bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement of NaNO
2
-Oxidizing Activity in
Nitrobacter vulgaris
by Coentrapment in Polyacrylamide Containing Polydimethylsiloxane Copolymer and DEAE-Sephadex
Authors: Zhang Songping , Norrlöw Olof , Dey Estera Szwajcer 
Published: October 2005

ABSTRACT

Removal of nitrite and nitrate from drinking water has attracted great attention in recent years because of the human health risk induced by the exposure to contaminated groundwater and surface water. We have therefore tested a model nitrite oxidation system by coentrapping the NaNO
2
oxidizer
Nitrobacter vulgaris
with polydimethylsiloxane (PDMS) copolymer and DEAE-Sephadex in a polyacrylamide gel. The copolymer and the anion exchanger facilitate the diffusion of oxygen and NaNO
2
, respectively, into the gel matrix. To test the nitrite-oxidizing activity, the entrapped cells were coupled to a thermal sensor. Coentrapment of 5% (wt/vol) DEAE-Sephadex with
Nitrobacter vulgaris
increased the nitrite-oxidizing activity by a factor of 3.7 compared to entrapped cells alone, and by the addition of 0.86% (wt/vol) artificial oxygen carrier PDMS copolymer increased the activity further to 4.3 times higher. Operational and storage stability of the coentrapped
N
.
vulgaris
also improved. This suggests that this enhanced immobilized cell system can also be used for nitrite oxidation to nitrate in drinking water as an on-line thermally monitored bioreactor.
Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community
Authors: Gich Frederic , Schubert Karin , Bruns Alke , Hoffelner Herbert , Overmann Jörg 
Published: October 2005

ABSTRACT

High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α
-Proteobacteria
, β
-Proteobacteria
,
Actinobacteria
,
Firmicutes
, or
Flavobacteria-Cytophaga
lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α-
Proteobacteria
16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of
Sandaracinobacter sibiricus
, the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll
a
bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.
Diversity and Functional Analysis of Bacterial Communities Associated with Natural Hydrocarbon Seeps in Acidic Soils at Rainbow Springs, Yellowstone National Park
Authors: Hamamura Natsuko , Olson Sarah H. , Ward David M. , Inskeep William P. 
Published: October 2005

ABSTRACT

In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g.,
n-
alkanes with chain lengths of C
15
to C
30
, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including
Acidisphaera
spp. and
Acidiphilium
spp. of the α-
Proteobacteria
. Clones related to the iron- and sulfur-oxidizing chemolithotroph
Acidithiobacillus
spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [
14
C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [
14
C]hexadecane added was recovered as
14
CO
2
during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an
alkB
gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils.
Development of an F57 Sequence-Based Real-Time PCR Assay for Detection ofMycobacterium aviumsubsp.paratuberculosisin Milk
Authors: Tasara T. , Stephan R. 
Published: October 2005

ABSTRACTA light cycler-based real-time PCR (LC-PCR) assay that amplifies the F57 sequence ofMycobacterium aviumsubsp.paratuberculosiswas developed. This assay also includes an internal amplification control template to monitor the amplification conditions in each reaction. The targeted F57 sequence element is unique forM.aviumsubsp.paratuberculosisand is not known to exist in any other bacterial species. The assay specificity was demonstrated by evaluation of 10 knownM. aviumsubsp.paratuberculosisisolates and 33 other bacterial strains. The LC-PCR assay has a broad linear range (2 × 101to 2 ×106copies) for quantitative estimation of the number ofM. aviumsubsp.paratuberculosisF57 target copies in positive samples. To maximize the assay's detection sensitivity, an efficient strategy for isolation ofM. aviumsubsp.paratuberculosisDNA from spiked milk samples was also developed. The integrated procedure combining optimalM. aviumsubsp.paratuberculosisDNA isolation and real-time PCR detection had a reproducible detection limit of about 10M. aviumsubsp.paratuberculosiscells per ml when a starting sample volume of 10 ml ofM. aviumsubsp.paratuberculosis-spiked milk was analyzed. The entire process can be completed within a single working day and is suitable for routine monitoring of milk samples forM. aviumsubsp.paratuberculosiscontamination. The applicability of this protocol for naturally contaminated milk was also demonstrated using milk samples from symptomaticM. aviumsubsp.paratuberculosis-infected cows, as well as pooled samples from a dairy herd with a confirmed history of paratuberculosis.
Geobacteraceae
Community Composition Is Related to Hydrochemistry and Biodegradation in an Iron-Reducing Aquifer Polluted by a Neighboring Landfill
Authors: Lin Bin , Braster Martin , van Breukelen Boris M. , van Verseveld Henk W. , Westerhoff Hans V. , Röling Wilfred F. M. 
Published: October 2005

