bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of Polychlorinated-Biphenyl-Degrading Bacteria in the Presence of Biphenyl and Chlorobiphenyls Generates Oxidative Stress and Massive Accumulation of Inorganic Polyphosphate
Authors: Chávez Francisco P. , Lünsdorf Heinrich , Jerez Carlos A. 
Published: May 2004

ABSTRACT

Inorganic polyphosphate (polyP) plays a significant role in increasing bacterial cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. Using transmission electron microscopy of the polychlorinated biphenyl (PCB)-degrading bacterium
Pseudomonas
sp. strain B4 grown in defined medium with biphenyl as the sole carbon source, we observed large and abundant electron-dense granules at all stages of growth and following a shift from glucose to biphenyl or chlorobiphenyls. Using energy dispersive X-ray analysis and electron energy loss spectroscopy with an integrated energy-filtered transmission electron microscope, we demonstrated that these granules were mainly composed of phosphate. Using sensitive enzymatic methods to quantify cellular polyP, we confirmed that this polymer accumulates in PCB-degrading bacteria when they grow in the presence of biphenyl and chlorobiphenyls. Concomitant increases in the levels of the general stress protein GroEl and reactive oxygen species were also observed in chlorobiphenyl-grown cells, indicating that these bacteria adjust their physiology with a stress response when they are confronted with compounds that serve as carbon and energy sources and at the same time are chemical stressors.
In Vivo Study of
Trichoderma
-Pathogen-Plant Interactions, Using Constitutive and Inducible Green Fluorescent Protein Reporter Systems
Authors: Lu Zexun , Tombolini Riccardo , Woo Sheridan , Zeilinger Susanne , Lorito Matteo , Jansson Janet K. 
Published: May 2004

ABSTRACT

Plant tissue colonization by
Trichoderma atroviride
plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in situ interactions between
gfp
-tagged biocontrol strains of
T. atroviride
and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of
T. atroviride
adhered to
Pythium ultimum
mycelia in coculture experiments. In mycoparasitic interactions of
T. atroviride
with
P. ultimum
or
Rhizoctonia solani
, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of
T. atroviride
mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of
P. ultimum
by
T. atroviride
occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific
Trichoderma
genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or
Rhizoctonia
by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.
Novel Forms of Structural Integration between Microbes and a Hydrothermal Vent Gastropod from the Indian Ocean
Authors: Goffredi Shana K. , Warén Anders , Orphan Victoria J. , Van Dover Cindy L. , Vrijenhoek Robert C. 
Published: May 2004

ABSTRACT
Here we describe novel forms of structural integration between endo- and episymbiotic microbes and an unusual new species of snail from hydrothermal vents in the Indian Ocean. The snail houses a dense population of γ-proteobacteria within the cells of its greatly enlarged esophageal gland. This tissue setting differs from that of all other vent mollusks, which harbor sulfur-oxidizing endosymbionts in their gills. The significantly reduced digestive tract, the isotopic signatures of the snail tissues, and the presence of internal bacteria suggest a dependence on chemoautotrophy for nutrition. Most notably, this snail is unique in having a dense coat of mineralized scales covering the sides of its foot, a feature seen in no other living metazoan. The scales are coated with iron sulfides (pyrite and greigite) and heavily colonized by ε- and δ-proteobacteria, likely participating in mineralization of the sclerites. This novel metazoan-microbial collaboration illustrates the great potential of organismal adaptation in chemically and physically challenging deep-sea environments.
Vanadium Respiration by
Geobacter metallireducens
: Novel Strategy for In Situ Removal of Vanadium from Groundwater
Authors: Ortiz-Bernad Irene , Anderson Robert T. , Vrionis Helen A. , Lovley Derek R. 
Published: May 2004

