bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of Indigenous Plant-Microbe Symbioses Aids Restoration of Desertified Ecosystems
Authors: Requena Natalia , Perez-Solis Estefania , Azcón-Aguilar Concepción , Jeffries Peter , Barea José-Miguel 
Published: July 2002

ABSTRACT
Disturbance of natural plant communities is the first visible indication of a desertification process, but damage to physical, chemical, and biological soil properties is known to occur simultaneously. Such soil degradation limits reestablishment of the natural plant cover. In particular, desertification causes disturbance of plant-microbe symbioses which are a critical ecological factor in helping further plant growth in degraded ecosystems. Here we demonstrate, in two long-term experiments in a desertified Mediterranean ecosystem, that inoculation with indigenous arbuscular mycorrhizal fungi and with rhizobial nitrogen-fixing bacteria not only enhanced the establishment of key plant species but also increased soil fertility and quality. The dual symbiosis increased the soil nitrogen (N) content, organic matter, and hydrostable soil aggregates and enhanced N transfer from N-fixing to nonfixing species associated within the natural succession. We conclude that the introduction of target indigenous species of plants associated with a managed community of microbial symbionts is a successful biotechnological tool to aid the recovery of desertified ecosystems.
Discovery and Description of Giant Submarine Smectite Cones on the Seafloor in Eyjafjordur, Northern Iceland, and a Novel Thermal Microbial Habitat
Authors: Marteinsson Viggó Thór , Kristjánsson Jakob K. , Kristmannsdóttir Hrefna , Dahlkvist Maria , Sæmundsson Kristján , Hannington Mark , Pétursdóttir Sólveig K. , Geptner Alfred , Stoffers Peter 
Published: July 2002

ABSTRACTWith the submersible JAGO and by scuba diving we discovered three remarkable geothermal cones, rising 33, 25, and 45 m from the seafloor at a depth of 65 m in Eyjafjordur, northern Iceland. The greatest geothermal activity was on the highest cone, which discharged up to 50 liters of freshwater per s at 72°C and pH 10.0. The cones were built up from precipitated smectite, formed by mixing of the hot SiO2-rich geothermal fluid with the cold Mg-rich seawater. By connecting a rubber hose to one outflow, about 240 liters of pure geothermal fluids was concentrated through a 0.2-μm-pore-size filter. Among 50 thermophilic isolates, we found members ofBacillusandThermonemaand a new unidentified low-G+C gram-positive member of theBacteriaas well as one member of theArchaea,Desulfurococcus mobilis. Analysis of small-subunit rRNA genes PCR amplified and cloned directly from environmental DNA showed that 41 out of 45Bacteriasequences belonged to members of theAquificales, whereas all of the 10Archaeasequences belonged to theKorarchaeota. The physiological characteristics of isolates from different parts of the cones indicate a completely freshwater habitat, supporting the possibility of subterranean transmittance of terrestrial organisms.
Differentiation of Environmental and Clinical Isolates of
Vibrio mimicus
from
Vibrio cholerae
by Multilocus Enzyme Electrophoresis
Authors: Vieira Verônica V. , Teixeira Luiz Fernando M. , Vicente Ana Carolina P. , Momen Hooman , Salles Carlos André 
Published: July 2002

ABSTRACT

In this study, we demonstrated that analyzed strains of
Vibrio mimicus
and
Vibrio cholerae
could be separated in two groups by using multilocus enzyme electrophoresis (MEE) data from 14 loci. We also showed that the combination of four enzymatic loci enables us to differentiate these two species. Our results showed that the ribosomal intergenic spacer regions PCR-mediated identification system failed, in some cases, to differentiate between
V. mimicus
and
V. cholerae
. On the other hand, MEE proved to be a powerful molecular tool for the discrimination of these two species even when atypical strains were analyzed.
Surface Binding of Aflatoxin B
1
by Lactic Acid Bacteria
Authors: Haskard Carolyn A. , El-Nezami Hani S. , Kankaanpää Pasi E. , Salminen Seppo , Ahokas Jorma T. 
Published: July 2002