ABSTRACT

Relationships between community composition of the iron-reducing
Geobacteraceae
, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent
Geobacteraceae
16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high
Geobacteraceae
diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of
Geobacteraceae
. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.
Identifying Host Sources of Fecal Pollution: Diversity of
Escherichia coli
in Confined Dairy and Swine Production Systems
Authors: Lu Zexun , Lapen David , Scott Andrew , Dang Angela , Topp Edward 
Published: October 2005

ABSTRACT

Repetitive extragenic palindromic PCR fingerprinting of
Escherichia coli
is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of
E. coli
obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the
E. coli
populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the
E. coli
community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of
E. coli
populations obtained from 10 different locations in either holding tank suggested that spatial variability in the
E. coli
community should be accounted for when sampling. Overall, the diversity in
E. coli
populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications.
pH-, Lactic Acid-, and Non-Lactic Acid-Dependent Activities of Probiotic Lactobacilli against
Salmonella enterica
Serovar Typhimurium
Authors: Fayol-Messaoudi Domitille , Berger Cédric N. , Coconnier-Polter Marie-Hélène , Liévin-Le Moal Vanessa , Servin Alain L. 
Published: October 2005

ABSTRACT

The mechanism(s) underlying the antibacterial activity of probiotic
Lactobacillus
strains appears to be multifactorial and includes lowering of the pH and the production of lactic acid and of antibacterial compounds, including bacteriocins and nonbacteriocin, non-lactic acid molecules. Addition of Dulbecco's modified Eagle's minimum essential medium to the incubating medium delays the killing activity of lactic acid. We found that the probiotic strains
Lactobacillus johnsonii
La1,
Lactobacillus rhamnosus
GG,
Lactobacillus casei
Shirota YIT9029,
L. casei
DN-114 001, and
L. rhamnosus
GR1 induced a dramatic decrease in the viability of
Salmonella enterica
serovar Typhimurium SL1344 mainly attributable to non-lactic acid molecule(s) present in the cell-free culture supernatant (CFCS). These molecules were more active against serovar Typhimurium SL1344 in the exponential growth phase than in the stationary growth phase. We also showed that the production of the non-lactic acid substance(s) responsible for the killing activity was dependent on growth temperature and that both unstable and stable substances with killing activity were present in the CFCSs. We found that the complete inhibition of serovar Typhimurium SL1344 growth results from a pH-lowering effect.
Clustering of
Mycobacterium avium
subsp.
paratuberculosis
in Rabbits and the Environment: How Hot Is a Hot Spot?
Authors: Judge Johanna , Kyriazakis Ilias , Greig Alastair , Allcroft David J. , Hutchings Michael R. 
Published: October 2005

ABSTRACT

Clustering of pathogens in the environment leads to hot spots of diseases at local, regional, national, and international levels. Scotland contains regional hot spots of Johne's disease (caused by
Mycobacterium avium
subsp.
paratuberculosis
) in rabbits, and there is increasing evidence of a link between paratuberculosis infections in rabbits and cattle. The spatial and temporal dynamics of paratuberculosis in rabbits within a hot spot region were studied with the overall aim of determining environmental patterns of infection and thus the risk of interspecies transmission to livestock. The specific aims were to determine if prevalence of paratuberculosis in rabbits varies temporally between seasons and whether the heterogeneous spatial environmental distribution of
M. avium
subsp.
paratuberculosis
on a large scale (i.e., regional hot spots) is replicated at finer resolutions within a hot spot. The overall prevalence of
M. avium
subsp.
paratuberculosis
in rabbits was 39.7%; the temporal distribution of infection in rabbits followed a cyclical pattern, with a peak in spring of 55.4% and a low in summer of 19.4%. Spatially,
M. avium
subsp.
paratuberculosis
-infected rabbits and, thus, the risk of interspecies transmission were highly clustered in the environment. However, this is mostly due to the clustered distribution of rabbits. The patterns of
M. avium
subsp.
paratuberculosis
infection in rabbits are discussed in relation to the host's socioecology and risk to livestock.
Use of Rotavirus Virus-Like Particles as Surrogates To Evaluate Virus Persistence in Shellfish
Authors: Loisy Fabienne , Atmar Robert L. , Le Saux Jean-Claude , Cohen Jean , Caprais Marie-Paule , Pommepuy Monique , Le Guyader Françoise S. 
Published: October 2005