ABSTRACT

Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the
Geobacteraceae
, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V),
Geobacter metallireducens
was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of
Geobacteraceae
in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that
G. metallireducens
can grow via vanadium(V) respiration and that stimulating the activity of
Geobacteraceae
, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.
Anaerobic Nitrogen-Fixing Consortia Consisting of Clostridia Isolated from Gramineous Plants
Authors: Minamisawa Kiwamu , Nishioka Kiyo , Miyaki Taro , Ye Bin , Miyamoto Takuya , You Mu , Saito Asami , Saito Masanori , Barraquio Wilfredo L. , Teaumroong Neung , Sein Than , Sato Tadashi 
Published: May 2004

ABSTRACT

We report here the existence of anaerobic nitrogen-fixing consortia (ANFICOs) consisting of N
2
-fixing clostridia and diverse nondiazotrophic bacteria in nonleguminous plants; we found these ANFICOs while attempting to overcome a problem with culturing nitrogen-fixing microbes from various gramineous plants. A major feature of ANFICOs is that N
2
fixation by the anaerobic clostridia is supported by the elimination of oxygen by the accompanying bacteria in the culture. In a few ANFICOs, nondiazotrophic bacteria specifically induced nitrogen fixation of the clostridia in culture. ANFICOs are widespread in wild rice species and pioneer plants, which are able to grow in unfavorable locations. These results indicate that clostridia are naturally occurring endophytes in gramineous plants and that clostridial N
2
fixation arises in association with nondiazotrophic endophytes.
Negative Cross-Communication among Wheat Rhizosphere Bacteria: Effect on Antibiotic Production by the Biological Control Bacterium
Pseudomonas aureofaciens
30-84
Authors: Morello J. E. , Pierson E. A. , Pierson L. S. 
Published: May 2004

ABSTRACT

Phenazine antibiotic production in the biological control bacterium
Pseudomonas aureofaciens
30-84 is regulated in part via the PhzR/PhzI
N
-acyl homoserine lactone (AHL) system. Previous work showed that a subpopulation of the wheat rhizosphere community positively affected phenazine gene expression in strain 30-84 via AHL signals (E. A. Pierson, D. W. Wood, J. A. Cannon, F. M. Blachere, and L. S. Pierson III, Mol. Plant-Microbe Interact.
11:
1078-1084, 1998). In the present work, a second subpopulation, one that negatively affected phenazine gene expression, was identified from this rhizosphere community. Strain 30-84 grown in conditioned medium (CM) from several strains produced lower levels of phenazines (1.5- to 9.3-fold) than control when grown in CM from the strain 30-84I
1
/I
2
. Growth of the
phzB
::
lacZ
reporter strain 30-84Z in this CM resulted in decreased
lacZ
expression (4.3- to 9.2-fold) compared to growth of the control strain in CM, indicating that inhibition of
phzB
occurred at the level of gene expression. Preliminary chemical and biological characterizations suggested that these signals, unlike other identified negative signals, were not extractable in ethyl acetate. Introduction of extra copies of
phzR
and
phzI
, but not
phzI
alone, in
trans
into strain 30-84Z reduced the negative effect on
phzB
::
lacZ
expression. The presence of negative-signal-producing strains in a mixture with strain 30-84 reduced strain 30-84's ability to inhibit the take-all disease pathogen in vitro. Together, the results from the previous work on the positive-signal subpopulation and the present work on the negative-signal subpopulation suggest that cross-communication among members of the rhizosphere community and strain 30-84 may control secondary metabolite production and pathogen inhibition.
Bifidobacterium lactisDSM 10140: Identification of theatp(atpBEFHAGDC) Operon and Analysis of Its Genetic Structure, Characteristics, and Phylogeny
Authors: Ventura Marco , Canchaya Carlos , van Sinderen Douwe , Fitzgerald Gerald F. , Zink Ralf 
Published: May 2004

ABSTRACTTheatpoperon is highly conserved among eubacteria, and it has been considered a molecular marker as an alternative to the 16S rRNA gene. PCR primers were designed from the consensus sequences of theatpDgene to amplify partialatpDsequences from 12Bifidobacteriumspecies and nineLactobacillusspecies. All PCR products were sequenced and aligned with otheratpDsequences retrieved from public databases. Genes encoding the subunits of the F1F0-ATPase ofBifidobacterium lactisDSM 10140 (atpBEFHAGDC) were cloned and sequenced. The deduced amino acid sequences of these subunits showed significant homology with the sequences of other organisms. We identified specific sequence signatures for the genusBifidobacteriumand for the closely related taxaBifidobacterium lactisandBifidobacterium animalisandLactobacillus gasseriandLactobacillus johnsonii, which could provide an alternative to current methods for identification of lactic acid bacterial species. Northern blot analysis showed that there was a transcript at approximately 7.3 kb, which corresponded to the size of theatpoperon, and a transcript at 4.5 kb, which corresponded to theatpC,atpD,atpG, andatpAgenes. The transcription initiation sites of these two mRNAs were mapped by primer extension, and the results revealed no consensus promoter sequences. Phylogenetic analysis of theatpDgenes demonstrated that theLactobacillus atpDgene clustered with the generaListeria,Lactococcus,Streptococcus, andEnterococcusand that the higher G+C content and highly biased codon usage with respect to the genome average support the hypothesis that there was probably horizontal gene transfer. The acid inducibility of theatpoperon ofB. lactisDSM 10140 was verified by slot blot hybridization by using RNA isolated from acid-treated cultures ofB. lactisDSM 10140. The rapid increase in the level ofatpoperon transcripts upon exposure to low pH suggested that the ATPase complex ofB. lactisDSM 10140 was regulated at the level of transcription and not at the enzyme assembly step.
Isolation, Characterization, and In Situ Detection of a Novel Chemolithoautotrophic Sulfur-Oxidizing Bacterium in Wastewater Biofilms Growing under Microaerophilic Conditions
Authors: Ito Tsukasa , Sugita Kenichi , Okabe Satoshi 
Published: May 2004

ABSTRACT

We successfully isolated a novel aerobic chemolithotrophic sulfur-oxidizing bacterium, designated strain SO07, from wastewater biofilms growing under microaerophilic conditions. For isolation, the use of elemental sulfur (S
0
), which is the most abundant sulfur pool in the wastewater biofilms, as the electron donor was an effective measure to establish an enrichment culture of strain SO07 and further isolation. 16S rRNA gene sequence analysis revealed that newly isolated strain SO07 was affiliated with members of the genus
Halothiobacillus
, but it was only distantly related to previously isolated species (89% identity). Strain SO07 oxidized elemental sulfur, thiosulfate, and sulfide to sulfate under oxic conditions. Strain SO07 could not grow on nitrate. Organic carbons, including acetate, propionate, and formate, could not serve as carbon and energy sources. Unlike other aerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 150 mM was negligible. In situ hybridization combined with confocal laser scanning microscopy revealed that a number of rod-shaped cells hybridized with a probe specific for strain SO07 were mainly present in the oxic biofilm strata (ca. 0 to 100 μm) and that they often coexisted with sulfate-reducing bacteria in this zone. These results demonstrated that strain SO07 was one of the important sulfur-oxidizing populations involved in the sulfur cycle occurring in the wastewater biofilm and was primarily responsible for the oxidation of H
2
S and S
0
to SO
4
2−
under oxic conditions.
Functional Expression of the Ectoine Hydroxylase Gene (
thpD
) from
Streptomyces chrysomallus
in
Halomonas elongata
Authors: Prabhu Julia , Schauwecker Florian , Grammel Nicolas , Keller Ullrich , Bernhard Michael 
Published: May 2004

ABSTRACT

The formation of hydroxyectoine in the industrial ectoine producer
Halomonas elongata
was improved by the heterologous expression of the ectoine hydroxylase gene,
thpD
, from
Streptomyces chrysomallus.
The efficient conversion of ectoine to hydroxyectoine was achieved by the concerted regulation of
thpD
by the
H. elongata ectA
promoter.
Antimicrobial Resistance of
Enterococcus
Species Isolated from Produce
Authors: Johnston Lynette M. , Jaykus Lee-Ann 
Published: May 2004