ABSTRACT

Specific lactic acid bacterial strains remove toxins from liquid media by physical binding. The stability of the aflatoxin B
1
complexes formed with 12 bacterial strains in both viable and nonviable (heat- or acid-treated) forms was assessed by repetitive aqueous extraction. By the fifth extraction, up to 71% of the total aflatoxin B
1
remained bound. Nonviable bacteria retained the highest amount of aflatoxin B
1
.
Lactobacillus rhamnosus
strain GG (ATCC 53103) and
L. rhamnosus
strain LC-705 (DSM 7061) removed aflatoxin B
1
from solution most efficiently and were selected for further study. The accessibility of bound aflatoxin B
1
to an antibody in an indirect competitive inhibition enzyme-linked immunosorbent assay suggests that surface components of these bacteria are involved in binding. Further evidence is the recovery of around 90% of the bound aflatoxin from the bacteria by solvent extraction. Autoclaving and sonication did not release any detectable aflatoxin B
1
. Variation in temperature (4 to 37°C) and pH (2 to 10) did not have any significant effect on the amount of aflatoxin B
1
released. Binding of aflatoxin B
1
appears to be predominantly extracellular for viable and heat-treated bacteria. Acid treatment may permit intracellular binding. In all cases, binding is of a reversible nature, but the stability of the complexes formed depends on strain, treatment, and environmental conditions.
Utilization of the
rpoB
Gene as a Specific Chromosomal Marker for Real-Time PCR Detection of
Bacillus anthracis
Authors: Qi Yuan , Patra Guy , Liang Xudong , Williams Leanne E. , Rose Sharon , Redkar Rajendra J. , DelVecchio Vito G. 
Published: July 2002

ABSTRACT

The potential use of
Bacillus anthracis
as a weapon of mass destruction poses a threat to humans, domesticated animals, and wildlife and necessitates the need for a rapid and highly specific detection assay. We have developed a real-time PCR-based assay for the specific detection of
B. anthracis
by taking advantage of the unique nucleotide sequence of the
B. anthracis rpoB
gene. Variable region 1 of the
rpoB
gene was sequenced from 36
Bacillus
strains, including 16
B. anthracis
strains and 20 other related bacilli, and four nucleotides specific for
B. anthracis
were identified. PCR primers were selected so that two
B. anthracis
-specific nucleotides were at their 3′ ends, whereas the remaining bases were specific to the probe region. This format permitted the PCR reactions to be performed on a LightCycler via fluorescence resonance energy transfer (FRET). The assay was found to be specific for 144
B. anthracis
strains from different geographical locations and did not cross-react with other related bacilli (175 strains), with the exception of one strain. The PCR assay can be performed on isolated DNA as well as crude vegetative cell lysates in less than 1 h. Therefore, the
rpoB
-FRET assay could be used as a new chromosomal marker for rapid detection of
B. anthracis
.
Evidence for Iron-Dependent Nitrate Respiration in the Dissimilatory Iron-Reducing Bacterium
Geobacter metallireducens
Authors: Senko John M. , Stolz John F. 
Published: July 2002

ABSTRACT

The dissimilatory iron-reducing bacterium
Geobacter metallireducens
was found to require iron at a concentration in excess of 50 μM for continuous cultivation on nitrate. Growth yield (∼3-fold), cytochrome
c
content (∼7-fold), and nitrate (∼4.5-fold) and nitrite (∼70-fold) reductase activities were all increased significantly when the growth medium was amended with 500 μM iron.
Comparison of
pmoA
PCR Primer Sets as Tools for Investigating Methanotroph Diversity in Three Danish Soils
Authors: Bourne David G. , McDonald Ian R. , Murrell J. Colin 
Published: July 2002

