bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Heat, Acidification, and Chlorination on
Salmonella enterica
Serovar Typhimurium Cells in a Biofilm Formed at the Air-Liquid Interface
Authors: Scher Keren , Romling Ute , Yaron Sima 
Published: March 2005

ABSTRACT

Bacterial biofilms have great significance for public health, since biofilm-associated microorganisms exhibit dramatically decreased susceptibility to antimicrobial agents and treatments. To date most attention has focused on biofilms that arise from the colonization of solid-liquid or solid-air interfaces. It is of interest that colonization of the interface between air and liquid, which can be selectively advantageous for aerobic or facultative aerobic bacteria, has been rarely studied, although it may present a major problem in industrial aquatic systems. In this work we investigated the role of a biofilm at the interface between air and liquid (pellicle) in the susceptibility of
Salmonella enterica
serovar Typhimurium to stress conditions. For a control we used a mutant that had lost its ability to synthesize cellulose and thin aggregative fimbriae and thus did not produce the pellicle. Resistance of bacteria from the pellicle to heat, acidification, and chlorination was compared to resistance of planktonic cells from the logarithmic and stationary phases of growth. Pellicle cells were significantly more resistant to chlorination, and thus the surrounding matrix conferred protection against the reactive sodium hypochlorite. However, the stress management of pellicle cells in response to heat and low pH was not enhanced compared to that of stationary-phase cells. A long-period of incubation resulted in endogenous hydrolysis of the pellicle matrix. This phenomenon provides a potential new approach to combat microbial cells in biofilms.
Mycobacterium aviumSubspeciesparatuberculosisCultured from Locally and Commercially Pasteurized Cow's Milk in the Czech Republic
Authors: Ayele Wuhib Y. , Svastova Petra , Roubal Petr , Bartos Milan , Pavlik Ivo 
Published: March 2005

ABSTRACTBetween November 2002 and April 2003, 244 bottles and cartons of commercially pasteurized cow's milk were obtained at random from retail outlets throughout the Czech Republic. During the same period, samples of raw milk and of milk that was subsequently subjected to a minimum of 71.7°C for 15 s in a local pasteurization unit were also obtained from two dairy herds, designated herds A and B, with low and high levels, respectively, of subclinicalMycobacterium aviumsubsp.paratuberculosisinfection, and from one herd, herd C, without infection. Infection in individual cows in each herd was tested by fecal culturing. Milk samples were brought to the Veterinary Research Institute in Brno, Czech Republic, processed, inoculated onto Herrold's egg yolk slants, and incubated for 32 weeks. Colonies were characterized by morphology, Ziehl-Neelsen staining, mycobactin J dependency, and IS900PCR results.M. aviumsubsp.paratuberculosiswas cultured from 4 of 244 units (1.6%) of commercially pasteurized retail milk.M. aviumsubsp.paratuberculosiswas also cultured from 2 of 100 (2%) cartons of locally pasteurized milk derived from infected herds A and B and from 0 of 100 cartons of milk from uninfected herd C. Raw milk from 1 of 10 (10%) fecal culture-positive cows in herd A and from 13 of 66 (19.7%) fecal culture-positive cows in herd B was culture positive forM. aviumsubsp.paratuberculosis.These findings confirm thatM. aviumsubsp.paratuberculosisis present in raw milk from subclinically infected dairy cows. The culture ofM. aviumsubsp.paratuberculosisin the Czech Republic from retail milk that had been pasteurized locally or commercially to the required national and European Union standards is in agreement with similar research on milk destined for consumers in the United Kingdom and the United States and shows that humans are being exposed to this chronic enteric pathogen by this route.
Heterologous Production, Assembly, and Secretion of a Minicellulosome by
Clostridium acetobutylicum
ATCC 824
Authors: Mingardon Florence , Perret Stéphanie , Bélaïch Anne , Tardif Chantal , Bélaïch Jean-Pierre , Fierobe Henri-Pierre 
Published: March 2005

