bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of Bacterial Communities in Mesophilic and Thermophilic Bioreactors Treating Pharmaceutical Wastewater
Authors: LaPara Timothy M. , Nakatsu Cindy H. , Pantea Lisa , Alleman James E. 
Published: July 2002

ABSTRACT

The phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. These reactors were operated at both mesophilic (28 to 32°C) and thermophilic (50 to 58°C) temperatures. Community fingerprint analysis by denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified V3 region of the 16S rRNA gene from the domain
Bacteria
revealed that these seven reactors supported three distinct microbial communities. A band-counting analysis of the PCR-DGGE results suggested that elevated reactor temperatures corresponded with reduced species richness. Cloning of nearly complete 16S rRNA genes also suggested a reduced species richness in the thermophilic reactors by comparing the number of clones with different nucleotide inserts versus the total number of clones screened. While these results imply that elevated temperature can reduce species richness, other factors also could have impacted the number of populations that were detected. Nearly complete 16S rDNA sequence analysis showed that the thermophilic reactors were dominated by members from the β subdivision of the division
Proteobacteria
(β-proteobacteria) in addition to anaerobic phylotypes from the low-G+C gram-positive and
Synergistes
divisions. The mesophilic reactors, however, included at least six bacterial divisions, including
Cytophaga-Flavobacterium-Bacteroides
,
Synergistes
,
Planctomycetes
, low-G+C gram-positives,
Holophaga-Acidobacterium
, and
Proteobacteria
(α-proteobacteria, β-proteobacteria, γ-proteobacteria and δ-proteobacteria subdivisions). The two PCR-based techniques detected the presence of similar bacterial populations but failed to coincide on the relative distribution of these phylotypes. This suggested that at least one of these methods is insufficiently quantitative to determine total community biodiversity—a function of both the total number of species present (richness) and their relative distribution (evenness).
Effect of Oxygen on Formation and Structure of
Azotobacter vinelandii
Alginate and Its Role in Protecting Nitrogenase
Authors: Sabra W. , Zeng A.-P. , Lünsdorf H. , Deckwer W.-D. 
Published: July 2002

ABSTRACT

The activity of nitrogenase in the nitrogen-fixing bacterium
Azotobacter vinelandii
grown diazotrophically under aerobic conditions is generally considered to be protected against O
2
by a high respiration rate. In this work, we have shown that a high rate of respiration is not the prevailing mechanism for nitrogenase protection in
A. vinelandii
grown in phosphate-limited nitrogen-free chemostat culture. Instead, the formation of alginate appeared to play a decisive role in protecting the nitrogenase that is required for cell growth in this culture. Depending on the O
2
tension and cell growth rate, the formation rate and composition of alginate released into the culture broth varied significantly. Furthermore, transmission electron microscopic analysis of cell morphology and the cell surface revealed the existence of an alginate capsule on the surface of
A. vinelandii
. The composition, thickness, and compactness of this alginate capsule also varied significantly. In general, increasing O
2
tension led to the formation of alginate with a higher molecular weight and a greater
l
-guluronic acid content. The alginate capsule was accordingly thicker and more compact. In addition, the formation of the alginate capsule was found to be strongly affected by the shear rate in a bioreactor. Based on these experimental results, it is suggested that the production of alginate, especially the formation of an alginate capsule on the cell surface, forms an effective barrier for O
2
transfer into the cell. It is obviously the quality, not the quantity, of alginate that is decisive for the protection of nitrogenase.
Resuscitation by Ferrioxamine E of Stressed
Salmonella enterica
Serovar Typhimurium from Soil and Water Microcosms
Authors: Reissbrodt R. , Heier H. , Tschäpe H. , Kingsley R. A. , Williams P. H. 
Published: July 2002

ABSTRACT

Storage of
Salmonella enterica
serovar Typhimurium strains in soil and water microcosms resulted in loss of culturability on standard plating media. Prior incubation in buffered peptone water supplemented with ferrioxamine E markedly extended the time that bacteria were recoverable by plating, except in the case of mutants deficient in ferrioxamine E uptake.
Inhibition of
Giardia intestinalis
by Extracellular Factors from Lactobacilli: an In Vitro Study
Authors: Pérez Pablo F. , Minnaard Jessica , Rouvet Martine , Knabenhans Christian , Brassart Dominique , De Antoni Graciela L. , Schiffrin Eduardo J. 
Published: July 2002