ABSTRACT

Three particulate methane monooxygenase PCR primer sets (A189-A682, A189-A650, and A189-mb661) were investigated for their ability to assess methanotroph diversity in soils from three sites, i.e., heath, oak, and sitka, each of which was capable of oxidizing atmospheric concentrations of methane. Each PCR primer set was used to construct a library containing 50 clones from each soil type. The clones from each library were grouped by restriction fragment length polymorphism, and representatives from each group were sequenced and analyzed. Libraries constructed with the A189-A682 PCR primer set were dominated by
amoA
-related sequences or nonspecific PCR products with nonsense open reading frames. The primer set could not be used to assess methanotroph diversity in these soils. A new
pmoA-
specific primer, A650, was designed in this study. The A189-A650 primer set demonstrated distinct biases both in clone library analysis and when incorporated into denaturing gradient gel electrophoresis analysis. The A189-mb661 PCR primer set demonstrated the largest retrieval of methanotroph diversity of all of the primer sets. However, this primer set did not retrieve sequences linked with novel high-affinity methane oxidizers from the soil libraries, which were detected using the A189-A650 primer set. A combination of all three primer sets appears to be required to examine both methanotroph diversity and the presence of novel methane monooxygenase sequences.
Fluorescent Method for Monitoring Cheese Starter Permeabilization and Lysis
Authors: Bunthof Christine J. , van Schalkwijk Saskia , Meijer Wilco , Abee Tjakko , Hugenholtz Jeroen 
Published: July 2002

ABSTRACT

A fluorescence method to monitor lysis of cheese starter bacteria using dual staining with the LIVE/DEAD
Bac
Light bacterial viability kit is described. This kit combines membrane-permeant green fluorescent nucleic acid dye SYTO 9 and membrane-impermeant red fluorescent nucleic acid dye propidium iodide (PI), staining damaged membrane cells fluorescent red and intact cells fluorescent green. For evaluation of the fluorescence method, cells of
Lactococcus lactis
MG1363 were incubated under different conditions and subsequently labeled with SYTO 9 and PI and analyzed by flow cytometry and epifluorescence microscopy. Lysis was induced by treatment with cell wall-hydrolyzing enzyme mutanolysin. Cheese conditions were mimicked by incubating cells in a buffer with high protein, potassium, and magnesium, which stabilizes the cells. Under nonstabilizing conditions a high concentration of mutanolysin caused complete disruption of the cells. This resulted in a decrease in the total number of cells and release of cytoplasmic enzyme lactate dehydrogenase. In the stabilizing buffer, mutanolysin caused membrane damage as well but the cells disintegrated at a much lower rate. Stabilizing buffer supported permeabilized cells, as indicated by a high number of PI-labeled cells. In addition, permeable cells did not release intracellular aminopeptidase N, but increased enzyme activity was observed with the externally added and nonpermeable peptide substrate lysyl-
p
-nitroanilide. Finally, with these stains and confocal scanning laser microscopy the permeabilization of starter cells in cheese could be analyzed.
Quantification of
Nitrosomonas oligotropha
-Like Ammonia-Oxidizing Bacteria and
Nitrospira
spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR
Authors: Dionisi Hebe M. , Layton Alice C. , Harms Gerda , Gregory Igrid R. , Robinson Kevin G. , Sayler Gary S. 
Published: July 2002

ABSTRACT

Utilizing the principle of competitive PCR, we developed two assays to enumerate
Nitrosomonas oligotropha
-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus
Nitrospira
. The specificities of two primer sets, which were designed for two target regions, the
amoA
gene and
Nitrospira
16S ribosomal DNA (rDNA), were verified by DNA sequencing. Both assays were optimized and applied to full-scale, activated sludge wastewater treatment plant (WWTP) samples. If it was assumed that there was an average of 3.6 copies of 16S rDNA per cell in the total population and two copies of the
amoA
gene per ammonia-oxidizing bacterial cell, the ammonia oxidizers examined represented 0.0033% ± 0.0022% of the total bacterial population in a municipal WWTP.
N. oligotropha
-like ammonia-oxidizing bacteria were not detected in an industrial WWTP. If it was assumed that there was one copy of the 16S rDNA gene per nitrite-oxidizing bacterial cell,
Nitrospira
spp. represented 0.39% ± 0.28% of the biosludge population in the municipal WWTP and 0.37% ± 0.23% of the population in the industrial WWTP. The number of
Nitrospira
sp. cells in the municipal WWTP was more than 62 times greater than the number of
N. oligotropha
-like cells, based on a competitive PCR analysis. The results of this study extended our knowledge of the comparative compositions of nitrifying bacterial populations in wastewater treatment systems. Importantly, they also demonstrated that we were able to quantify these populations, which ultimately will be required for accurate prediction of process performance and stability for cost-effective design and operation of WWTPs.
Homology of
Escherichia coli
R773
arsA
,
arsB
, and
arsC
Genes in Arsenic-Resistant Bacteria Isolated from Raw Sewage and Arsenic-Enriched Creek Waters
Authors: Saltikov Chad W. , Olson Betty H. 
Published: July 2002

