bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of
rpoS
in Escherichia coli O157:H7 Strain H32 Biofilm Development and Survival
Authors: Sheldon Jessica R. , Yim Mi-Sung , Saliba Jessica H. , Chung Wai-Hong , Wong Kwok-Yin , Leung Kam Tin 
Published: September 2012

ABSTRACT

The protein RpoS is responsible for mediating cell survival during the stationary phase by conferring cell resistance to various stressors and has been linked to biofilm formation. In this study, the role of the
rpoS
gene in
Escherichia coli
O157:H7 biofilm formation and survival in water was investigated. Confocal scanning laser microscopy of biofilms established on coverslips revealed a nutrient-dependent role of
rpoS
in biofilm formation, where the biofilm biomass volume of the
rpoS
mutant was 2.4- to 7.5-fold the size of its
rpoS
+
wild-type counterpart in minimal growth medium. The enhanced biofilm formation of the
rpoS
mutant did not, however, translate to increased survival in sterile double-distilled water (ddH
2
O), filter-sterilized lake water, or unfiltered lake water. The
rpoS
mutant had an overall reduction of 3.10 and 5.30 log
10
in sterile ddH
2
O and filter-sterilized lake water, respectively, while only minor reductions of 0.53 and 0.61 log
10
in viable counts were observed for the wild-type form in the two media over a 13-day period, respectively. However, the survival rates of the detached biofilm-derived
rpoS
+
and
rpoS
mutant cells were comparable. Under the competitive stress conditions of unfiltered lake water, the advantage conferred by the presence of
rpoS
was lost, and both the wild-type and knockout forms displayed similar declines in viable counts. These results suggest that
rpoS
does have an influence on both biofilm formation and survival of
E. coli
O157:H7 and that the advantage conferred by
rpoS
is contingent on the environmental conditions.
Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis
Authors: Jacques Marie-Agnès , Durand Karine , Orgeur Geoffrey , Balidas Samuel , Fricot Céline , Bonneau Sophie , Quillévéré Anne , Audusseau Corinne , Olivier Valérie , Grimault Valérie , Mathis René 
Published: September 2012

ABSTRACT

The genus
Clavibacter
comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose.
Clavibacter michiganensis
subsp.
michiganensis
is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of
C. michiganensis
subsp.
michiganensis
strains, relatives (strains from the four other
C. michiganensis
subspecies), and nonpathogenic
Clavibacter
-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (
atpD
,
dnaK
,
gyrB
,
ppK
,
recA
, and
rpoB
). We compared this “framework” with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main
C. michiganensis
subsp.
michiganensis
pathogenicity determinants. We showed that
C. michiganensis
subsp.
michiganensis
is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic
Clavibacter
-like strains were identified as
C. michiganensis
using 16S rRNA gene sequencing. These strains, while cross-reacting with
C. michiganensis
subsp.
michiganensis
identification tools, are phylogenetically distinct from the pathogenic strains but belong to the
C. michiganensis
clade.
C. michiganensis
subsp.
michiganensis
clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced.
Preferential Utilization of
d
-Lactate by Shewanella oneidensis
Authors: Brutinel Evan D. , Gralnick Jeffrey A. 
Published: September 2012

ABSTRACT

Shewanella oneidensis
couples oxidation of lactate to respiration of many substrates. Here we report that
llpR
(

l

-
l
actate-
p
ositive
r
egulator, SO_3460) encodes a positive regulator of
l
-lactate utilization distinct from previously studied regulators. We also demonstrate
d
-lactate inhibition of
l
-lactate utilization in
S. oneidensis
, resulting in preferential utilization of the
d
isomer.
Different Antibiotic Resistance and Sporulation Properties within Multiclonal Clostridium difficile PCR Ribotypes 078, 126, and 033 in a Single Calf Farm
Authors: Zidaric Valerija , Pardon Bart , dos Vultos Tiago , Deprez Piet , Brouwer Michael Sebastiaan Maria , Roberts Adam P. , Henriques Adriano O. , Rupnik Maja 
Published: September 2012

ABSTRACT

Clostridium difficile
strains were sampled periodically from 50 animals at a single veal calf farm over a period of 6 months. At arrival, 10% of animals were
C. difficile
positive, and the peak incidence was determined to occur at the age of 18 days (16%). The prevalence then decreased, and at slaughter,
C. difficile
could not be isolated. Six different PCR ribotypes were detected, and strains within a single PCR ribotype could be differentiated further by pulsed-field gel electrophoresis (PFGE). The PCR ribotype diversity was high up to the animal age of 18 days, but at later sampling points, PCR ribotype 078 and the highly related PCR ribotype 126 predominated. Resistance to tetracycline, doxycycline, and erythromycin was detected, while all strains were susceptible to amoxicillin and metronidazole. Multiple variations of the resistance gene
tet
(M) were present at the same sampling point, and these changed over time. We have shown that PCR ribotypes often associated with cattle (ribotypes 078, 126, and 033) were not clonal but differed in PFGE type, sporulation properties, antibiotic sensitivities, and tetracycline resistance determinants, suggesting that multiple strains of the same PCR ribotype infected the calves and that calves were likely to be infected prior to arrival at the farm. Importantly, strains isolated at later time points were more likely to be resistant to tetracycline and erythromycin and showed higher early sporulation efficiencies
in vitro
, suggesting that these two properties converge to promote the persistence of
C. difficile
in the environment or in hosts.
“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens
Authors: Paul Kristina , Nonoh James O. , Mikulski Lena , Brune Andreas 
Published: September 2012

