bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pyridine-2,6-Bis(Thiocarboxylic Acid) Produced by
Pseudomonas stutzeri
KC Reduces and Precipitates Selenium and Tellurium Oxyanions
Authors: Zawadzka Anna M. , Crawford Ronald L. , Paszczynski Andrzej J. 
Published: May 2006

ABSTRACT

The siderophore of
Pseudomonas stutzeri
KC, pyridine-2,6-bis(thiocarboxylic acid) (pdtc), is shown to detoxify selenium and tellurium oxyanions in bacterial cultures. A mechanism for pdtc's detoxification of tellurite and selenite is proposed. The mechanism is based upon determination using mass spectrometry and energy-dispersive X-ray spectrometry of the chemical structures of compounds formed during initial reactions of tellurite and selenite with pdtc. Selenite and tellurite are reduced by pdtc or its hydrolysis product H
2
S, forming zero-valent pdtc selenides and pdtc tellurides that precipitate from solution. These insoluble compounds then hydrolyze, releasing nanometer-sized particles of elemental selenium or tellurium. Electron microscopy studies showed both extracellular precipitation and internal deposition of these metalloids by bacterial cells. The precipitates formed with synthetic pdtc were similar to those formed in pdtc-producing cultures of
P. stutzeri
KC. Culture filtrates of
P. stutzeri
KC containing pdtc were also active in removing selenite and precipitating elemental selenium and tellurium. The pdtc-producing wild-type strain KC conferred higher tolerance against selenite and tellurite toxicity than a pdtc-negative mutant strain, CTN1. These observations support the hypothesis that pdtc not only functions as a siderophore but also is involved in an initial line of defense against toxicity from various metals and metalloids.
Effect of Nutrient Periodicity on Microbial Community Dynamics
Authors: Carrero-Colón Militza , Nakatsu Cindy H. , Konopka Allan 
Published: May 2006

ABSTRACT

When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h
−1
to 0.15 h
−1
as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions,
Bacteroidetes
,
Proteobacteria
, and
Actinobacteria
. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.
Alicyclobacillus acidocaldariusThermophilic Esterase EST2's Activity in Milk and Cheese Models
Authors: Mandrich Luigi , Manco Giuseppe , Rossi Mosè , Floris Esther , Jansen-van den Bosch Tanja , Smit Gerrit , Wouters Jeroen A. 
Published: May 2006

ABSTRACTThe aim of this work was to investigate the behavior of thermophilic esterase EST2 fromAlicyclobacillus acidocaldariusin milk and cheese models. The pure enzyme was used to compare the EST2 hydrolytic activity to the activity of endogenous esterase EstA fromLactococcus lactis. The results indicate that EST2 exhibits 30-fold-higher esterase activity than EstA. As EstA has thioesterase activity, EST2 was assayed for this activity under the optimal conditions determined for EstA (namely, 30°C and pH 7.5). Although it is a thermophilic enzyme, EST2 exhibited eightfold-higher thioesterase activity than EstA withS-methyl thiobutanoate. The abilities of EST2 and EstA to synthesize short-chain fatty acid esters were compared. Two methods were developed to do this. In the first method a spectrophotometric assay was used to monitor the synthesis of esters by the pure enzymes usingp-nitrophenol as the alcohol substrate. The synthetic activities were also evaluated under conditions that mimicked those present in milk and/or cheese. The second method involved evaluation of the synthetic abilities of the enzymes when they were directly added to a model cheese matrix. Substantial ester synthesis by EST2 was observed under both conditions. Finally, esterase and thioesterase activities were evaluated in milk using the purified EST2 enzyme and in the model cheese matrix using a strain ofL. lactisNZ9000 harboring the EST2 gene and thus overproducing EST2. Both the esterase and thioesterase activities measured in milk and in the cheese matrix were much greater than the activities of the controls.
Characterization of the Replication, Maintenance, and Transfer Features of the IncP-7 Plasmid pCAR1, Which Carries Genes Involved in Carbazole and Dioxin Degradation
Authors: Shintani Masaki , Yano Hirokazu , Habe Hiroshi , Omori Toshio , Yamane Hisakazu , Tsuda Masataka , Nojiri Hideaki 
Published: May 2006

ABSTRACT

Isolated from
Pseudomonas resinovorans
CA10, pCAR1 is a 199-kb plasmid that carries genes involved in the degradation of carbazole and dioxin. The nucleotide sequence of pCAR1 has been determined previously. In this study, we characterized pCAR1 in terms of its replication, maintenance, and conjugation. By constructing miniplasmids of pCAR1 and testing their establishment in
Pseudomonas putida
DS1, we show that pCAR1 replication is due to the
repA
gene and its upstream DNA region. The
repA
gene and putative
oriV
region could be separated in
P. putida
DS1, and the
oriV
region was determined to be located within the 345-bp region between the
repA
and
parW
genes. Incompatibility testing using the minireplicon of pCAR1 and IncP plasmids indicated that pCAR1 belongs to the IncP-7 group. Monitoring of the maintenance properties of serial miniplasmids in nonselective medium, and mutation and complementation analyses of the
parWABC
genes, showed that the stability of pCAR1 is attributable to the products of the
parWAB
genes. In mating assays, the transfer of pCAR1 from CA10 was detected in a CA10 derivative that was cured of pCAR1 (CA10dm4) and in
P. putida
KT2440 at frequencies of 3 × 10
−1
and 3 × 10
−3
per donor strain, respectively. This is the first report of the characterization of this completely sequenced IncP-7 plasmid.
Stolbur Phytoplasma Genome Survey Achieved Using a Suppression Subtractive Hybridization Approach with High Specificity
Authors: Cimerman Agnès , Arnaud Guillaume , Foissac Xavier 
Published: May 2006

ABSTRACT

Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, suppression subtractive hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83% were homologous to “
Candidatus
Phytoplasma asteris” (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase.
Characterization of Novel Carbazole Catabolism Genes from Gram-Positive Carbazole Degrader
Nocardioides aromaticivorans
IC177
Authors: Inoue Kengo , Habe Hiroshi , Yamane Hisakazu , Nojiri Hideaki 
Published: May 2006

ABSTRACT

Nocardioides aromaticivorans
IC177 is a gram-positive carbazole degrader. The genes encoding carbazole degradation (
car
genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. The
car
genes were clustered into the
carAaCBaBbAcAd
and
carDFE
gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme A, respectively. The conserved amino acid motifs proposed to bind the Rieske-type [2Fe-2S] cluster and mononuclear iron, the Rieske-type [2Fe-2S] cluster, and flavin adenine dinucleotide were found in the deduced amino acid sequences of
carAa
,
carAc
, and
carAd
, respectively, which showed similarities with CarAa from
Sphingomonas
sp. strain KA1 (49% identity), CarAc from
Pseudomonas resinovorans
CA10 (31% identity), and AhdA4 from
Sphingomonas
sp. strain P2 (37% identity), respectively.
E
s
cherichia coli
cells expressing CarAaAcAd exhibited major carbazole 1,9a-dioxygenase (CARDO) activity. These data showed that the IC177 CARDO is classified into class IIB, while gram-negative CARDOs are classified into class III or IIA, indicating that the respective CARDOs have diverse types of electron transfer components and high similarities of the terminal oxygenase. Reverse transcription-PCR (RT-PCR) experiments showed that the
carAaCBaBbAcAd
and
carDFE
gene clusters are operonic. The results of quantitative RT-PCR experiments indicated that transcription of both operons is induced by carbazole or its metabolite, whereas anthranilate is not an inducer. Biotransformation analysis showed that the IC177 CARDO exhibits significant activities for naphthalene, carbazole, and dibenzo-
p
-dioxin but less activity for dibenzofuran and biphenyl.
Development of a Biofilm Production-Deficient
Escherichia coli
Strain as a Host for Biotechnological Applications
Authors: Sung Bong Hyun , Lee Choong Hoon , Yu Byung Jo , Lee Jun Hyoung , Lee Ju Young , Kim Mi Sun , Blattner Frederick R. , Kim Sun Chang 
Published: May 2006

ABSTRACT

Bacteria form biofilms by adhering to biotic or abiotic surfaces. This phenomenon causes several problems, including a reduction in the transport of mass and heat, an increase in resistance to antibiotics, and a shortening of the lifetimes of modules in bioindustrial fermentors. To overcome these difficulties, we created a biofilm production-deficient
Escherichia coli
strain, BD123, by deleting genes involved in curli biosynthesis and assembly, Δ(
csgG-csgC
); colanic acid biosynthesis and assembly, Δ(
wcaL-wza
); and type I pilus biosynthesis, Δ(
fimB-fimH
).
E. coli
BD123 remained mostly in the form of planktonic cells under the conditions tested and became more sensitive to the antibiotics streptomycin and rifampin than the wild-type
E. coli
MG1655: the growth of BD123 was inhibited by one-fourth of the concentrations needed to inhibit MG1655. In addition, the transformation efficiency of BD123 was about 20 times higher than that of MG1655, and the production and secretion of recombinant proteins were ∼16% and ∼25% greater, respectively, with BD123 than with MG1655. These results indicate that the newly created biofilm production-deficient strain of
E. coli
displays several key properties that substantially enhance its utility in the biotechnology arena.
Modeling for Gellan Gum Production by
Sphingomonas paucimobilis
ATCC 31461 in a Simplified Medium
Authors: Wang Xia , Xu Ping , Yuan Yong , Liu Changlong , Zhang Dezhong , Yang Zhengting , Yang Chunyu , Ma Cuiqing 
Published: May 2006

ABSTRACT

Gellan gum production was carried out by
Sphingomonas paucimobilis
ATCC 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. The results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter
−1
. As for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rotary shaker. Under the optimized conditions, the maximum level of gellan gum (14.75 g liter
−1
) and the highest conversion efficiency (49.17%) were obtained in a 30-liter fermentor in batch fermentation. Logistic and Luedeking-Piret models were confirmed to provide a good description of gellan gum fermentation, which gave some support for the study of gellan gum fermentation kinetics. Additionally, this study is the first demonstration that gellan gum production is largely growth associated by analysis of kinetics in its batch fermentation process. Based on model prediction, higher gellan gum production (17.71 g liter
−1
) and higher conversion efficiency (57.12%) were obtained in fed-batch fermentation at the same total glucose concentration (30 g liter
−1
).
Role of Efflux Pumps in Adaptation and Resistance of
Listeria monocytogenes
to Benzalkonium Chloride
Authors: Romanova N. A. , Wolffs P. F. G. , Brovko L. Y. , Griffiths M. W. 
Published: May 2006

ABSTRACT

In this study, potential mechanisms underlying resistance and adaptation to benzalkonium chloride (BC) in
Listeria monocytogenes
were investigated. Two groups of strains were studied. The first group consisted of strains naturally sensitive to BC which could be adapted to BC. The second group consisted of naturally resistant strains. For all adapted isolates, there was a correlation between the resistance to BC and ethidium bromide, but this was not the case for the naturally resistant isolates. To investigate the role of efflux pumps in adaptation or resistance, reserpine, an efflux pump inhibitor, was added to the strains. Addition of reserpine to the sensitive and adapted strains resulted in a decrease in the MIC for BC, whereas no such decrease was observed for the resistant strains, indicating that efflux pumps played no role in the innate resistance of certain strains of
L. monocytogenes
to this compound. Two efflux pumps (MdrL and Lde) have been described in
L. monocytogenes
. Studies showed low and intermediate levels of expression of the genes encoding the efflux pumps for two selected resistant strains, H7764 and H7962, respectively. Adaptation to BC of sensitive isolates of
L. monocytogenes
resulted in significant increases in expression of
mdrl
(
P
< 0.05), but no such increase was observed for
lde
for two adapted strains of
L. monocytogenes
, LJH 381 (
P
= 0.91) and C719 (
P
= 0.11). This indicates that the efflux pump Mdrl is at least partly responsible for the adaptation to BC.
Auxofuran, a Novel Metabolite That Stimulates the Growth of Fly Agaric, Is Produced by the Mycorrhiza Helper Bacterium
Streptomyces
Strain AcH 505
Authors: Riedlinger Julia , Schrey Silvia D. , Tarkka Mika T. , Hampp Rüdiger , Kapur Manmohan , Fiedler Hans-Peter 
Published: May 2006

ABSTRACT

The mycorrhiza helper bacterium
Streptomyces
strain AcH 505 improves mycelial growth of ectomycorrhizal fungi and formation of ectomycorrhizas between
Amanita muscaria
and spruce but suppresses the growth of plant-pathogenic fungi, suggesting that it produces both fungal growth-stimulating and -suppressing compounds. The dominant fungal-growth-promoting substance produced by strain AcH 505, auxofuran, was isolated, and its effect on the levels of gene expression of
A. muscaria
was investigated. Auxofuran and its synthetic analogue 7-dehydroxy-auxofuran were most effective at a concentration of 15 μM, and application of these compounds led to increased lipid metabolism-related gene expression. Cocultivation of strain AcH 505 and
A. muscaria
stimulated auxofuran production by the streptomycete. The antifungal substances produced by strain AcH 505 were identified as the antibiotics WS-5995 B and C. WS-5995 B completely blocked mycelial growth at a concentration of 60 μM and caused a cell stress-related gene expression response in
A. muscaria
. Characterization of these compounds provides the foundation for molecular analysis of the fungus-bacterium interaction in the ectomycorrhizal symbiosis between fly agaric and spruce.
Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat
Authors: Ley Ruth E. , Harris J. Kirk , Wilcox Joshua , Spear John R. , Miller Scott R. , Bebout Brad M. , Maresca Julia A. , Bryant Donald A. , Sogin Mitchell L. , Pace Norman R. 
Published: May 2006

ABSTRACT

We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (≥97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O
2
and H
2
S. Bacteria of the phylum
Chloroflexi
formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments),
Chloroflexi
sequences were conspicuous throughout the mat. Filamentous
Chloroflexi
bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium
Microcoleus chthonoplastes
, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.
Improved Methodology for Bioremoval of Black Crusts on Historical Stone Artworks by Use of Sulfate-Reducing Bacteria
Authors: Cappitelli Francesca , Zanardini Elisabetta , Ranalli Giancarlo , Mello Emilio , Daffonchio Daniele , Sorlini Claudia 
Published: May 2006

ABSTRACTAn improved methodology to remove black crusts from stone by usingDesulfovibrio vulgarissubsp.vulgarisATCC 29579, a sulfate-reducing bacterium, is presented. The strain removed 98% of the sulfates of the crust in a 45-h treatment. Precipitation of black iron sulfide was avoided using filtration of a medium devoid of iron. Among three cell carriers, Carbogel proved to be superior to both sepiolite and Hydrobiogel-97, as it allowed an easy application of the bacteria, kept the system in a state where microbial activity was maintained, and allowed easy removal of the cells after the treatment.
Multiniche Screening Reveals the Clinically Relevant Metallo-β-Lactamase VIM-2 in
Pseudomonas aeruginosa
Far from the Hospital Setting: an Ongoing Dispersion Process?
Authors: Quinteira Sandra , Peixe Luísa 
Published: May 2006

ABSTRACT

A screening study of the presence of metallo-β-lactamases (IMP and VIM types and SPM-1) in isolates from different nonhospital sources was conducted, and it revealed the presence of
bla
VIM-2
, associated with the In58 class 1 integron, in two unrelated
Pseudomonas aeruginosa
strains from aquatic habitats. The results suggest that the hospital setting was the possible origin of these
bla
VIM-2
-carrying strains.
Development and Validation of an Oligonucleotide Microarray for Detection of Multiple Virulence and Antimicrobial Resistance Genes in
Escherichia coli
Authors: Bruant Guillaume , Maynard Christine , Bekal Sadjia , Gaucher Isabelle , Masson Luke , Brousseau Roland , Harel Josée 
Published: May 2006

ABSTRACT

An oligonucleotide microarray detecting 189
Escherichia coli
virulence genes or markers and 30 antimicrobial resistance genes was designed and validated using DNA from known reference strains. This microarray was confirmed to be a powerful diagnostic tool for monitoring emerging
E. coli
pathotypes and antimicrobial resistance, as well as for environmental, epidemiological, and phylogenetic studies including the evaluation of genome plasticity.
Comparison of a Conventional Antimicrobial Susceptibility Assay to an Oligonucleotide Chip System for Detection of Drug Resistance in
Mycobacterium tuberculosis
Isolates
Authors: Park Heekyung , Song Eun Ju , Song Eun Sil , Lee Eun Yup , Kim Cheol Min , Jeong Seok Hoon , Shin Jeong Hwan , Jeong Joseph , Kim Sunjoo , Park Young Kil , Bai Gill-Han , Chang Chulhun L. 
Published: May 2006

ABSTRACT

An oligonucleotide chip (Combichip Mycobacteria chip) detecting specific mutations in the
rpoB
,
katG
, and
inhA
genes of
Mycobacterium tuberculosis
was compared with conventional antimicrobial susceptibility results. The probes detecting drug resistance were as follows: 7 wild-type and 13 mutant probes for rifampin and 2 wild-type and 3 mutant probes for isoniazid. Target DNA of
M. tuberculosis
was amplified by PCR, followed by hybridization and scanning. Direct sequencing was performed to verify the results of the oligonucleotide chip. One-hundred seven of 115 rifampin-resistant strains (93%) had mutations in the
rpoB
gene. Eighty-five of 119 isoniazid-resistant strains (71%) had mutations in the
katG
gene or
inhA
gene. The diagnostic oligonucleotide chip with mutation-specific probes is a reliable and useful tool for the rapid and accurate diagnosis of resistance against rifampin and isoniazid in
M. tuberculosis
isolates.
Emergence of an Invasive Clone of Nontoxigenic
Corynebacterium diphtheriae
in the Urban Poor Population of Vancouver, Canada
Authors: Romney M. G. , Roscoe D. L. , Bernard K. , Lai S. , Efstratiou A. , Clarke A. M. 
Published: May 2006

ABSTRACT

Invasive disease due to
Corynebacterium diphtheriae
is rare in North America. Here we describe the emergence of a predominant clone of a nontoxigenic strain of
C. diphtheriae
in the impoverished population of Vancouver's downtown core. This clone has caused significant morbidity and contributed to at least two deaths. Over a 5-year period, seven cases of bacteremia due to
C. diphtheriae
were detected in patients admitted to Vancouver hospitals. Injection drug use, diabetes mellitus, skin colonization/infection with
C. diphtheriae
, and homelessness all appeared to be related to the development of bacteremia with the organism. Ribotyping of isolates recovered from blood culture revealed a predominant ribotype pattern that has not previously been reported in North America.