ABSTRACT

Rotavirus virus-like particles (VLPs) and MS2 bacteriophages were bioaccumulated in bivalve mollusks to evaluate viral persistence in shellfish during depuration and relaying under natural conditions. Using this nonpathogenic surrogate virus, we were able to demonstrate that about 1 log
10
of VLPs was depurated after 1 week in warm seawater (22°C). Phage MS2 was depurated more rapidly (about 2 log
10
in 1 week) than were VLPs, as determined using a single-compartment model and linear regression analysis. After being relayed in the estuary under the influence of the tides, VLPs were detected in oysters for up to 82 days following seeding with high levels of VLPs (concentration range between 10
10
and 10
9
particles per g of pancreatic tissue) and for 37 days for lower contamination levels (10
5
particles per g of pancreatic tissue). These data suggest that viral particles may persist in shellfish tissues for several weeks.
Pelagic-Benthic Coupling and Diagenesis of Nucleic Acids in a Deep-Sea Continental Margin and an Open-Slope System of the Eastern Mediterranean
Authors: Dell'Anno Antonio , Corinaldesi Cinzia , Stavrakakis Spyros , Lykousis Vasilis , Danovaro Roberto 
Published: October 2005

ABSTRACT
Downward fluxes of nucleic acids adsorbed onto settling particles play a key role in the supply of organic phosphorus and genetic material to the ocean interior. However, information on pelagic-benthic coupling, diagenesis, and processes controlling nucleic acid preservation in deep-sea sediments is practically nonexistent. In this study, we compared nucleic acid fluxes, sedimentary DNA and RNA concentrations, and the enzymatically hydrolyzable fraction of DNA in a bathyal continental margin (North Aegean Sea) and an open-sea system (South Aegean Sea) of the Eastern Mediterranean. The two systems displayed contrasting patterns of nucleic acid fluxes, which increased significantly with depth in the North Aegean Sea and decreased with depth in the South Aegean Sea. These results suggest that in continental margin and open-ocean systems different processes control the nucleic acid supply to the sea floor. Differences in nucleic acid fluxes were reflected by nucleic acid concentrations in the sediments, which reached extremely high values in the North Aegean Sea. In this system, a large fraction of DNA may be buried, as suggested by the large fraction of DNA resistant to nuclease degradation and by estimates of burial efficiency (ca. eight times higher in the North than in the South Aegean Sea). Overall, the results reported here suggest that the preservation of DNA in deeper sediment layers may be favored in benthic systems characterized by high sedimentation rates.
Effects of Cattle Feeding Regimen and Soil Management Type on the Fate of
Escherichia coli
O157:H7 and
Salmonella enterica
Serovar Typhimurium in Manure, Manure-Amended Soil, and Lettuce
Authors: Franz Eelco , van Diepeningen Anne D. , de Vos Oscar J. , van Bruggen Ariena H. C. 
Published: October 2005

