bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodegradation ofcis-1,4-Polyisoprene Rubbers by Distinct Actinomycetes: Microbial Strategies and Detailed Surface Analysis
Authors: Linos Alexandros , Berekaa Mahmoud M. , Reichelt Rudolf , Keller Ulrike , Schmitt Jürgen , Flemming Hans-Curt , Kroppenstedt Reiner M. , Steinbüchel Alexander 
Published: July 2002

ABSTRACTSeveral actinomycetes isolated from nature were able to use both natural rubber (NR) and syntheticcis-1,4-polyisoprene rubber (IR) as a sole source of carbon. According to their degradation behavior, they were divided into two groups. Representatives of the first group grew only in direct contact to the rubber substrate and led to considerable disintegration of the material during cultivation. The second group consisted of weaker rubber decomposers that did not grow adhesively, as indicated by the formation of clear zones (translucent halos) around bacterial colonies after cultivation on NR dispersed in mineral agar. Taxonomic analysis of four selected strains based on 16S rRNA similarity examinations revealed twoGordoniasp. strains, VH2 and Kb2, and oneMycobacterium fortuitumstrain, NF4, belonging to the first group as well as oneMicromonospora aurantiacastrain, W2b, belonging to the second group. Schiff's reagent staining tests performed for each of the strains indicated colonization of the rubber surface, formation of a bacterial biofilm, and occurrence of compounds containing aldehyde groups during cultivation with NR latex gloves. Detailed analysis by means of scanning electron microscopy yielded further evidence for the two different microbial strategies and clarified the colonization efficiency. Thereby, strains VH2, Kb2, and NF4 directly adhered to and merged into the rubber material, while strain W2b produced mycelial corridors, especially on the surface of IR. Fourier transform infrared spectroscopy comprising the attenuated total reflectance technique was applied on NR latex gloves overgrown by cells of theGordoniastrains, which were the strongest rubber decomposers. Spectra demonstrated the decrease in number ofcis-1,4 double bonds, the formation of carbonyl groups, and the change of the overall chemical environment, indicating that an oxidative attack at the double bond is the first metabolic step of the biodegradation process.
Bile Salt Hydrolase of
Bifidobacterium longum
—Biochemical and Genetic Characterization
Authors: Tanaka Hiroshi , Hashiba Honoo , Kok Jan , Mierau Igor 
Published: July 2002

ABSTRACT

A bile salt hydrolase (BSH) was isolated from
Bifidobacterium longum
SBT2928, purified, and characterized. Furthermore, we describe for the first time cloning and analysis of the gene encoding BSH (
bsh
) in a member of the genus
Bifidobacterium
. The enzyme has a native molecular weight of 125,000 to 130,000 and a subunit molecular weight of 35,024, as determined from the deduced amino acid sequence, indicating that the enzyme is a tetramer. The pH optimum of
B. longum
BSH is between 5 and 7, and the temperature optimum is 40°C. The enzyme is strongly inhibited by thiol enzyme inhibitors, indicating that a Cys residue is likely to be involved in the catalytic reaction. The BSH of
B. longum
can hydrolyze all six major human bile salts and at least two animal bile salts. A slight preference for glycine-conjugated bile acids was detected based on both the specificity and the

K
m

values. The nucleotide sequence of
bsh
was determined and used for homology studies, transcript analysis, and construction and analysis of various mutants. The levels of homology with BSH of other bacteria and with penicillin V acylase (PVA) of
Bacillus sphaericus
were high. On the basis of the similarity of BSH and PVA, whose crystal structure has been elucidated, BSH can be classified as an N-terminal nucleophile hydrolase with Cys as the N-terminal amino acid. This classification was confirmed by the fact that a Cys1Ala exchange by site-directed mutagenesis resulted in an inactive protein. Reverse transcription-PCR experiments revealed that
bsh
is part of an operon containing at least two genes,
bsh
and
glnE
(GlnE is glutamine synthetase adenylyltransferase). Two UV-induced BSH-negative mutants and one spontaneous BSH-negative mutant were isolated from
B. longum
SBT2928 cultures and characterized. These mutants had point mutations that inactivated
bsh
by premature termination, frameshift, or amino acid exchange.
Restriction-Site-Specific PCR as a Rapid Test To Detect Enterohemorrhagic
Escherichia coli
O157:H7 Strains in Environmental Samples
Authors: Kimura Richard , Mandrell Robert E. , Galland John C. , Hyatt Doreene , Riley Lee W. 
Published: July 2002