ABSTRACT

The
Euryarchaeota
comprise both methanogenic and nonmethanogenic orders and many lineages of uncultivated archaea with unknown properties. One of these deep-branching lineages, distantly related to the
Thermoplasmatales
, has been discovered in various environments, including marine habitats, soil, and also the intestinal tracts of termites and mammals. By comparative phylogenetic analysis, we connected this lineage of 16S rRNA genes to a large clade of unknown
mcrA
gene sequences, a functional marker for methanogenesis, obtained from the same habitats. The identical topologies of 16S rRNA and
mcrA
gene trees and the perfect congruence of all branches, including several novel groups that we obtained from the guts of termites and cockroaches, strongly suggested that they stem from the same microorganisms. This was further corroborated by two highly enriched cultures of closely related methanogens from the guts of a higher termite (
Cubitermes ugandensis
) and a millipede (
Anadenobolus
sp.), which represented one of the arthropod-specific clusters in the respective trees. Numerous other pairs of habitat-specific sequence clusters were obtained from the guts of other termites and cockroaches but were also found in previously published data sets from the intestinal tracts of mammals (e.g., rumen cluster C) and other environments. Together with the recently described
Methanomassiliicoccus luminyensis
isolated from human feces, which falls into rice cluster III, the results of our study strongly support the idea that the entire clade of “uncultured
Thermoplasmatales
” in fact represents the seventh order of methanogenic archaea, for which the provisional name “
Methanoplasmatales
” is proposed.
Detection and Identification of Salmonella enterica, Escherichia coli, and Shigella spp. via PCR-Electrospray Ionization Mass Spectrometry: Isolate Testing and Analysis of Food Samples
Authors: Pierce Sarah E. , Bell Rebecca L. , Hellberg Rosalee S. , Cheng Chorng-Ming , Chen Kai-Shun , Williams-Hill Donna M. , Martin William B. , Allard Marc W. 
Published: September 2012

ABSTRACT

An assay to identify the common food-borne pathogens
Salmonella
,
Escherichia coli
,
Shigella
, and
Listeria monocytogenes
was developed in collaboration with Ibis Biosciences (a division of Abbott Molecular) for the Plex-ID biosensor system, a platform that uses electrospray ionization mass spectroscopy (ESI-MS) to detect the base composition of short PCR amplicons. The new food-borne pathogen (FBP) plate has been experimentally designed using four gene segments for a total of eight amplicon targets. Initial work built a DNA base count database that contains more than 140
Salmonella enterica
, 139
E. coli
, 11
Shigella
, and 36
Listeria
patterns and 18 other
Enterobacteriaceae
organisms. This assay was tested to determine the scope of the assay's ability to detect and differentiate the enteric pathogens and to improve the reference database associated with the assay. More than 800 bacterial isolates of
S. enterica
,
E. coli
, and
Shigella
species were analyzed. Overall, 100% of
S. enterica
, 99% of
E. coli
, and 73% of
Shigella
spp. were detected using this assay. The assay was also able to identify 30% of the
S. enterica
serovars to the serovar level. To further characterize the assay, spiked food matrices and food samples collected during regulatory field work were also studied. While analysis of preenrichment media was inconsistent, identification of
S. enterica
from selective enrichment media resulted in serovar-level identifications for 8 of 10 regulatory samples. The results of this study suggest that this high-throughput method may be useful in clinical and regulatory laboratories testing for these pathogens.
Biotin-Binding Proteins in the Defense of Mushrooms against Predators and Parasites
Authors: Bleuler-Martinez Silvia , Schmieder Stefanie , Aebi Markus , Künzler Markus 
Published: September 2012

ABSTRACT
Tamavidins are fungal biotin-binding proteins (BBPs) displaying antifungal activity against phytopathogens. Here we show high toxicity of tamavidins toward nematodes, insects, and amoebae. As these organisms represent important phyla of fungal predators and parasites, we propose that BBPs are part of the chemical defense system of fungi.
Chemotactic Behavior of Pathogenic and Nonpathogenic Leptospira Species
Authors: Lambert Ambroise , Takahashi Naoko , Charon Nyles W. , Picardeau Mathieu 
Published: September 2012