ABSTRACT

The gene
man5K
encoding the mannanase Man5K from
Clostridium cellulolyticum
was cloned alone or as an operon with the gene
cipC1
encoding a truncated scaffoldin (miniCipC1) of the same origin in the solventogenic
Clostridium acetobutylicum
. The expression of the heterologous gene(s) was under the control of a weakened thiolase promoter P

thl

. The recombinant strains of the solventogenic bacterium were both found to secrete active Man5K in the range of milligrams per liter. In the case of the strain expressing only
man5K
, a large fraction of the recombinant enzyme was truncated and lost the N-terminal dockerin domain, but it remained active towards galactomannan. When
man5K
was coexpressed with
cipC1
in
C. acetobutylicum
, the recombinant strain secreted almost exclusively full-length mannanase, which bound to the scaffoldin miniCipC1, thus showing that complexation to the scaffoldin stabilized the enzyme. The secreted heterologous complex was found to be functional: it binds to crystalline cellulose via the carbohydrate binding module of the miniscaffoldin, and the complexed mannanase is active towards galactomannan. Taken together, these data show that
C. acetobutylicum
is a suitable host for the production, assembly, and secretion of heterologous minicellulosomes.
Analyses of Livestock Production, Waste Storage, and Pathogen Levels and Prevalences in Farm Manures
Authors: Hutchison M. L. , Walters L. D. , Avery S. M. , Munro F. , Moore A. 
Published: March 2005

ABSTRACTSurvey results describing the levels and prevalences of zoonotic agents in 1,549 livestock waste samples were analyzed for significance with livestock husbandry and farm waste management practices. Statistical analyses of survey data showed that livestock groups containing calves of <3 months of age, piglets, or lambs had higher prevalences and levels ofCampylobacterspp. andEscherichia coliO157 in their wastes. Younger calves that were still receiving milk, however, had significantly lower levels and prevalence ofE. coliO157. Furthermore, when wastes contained any form of bedding, they had lowered prevalences and levels of both pathogenicListeriaspp. andCampylobacter spp. Livestock wastes generated by stock consuming a diet composed principally of grass were less likely to harborE. coliO157 orSalmonellaspp. Stocking density did not appear to influence either the levels or prevalences of bacterial pathogens. Significant seasonal differences in prevalences were detected in cattle wastes;Listeriaspp. were more likely to be isolated in March to June, andE. coliO157 was more likely to be found in May and June. Factors such as livestock diet and age also had significant influence on the levels and prevalences of some zoonotic agents in livestock wastes. A number of the correlations identified could be used as the basis of a best-practice disposal document for farmers, thereby lowering the microbiological risks associated with applying manures of contaminated livestock to land.
Degradation of 1,4-Dioxane and Cyclic Ethers by an Isolated Fungus
Authors: Nakamiya Kunichika , Hashimoto Syunji , Ito Hiroyasu , Edmonds John S. , Morita Masatoshi 
Published: March 2005

ABSTRACT

By using 1,4-dioxane as the sole source of carbon, a 1,4-dioxane-degrading microorganism was isolated from soil. The fungus, termed strain A, was able to utilize 1,4-dioxane and many kinds of cyclic ethers as the sole source of carbon and was identified as
Cordyceps sinensis
from its 18S rRNA gene sequence. Ethylene glycol was identified as a degradation product of 1,4-dioxane by the use of deuterated 1,4-dioxane-
d
8
and gas chromatography-mass spectrometry analysis. A degradation pathway involving ethylene glycol, glycolic acid, and oxalic acid was proposed, followed by incorporation of the glycolic acid and/or oxalic acid via glyoxylic acid into the tricarboxylic acid cycle.
Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils
Authors: Wang Ya-Juan , Leadbetter Jared Renton 
Published: March 2005

ABSTRACT

Signal degradation impacts all communications. Although acyl-homoserine lactone (acyl-HSL) quorum-sensing signals are known to be degraded by defined laboratory cultures, little is known about their stability in nature. Here, we show that acyl-HSLs are biodegraded in soils sampled from diverse U.S. sites and by termite hindgut contents. When amended to samples at physiologically relevant concentrations,
14
C-labeled acyl-HSLs were mineralized to
14
CO
2
rapidly and, at most sites examined, without lag. A lag-free turf soil activity was characterized in further detail. Heating or irradiation of the soil prior to the addition of radiolabel abolished mineralization, whereas protein synthesis inhibitors did not. Mineralization exhibited an apparent

K
m

of 1.5 μM acyl-HSL, ca. 1,000-fold lower than that reported for a purified acyl-HSL lactonase. Under optimal conditions, acyl-HSL degradation proceeded at a rate of 13.4 nmol · h
−1
· g of fresh weight soil
−1
. Bioassays established that the final extent of signal inactivation was greater than for its full conversion to CO
2
but that the two processes were well coupled kinetically. A most probable number of 4.6 × 10
5
cells · g of turf soil
−1
degraded physiologically relevant amounts of hexanoyl-[1-
14
C]HSL to
14
CO
2
. It would take chemical lactonolysis months to match the level of signal decay achieved in days by the observed biological activity. Rapid decay might serve either to quiet signal cross talk that might otherwise occur between spatially separated microbial aggregates or as a full system reset. Depending on the context, biological signal decay might either promote or complicate cellular communications and the accuracy of population density-based controls on gene expression in species-rich ecosystems.
Rhizobial 16S rRNA and
dnaK
Genes: Mosaicism and the Uncertain Phylogenetic Placement of
Rhizobium galegae
Authors: Eardly B. D. , Nour S. M. , van Berkum P. , Selander R. K. 
Published: March 2005

ABSTRACT

The phylogenetic relatedness among 12 agriculturally important species in the order
Rhizobiales
was estimated by comparative 16S rRNA and
dnaK
sequence analyses. Two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. One group consisted of
Mesorhizobium loti
and
Mesorhizobium ciceri
, and the other group consisted of
Agrobacterium rhizogenes
,
Rhizobium tropici
,
Rhizobium etli
, and
Rhizobium leguminosarum
. Although bootstrap support for the placement of the remaining six species varied,
A. tumefaciens
,
Agrobacterium rubi
, and
Agrobacterium vitis
were consistently associated in the same subcluster. The three other species included
Rhizobium galegae
,
Sinorhizobium meliloti
, and
Brucella ovis
. Among these, the placement of
R. galegae
was the least consistent, in that it was placed flanking the
A. rhizogenes
-
Rhizobium
cluster in the
dnaK
nucleotide sequence trees, while it was placed with the other three
Agrobacterium
species in the 16S rRNA and the DnaK amino acid trees. In an effort to explain the inconsistent placement of
R. galegae
, we examined polymorphic site distribution patterns among the various species. Localized runs of nucleotide sequence similarity were evident between
R. galegae
and certain other species, suggesting that the
R. galegae
genes are chimeric. These results provide a tenable explanation for the weak statistical support often associated with the phylogenetic placement of
R. galegae
, and they also illustrate a potential pitfall in the use of partial sequences for species identification.
Fingerprinting of
Bacillus thuringiensis
Type Strains and Isolates by Using
Bacillus cereus
Group-Specific Repetitive Extragenic Palindromic Sequence-Based PCR Analysis
Authors: Reyes-Ramirez Arturo , Ibarra Jorge E. 
Published: March 2005

ABSTRACT

A total of 119
Bacillus thuringiensis
strains (83 type strains and 26 native isolates), as well as five
B. cereus
group species, were analyzed by repetitive extragenic palindromic sequence-based PCR analysis (Rep-PCR) fingerprinting. Primers Bc-REP-1 and Bc-REP-2 were specifically designed according to an extragenic 26-bp repeated sequence found in the six
B. cereus
group genomes reported. A total of 47 polymorphic bands were detected, and the patterns varied from 5 to 13 bands in number and from 0.2 to 3.8 kb in size. Virtually each type strain showed a distinctive
B. cereus
(Bc)-Rep-PCR pattern, except for
B. thuringiensis
serovars dakota (H serotype 15 [H15]) and sotto (H4a,4b), as well as serovars amagiensis (H29) and seoulensis (H35), which shared the same patterns. As expected, serovar entomocidus (H6) and its biovar subtoxicus showed an identical pattern; similarly, serovars sumiyoshiensis (H3a,3d) and fukuokaensis (H3a,3d,3e), which share two antigenic determinants, also showed identical Bc-Rep-PCR patterns. Interestingly, serovars israelensis (H14) and malaysiensis (H36), which share several phenotypic attributes, also showed identical Bc-Rep-PCR patterns. Native, coleopteran-active strains, including the self-agglutinated LBIT-74 strain, showed Bc-Rep-PCR patterns identical or very similar to that of the tenebrionis strain. Likewise, native mosquitocidal strains (including some self-agglutinated strains) also showed patterns identical or very similar to that of the serovar israelensis IPS-82 strain. Additionally, native β-exotoxin-producing strains from serovar thuringiensis showed patterns identical to that of the
B. thuringiensis
type strain. The
B. cereus
group-specific Bc-Rep-PCR fingerprinting technique was shown to be highly discriminative, fast, easy, and able to identify
B. thuringiensis
serotypes, including nonflagellar and self-agglutinated strains.
The Doubly Phosphorylated Form of HPr, HPr(Ser-P)(His∼P), Is Abundant in Exponentially Growing Cells ofStreptococcus thermophilusand Phosphorylates the Lactose Transporter LacS as Efficiently as HPr(His∼P)
Authors: Cochu Armelle , Roy Denis , Vaillancourt Katy , LeMay Jean-Dominique , Casabon Israël , Frenette Michel , Moineau Sylvain , Vadeboncoeur Christian 
Published: March 2005

ABSTRACTInStreptococcus thermophilus, lactose is taken up by LacS, a transporter that comprises a membrane translocator domain and a hydrophilic regulatory domain homologous to the IIA proteins and protein domains of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). The IIA domain of LacS (IIALacS) possesses a histidine residue that can be phosphorylated by HPr(His∼P), a protein component of the PTS. However, determination of the cellular levels of the different forms of HPr, namely, HPr, HPr(His∼P), HPr(Ser-P), and HPr(Ser-P)(His∼P), in exponentially lactose-growing cells revealed that the doubly phosphorylated form of HPr represented 75% and 25% of the total HPr inS. thermophilusATCC 19258 andS. thermophilusSMQ-301, respectively. Experiments conducted with [32P]PEP and purified recombinantS. thermophilusATCC 19258 proteins (EI, HPr, and IIALacS) showed that IIALacSwas reversibly phosphorylated by HPr(Ser-P)(His∼P) at a rate similar to that measured with HPr(His∼P). Sequence analysis of the IIALacSprotein domains from severalS. thermophilusstrains indicated that they can be divided into two groups on the basis of their amino acid sequences. The amino acid sequence of IIALacSfrom group I, to which strain 19258 belongs, differed from that of group II at 11 to 12 positions. To ascertain whether IIALacSfrom group II could also be phosphorylated by HPr(His∼P) and HPr(Ser-P)(His∼P), in vitro phosphorylation experiments were conducted with purified proteins fromStreptococcus salivariusATCC 25975, which possesses a IIALacSvery similar to group IIS. thermophilusIIALacS. The results indicated thatS. salivariusIIALacSwas phosphorylated by HPr(Ser-P)(His∼P) at a higher rate than that observed with HPr(His∼P). Our results suggest that the reversible phosphorylation of IIALacSinS. thermophilusis accomplished by HPr(Ser-P)(His∼P) as well as by HPr(His∼P).
16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order “Rhodocyclales”
Authors: Loy Alexander , Schulz Claudia , Lücker Sebastian , Schöpfer-Wendels Andreas , Stoecker Kilian , Baranyi Christian , Lehner Angelika , Wagner Michael 
Published: March 2005

ABSTRACTFor simultaneous identification of members of the betaproteobacterial order “Rhodocyclales” in environmental samples, a 16S rRNA gene-targeted oligonucleotide microarray (RHC-PhyloChip) consisting of 79 probes was developed. Probe design was based on phylogenetic analysis of available 16S rRNA sequences from all cultured and as yet uncultured members of the “Rhodocyclales.” The multiple nested probe set was evaluated for microarray hybridization with 16S rRNA gene PCR amplicons from 29 reference organisms. Subsequently, the RHC-PhyloChip was successfully used for cultivation-independent “Rhodocyclales” diversity analysis in activated sludge from an industrial wastewater treatment plant. The implementation of a newly designed “Rhodocyclales”-selective PCR amplification system prior to microarray hybridization greatly enhanced the sensitivity of the RHC-PhyloChip and thus enabled the detection of “Rhodocyclales” populations with relative abundances of less than 1% of all bacteria (as determined by fluorescence in situ hybridization) in the activated sludge. The presence of as yet unculturedZoogloea-,Ferribacterium/Dechloromonas-, andSterolibacterium-related bacteria in the industrial activated sludge, as indicated by the RHC-PhyloChip analysis, was confirmed by retrieval of their 16S rRNA gene sequences and subsequent phylogenetic analysis, demonstrating the suitability of the RHC-PhyloChip as a novel monitoring tool for environmental microbiology.
Isolation and Characterization of Novel Giant
Stenotrophomonas maltophilia
Phage φSMA5
Authors: Chang Hsiao-Chuan , Chen Chiy-Rong , Lin Juey-Wen , Shen Gwan-Han , Chang Kai-Ming , Tseng Yi-Hsiung , Weng Shu-Fen 
Published: March 2005