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 is an important food-borne pathogen in industrialized countries. We developed a rapid and simple test for detecting
E. coli
O157:H7 using a method based on restriction site polymorphisms. Restriction-site-specific PCR (RSS-PCR) involves the amplification of DNA fragments using primers based on specific restriction enzyme recognition sequences, without the use of endonucleases, to generate a set of amplicons that yield “fingerprint” patterns when resolved electrophoretically on an agarose gel. The method was evaluated in a blinded study of
E. coli
isolates obtained from environmental samples collected at beef cattle feedyards. The 54 isolates were all initially identified by a commonly used polyclonal antibody test as belonging to O157:H7 serotype. They were retested by anti-O157 and anti-H7 monoclonal antibody enzyme-linked immunosorbent assay (ELISA). The RSS-PCR method identified all 28 isolates that were shown to be
E. coli
O157:H7 by the monoclonal antibody ELISA as belonging to the O157:H7 serotype. Of the remaining 26 ELISA-confirmed non-O157:H7 strains, the method classified 25 strains as non-O157:H7. The specificity of the RSS-PCR results correlated better with the monoclonal antibody ELISA than with the polyclonal antibody latex agglutination tests. The RSS-PCR method may be a useful test to distinguish
E. coli
O157:H7 from a large number of
E. coli
isolates from environmental samples.
The Common Nodulation Genes of
Astragalus sinicus
Rhizobia Are Conserved despite Chromosomal Diversity
Authors: Zhang Xue-Xian , Turner Sarah L. , Guo Xian-Wu , Yang Hui-Jun , Debellé Frédéric , Yang Guo-Ping , Dénarié Jean , Young J. Peter W. , Li Fu-Di 
Published: July 2002

ABSTRACT

The nodulation genes of
Mesorhizobium
sp. (
Astragalus sinicus
) strain 7653R were cloned by functional complementation of
Sinorhizobium meliloti nod
mutants. The common
nod
genes,
nodD
,
nodA
, and
nodBC
, were identified by heterologous hybridization and sequence analysis. The
nodA
gene was found to be separated from
nodBC
by approximately 22 kb and was divergently transcribed. The 2.0-kb
nodDBC
region was amplified by PCR from 24 rhizobial strains nodulating
A. sinicus
, which represented different chromosomal genotypes and geographic origins. No polymorphism was found in the size of PCR products, suggesting that the separation of
nodA
from
nodBC
is a common feature of
A. sinicus
rhizobia. Sequence analysis of the PCR-amplified
nodA
gene indicated that seven strains representing different 16S and 23S ribosomal DNA genotypes had identical
nodA
sequences. These data indicate that, whereas microsymbionts of
A. sinicus
exhibit chromosomal diversity, their nodulation genes are conserved, supporting the hypothesis of horizontal transfer of
nod
genes among diverse recipient bacteria.
Fungal Colonization and Biodeterioration of Plasticized Polyvinyl Chloride
Authors: Webb Jeremy S. , Nixon Marianne , Eastwood Ian M. , Greenhalgh Malcolm , Robson Geoffrey D. , Handley Pauline S. 
Published: July 2002