ABSTRACT

The purpose of this study was to characterize the antibiotic resistance profiles of
Enterococcus
species isolated from fresh produce harvested in the southwestern United States. Among the 185
Enterococcus
isolates obtained, 97 (52%) were
Enterococcus faecium
, 38 (21%) were
Enterococcus faecalis
, and 50 (27%) were other
Enterococcus
species. Of human clinical importance,
E. faecium
strains had a much higher prevalence of resistance to ciprofloxacin, tetracycline, and nitrofurantoin than
E. faecalis. E. faecalis
strains had a low prevalence of resistance to antibiotics used to treat
E. faecalis
infections of both clinical and of agricultural relevance, excluding its intrinsic resistance patterns. Thirty-four percent of the isolates had multiple-drug-resistance patterns, excluding intrinsic resistance. Data on the prevalence and types of antibiotic resistance in
Enterococcus
species isolated from fresh produce may be used to describe baseline antibiotic susceptibility profiles associated with
Enterococcus
spp. isolated from the environment. The data collected may also help elucidate the role of foods in the transmission of antibiotic-resistant strains to human populations.
pmoA
-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment
Authors: Pester Michael , Friedrich Michael W. , Schink Bernhard , Brune Andreas 
Published: May 2004

ABSTRACT

Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the
pmoA
gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and the inactive community in an anoxic sediment layer at a 10-cm depth. There were also no major changes in community structure between littoral sediment cores sampled in summer and winter. By contrast, the fingerprint patterns showed substantial differences between the methanotrophic communities of littoral and profundal sediments.
Plastic Encapsulation of Stabilized
Escherichia coli
and
Pseudomonas putida
Authors: Manzanera M. , Vilchez S. , Tunnacliffe A. 
Published: May 2004

ABSTRACT

Escherichia coli
and
Pseudomonas putida
dried in hydroxyectoine or trehalose are shown to be highly resistant to the organic solvents chloroform and acetone, and consequently, they can be encapsulated in a viable form in solid plastic materials. Bacteria are recovered by rehydration after physical disruption of the plastic.
P. putida
incorporated into a plastic coating of maize seeds was shown to colonize roots efficiently after germination.
Transformation of Folate-Consuming
Lactobacillus gasseri
into a Folate Producer
Authors: Wegkamp Arno , Starrenburg Marjo , de Vos Willem M. , Hugenholtz Jeroen , Sybesma Wilbert 
Published: May 2004

ABSTRACT

Five genes essential for folate biosynthesis in
Lactococcus lactis
were cloned on a broad-host-range lactococcal vector and were transferred to the folate auxotroph
Lactobacillus gasseri
. As a result
L. gasseri
changed from a folate consumer to a folate producer. This principle can be used to increase folate levels in many fermented food products.
Characterization of
Nocardia asteroides
Isolates from Different Ecological Habitats on the Basis of Repetitive Extragenic Palindromic-PCR Fingerprinting
Authors: Yamamura Hideki , Hayakawa Masayuki , Nakagawa Youji , Iimura Yuzuru 
Published: May 2004

ABSTRACT

Thirteen isolates of
Nocardia asteroides
from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.
Salinity Decreases Nitrite Reductase Gene Diversity in Denitrifying Bacteria of Wastewater Treatment Systems
Authors: Yoshie Sachiko , Noda Naohiro , Tsuneda Satoshi , Hirata Akira , Inamori Yuhei 
Published: May 2004

ABSTRACT

Investigation of the diversity of
nirK
and
nirS
in denitrifying bacteria revealed that salinity decreased the diversity in a nitrate-containing saline wastewater treatment system. The predominant
nirS
clone was related to
nirS
derived from marine bacteria, and the predominant
nirK
clone was related to
nirK
of the genus
Alcaligenes
.
Bacteriophage-Based Genetic System for Selection of Nonsplicing Inteins
Authors: Cann Isaac K. O. , Amaya Kensey R. , Southworth Maurice W. , Perler Francine B. 
Published: May 2004