ABSTRACT

We have developed a capillary tube assay in combination with real-time PCR to quantitate the number of chemoattracted
Leptospira
cells. We identified Tween 80, glucose, sucrose, and pyruvate as attractants for
Leptospira
cells; amino acids and vitamin B
12
were found to be nonchemotactic or weakly chemotactic. This assay has the general applicability to further our understanding of leptospiral chemotaxis.
Oxygen Response of the Wine Yeast Saccharomyces cerevisiae EC1118 Grown under Carbon-Sufficient, Nitrogen-Limited Enological Conditions
Authors: Aceituno Felipe F. , Orellana Marcelo , Torres Jorge , Mendoza Sebastián , Slater Alex W. , Melo Francisco , Agosin Eduardo 
Published: September 2012

ABSTRACTDiscrete additions of oxygen play a critical role in alcoholic fermentation. However, few studies have quantitated the fate of dissolved oxygen and its impact on wine yeast cell physiology under enological conditions. We simulated the range of dissolved oxygen concentrations that occur after a pump-over during the winemaking process by sparging nitrogen-limited continuous cultures with oxygen-nitrogen gaseous mixtures. When the dissolved oxygen concentration increased from 1.2 to 2.7 μM, yeast cells changed from a fully fermentative to a mixed respirofermentative metabolism. This transition is characterized by a switch in the operation of the tricarboxylic acid cycle (TCA) and an activation of NADH shuttling from the cytosol to mitochondria. Nevertheless, fermentative ethanol production remained the major cytosolic NADH sink under all oxygen conditions, suggesting that the limitation of mitochondrial NADH reoxidation is the major cause of the Crabtree effect. This is reinforced by the induction of several key respiratory genes by oxygen, despite the high sugar concentration, indicating that oxygen overrides glucose repression. Genes associated with other processes, such as proline uptake, cell wall remodeling, and oxidative stress, were also significantly affected by oxygen. The results of this study indicate that respiration is responsible for a substantial part of the oxygen response in yeast cells during alcoholic fermentation. This information will facilitate the development of temporal oxygen addition strategies to optimize yeast performance in industrial fermentations.
Impact of Sorbic Acid on Germination and Outgrowth Heterogeneity of Bacillus cereus ATCC 14579 Spores
Authors: den Besten Heidy M. W. , van Melis Clint C. J. , Sanders Jan Willem , Nierop Groot Masja N. , Abee Tjakko 
Published: September 2012

ABSTRACT
Population heterogeneity complicates the predictability of the outgrowth kinetics of individual spores. Flow cytometry sorting and monitoring of the germination and outgrowth of single dormant spores allowed the quantification of acid-induced spore population heterogeneity at pH 5.5 and in the presence of sorbic acid. This showed that germination efficiency was not a good predictor for heterogeneity in final outgrowth.
Methicillin-Resistant Staphylococcus aureus Phage Plaque Size Enhancement Using Sublethal Concentrations of Antibiotics
Authors: Kaur Sandeep , Harjai Kusum , Chhibber Sanjay 
Published: September 2012

ABSTRACTPhage therapy presents an alternative approach against the emerging methicillin-resistantStaphylococcus aureus(MRSA) threat. Some of the problems encountered during isolation of MRSA phages include the high prevalence of enteric phages in natural sources, nonspecific absorption of viable phage, and the formation of pinpoint or tiny plaques. The phage isolated in this study, MR-5, also formed tiny plaques against its hostS. aureusATCC 43300 (MRSA), making its detection and enumeration difficult. An improved method of increasing the plaque size of MRSA phage by incorporating sublethal concentrations of three different classes of antibiotics (inhibitors of protein synthesis) in the classical double-layer agar (DLA) method was investigated. The β-lactam and quinolone antibiotics commonly employed in earlier studies for increasing the plaque size did not show any significant effect on the plaque size of isolated MR-5 phage. Linezolid (oxazolidinone class), tetracycline, and ketolide antibiotics brought significant enhancements (3 times the original size) in the plaque size of MR-5 phage. Prior treatment with these antibiotics resulted in significant reductions in the time of adsorption and the latent period of MR-5 phage. To rule out whether the action of linezolid (which brought the maximum increase in plaque size) was specific for a single phage only, its effect on the plaque size of seven otherS. aureus-specific phages was also assessed. Significant enhancements in the plaque size of these phages were observed. These results indicate that this modification can therefore safely be incorporated in the traditional DLA overlay method to search for new MRSA-virulent phages.
Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community
Authors: Marshall Christopher W. , Ross Daniel E. , Fichot Erin B. , Norman R. Sean , May Harold D. 
Published: September 2012