ABSTRACTSignificant substratum damage can occur when plasticized PVC (pPVC) is colonized by microorganisms. We investigated microbial colonization of pPVC in an in situ, longitudinal study. Pieces of pPVC containing the plasticizers dioctyl phthalate and dioctyl adipate (DOA) were exposed to the atmosphere for up to 2 years. Fungal and bacterial populations were quantified, and colonizing fungi were identified by rRNA gene sequencing and morphological characteristics.Aureobasidium pullulanswas the principal colonizing fungus, establishing itself on the pPVC between 25 and 40 weeks of exposure. A group of yeasts and yeast-like fungi, includingRhodotorula aurantiacaandKluyveromycesspp., established themselves on the pPVC much later (after 80 weeks of exposure). Numerically, these organisms dominatedA. pullulansafter 95 weeks, with a mean viable count ± standard error of 1,000 ± 200 yeast CFU cm−2, compared to 390 ± 50A. pullulansCFU cm−2. No bacterial colonization was observed. We also used in vitro tests to characterize the deteriogenic properties of fungi isolated from the pPVC. All strains ofA. pullulanstested could grow with the intact pPVC formulation as the sole source of carbon, degrade the plasticizer DOA, produce extracellular esterase, and cause weight loss of the substratum during growth in vitro. In contrast, several yeast isolates could not grow on pPVC or degrade DOA. These results suggest that microbial succession may occur during the colonization of pPVC and thatA. pullulansis critical to the establishment of a microbial community on pPVC.
Analysis of
gyrB
and
toxR
Gene Sequences of
Vibrio hollisae
and Development of
gyrB
- and
toxR
-Targeted PCR Methods for Isolation of
V. hollisae
from the Environment and Its Identification
Authors: Vuddhakul Varaporn , Nakai Toshihiro , Matsumoto Chiho , Oh Takanori , Nishino Takeshi , Chen Chien-Hsien , Nishibuchi Mitsuaki , Okuda Jun 
Published: July 2002

ABSTRACT

Isolation of
Vibrio hollisae
strains, particularly from the environment, is rare. This may be due, in part, to the difficulty encountered when using conventional biochemical tests to identify the microorganism. In this study, we evaluated whether two particular genes may be useful for the identification of
V. hollisae
. The two genes are presumed to be conserved among the bacterial species (
gyrB
) or among the species of the genus
Vibrio
(
toxR
). A portion of the
gyrB
sequence of
V. hollisae
was cloned by PCR using a set of degenerate primers. The sequence showed 80% identity with the corresponding
Vibrio parahaemolyticus gyrB
sequence. The
toxR
gene of
V. hollisae
was cloned utilizing a
htpG
gene probe derived from the
V. parahaemolyticus htpG
gene, which is known to be linked to the
toxR
gene in
V. hollisae
. The coding sequence of the cloned
V. hollisae toxR
gene had 59% identity with the
V. parahaemolyticus toxR
coding sequence. The results of DNA colony hybridization tests using the DNA probes derived from the two genes of
V. hollisae
indicated that these gene sequences could be utilized for differentiation of
V. hollisae
from other
Vibrio
species and from microorganisms found in marine fish. PCR methods targeting the two gene sequences were established. Both PCR methods were shown to specifically detect the respective target sequences of
V. hollisae
but not other organisms. A strain of
V. hollisae
added at a concentration of 1 to 10
2
CFU/ml to alkaline peptone water containing a seafood sample could be detected by a 4-h enrichment incubation in alkaline peptone water at 37°C followed by quick DNA extraction with an extraction kit and 35-cycle PCR specific for the
V. hollisae toxR
gene. We conclude that screening of seafood samples by this 35-cycle,
V. hollisae toxR
-specific PCR, followed by isolation on a differential medium and identification by the above
htpG
- and
toxR
-targeted PCR methods, can be useful for isolation from the environment and identification of
V. hollisae
.
Purification and Characterization of Novel Antifungal Compounds from the Sourdough
Lactobacillus plantarum
Strain 21B
Authors: Lavermicocca Paola , Valerio Francesca , Evidente Antonio , Lazzaroni Silvia , Corsetti Aldo , Gobbetti Marco 
Published: July 2002