ABSTRACT

Survival of the green fluorescent protein-transformed human pathogens
Escherichia coli
O157:H7 and
Salmonella enterica
serovar Typhimurium was studied in a laboratory-simulated lettuce production chain. Dairy cows were fed three different roughage types: high-digestible grass silage plus maize silage (6:4), low-digestible grass silage, and straw. Each was adjusted with supplemental concentrates to high and low crude protein levels. The pathogens were added to manure, which was subsequently mixed (after 56 and 28 days for
E. coli
O157:H7 and
Salmonella
serovar Typhimurium, respectively) with two pairs of organically and conventionally managed loamy and sandy soil. After another 14 days, iceberg lettuce seedlings were planted and then checked for pathogens after 21 days of growth. Survival data were fitted to a logistic decline function (exponential for
E. coli
O157:H7 in soil). Roughage type significantly influenced the rate of decline of
E. coli
O157:H7 in manure, with the fastest decline in manure from the pure straw diet and the slowest in manure from the diet of grass silage plus maize silage. Roughage type showed no effect on the rate of decline of
Salmonella
serovar Typhimurium, although decline was significantly faster in the manure derived from straw than in the manure from the diet of grass silage plus maize silage. The pH and fiber content of the manure were significant explanatory factors and were positively correlated with the rate of decline. With
E. coli
O157:H7 there was a trend of faster decline in organic than in conventional soils. No pathogens were detected in the edible lettuce parts. The results indicate that cattle diet and soil management are important factors with respect to the survival of human pathogens in the environment.
Engineering of a Novel
Saccharomyces cerevisiae
Wine Strain with a Respiratory Phenotype at High External Glucose Concentrations
Authors: Henricsson C. , de Jesus Ferreira M. C. , Hedfalk K. , Elbing K. , Larsson C. , Bill R. M. , Norbeck J. , Hohmann S. , Gustafsson L. 
Published: October 2005

ABSTRACT

The recently described respiratory strain
Saccharomyces cerevisiae
KOY.TM6*P is, to our knowledge, the only reported strain of
S. cerevisiae
which completely redirects the flux of glucose from ethanol fermentation to respiration, even at high external glucose concentrations (27). In the KOY.TM6*P strain, portions of the genes encoding the predominant hexose transporter proteins, Hxt1 and Hxt7, were fused within the regions encoding transmembrane (TM) domain 6. The resulting chimeric gene,
TM6*
, encoded a chimera composed of the amino-terminal half of Hxt1 and the carboxy-terminal half of Hxt7. It was subsequently integrated into the genome of an
hxt
null strain. In this study, we have demonstrated the transferability of this respiratory phenotype to the V5
hxt1-7
Δ strain, a derivative of a strain used in enology. We also show by using this mutant that it is not necessary to transform a complete
hxt
null strain with the
TM6*
construct to obtain a non-ethanol-producing phenotype. The resulting V5.TM6*P strain, obtained by transformation of the V5
hxt1-7
Δ strain with the
TM6*
chimeric gene, produced only minor amounts of ethanol when cultured on external glucose concentrations as high as 5%. Despite the fact that glucose flux was reduced to 30% in the V5.TM6*P strain compared with that of its parental strain, the V5.TM6*P strain produced biomass at a specific rate as high as 85% that of the V5 wild-type strain. Even more relevant for the potential use of such a strain for the production of heterologous proteins and also of low-alcohol beverages is the observation that the biomass yield increased 50% with the mutant compared to its parental strain.
Autotrophic and Mixotrophic Hydrogen Photoproduction in Sulfur-Deprived
Chlamydomonas
Cells
Authors: Fouchard Swanny , Hemschemeier Anja , Caruana Amandine , Pruvost Jérémy , Legrand Jack , Happe Thomas , Peltier Gilles , Cournac Laurent 
Published: October 2005

ABSTRACT

In
Chlamydomonas reinhardtii
cells, H
2
photoproduction can be induced in conditions of sulfur deprivation in the presence of acetate. The decrease in photosystem II (PSII) activity induced by sulfur deprivation leads to anoxia, respiration becoming higher than photosynthesis, thereby allowing H
2
production. Two different electron transfer pathways, one PSII dependent and the other PSII independent, have been proposed to account for H
2
photoproduction. In this study, we investigated the contribution of both pathways as well as the acetate requirement for H
2
production in conditions of sulfur deficiency. By using 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), a PSII inhibitor, which was added at different times after the beginning of sulfur deprivation, we show that PSII-independent H
2
photoproduction depends on previously accumulated starch resulting from previous photosynthetic activity. Starch accumulation was observed in response to sulfur deprivation in mixotrophic conditions (presence of acetate) but also in photoautotrophic conditions. However, no H
2
production was measured in photoautotrophy if PSII was not inhibited by DCMU, due to the fact that anoxia was not reached. When DCMU was added at optimal starch accumulation, significant H
2
production was measured. H
2
production was enhanced in autotrophic conditions by removing O
2
using N
2
bubbling, thereby showing that substantial H
2
production can be achieved in the absence of acetate by using the PSII-independent pathway. Based on these data, we discuss the possibilities of designing autotrophic protocols for algal H
2
photoproduction.