ABSTRACT

The occurrence and diversity of the
Escherichia coli
R773
ars
operon were investigated among arsenic-resistant enteric and nonenteric bacteria isolated from raw sewage and arsenic-enriched creek waters. Selected isolates from each creek location were screened for
ars
genes by colony hybridization and PCR. The occurrence of
arsA
,
arsB
, and
arsC
determined by low-stringency colony hybridization (31 to 53% estimated mismatch) was 81, 87, and 86%, respectively, for 84 bacteria isolated on arsenate- and arsenite-amended media from three locations. At moderate stringency (21 to 36% estimated mismatch), the occurrence decreased to 42, 56, and 63% for
arsA
,
arsB
, and
arsC
, respectively. PCR results showed that the
ars
operon is conserved in some enteric bacteria isolated from creek waters and raw sewage. The occurrence of the
arsBC
genotype was about 50% in raw sewage enteric bacteria, while
arsA
was detected in only 9.4% of the isolates (
n
= 32). The
arsABC
and
arsBC
genotypes occurred more frequently in enteric bacteria isolated from creek samples: 71.4 and 85.7% (
n
= 7), respectively. Average sequence divergence within
arsB
for six creek enteric bacteria was 20% compared to that of the
E. coli
R773
ars
operon. Only 1 of 11 pseudomonads screened by PCR was positive for
arsB
. The results from this study suggest that significant divergence has occurred in the
ars
operon among As-resistant
E. coli
strains and in
Pseudomonas
spp.
Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces
Authors: Frias-Lopez Jorge , Zerkle Aubrey L. , Bonheyo George T. , Fouke Bruce W. 
Published: July 2002

ABSTRACT

Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Curaçao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including
Clostridium
spp.,
Arcobacter
spp.,
Campylobacter
spp.,
Cytophaga fermentans
,
Cytophaga columnaris
, and
Trichodesmium tenue
.
Rapid and Quantitative Detection of the Microbial Spoilage of Meat by Fourier Transform Infrared Spectroscopy and Machine Learning
Authors: Ellis David I. , Broadhurst David , Kell Douglas B. , Rowland Jem J. , Goodacre Royston 
Published: July 2002

ABSTRACT

Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable “fingerprints.” Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 10
7
bacteria·g
−1
the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels.
Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria
Authors: Pernthaler Annelie , Pernthaler Jakob , Amann Rudolf 
Published: July 2002

ABSTRACT

Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. Penetration of the HRP molecule into bacterial cells requires permeabilization procedures that cause high and most probably species-selective cell loss. Here we present an improved protocol for CARD-FISH of marine planktonic and benthic microbial assemblages. After concentration of samples onto membrane filters and subsequent embedding of filters in low-gelling-point agarose, no decrease in bacterial cell numbers was observed during 90 min of lysozyme incubation (10 mg ml
−1
at 37°C). The detection rates of coastal North Sea bacterioplankton by CARD-FISH with a general bacterial probe (EUB338-HRP) were significantly higher (mean, 94% of total cell counts; range, 85 to 100%) than that with a monolabeled probe (EUB338-mono; mean, 48%; range, 19 to 66%). Virtually no unspecific staining was observed after CARD-FISH with an antisense EUB338-HRP. Members of the marine SAR86 clade were undetectable by FISH with a monolabeled probe; however, a substantial population was visualized by CARD-FISH (mean, 7%; range, 3 to 13%). Detection rates of EUB338-HRP in Wadden Sea sediments (mean, 81%; range, 53 to 100%) were almost twice as high as the detection rates of EUB338-mono (mean, 44%; range, 25 to 71%). The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment.
Conjugation of Hydroxyethyl Starch to Desferrioxamine (DFO) Modulates the Dual Role of DFO in
Yersinia enterocolitica
Infection
Authors: Schubert Sören , Autenrieth Ingo B. 
Published: July 2002