ABSTRACT

Sourdough lactic acid bacteria were selected for antifungal activity by a conidial germination assay. The 10-fold-concentrated culture filtrate of
Lactobacillus plantarum
21B grown in wheat flour hydrolysate almost completely inhibited
Eurotium repens
IBT18000,
Eurotium rubrum
FTDC3228,
Penicillium corylophilum
IBT6978,
Penicillium roqueforti
IBT18687,
Penicillium expansum
IDM/FS2,
Endomyces fibuliger
IBT605 and IDM3812,
Aspergillus niger
FTDC3227 and IDM1,
Aspergillus flavus
FTDC3226,
Monilia sitophila
IDM/FS5, and
Fusarium graminearum
IDM623. The nonconcentrated culture filtrate of
L. plantarum
21B grown in whole wheat flour hydrolysate had similar inhibitory activity. The activity was fungicidal. Calcium propionate at 3 mg ml
−1
was not effective under the same assay conditions, while sodium benzoate caused inhibition similar to
L. plantarum
21B. After extraction with ethyl acetate, preparative silica gel thin-layer chromatography, and chromatographic and spectroscopic analyses, novel antifungal compounds such as phenyllactic and 4-hydroxy-phenyllactic acids were identified in the culture filtrate of
L. plantarum
21B. Phenyllactic acid was contained at the highest concentration in the bacterial culture filtrate and had the highest activity. It inhibited all the fungi tested at a concentration of 50 mg ml
−1
except for
P. roqueforti
IBT18687 and
P. corylophilum
IBT6978 (inhibitory concentration, 166 mg ml
−1
).
L. plantarum
20B, which showed high antimold activity, was also selected. Preliminary studies showed that phenyllactic and 4-hydroxy-phenyllactic acids were also contained in the bacterial culture filtrate of strain 20B. Growth of
A. niger
FTDC3227 occurred after 2 days in breads started with
Saccharomyces cerevisiae
141 alone or with
S. cerevisiae
and
Lactobacillus brevis
1D, an unselected but acidifying lactic acid bacterium, while the onset of fungal growth was delayed for 7 days in bread started with
S. cerevisiae
and selected
L. plantarum
21B.
The Sigma Factor AlgU (AlgT) Controls Exopolysaccharide Production and Tolerance towards Desiccation and Osmotic Stress in the Biocontrol Agent
Pseudomonas fluorescens
CHA0
Authors: Schnider-Keel Ursula , Lejbølle Kirsten Bang , Baehler Eric , Haas Dieter , Keel Christoph 
Published: July 2002

ABSTRACT

A variety of stress situations may affect the activity and survival of plant-beneficial pseudomonads added to soil to control root diseases. This study focused on the roles of the sigma factor AlgU (synonyms, AlgT, RpoE, and ς
22
) and the anti-sigma factor MucA in stress adaptation of the biocontrol agent
Pseudomonas fluorescens
CHA0. The
algU
-
mucA
-
mucB
gene cluster of strain CHA0 was similar to that of the pathogens
Pseudomonas aeruginosa
and
Pseudomonas syringae
. Strain CHA0 is naturally nonmucoid, whereas a
mucA
deletion mutant or
algU
-overexpressing strains were highly mucoid due to exopolysaccharide overproduction. Mucoidy strictly depended on the global regulator GacA. An
algU
deletion mutant was significantly more sensitive to osmotic stress than the wild-type CHA0 strain and the
mucA
mutant were. Expression of an
algU
′
-
′
lacZ
reporter fusion was induced severalfold in the wild type and in the
mucA
mutant upon exposure to osmotic stress, whereas a lower, noninducible level of expression was observed in the
algU
mutant. Overexpression of
algU
did not enhance tolerance towards osmotic stress. AlgU was found to be essential for tolerance of
P. fluorescens
towards desiccation stress in a sterile vermiculite-sand mixture and in a natural sandy loam soil. The size of the population of the
algU
mutant declined much more rapidly than the size of the wild-type population at soil water contents below 5%. In contrast to its role in pathogenic pseudomonads, AlgU did not contribute to tolerance of
P. fluorescens
towards oxidative and heat stress. In conclusion, AlgU is a crucial determinant in the adaptation of
P. fluorescens
to dry conditions and hyperosmolarity, two major stress factors that limit bacterial survival in the environment.
gfp
-Based
N
-Acyl Homoserine-Lactone Sensor Systems for Detection of Bacterial Communication
Authors: Andersen Jens Bo , Heydorn Arne , Hentzer Morten , Eberl Leo , Geisenberger Otto , Christensen Bjarke Bak , Molin So/ren , Givskov Michael 
Published: July 2002

ABSTRACT

In order to perform single-cell analysis and online studies of
N
-acyl homoserine lactone (AHL)-mediated communication among bacteria, components of the
Vibrio fischeri
quorum sensor encoded by

luxR-P
luxI

have been fused to modified versions of
gfp
mut3∗ genes encoding unstable green fluorescent proteins. Bacterial strains harboring this green fluorescent sensor detected a broad spectrum of AHL molecules and were capable of sensing the presence of 5 nM
N
-3-oxohexanoyl-
l
-homoserine lactone in the surroundings. In combination with epifluorescent microscopy, the sensitivity of the sensor enabled AHL detection at the single-cell level and allowed for real-time measurements of fluctuations in AHL concentrations. This green fluorescent AHL sensor provides a state-of-the-art tool for studies of communication between the individuals present in mixed bacterial communities.
Genetic Evidence for a Defective Xylan Degradation Pathway in
Lactococcus lactis
Authors: Erlandson Karn A. , Delamarre Soazig C. , Batt Carl A. 
Published: July 2002

ABSTRACT

Genetic and biochemical evidence for a defective xylan degradation pathway was found linked to the xylose operon in three lactococcal strains,
Lactococcus lactis
210,
L. lactis
IO-1, and
L. lactis
NRRL B-4449. Immediately downstream of the xylulose kinase gene (
xylB
) (K. A. Erlandson, J.-H. Park, W. El Khal, H.-H. Kao, P. Basaran, S. Brydges, and C. A. Batt, Appl. Environ. Microbiol. 66:3974–3980, 1999) are two open reading frames encoding a mutarotase (
xylM
) and a xyloside transporter (
xynT
) and a partial open reading frame encoding a β-xylosidase (
xynB
). These are functions previously unreported for lactococci or lactobacilli. The mutarotase activity of the putative
xylM
gene product was confirmed by overexpression of the
L. lactis
enzyme in
Escherichia coli
and purification of recombinant XylM. We hypothesize that the mutarotase links xylan degradation to xylose metabolism due to the anomeric preference of xylose isomerase. In addition, Northern hybridization experiments suggested that the
xylM
and
xynTB
genes are cotranscribed with the
xylRAB
genes, responsible for xylose metabolism. Although none of the three strains appeared to metabolize xylan or xylobiose, they exhibited xylosidase activity, and
L. lactis
IO-1 and
L. lactis
NRRL B-4449 had functional mutarotases.
Occurrence and Diversity of Tetracycline Resistance Genes in Lagoons and Groundwater Underlying Two Swine Production Facilities
Authors: Chee-Sanford J. C. , Aminov R. I. , Krapac I. J. , Garrigues-Jeanjean N. , Mackie R. I. 
Published: July 2002