ABSTRACT

The aim of the present work was to evaluate the effect of spent culture supernatants of different strains of lactobacilli on giardia trophozoites. The growth of
Giardia intestinalis
strain WB, as well as the attachment to the human intestinal epithelial cell line Caco-2, was evaluated by using proliferation and adhesion assays with radiolabeled parasites. In addition, scanning electron microscopy and flow cytometric analysis were performed. The effect of spent culture supernatants from lactobacilli was strain dependent.
Lactobacillus johnsonii
La1 significantly inhibited the proliferation of
G. intestinalis
trophozoites. Although the effect was strongly pH dependent, it was not simply due to lactic acid. According to flow cytometric analysis, trophozoites were arrested in G
1
phase but neither significant necrosis nor apoptosis could be detected. Bacterial cells or their spent culture supernatants were unable to modify trophozoite attachment to Caco-2 cells. However, trophozoites treated with spent culture supernatants had little, if any, proliferative capacity. These results suggest that La1 produces some substance(s) able to inhibit proliferation of
Giardia
trophozoites. Partial characterization of the factors involved in the antigiardiasic action showed that they have a low molecular mass and are inactivated by heating. On this basis, it seems worthwhile to explore how colonization of the proximal small bowel with these lactic acid bacteria could interfere with giardiasis in vivo.
High Genetic Variability for Resistance to
Bacillus thuringiensis
Toxins in a Single Population of Diamondback Moth
Authors: González-Cabrera Joel , Herrero Salvador , Ferré Juan 
Published: July 2002

ABSTRACT
The long-term benefit of insecticidal products based on Cry toxins, either in sprays or as transgenic crops, is threatened by the development of resistance by target pests. The models used to predict evolution of resistance to Cry toxins most often are monogenic models in which two alleles are used. Moreover, the high-dose/refuge strategy recommended for implementation with transgenic crops relies on the assumption that the resistance allele is recessive. Using selection experiments, we demonstrated the occurrence in a laboratory colony of diamondback moth of two different genes (either allelic or nonallelic) that confer resistance to Cry1Ab. At the concentration tested, resistance was dominant in one selection line and partially recessive in the other. Resistant insects from the two selection lines also differed in their cross-resistance patterns. The diamondback moth colony was derived from a field population from the Philippines, which originally showed a different resistance phenotype. This is the first time that an insect population has been directly shown to carry more than one gene conferring resistance to the same Cry toxin.
Examination of Peak Power Dependence in the UV Inactivation of Bacterial Spores
Authors: Rice Jane K. , Ewell Michael 
Published: July 2002

ABSTRACT

We examine whether the rate of delivery of photons from a UV radiation source has an effect on the inactivation of spores. We directly compare the output of a high-peak-power UV laser source at 248 nm to a low-power continuous lamp source (254 nm) in the inactivation of
Bacillus
subtilis
spores. The two UV sources differ by a factor of 10
8
in peak power. Contrary to previous reports, no clear differences in spore survival were observed.
Dissection of Central Carbon Metabolism of Hemoglobin-Expressing
Escherichia coli
by
13
C Nuclear Magnetic Resonance Flux Distribution Analysis in Microaerobic Bioprocesses
Authors: Frey Alexander D. , Fiaux Jocelyne , Szyperski Thomas , Wüthrich Kurt , Bailey James E. , Kallio Pauli T. 
Published: July 2002

ABSTRACT

Escherichia coli
MG1655 cells expressing
Vitreoscilla
hemoglobin (VHb),
Alcaligenes eutrophus
flavohemoprotein (FHP), the N-terminal hemoglobin domain of FHP (FHPg), and a fusion protein which comprises VHb and the
A. eutrophus
C-terminal reductase domain (VHb-Red) were grown in a microaerobic bioreactor to study the effects of low oxygen concentrations on the central carbon metabolism, using fractional
13
C-labeling of the proteinogenic amino acids and two-dimensional [
13
C,
1
H]-correlation nuclear magnetic resonance (NMR) spectroscopy. The NMR data revealed differences in the intracellular carbon fluxes between
E. coli
cells expressing either VHb or VHb-Red and cells expressing
A. eutrophus
FHP or the truncated heme domain (FHPg).
E. coli
MG1655 cells expressing either VHb or VHb-Red were found to function with a branched tricarboxylic acid (TCA) cycle. Furthermore, cellular demands for ATP and reduction equivalents in VHb- and VHb-Red-expressing cells were met by an increased flux through glycolysis. In contrast, in
E. coli
cells expressing
A. eutrophus
hemeproteins, the TCA cycle is running cyclically, indicating a shift towards a more aerobic regulation. Consistently,
E. coli
cells displaying FHP and FHPg activity showed lower production of the typical anaerobic by-products formate, acetate, and
d
-lactate. The implications of these observations for biotechnological applications are discussed.
Genetic Diversity among 3-Chloroaniline- and Aniline-Degrading Strains of the
Comamonadaceae
Authors: Boon Nico , Goris Johan , De Vos Paul , Verstraete Willy , Top Eva M. 
Published: July 2002