ABSTRACT

A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at −590 mV versus the standard hydrogen electrode (SHE) with CO
2
as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant
Archaea
population of
Methanobacterium
spp. and a shifting
Bacteria
population.
Acetobacterium
spp. were the most abundant
Bacteria
on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day
−1
(per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day
−1
(accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day
−1
(versus 0.045 mM day
−1
abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of −460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.
Two Enzymes of a Complete Degradation Pathway for Linear Alkylbenzenesulfonate (LAS) Surfactants: 4-Sulfoacetophenone Baeyer-Villiger Monooxygenase and 4-Sulfophenylacetate Esterase in Comamonas testosteroni KF-1
Authors: Weiss Michael , Denger Karin , Huhn Thomas , Schleheck David 
Published: September 2012

ABSTRACT

Complete biodegradation of the surfactant linear alkylbenzenesulfonate (LAS) is accomplished by complex bacterial communities in two steps. First, all LAS congeners are degraded into about 50 sulfophenylcarboxylates (SPC), one of which is 3-(4-sulfophenyl)butyrate (3-C
4
-SPC). Second, these SPCs are mineralized. 3-C
4
-SPC is mineralized by
Comamonas testosteroni
KF-1 in a process involving 4-sulfoacetophenone (SAP) as a metabolite and an unknown inducible Baeyer-Villiger monooxygenase (BVMO) to yield 4-sulfophenyl acetate (SPAc) from SAP (SAPMO enzyme); hydrolysis of SPAc to 4-sulfophenol and acetate is catalyzed by an unknown inducible esterase (SPAc esterase). Transcriptional analysis showed that one of four candidate genes for BVMOs in the genome of strain KF-1, as well as an SPAc esterase candidate gene directly upstream, was inducibly transcribed during growth with 3-C
4
-SPC. The same genes were identified by enzyme purification and peptide fingerprinting-mass spectrometry when SAPMO was enriched and SPAc esterase purified to homogeneity by protein chromatography. Heterologously overproduced pure SAPMO converted SAP to SPAc and was active with phenylacetone and 4-hydroxyacetophenone but not with cyclohexanone and progesterone. SAPMO showed the highest sequence homology to the archetypal phenylacetone BVMO (57%), followed by steroid BVMO (55%) and 4-hydroxyacetophenone BVMO (30%). Finally, the two pure enzymes added sequentially, SAPMO with NADPH and SAP, and then SPAc esterase, catalyzed the conversion of SAP via SPAc to 4-sulfophenol and acetate in a 1:1:1:1 molar ratio. Hence, the first two enzymes of a complete LAS degradation pathway were identified, giving evidence for the recruitment of members of the very versatile type I BVMO and carboxylester hydrolase enzyme families for the utilization of a xenobiotic compound by bacteria.
Anaerobic Benzene Oxidation by Geobacter Species
Authors: Zhang Tian , Bain Timothy S. , Nevin Kelly P. , Barlett Melissa A. , Lovley Derek R. 
Published: September 2012

ABSTRACTThe abundance ofGeobacterspecies in contaminated aquifers in which benzene is anaerobically degraded has led to the suggestion that someGeobacterspecies might be capable of anaerobic benzene degradation, but this has never been documented. A strain ofGeobacter, designated strain Ben, was isolated from sediments from the Fe(III)-reducing zone of a petroleum-contaminated aquifer in which there was significant capacity for anaerobic benzene oxidation. Strain Ben grew in a medium with benzene as the sole electron donor and Fe(III) oxide as the sole electron acceptor. Furthermore, additional evaluation ofGeobacter metallireducensdemonstrated that it could also grow in benzene-Fe(III) medium. In both strain Ben andG. metallireducensthe stoichiometry of benzene metabolism and Fe(III) reduction was consistent with the oxidation of benzene to carbon dioxide with Fe(III) serving as the sole electron acceptor. With benzene as the electron donor, and Fe(III) oxide (strain Ben) or Fe(III) citrate (G. metallireducens) as the electron acceptor, the cell yields of strain Ben andG. metallireducenswere 3.2 × 109and 8.4 × 109cells/mmol of Fe(III) reduced, respectively. Strain Ben also oxidized benzene with anthraquinone-2,6-disulfonate (AQDS) as the sole electron acceptor with cell yields of 5.9 × 109cells/mmol of AQDS reduced. Strain Ben serves as model organism for the study of anaerobic benzene metabolism in petroleum-contaminated aquifers, andG. metallireducensis the first anaerobic benzene-degrading organism that can be genetically manipulated.
Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms
Authors: Fida Tekle Tafese , Breugelmans Philip , Lavigne Rob , Coronado Edith , Johnson David R. , van der Meer Jan Roelof , Mayer Antonia P. , Heipieper Hermann J. , Hofkens Johan , Springael Dirk 
Published: September 2012

ABSTRACTMembers of the genusSphingomonasare important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degradingSphingomonassp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity.