bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of Passive Diffusion in the Uptake of Polychlorinated Biphenyls by Phagotrophic Protozoa
Authors: Kujawinski Elizabeth B. , Farrington John W. , Moffett James W. 
Published: July 2002

ABSTRACT

Unicellular protozoan grazers represent a size class of organisms where a transition in the mechanism of chlorobiphenyl (CB) introduction, from diffusion through surface membranes to ingestion of contaminated prey, could occur. This study compares the relative importance of these two processes in the overall uptake of polychlorinated biphenyls by protists. Uptake rates and steady-state concentrations were compared in laboratory cultures of grazing and nongrazing protozoa. These experiments were conducted with a 10-μm marine scuticociliate (
Uronema
sp.), bacterial prey (
Halomonas halodurans
), and a suite of 21 CB congeners spanning a range of aqueous solubilities. The dominant pathway of CB uptake by both grazing and nongrazing protozoa was diffusion. Organic-carbon-normalized CB concentrations (in the protozoan cell) were equivalent in grazing and nongrazing protozoa for all congeners studied. Rate constants for uptake into and loss from the protozoan cell were independently determined by using [3,3′,4,4′-
14
C]tetrachlorobiphenyl (IUPAC no. 77), 0.38 ± 0.03 min
−1
and (1.1 ± 0.1) × 10
−5
(g of organic carbon)
−1
min
−1
, respectively. Magnitudes of the uptake and loss processes were calculated and compared by using a numerical model. The model result was consistent with data from the bioaccumulation experiment and supported the hypothesis that diffusive uptake is faster than ingestive uptake in phagotrophic unicellular protozoa.
Monitoring Precursor 16S rRNAs of
Acinetobacter
spp. in Activated Sludge Wastewater Treatment Systems
Authors: Oerther Daniel B. , Pernthaler Jakob , Schramm Andreas , Amann Rudolf , Raskin Lutgarde 
Published: July 2002

ABSTRACT

Recently, Cangelosi and Brabant used oligonucleotide probes targeting the precursor 16S rRNA of
Escherichia coli
to demonstrate that the levels of precursor rRNA were more sensitive to changes in growth phase than the levels of total rRNA (G. A. Cangelosi and W. H. Brabant, J. Bacteriol. 179:4457–4463, 1997). In order to measure changes in the levels of precursor rRNA in activated sludge systems, we designed oligonucleotide probes targeting the 3′ region of the precursor 16S rRNA of
Acinetobacter
spp. We used these probes to monitor changes in the level of precursor 16S rRNA during batch growth of
Acinetobacter
spp. in Luria-Bertani (LB) medium, filtered wastewater, and in lab- and full-scale wastewater treatment systems. Consistent with the previous reports for
E. coli
, results obtained with membrane hybridizations and fluorescence in situ hybridizations with
Acinetobacter calcoaceticus
grown in LB medium showed a more substantial and faster increase in precursor 16S rRNA levels compared to the increase in total 16S rRNA levels during exponential growth. Diluting an overnight culture of
A. calcoaceticus
grown in LB medium with filtered wastewater resulted in a pattern of precursor 16S rRNA levels that appeared to follow diauxic growth. In addition, fluorescence in situ hybridizations with oligonucleotide probes targeting total 16S rRNA and precursor 16S rRNA showed that individual cells of
A. calcoaceticus
expressed highly variable levels of precursor 16S rRNA when adapting from LB medium to filtered sewage. Precursor 16S rRNA levels of
Acinetobacter
spp. transiently increased when activated sludge was mixed with influent wastewater in lab- and full-scale wastewater treatment systems. These results suggest that
Acinetobacter
spp. experience a change in growth activity within wastewater treatment systems.
Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability
Authors: Friedrich M. , Grosser R. J. , Kern E. A. , Inskeep W. P. , Ward D. M. 
Published: July 2002

ABSTRACT

Reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. We established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (R. J. Grosser, M. Friedrich, D. M. Ward, and W. P. Inskeep, Appl. Environ. Microbiol. 66:2695–2702, 2000). Bacteria enriched and isolated from contaminated soils under these conditions were analyzed by denaturing gradient gel electrophoresis (DGGE) and sequencing of PCR-amplified 16S ribosomal DNA segments. Compared to DGGE patterns obtained with enrichment cultures containing sand or no sorptive solid phase, different DGGE patterns were obtained with enrichment cultures containing phenanthrene sorbed to beads of Amberlite IRC-50 (AMB), a weak cation-exchange resin, and especially Biobead SM7 (SM7), a polyacrylic resin that sorbed phenanthrene more strongly. SM7 enrichments selected for mycobacterial phenanthrene mineralizers, whereas AMB enrichments selected for a
Burkholderia
sp. that degrades phenanthrene. Identical mycobacterial and
Burkholderia
16S rRNA sequence segments were found in SM7 and AMB enrichment cultures inoculated with contaminated soil from two geographically distant sites. Other closely related
Burkholderia
sp. populations, some of which utilized phenanthrene, were detected in sand and control enrichment cultures. Our results are consistent with the hypothesis that different phenanthrene-utilizing bacteria inhabiting the same soils may be adapted to different phenanthrene bioavailabilities.
Production and Characterization of Two Monoclonal Antibodies Specific for
Plasmopara halstedii
Authors: Bouterige S. , Robert R. , Bouchara J. P. , Marot-Leblond A. , Molinero V. , Senet J. M. 
Published: July 2002

ABSTRACT

Sunflower downy mildew, caused by the fungus
Plasmopara halstedii
, is a potentially devastating disease. We produced two monoclonal antibodies (MAbs) (12C9 and 18E2) by immunizing mice with a partially purified extract of
P. halstedii
race 1. Both MAbs detected in enzyme-linked immunosorbent assay (ELISA) all races of
P. halstedii
present in France. No cross-reactions were observed with
Plasmopara viticola
or with other fungi commonly associated with sunflowers. Both MAbs recognized the same three fungal antigens with molecular masses of 68, 140, and 192 kDa. However, the epitopes on the fungal antigens were distinct and repetitive. Seed homogenates from infected plants were incubated in wells coated with MAb 18E2. This resulted in the trapping of
P. halstedii
antigens that were identified with biotinylated MAb 12C9. No reactions were seen with seed homogenates from healthy plants. Thus, our results suggest that these MAbs might be used to develop a sandwich ELISA detection system for
P. halstedii
in infected seeds.
Polyclonal Antibodies Recognizing the AmoB Protein of Ammonia Oxidizers of the β-Subclass of the Class
Proteobacteria
Authors: Pinck Claudia , Coeur Caroline , Potier Patrick , Bock Eberhard 
Published: July 2002

ABSTRACT

A 41-kDa protein of
Nitrosomonas eutropha
was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the β-subclass of
Proteobacteria
(
Nitrosomonas
, including
Nitrosococcus mobilis
, which belongs phylogenetically to
Nitrosomonas
;
Nitrosospira
;
Nitrosolobus
; and
Nitrosovibrio
). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the γ-subclass of
Proteobacteria
(
Nitrosococcus oceani
and
Nitrosococcus halophilus
). Moreover, methane oxidizers (
Methylococcus capsulatus
,
Methylocystis parvus
, and
Methylomonas methanica
) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of
N. eutropha
consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when
N. eutropha
was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of
Nitrosomonas
after 1 year of ammonia starvation.
Green Fluorescent Protein as a Novel Indicator of Antimicrobial Susceptibility in
Aureobasidium pullulans
Authors: Webb Jeremy S. , Barratt Sarah R. , Sabev Hristo , Nixon Marianne , Eastwood Ian M. , Greenhalgh Malcolm , Handley Pauline S. , Robson Geoffrey D. 
Published: July 2002

ABSTRACT

Presently there is no method available that allows noninvasive and real-time monitoring of fungal susceptibility to antimicrobial compounds. The green fluorescent protein (GFP) of the jellyfish
Aequoria victoria
was tested as a potential reporter molecule for this purpose.
Aureobasidium pullulans
was transformed to express cytosolic GFP using the vector pTEFEGFP (A. J. Vanden Wymelenberg, D. Cullen, R. N. Spear, B. Schoenike, and J. H. Andrews, BioTechniques 23:686–690, 1997). The transformed strain Ap1
gfp
showed bright fluorescence that was amenable to quantification using fluorescence spectrophotometry. Fluorescence levels in Ap1
gfp
blastospore suspensions were directly proportional to the number of viable cells determined by CFU plate counts (
r
2
> 0.99). The relationship between cell viability and GFP fluorescence was investigated by adding a range of concentrations of each of the biocides sodium hypochlorite and 2-
n
-octylisothiozolin-3-one (OIT) to suspensions of Ap1
gfp
blastospores (pH 5 buffer). These biocides each caused a rapid (<25-min) loss of fluorescence of greater than 90% when used at concentrations of 150 μg of available chlorine ml
−1
and 500 μg ml
−1
, respectively. Further, loss of GFP fluorescence from
A. pullulans
cells was highly correlated with a decrease in the number of viable cells (
r
2
> 0.92). Losses of GFP fluorescence and cell viability were highly dependent on external pH; maximum losses of fluorescence and viability occurred at pH 4, while reduction of GFP fluorescence was absent at pH 8.0 and was associated with a lower reduction in viability. When
A. pullulans
was attached to the surface of plasticized poly(vinylchloride) containing 500 ppm of OIT, fluorescence decreased more slowly than in cell suspensions, with >95% loss of fluorescence after 27 h. This technique should have broad applications in testing the susceptibility of
A. pullulans
and other fungal species to antimicrobial compounds.
Purification, Stability, and Mineralization of 3-Hydroxy-2- Formylbenzothiophene, a Metabolite of Dibenzothiophene
Authors: Bressler David C. , Fedorak Phillip M. 
Published: July 2002

ABSTRACT

3-Hydroxy-2-formylbenzothiophene (HFBT) is a metabolite found in many bacterial cultures that degrade dibenzothiophene (DBT) via the Kodama pathway. The fate of HFBT in cultures and in the environment is unknown. In this study, HFBT was produced by a DBT-degrading bacterium and purified by sublimation. When stored in organic solvent or as a crystal, the HFBT slowly decomposed, yielding colored products. Two of these were identified as thioindigo and
cis
-thioindigo. The supernatant of the DBT-degrading culture contained thioindigo, which has not been reported previously as a product of DBT biodegradation. In mineral salts medium, HFBT was sufficiently stable to allow biodegradation studies with a mixed microbial culture over a 3- to 4-week period. High-performance liquid chromatography analyses showed that HFBT was removed from the medium. 2-Mercaptophenylglyoxalate, detected as benzothiophene-2,3-dione, was found in an HFBT-degrading mixed culture, and the former appears to be a metabolite of HFBT. This mixed culture also mineralized HFBT to CO
2
.
Naturally Occurring Lactococcal Plasmid pAH90 Links Bacteriophage Resistance and Mobility Functions to a Food-Grade Selectable Marker
Authors: O' Sullivan David , Ross R. Paul , Twomey Denis P. , Fitzgerald Gerald F. , Hill Colin , Coffey Aidan 
Published: July 2002