ABSTRACT

We examined the diversity of the plasmids and of the gene
tdnQ
, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-CA). Three strains have been described and identified previously, i.e.,
Comamonas testosteroni
I2 and
Delftia acidovorans
CA28 and BN3.1. Strains LME1 and B8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as
D. acidovorans
. Both
Delftia
and
Comamonas
belong to the family
Comamonadaceae
. All five strains possess a large plasmid of ca. 100 kb, but the plasmids from only four strains could be transferred to a recipient strain by selection on aniline or 3-CA as a sole source of carbon and/or nitrogen. Plasmid transfer experiments and Southern hybridization revealed that the plasmid of strain I2 was responsible for total aniline but not 3-CA degradation, while the plasmids of strains LME1 and B8c were responsible only for the oxidative deamination of aniline. Several transconjugant clones that had received the plasmid from strain CA28 showed different degradative capacities: all transconjugants could use aniline as a nitrogen source, while only some of the transconjugants could deaminate 3-CA. For all four plasmids, the IS
1071
insertion sequence of Tn
5271
was found to be located on a 1.4-kb restriction fragment, which also hybridized with the
tdnQ
probe. This result suggests the involvement of this insertion sequence element in the dissemination of aniline degradation genes in the environment. By use of specific primers for the
tdnQ
gene from
Pseudomonas putida
UCC22, the diversity of the PCR-amplified fragments in the five strains was examined by denaturing gradient gel electrophoresis (DGGE). With DGGE, three different clusters of the
tdnQ
fragment could be distinguished. Sequencing data showed that the
tdnQ
sequences of I2, LME1, B8c, and CA28 were very closely related, while the
tdnQ
sequences of BN3.1 and
P. putida
UCC22 were only about 83% identical to the other sequences. Northern hybridization revealed that the
tdnQ
gene is transcribed only in the presence of aniline and not when only 3-CA is present.
Evidence for a Genetically Stable Strain of
Campylobacter jejuni
Authors: Manning G. , Duim B. , Wassenaar T. , Wagenaar J. A. , Ridley A. , Newell D. G. 
Published: July 2002

ABSTRACT

The genetic stability of selected epidemiologically linked strains of
Campylobacter jejuni
during outbreak situations was investigated by using subtyping techniques. Strains isolated from geographically related chicken flock outbreaks in 1998 and from a human outbreak in 1981 were investigated. There was little similarity in the strains obtained from the different chicken flock outbreaks; however, the strains from each of three chicken outbreaks, including strains isolated from various environments, were identical as determined by
fla
typing, amplified fragment length polymorphism (AFLP) analysis, and pulsed-field gel electrophoresis, which confirmed the genetic stability of these strains during the short time courses of chicken flock outbreaks. The human outbreak samples were compared with strain 81116, which originated from the same outbreak but has since undergone innumerable laboratory passages. Two main AFLP profiles were recognized from this outbreak, which confirmed the serotyping results obtained at the time of the outbreak. The major type isolated from this outbreak (serotype P6:L6) was exemplified by strain 81116. Despite the long existence of strain 81116 as a laboratory strain, the AFLP profile of this strain was identical to the profiles of all the other historical P6:L6 strains from the outbreak, indicating that the genotype has remained stable for almost 20 years. Interestingly, the AFLP profiles of the P6:L6 group of strains from the human outbreak and the strains from one of the recent chicken outbreaks were also identical. This similarity suggests that some clones of
C. jejuni
remain genetically stable in completely different environments over long periods of time and considerable geographical distances.
Cytotoxicity Associated with Trichloroethylene Oxidation in
Burkholderia cepacia
G4
Authors: Yeager Chris M. , Bottomley Peter J. , Arp Daniel J. 
Published: July 2002