ABSTRACT

The iron chelator desferrioxamine (DFO) B is widely used in the therapy of patients with iron overload. As a side effect, DFO may favor the occurrence of fulminant
Yersinia
infections. Previous work from our laboratory showed that this might be due to a dual role of DFO: growth promotion of the pathogen and immunosuppression of the host. In this study, we sought to determine whether conjugation of DFO to hydroxyethyl starch (HES-DFO) may prevent exacerbation of
Yersinia
infection in mice. We found HES-DFO to promote neither growth of
Yersinia enterocolitica
nor mitogen-induced T-cell proliferation and gamma interferon production by T cells in vitro. Nevertheless, in vivo HES-DFO promoted growth of
Y. enterocolitica
possibly due to cleavage of HES and release of DFO. The pretreatment of mice with DFO resulted in death of all mice 2 to 5 days after application of a normally sublethal inoculum of
Y. enterocolitica
, while none of the mice pretreated with HES-DFO died within the first 7 days postinfection. However, some of the HES-DFO-treated mice died 8 to 14 days postinfection. Thus, due to the delayed in vivo effect HES-DFO failed to trigger
Yersinia
-induced septic shock, which accounts for early mortality in DFO-associated septicemia. Moreover, our data suggest that DFO needs to be taken up by host cells in order to exert its immunosuppressive action. These results strongly suggest that HES-DFO might be a favorable drug with fewer side effects than DFO in terms of DFO-promoted fulminant infections.
Comparison of Two Commercial Microimmunofluorescence Kits and an Enzyme Immunoassay Kit for Detection of Serum Immunoglobulin G Antibodies to
Chlamydia pneumoniae
Authors: Messmer Trudy O. , Martinez Joseph , Hassouna Fadwa , Zell Elizabeth R. , Harris Wayne , Dowell Scott , Carlone George M. 
Published: July 2002

ABSTRACT

We compared the MRL and the Labsystems
Chlamydia pneumoniae
microimmunofluorescence (MIF) immunoglobulin G (IgG) kits and the Labsystems enzyme immunoassay (EIA) kit in a blinded study of 83 serum samples in which we evaluated titers, cross-reactivity to other species, and reproducibility. There was no statistically significant difference between the MRL and the Labsystems MIF kits in the endpoint titers of IgG antibody to
C. pneumoniae
. The correlation between the results obtained with these two MIF kits was excellent (
r
= 0.95;
P
= 0.001). The cross-reactivity of the
C. pneumoniae
-positive sera with
C. trachomatis
- and
C. psittaci
-positive sera was assessed for each MIF kit. For
C. pneumoniae
-positive sera with titers of ≥32, the Labsystems MIF kit exhibited more cross-reactivity to
C. psittaci
than the MRL kit did. The values obtained with the Labsystems EIA kit represented single dilutions of serum specimens expressed as enzymeimmuno units on a continuous scale. The results obtained with the Labsystems EIA kit correlated moderately well with those obtained with each MIF kit when they were compared for their abilities to detect IgG antibodies to
C. pneumoniae
(for the MRL MIF kit,
r
= 0.79 [
P
= 0.001]; for the Labsystems MIF kit,
r
= 0.78 [
P
= 0.001]). The results obtained with the commercial MRL and Labsystems MIF kits and the Labsystems EIA kit tested were reproducible; and the kits were standardized, had quality control reagents, and are suitable for detection of
C. pneumoniae
antibodies in serum and for use in interlaboratory studies. Validation of the use of these kits for clinical diagnosis still needs further evaluation.