ABSTRACT

The bacteriophage resistance plasmid pAH90 (26,490 bp) is a natural cointegrate plasmid formed via homologous recombination between the type I restriction-modification specificity determinants (
hsdS
) of two smaller lactococcal plasmids, pAH33 (6,159 bp) and pAH82 (20,331 bp), giving rise to a bacteriophage-insensitive mutant following phage challenge (D. O'Sullivan, D. P. Twomey, A. Coffey, C. Hill, G. F. Fitzgerald, and R. P. Ross, Mol. Microbiol. 36:866–876; 2000). In this communication we provide evidence that the recombination event is favored by phage infection. The entire nucleotide sequence of plasmid pAH90 was determined and found to contain 24 open reading frames (ORFs) responsible for phenotypes which include restriction-modification, phage adsorption inhibition, plasmid replication, cadmium resistance, cobalt transport, and conjugative mobilization. The cadmium resistance property, encoded by the
cadA
gene, which has an associated regulatory gene (
cadC
), is of particular interest, as it facilitated the selection of pAH90 in other phage-sensitive lactococci after electroporation. In addition, we report the identification of a group II self-splicing intron bounded by two exons which have the capacity to encode a relaxase implicated in conjugation in gram-positive bacteria. The functionality of this intron was evident by demonstrating splicing in vivo. Given that pAH90 encodes potent phage defense systems which act at different stages in the phage lytic cycle, the linkage of these with a food-grade selectable marker on a replicon that can be mobilized among lactococci has significant potential for natural strain improvement for industrial dairy fermentations which are susceptible to phage inhibition.
Biogeochemical and Molecular Signatures of Anaerobic Methane Oxidation in a Marine Sediment
Authors: Thomsen Trine R. , Finster Kai , Ramsing Niels B. 
Published: July 2002

ABSTRACT

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for
Archaea
. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802–805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera
Desulfonema
,
Desulfococcus
, and
Desulfosarcina
. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.
Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods
Authors: Smit Eric , Leeflang Paula , Gommans Suzanne , van den Broek Jan , van Mil Saskia , Wernars Karel 
Published: July 2002

ABSTRACT

There is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. For this purpose the soil microbial community of a wheat field on an experimental farm in The Netherlands was studied by using both cultivation-based and molecule-based methods. Samples were taken in the different seasons over a 1-year period. Fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacteria, and only a few isolates appeared to belong to the
Proteobacteria
and green sulfur bacteria. Some genera, such as
Micrococcus
,
Arthrobacter
, and
Corynebacterium
were detected throughout the year, while
Bacillus
was found only in July. Isolate diversity was lowest in July, and the most abundant species,
Arthrobacter oxydans
, and members of the genus
Pseudomonas
were found in reduced numbers in July. Analysis by molecular techniques showed that diversity of cloned 16S ribosomal DNA (rDNA) sequences was greater than the diversity among cultured isolates. Moreover, based on analysis of 16S rDNA sequences, there was a more even distribution among five main divisions,
Acidobacterium
,
Proteobacteria
,
Nitrospira
, cyanobacteria, and green sulfur bacteria. No clones were found belonging to the gram-positive bacteria, which dominated the cultured isolates. Seasonal fluctuations were assessed by denaturing gradient gel electrophoresis. Statistical analysis of the banding patterns revealed significant differences between samples taken in different seasons. Cluster analysis of the patterns revealed that the bacterial community in July clearly differed from those in the other months. Although the molecule- and cultivation-based methods allowed the detection of different parts of the bacterial community, results from both methods indicated that the community present in July showed the largest difference from the communities of the other months. Efforts were made to use the sequence data for providing insight into more general ecological relationships. Based on the distribution of 16S rDNA sequences among the bacterial divisions found in this work and in literature, it is suggested that the ratio between the number of
Proteobacteria
and
Acidobacterium
organisms might be indicative of the trophic level of the soil.
Identification of a Small Tetraheme Cytochrome
c
and a Flavocytochrome
c
as Two of the Principal Soluble Cytochromes
c
in
Shewanella oneidensis
Strain MR1
Authors: Tsapin A. I. , Vandenberghe I. , Nealson K. H. , Scott J. H. , Meyer T. E. , Cusanovich M. A. , Harada E. , Kaizu T. , Akutsu H. , Leys D. , Van Beeumen J. J. 
Published: July 2002

