotic phenazine-1-carboxamide on rhizosphere colonization by
Pseudomonas chlororaphis
, a gnotobiotic system based on
Arabidopsis thaliana
seedlings in soil was investigated. Transposon insertion mutants of
P. chlororaphis
isolate SPR044 carrying insertions in different genes required for the production of
N
-acyl-homoserine lactones and phenazine-1-carboxamide were generated. Analysis of solitary rhizosphere colonization revealed that after prolonged growth, the population of the wild type was significantly larger than that of the homoserine lactone-negative
gacS
mutant and that of a phenazine-1-carboxamide-overproducing strain. In cocultivation experiments, however, the population size of the
gacS
mutant was similar to that of the wild type after extended growth in the rhizosphere. A detailed analysis of growth kinetics was performed to explain this phenomenon. After cells grown to the stationary phase were transferred to fresh medium, the
gacS
mutant had a reduced lag phase, and production of the stationary-phase-specific sigma factor RpoS was strongly reduced. This may provide a relative competitive advantage in cocultures with other bacteria, because it permits faster reinitiation of growth after a change to nutrient-rich conditions. In addition, delayed entry into the stationary phase may allow more efficient nutrient utilization. Thus, GacS-GacA-regulated processes are not absolutely required for efficient rhizosphere colonization in populations containing the wild type and Gac
−
mutants.
The Competitiveness of
Pseudomonas chlororaphis
Carrying pJP4 Is Reduced in the
Arabidopsis thaliana
Rhizosphere
Authors: Schmidt-Eisenlohr Heike , Baron Christian 
Published: March 2003

ABSTRACT

The effect of the large catabolic IncP plasmid pJP4 on the competitiveness of
Pseudomonas chlororaphis
SPR044 and on its derivatives SPR244 (GacS deficient), SPR344 (phenazine-1-carboxamide overproducer), and SPR644 (phenazine-1-carboxamide deficient) in the
Arabidopsis thaliana
rhizosphere was assessed. Solitary rhizosphere colonization by the wild type, SPR244, and SPR644 was not affected by the plasmid. The size of the population of SPR344 carrying pJP4, however, was significantly reduced compared to the size of the population of the plasmid-free derivative. The abiotic stress caused by phenazine-1-carboxamide overproduction probably resulted in a selective disadvantage for cells carrying pJP4. Next, the effect of biotic stress caused by coinoculation of other bacteria was analyzed. Cells carrying pJP4 had a selective disadvantage compared to plasmid-free cells in the presence of the efficient colonizer
Pseudomonas fluorescens
WCS417r. This effect was not observed after coinoculation with a variety of other bacteria, and it was independent of quorum sensing and phenazine-1-carboxamide production. Thus, the presence of large catabolic plasmids imposes a detectable metabolic burden in the presence of biotic stress. Plasmid transfer in the
A. thaliana
rhizosphere from
P. chlororaphis
and its derivatives to
Ralstonia eutropha
was determined by using culture-dependent and culture-independent techniques. With the cultivation-independent technique we detected a significantly higher portion of exconjugants, but pJP4 transfer was independent of the quorum-sensing system and of phenazine-1-carboxamide production.
Evidence for the Existence of Psychrophilic Methanogenic Communities in Anoxic Sediments of Deep Lakes
Authors: Nozhevnikova Alla N. , Zepp Kornelia , Vazquez Francisco , Zehnder Alexander J. B. , Holliger Christof 
Published: March 2003

ABSTRACTIn order to obtain evidence for the existence of psychrophilic methanogenic communities in sediments of deep lakes that are low-temperature environments (4 to 5°C), slurries were first incubated at temperatures between 4 and 60°C for several weeks, at which time they were amended, or not, with an additional substrate, such as cellulose, butyrate, propionate, acetate, or hydrogen, and further incubated at 6°C. Initial methane production rates were highest in slurries preincubated at temperatures between 4 and 15°C, with maximal rates in slurries kept at 6°C. Hydrogen-amended cultures were the only exceptions, with the highest methane production rates at 6°C after preincubation at 30°C.
Comparison of Ribotyping and Repetitive Extragenic Palindromic-PCR for Identification of Fecal
Escherichia coli
from Humans and Animals
Authors: Carson C. Andrew , Shear Brian L. , Ellersieck Mark R. , Schnell Jennifer D. 
Published: March 2003

ABSTRACT

This report compares the performances of two popular genotypic methods used for tracking the sources of fecal pollution in water, ribotyping and repetitive extragenic palindromic-PCR (rep-PCR). The rep-PCR was more accurate, reproducible, and efficient in associating DNA fingerprints of fecal
Escherichia coli
with human and animal hosts of origin.
Antigenic Hepatitis A Virus Structures May Be Produced in
Escherichia coli
Authors: Sánchez Glòria , Caballero Santiago , Guix Susana , Bosch Albert , Pintó Rosa M. 
Published: March 2003

ABSTRACT

The synthesis of 14S pentamers and 70S empty capsids of hepatitis A virus (HAV) has been accomplished by expressing the viral genome for periods of time longer than 4 h in
Escherichia coli
. HAV pentamers (14S) self-assembled into capsids (70S) in vitro. The antibodies induced by these structures recognized and neutralized HAV.
Comparison of Methods for DNA Isolation from Food Samples for Detection of Shiga Toxin-Producing
Escherichia coli
by Real-Time PCR
Authors: Heller Loree C. , Davis Carisa R. , Peak K. Kealy , Wingfield David , Cannons Andrew C. , Amuso Philip T. , Cattani Jacqueline 
Published: March 2003

ABSTRACT

In this study, food samples were intentionally contaminated with
Escherichia coli
O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly.
Cr(VI) Reduction by Sulfidogenic and Nonsulfidogenic Microbial Consortia
Authors: Arias Y. Meriah , Tebo Bradley M. 
Published: March 2003

ABSTRACT
In time course experiments, bacterial community compositions were compared between a sulfidogenic and two nonsulfidogenic Cr(VI)-reducing consortia enriched from metal-contaminated sediments. The consortia were subjected to 0 and 0.85 mM or 1.35 mM Cr(VI), and Cr(VI) reduction, growth, and denaturing gradient gel electrophoresis profiles of PCR products of small-subunit (16S) ribosomal genes were compared. Results showed that although Cr(VI) was completely reduced by the three consortia, Cr(VI) inhibited cell growth, with sulfate-reducing bacteria being particularly sensitive to Cr(VI) toxicity relative to other bacteria in the consortia.