ABSTRACT

Stenotrophomonas maltophilia
is one of the most prevalent opportunistic bacteria causing nosocomial infections. It has become problematic because most of the isolates are resistant to multiple antibiotics, and therefore, development of phage therapy has attracted strong attention. In this study, eight
S. maltophilia
phages were isolated from clinical samples including patient specimens, catheter-related devices, and wastewater. These phages can be divided into four distinct groups based on host range and digestibility of the phage DNAs with different restriction endonucleases. One of them, designated φSMA5, was further characterized. Electron microscopy showed it resembled
Myoviridae
, with an isometric head (90 nm in diameter), a tail (90 nm long), a baseplate (25 nm wide), and short tail fibers. The φSMA5 double-stranded DNA, refractory to digestion by most restriction enzymes, was tested and estimated to be 250 kb by pulsed-field gel electrophoresis. This genome size is second to that of the largest phage, φKZ of
Pseudomonas aeruginosa
. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, 25 virion proteins were visualized. N-terminal sequencing of four of them suggested that each of them might have had its N terminus cleaved off. Among the 87
S. maltophilia
strains collected in this study, only 61 were susceptible to φSMA5, indicating that more phages are needed toward a phage therapy strategy. Since literature search yielded no information about
S. maltophilia
phages, φSMA5 appears to be the first reported.
Flow-Cytometric Cell Sorting and Subsequent Molecular Analyses for Culture-Independent Identification of Bacterioplankton Involved in Dimethylsulfoniopropionate Transformations
Authors: Mou Xiaozhen , Moran Mary Ann , Stepanauskas Ramunas , González José M. , Hodson Robert E. 
Published: March 2005

ABSTRACT

Marine bacterioplankton transform dimethylsulfoniopropionate (DMSP) into the biogeochemically important and climatically active gas dimethylsulfide. In order to identify specific bacterial taxa mediating DMSP processing in a natural marine ecosystem, we amended water samples from a southeastern U.S. salt marsh with 20 μM DMSP and tracked community shifts with flow cytometry (FCM) coupled to 16S rRNA gene analyses. In two out of four seasons studied, DMSP amendments induced the formation of distinct bacterioplankton populations with elevated nucleic acid (NA) content within 24 h, indicative of cells actively utilizing DMSP. The 16S rRNA genes of the cells with and without elevated NA content were analyzed following cell sorting and PCR amplification with sequencing and terminal restriction fragment length polymorphism approaches. Compared to cells in the control FCM populations, bacteria with elevated NA content in the presence of DMSP were relatively enriched in taxa related to
Loktanella
,
Oceanicola
, and
Sulfitobacter
(
Roseobacter
lineage, α
-Proteobacteria
);
Caulobacter
(α
-Proteobacteria
); and
Brachymonas
and
Xenophilus
(β
-Proteobacteria
) in the May-02 sample and to
Ketogulonicigenium
(
Roseobacter
lineage, α
-Proteobacteria
) and novel γ
-Proteobacteria
in the Sept-02 sample. Our study suggests that diverse bacterioplankton participate in the metabolism of DMSP in coastal marine systems and that their relative importance varies temporally.
Quantitative Molecular Assay for Fingerprinting Microbial Communities of Wastewater and Estrogen-Degrading Consortia
Authors: Yu Chang-Ping , Ahuja Rajiv , Sayler Gary , Chu Kung-Hui 
Published: March 2005

ABSTRACTA quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-RFLP) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. The real-time-t-RFLP assay was developed by incorporating the quantitative feature of real-time PCR and the fingerprinting feature of t-RFLP analysis. The assay was validated by using a model microbial community containing three pure strains, anEscherichia colistrain (gram negative), aPseudomonas fluorescensstrain (gram negative), and aBacillus thuringiensisstrain (gram positive). Subsequently, the real-time-t-RFLP assay was applied to and proven to be useful for environmental samples; the richness and abundance of species in microbial communities (expressed as the number of 16S rRNA gene copies of each ribotype per milliliter) of wastewater and estrogen-degrading consortia (enriched with 17α-estradiol, 17β-estradiol, or estrone) were successfully characterized. The results of this study strongly suggested that the real-time-t-RFLP assay can be a powerful molecular tool for gaining insight into microbial communities in various engineered systems and natural habitats.