ABSTRACT

The effects of trichloroethylene (TCE) oxidation on toluene 2-monooxygenase activity, general respiratory activity, and cell culturability were examined in the toluene-oxidizing bacterium
Burkholderia cepacia
G4. Nonspecific damage outpaced inactivation of toluene 2-monooxygenase in
B. cepacia
G4 cells. Cells that had degraded approximately 0.5 μmol of TCE (mg of cells
−1
) lost 95% of their acetate-dependent O
2
uptake activity (a measure of general respiratory activity), yet toluene-dependent O
2
uptake activity decreased only 35%. Cell culturability also decreased upon TCE oxidation; however, the extent of loss varied greatly (up to 3 orders of magnitude) with the method of assessment. Addition of catalase or sodium pyruvate to the surfaces of agar plates increased enumeration of TCE-injured cells by as much as 100-fold, indicating that the TCE-injured cells were ultrasensitive to oxidative stress. Cell suspensions that had oxidized TCE recovered the ability to grow in liquid minimal medium containing lactate or phenol, but recovery was delayed substantially when TCE degradation approached 0.5 μmol (mg of cells
−1
) or 66% of the cells' transformation capacity for TCE at the cell density utilized. Furthermore, among
B. cepacia
G4 cells isolated on Luria-Bertani agar plates from cultures that had degraded approximately 0.5 μmol of TCE (mg of cells
−1
), up to 90% were Tol
−
variants, no longer capable of TCE degradation. These results indicate that a toxicity threshold for TCE oxidation exists in
B. cepacia
G4 and that once a cell suspension has exceeded this toxicity threshold, the likelihood of reestablishing an active, TCE-degrading biomass from the cells will decrease significantly.
Kinetics of Methyl
t
-Butyl Ether Cometabolism at Low Concentrations by Pure Cultures of Butane-Degrading Bacteria
Authors: Liu Catherine Y. , Speitel Gerald E. , Georgiou George 
Published: July 2002

ABSTRACT

Butane-oxidizing
Arthrobacter
(ATCC 27778) bacteria were shown to degrade low concentrations of methyl
t
-butyl ether (MTBE; range, 100 to 800 μg/liter) with an apparent half-saturation concentration (
K

s

) of 2.14 mg/liter and a maximum substrate utilization rate (k
c
) of 0.43 mg/mg of total suspended solids per day.
Arthrobacter
bacteria demonstrated MTBE degradation activity when grown on butane but not when grown on glucose, butanol, or tryptose phosphate broth. The presence of butane,
tert
-butyl alcohol, or acetylene had a negative impact on the MTBE degradation rate. Neither
Methylosinus trichosporium
OB3b nor
Streptomyces griseus
was able to cometabolize MTBE.
Effect of Fermented Feed on the Microbial Population of the Gastrointestinal Tracts of Pigs
Authors: van Winsen René L. , Urlings Bert A. P. , Lipman Len J. A. , Snijders Jos M. A. , Keuzenkamp David , Verheijden Jos H. M. , van Knapen Frans 
Published: July 2002

ABSTRACT

An in vivo experiment was performed with pigs to study the inhibitory effect of fermented feed on the bacterial population of the gastrointestinal tract. Results demonstrated a significant positive correlation between pH and lactobacilli in the stomach contents of pigs in dry feed as well as in the stomach contents of pigs fed fermented feed. Furthermore, a significant positive correlation between the pH and the numbers of bacteria in the family
Enterobacteriaceae
in the contents of the stomach of pigs fed dry feed was found. In the stomach contents of pigs fed fermented feed, a significant negative correlation was found between the concentration of the undissociated form of lactic acid and the numbers of
Enterobacteriaceae
. The numbers of
Enterobacteriaceae
in the contents of the stomach, ileum, cecum, colon, and rectum of pigs fed fermented feed were significantly lower compared with the contents of the stomach, ileum, caecum, colon, and rectum of pigs fed dry feed. The numbers of total lactobacilli were significantly higher in the stomach contents of pigs fed fermented feed and in the ileum contents of one pig group fed fermented feed compared with the contents of pigs fed dry feed. However, the influence of lactobacilli on numbers of
Enterobacteriaceae
could not be demonstrated. It was concluded that fermented feed influences the bacterial ecology of the gastrointestinal tract and reduces the levels of
Enterobacteriaceae
in the different parts of the gastrointestinal tract.
Fate of the Biological Control Agent
Pseudomonas aureofaciens
TX-1 after Application to Turfgrass
Authors: Sigler William V. , Nakatsu Cindy H. , Reicher Zachary J. , Turco Ronald F. 
Published: July 2002