ABSTRACT

In this study, we used PCR typing methods to assess the presence of tetracycline resistance determinants conferring ribosomal protection in waste lagoons and in groundwater underlying two swine farms. All eight classes of genes encoding this mechanism of resistance [
tet
(O),
tet
(Q),
tet
(W),
tet
(M),
tetB
(P),
tet
(S),
tet
(T), and
otrA
] were found in total DNA extracted from water of two lagoons. These determinants were found to be seeping into the underlying groundwater and could be detected as far as 250 m downstream from the lagoons. The identities and origin of these genes in groundwater were confirmed by PCR-denaturing gradient gel electrophoresis and sequence analyses. Tetracycline-resistant bacterial isolates from groundwater harbored the
tet
(M) gene, which was not predominant in the environmental samples and was identical to
tet
(M) from the lagoons. The presence of this gene in some typical soil inhabitants suggests that the vector of antibiotic resistance gene dissemination is not limited to strains of gastrointestinal origin carrying the gene but can be mobilized into the indigenous soil microbiota. This study demonstrated that
tet
genes occur in the environment as a direct result of agriculture and suggested that groundwater may be a potential source of antibiotic resistance in the food chain.
Does the High Nucleic Acid Content of Individual Bacterial Cells Allow Us To Discriminate between Active Cells and Inactive Cells in Aquatic Systems?
Authors: Lebaron Philippe , Servais Pierre , Agogué Helene , Courties Claude , Joux Fabien 
Published: July 2002

ABSTRACT
The nucleic acid contents of individual bacterial cells as determined with three different nucleic acid-specific fluorescent dyes (SYBR I, SYBR II, and SYTO 13) and flow cytometry were compared for different seawater samples. Similar fluorescence patterns were observed, and bacteria with high apparent nucleic acid contents (HNA) could be discriminated from bacteria with low nucleic acid contents (LNA). The best discrimination between HNA and LNA cells was found when cells were stained with SYBR II. Bacteria in different water samples collected from seven freshwater, brackish water, and seawater ecosystems were prelabeled with tritiated leucine and then stained with SYBR II. After labeling and staining, HNA, LNA, and total cells were sorted by flow cytometry, and the specific activity of each cellular category was determined from leucine incorporation rates. The HNA cells were responsible for most of the total bacterial production, and the specific activities of cells in the HNA population varied between samples by a factor of seven. We suggest that nucleic acid content alone can be a better indicator of the fraction of growing cells than total counts and that this approach should be combined with other fluorescent physiological probes to improve detection of the most active cells in aquatic systems.
Genotypes Associated with Virulence in Environmental Isolates of
Vibrio cholerae
Authors: Rivera Irma N. G. , Chun Jongsik , Huq Anwar , Sack R. Brad , Colwell Rita R. 
Published: July 2002

ABSTRACT

Vibrio cholerae
is an autochthonous inhabitant of riverine and estuarine environments and also is a facultative pathogen for humans. Genotyping can be useful in assessing the risk of contracting cholera, intestinal, or extraintestinal infections via drinking water and/or seafood. In this study, environmental isolates of
V. cholerae
were examined for the presence of
ctxA, hlyA, ompU, stn/sto, tcpA, tcpI, toxR
, and
zot
genes, using multiplex PCR. Based on
tcpA
and
hlyA
gene comparisons, the strains could be grouped into Classical and El Tor biotypes. The
toxR, hlyA
, and
ompU
genes were present in 100, 98.6, and 87.0% of the
V. cholerae
isolates, respectively. The CTX genetic element and toxin-coregulated pilus El Tor (
tcpA
ET) gene were present in all toxigenic
V. cholerae
O1 and
V. cholerae
O139 strains examined in this study. Three of four nontoxigenic
V. cholerae
O1 strains contained
tcpA
ET. Interestingly, among the isolates of
V. cholerae
non-O1/non-O139, two had
tcpA
Classical, nine contained
tcpA
El Tor, three showed homology with both biotype genes, and four carried the
ctxA
gene. The
stn/sto
genes were present in 28.2% of the non-O1/non-O139 strains, in 10.5% of the toxigenic
V. cholerae
O1, and in 14.3% of the O139 serogroups. Except for
stn/sto
genes, all of the other genes studied occurred with high frequency in toxigenic
V. cholerae
O1 and O139 strains. Based on results of this study, surveillance of non-O1/non-O139
V. cholerae
in the aquatic environment, combined with genotype monitoring using
ctxA, stn/sto
, and
tcpA
ET genes, could be valuable in human health risk assessment.