ABSTRACT

Two abundant, low-redox-potential cytochromes
c
were purified from the facultative anaerobe
Shewanella oneidensis
strain MR1 grown anaerobically with fumarate. The small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. The small cytochrome
c
contains 91 residues and four heme binding sites. It is most similar to the cytochromes
c
from
Shewanella frigidimarina
(formerly
Shewanella putrefaciens
) NCIMB400 and the unclassified bacterial strain H1R (64 and 55% identity, respectively). The amount of the small tetraheme cytochrome is regulated by anaerobiosis, but not by fumarate. The larger of the two low-potential cytochromes contains tetraheme and flavin domains and is regulated by anaerobiosis and by fumarate and thus most nearly corresponds to the flavocytochrome
c
-fumarate reductase previously characterized from
S. frigidimarina
to which it is 59% identical. However, the genetic context of the cytochrome genes is not the same for the two
Shewanella
species, and they are not located in multicistronic operons. The small cytochrome
c
and the cytochrome domain of the flavocytochrome
c
are also homologous, showing 34% identity. Structural comparison shows that the
Shewanella
tetraheme cytochromes are not related to the
Desulfovibrio
cytochromes
c
3
but define a new folding motif for small multiheme cytochromes
c
.
Cluster Structure of Anaerobic Aggregates of an Expanded Granular Sludge Bed Reactor
Authors: Gonzalez-Gil G. , Lens P. N. L. , Van Aelst A. , Van As H. , Versprille A. I. , Lettinga G. 
Published: July 2002

ABSTRACT

The metabolic properties and ultrastructure of mesophilic aggregates from a full-scale expanded granular sludge bed reactor treating brewery wastewater are described. The aggregates had a very high methanogenic activity on acetate (17.19 mmol of CH
4
/g of volatile suspended solids [VSS]·day or 1.1 g of CH
4
chemical oxygen demand/g of VSS·day). Fluorescent in situ hybridization using 16S rRNA probes of crushed granules showed that 70 and 30% of the cells belonged to the archaebacterial and eubacterial domains, respectively. The spherical aggregates were black but contained numerous whitish spots on their surfaces. Cross-sectioning these aggregates revealed that the white spots appeared to be white clusters embedded in a black matrix. The white clusters were found to develop simultaneously with the increase in diameter. Energy-dispersed X-ray analysis and back-scattered electron microscopy showed that the whitish clusters contained mainly organic matter and no inorganic calcium precipitates. The white clusters had a higher density than the black matrix, as evidenced by the denser cell arrangement observed by high-magnification electron microscopy and the significantly higher effective diffusion coefficient determined by nuclear magnetic resonance imaging. High-magnification electron microscopy indicated a segregation of acetate-utilizing methanogens (
Methanosaeta
spp.) in the white clusters from syntrophic species and hydrogenotrophic methanogens (
Methanobacterium
-like and
Methanospirillum
-like organisms) in the black matrix. A number of physical and microbial ecology reasons for the observed structure are proposed, including the advantage of segregation for high-rate degradation of syntrophic substrates.
Survival of
Lactobacillus delbrueckii
subsp.
bulgaricus
and
Streptococcus thermophilus
in the Terminal Ileum of Fistulated Göttingen Minipigs
Authors: Lick Sonja , Drescher Karsten , Heller Knut J. 
Published: July 2002

ABSTRACT

The ability of
Lactobacillus delbrueckii
subsp.
bulgaricus
and
Streptococcus thermophilus
administered in yogurt to survive the passage through the upper gastrointestinal tract was investigated with Göttingen minipigs that were fitted with ileum T-cannulas. After ingestion of yogurt containing viable microorganisms, ileostomy samples were collected nearly every hour beginning 3 h after food uptake. Living
L. delbrueckii
subsp.
bulgaricus
and
S. thermophilus
were detected in the magnitude of 10
6
to 10
7
per gram of intestinal contents (wet weight) in all animals under investigation. A calculation of the minimum amount of surviving bacteria that had been administered is presented. Total DNA extracted from ileostomy samples was subjected to PCR, which was species specific for
L. delbrueckii
and
S. thermophilus
and subspecies specific for
L. delbrueckii
subsp.
bulgaricus
. All three bacterial groups could be detected by PCR after yogurt uptake but not after uptake of a semisynthetic diet. One pig apparently had developed an endogenous
L. delbrueckii
flora. When heat-treated yogurt was administered,
L. delbrueckii
was detected in all animals.
S. thermophilus
or
L. delbrueckii
subsp.
bulgaricus
was not detected, indicating that heat-inactivated cells and their DNAs had already been digested and their own
L. delbrueckii
flora had been stimulated for growth.