ABSTRACT

The fate and impact of
Pseudomonas aureofaciens
TX-1 following application as a biocontrol agent for fungi in turfgrass were studied. The organism was applied with a modified irrigation system by using a preparation containing 1 × 10
6
P. aureofaciens
TX-1 CFU ml
−1
about 100 times between May and August. We examined the impact of this repeated introduction of
P. aureofaciens
TX-1 (which is known to produce the antimicrobial compound phenazine-1-carboxylic acid) on the indigenous microbial community of the turfgrass system and on establishment of introduced bacteria in the soil system. A PCR primer-DNA hybridization probe combination was developed to accurately monitor the fate of
P. aureofaciens
TX-1 following application in irrigation water. To assess the impact of frequent
P. aureofaciens
TX-1 applications on the indigenous bacterial community, turfgrass canopy, thatch, and rhizosphere samples were obtained during the growing season from control and treated plots and subjected to DNA extraction procedures and denaturing gradient gel electrophoresis (DGGE). PCR amplification and hybridization of extracted DNA with the
P. aureofaciens
TX-1-specific primer-probe combination revealed that
P. aureofaciens
TX-1 not only became established in the rhizosphere and thatch but also was capable of overwintering. Separation of PCR-amplified partial 16S rRNA genes by DGGE showed that the repeated application of
P. aureofaciens
TX-1 in irrigation water resulted in transient displacement of a leaf surface bacterial community member. There was no obvious alteration of any dominant members of the thatch and rhizosphere microbial communities.
Bacillus
Spore Inactivation Methods Affect Detection Assays
Authors: Dang Jessica L. , Heroux Karen , Kearney John , Arasteh Ameneh , Gostomski Mark , Emanuel Peter A. 
Published: July 2002

ABSTRACT

Detection of biological weapons is a primary concern in force protection, treaty verification, and safeguarding civilian populations against domestic terrorism. One great concern is the detection of
Bacillus anthracis
, the causative agent of anthrax. Assays for detection in the laboratory often employ inactivated preparations of spores or nonpathogenic simulants. This study uses several common biodetection platforms to detect
B. anthracis
spores that have been inactivated by two methods and compares those data to detection of spores that have not been inactivated. The data demonstrate that inactivation methods can affect the sensitivity of nucleic acid- and antibody-based assays for the detection of
B. anthracis
spores. These effects should be taken into consideration when comparing laboratory results to data collected and assayed during field deployment.
Characterization by 16S rRNA Sequence Analysis of Pseudomonads Causing Blotch Disease of Cultivated
Agaricus bisporus
Authors: Godfrey S. A. C. , Harrow S. A. , Marshall J. W. , Klena J. D. 
Published: July 2002

ABSTRACT

Bacterial blotch of
Agaricus bisporus
has typically been identified as being caused by either
Pseudomonas tolaasii
(brown blotch) or
Pseudomonas gingeri
(ginger blotch). To address the relatedness of pseudomonads able to induce blotch, a pilot study was initiated in which pseudomonads were selectively isolated from mushroom farms throughout New Zealand. Thirty-three pseudomonad isolates were identified as being capable of causing different degrees of discoloration (separable into nine categories) of
A. bisporus
tissue in a bioassay. These isolates were also identified as unique using repetitive extragenic palindromic PCR and biochemical analysis. Relationships between these 33 blotch-causing organisms (BCO) and a further 22 selected pseudomonad species were inferred by phylogenetic analyses of near-full-length 16S rRNA gene nucleotide sequences. The 33 BCO isolates were observed to be distributed throughout the
Pseudomonas fluorescens
intrageneric cluster. These results show that in addition to known BCO (
P. tolaasii, P. gingeri
, and
Pseudomonas reactans
), a number of diverse pseudomonad species also have the ability to cause blotch diseases with various discolorations. Furthermore, observation of ginger blotch discoloration of
A. bisporus
being independently caused by many different pseudomonad species impacts on the homogeneity and classification of the previously described
P. gingeri
.