ABSTRACT
A genetic selection system that detects splicing and nonsplicing activities of inteins was developed based on the ability to rescue a T4 phage strain with a conditionally inactive DNA polymerase. This phage defect can be complemented by expression of plasmid-encoded phage RB69 DNA polymerase. Insertion of an intein gene into the active site of the RB69 DNA polymerase gene renders polymerase activity and phage viability dependent on protein splicing. The effectiveness of the system was tested by screening for thermosensitive splicing mutants. Development of genetic systems with the potential of identifying protein splicing inhibitors is a first step towards controlling proliferation of pathogenic microbes harboring inteins in essential proteins.
Degradation of Polycyclic Aromatic Hydrocarbons by a Newly Discovered Enteric Bacterium,
Leclercia adecarboxylata
Authors: Sarma Priyangshu Manab , Bhattacharya Dhruva , Krishnan S. , Lal Banwari 
Published: May 2004

ABSTRACT

A bacterial strain, PS4040, capable of degrading polycyclic aromatic hydrocarbons for use as the sole carbon source was isolated from oily-sludge-contaminated soil. The 16S rRNA gene showed 98.8% homology to that of
Leclercia adecarboxylata
. Comparative molecular typing with the clinical strain of
L. adecarboxylata
revealed that there were few comigrating and few distinct amplimers among them.
Albusin B, a Bacteriocin from the Ruminal Bacterium
Ruminococcus albus
7 That Inhibits Growth of
Ruminococcus flavefaciens
Authors: Chen Junqin , Stevenson David M. , Weimer Paul J. 
Published: May 2004

ABSTRACT

An ∼32-kDa protein (albusin B) that inhibited growth of
Ruminococcus flavefaciens
FD-1 was isolated from culture supernatants of
Ruminococcus albus
7. Traditional cloning and gene-walking PCR techniques revealed an open reading frame (
albB
) encoding a protein with a predicted molecular mass of 32,168 Da. A BLAST search revealed two homologs of AlbB from the unfinished genome of
R. albus
8 and moderate similarity to LlpA, a recently described 30-kDa bacteriocin from
Pseudomonas
sp. strain BW11M1.
Multiplex PCR with 16S rRNA Gene-Targeted Primers of
Bifidobacterium
spp. To Identify Sources of Fecal Pollution
Authors: Bonjoch X. , Ballesté E. , Blanch A. R. 
Published: May 2004

ABSTRACT

Bifidobacteria are one of the most common bacterial types found in the intestines of humans and other animals and may be used as indicators of human fecal pollution. The presence of nine human-related
Bifidobacterium
species was analyzed in human and animal wastewater samples of different origins by using species-specific primers based on 16S rRNA sequences. Only
B. adolescentis
and
B. dentium
were found exclusively in human sewage. A multiplex PCR approach with strain-specific primers was developed. The method showed a sensitivity threshold of 10 cells/ml. This new molecular method could provide useful information for the characterization of fecal pollution sources.
Osmotic Stress Leads to Decreased Intracellular pH of
Listeria monocytogenes
as Determined by Fluorescence Ratio-Imaging Microscopy
Authors: Fang Weihuan , Siegumfeldt Henrik , Budde Birgitte Bjørn , Jakobsen Mogens 
Published: May 2004

ABSTRACT

Intracellular pH (pH
i
) of
Listeria monocytogenes
was determined after exposure to NaCl or sorbitol in liquid and solid media (agar). Both compounds decreased pH
i
, and recovery on solid medium was impaired compared to that in liquid medium.
N
,
N
′-dicyclohexylcarbodiimide abolished pH
i
recovery, and lowering a
w
with glycerol showed no effect on pH
i
.
Specific PCR Assay for a Tannin-Tolerant
Selenomonas ruminantium
Isolate, Derived from Helicase Coding Sequences
Authors: Bishop Richard , Obura Moses , Odongo David , Odenyo Agnes 
Published: May 2004

ABSTRACT

Sequences from a tannin-tolerant
Selenomonas ruminantium
isolate (EAT2) that hydrolyzes gallic acid were identified. Two exhibited identity to helicases with a wide phylogenetic distribution. PCR amplification by using primers from one helicase gene detected 2,000 to 5,000 EAT2 genome equivalents but did not amplify total gastrointestinal microbial DNA of nine other ungulate species.