bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of
Mycobacterium ulcerans
in the Environment from Regions in Southeast Australia in Which It Is Endemic with Sequence Capture-PCR
Authors: Stinear Timothy , Davies John K. , Jenkin Grant A. , Hayman John A. , Oppedisano Frances , Johnson Paul D. R. 
Published: July 2002

ABSTRACT

We recently described the use of PCR to identify the environmental source of
Mycobacterium ulcerans
during an outbreak of ulcerative disease that occurred in a localized region of southeast Australia. The PCR used was based on amplification of the
M. ulcerans
-specific insertion sequence, IS
2404
. In this study we developed a new test that is a substantial improvement over the original PCR method in terms of sensitivity, reliability, and ease of use. In the new method magnetic bead sequence capture-PCR is used to detect two
M. ulcerans
sequences (IS
2404
and IS
2606
) and total mycobacterial 16S ribosomal DNA. We used sequence capture-PCR to test water and plant material collected over a 12-month period during 1998 and 1999 from sites near the centers of two distinct foci of
M. ulcerans
infections. A golf course irrigation system in one area and a small shallow lake in another area repeatedly were PCR positive for
M. ulcerans
. Nearby sites and sites unrelated to the endemic areas were negative. Based on the PCR data, a most-probable-number method was used to estimate the concentration of
M. ulcerans
cells in positive samples from both regions. This procedure resulted in average concentrations of 0.5 cell per 100 ml of water and 40 cells per 100 g of detritus. Loss of the PCR signal coincided with a decrease in ulcerative disease in each area. These results provide further evidence that
M. ulcerans
may be transmitted from a point environmental source and demonstrate the utility of magnetic bead sequence capture-PCR for identification of nonculturable microbial pathogens in the environment.
Evaluation of Fluorescently Labeled Lectins for Noninvasive Localization of Extracellular Polymeric Substances in
Sphingomonas
Biofilms
Authors: Johnsen Anders R. , Hausner Martina , Schnell Annette , Wuertz Stefan 
Published: July 2002

ABSTRACT

Three strains of
Sphingomonas
were grown as biofilms and tested for binding of five fluorescently labeled lectins (Con A-type IV-TRITC or -Cy5, Pha-E-TRITC, PNA-TRITC, UEA 1-TRITC, and WGA-Texas red). Only ConA and WGA were significantly bound by the biofilms. Binding of the five lectins to artificial biofilms made of the commercially available
Sphingomonas
extracellular polysaccharides was similar to binding to living biofilms. Staining of the living and artificial biofilms by ConA might be explained as binding of the lectin to the terminal mannosyl and terminal glucosyl residues in the polysaccharides secreted by
Sphingomonas
as well as to the terminal mannosyl residue in glycosphingolipids. Staining of the biofilms by WGA could only be explained as binding to the
Sphingomonas
glycosphingolipid membrane, binding to the cell wall, or nonspecific binding. Glycoconjugation of ConA and WGA with the target sugars glucose and
N
-acetylglucosamine, respectively, was used as a method for evaluation of the specificity of the lectins towards
Sphingomonas
biofilms and
Sphingomonas
polysaccharides. Our results show that the binding of lectins to biofilms does not necessarily prove the presence of specific target sugars in the extracellular polymeric substances (EPS) in biofilms. The lectins may bind to non-EPS targets or adhere nonspecifically to components of the biofilm matrix.
Applicability of an Arrhenius Model for the Combined Effect of Temperature and CO
2
Packaging on the Spoilage Microflora of Fish
Authors: Koutsoumanis Konstantinos P. , Taoukis Petros S. , Drosinos Eleftherios H. , Nychas George-John E. 
Published: July 2002

ABSTRACT

The temperature behavior of the natural microflora on the Mediterranean fish red mullet (
Mullus barbatus
) was examined as a case study. The growth of the spoilage bacteria
Pseudomonas
spp.,
Shewanella putrefaciens
,
Brochothrix thermosphacta
, and lactic acid bacteria was modeled as a function of temperature and the concentration of carbon dioxide in modified atmosphere packaging. Combined models were developed and comparatively assessed based on polynomial, Belehradek, and Arrhenius equations. The activation energy parameter of the Arrhenius model,

E
A

, was independent of the packaging atmosphere and ranged from 75 to 85 kJ/mol for the different bacteria, whereas the preexponential constant decreased exponentially with the packaging CO
2
concentration. We evaluated the applicability of the models developed by using experimental bacterial growth rates obtained from 42 independent experiments performed with three Mediterranean fish species and growth rates predicted from the models under the same temperature and packaging conditions. The accuracy factor and bias factor were used as statistical tools for evaluation, and the developed Arrhenius model and the Belehradek model were judged satisfactory overall.
Mycophenolic Acid in Silage
Authors: Schneweis Isabell , Meyer Karsten , Hörmansdorfer Stefan , Bauer Johann 
Published: July 2002

ABSTRACT

We examined 233 silage samples and found that molds were present in 206 samples with counts between 1 × 10
3
and 8.9 × 10
7
(mean, 4.7 × 10
6
) CFU/g. Mycophenolic acid, a metabolite of
Penicillium roqueforti
, was detected by liquid chromatography-mass spectrometry in 74 (32%) of these samples at levels ranging from 20 to 35,000 (mean, 1,400) μg/kg. This compound has well-known immunosuppressive properties, so feeding with contaminated silage may promote the development of infectious diseases in livestock.
Effects of High Pressure on Survival and Metabolic Activity of
Lactobacillus plantarum
TMW1.460
Authors: Ulmer Helge M. , Gänzle Michael G. , Vogel Rudi F. 
Published: July 2002

ABSTRACT

The application of high pressure (HP) for food preservation requires insight into mechanisms of HP-mediated cell injury and death. The HP inactivation in model beer of
Lactobacillus plantarum
TMW1.460, a beer-spoiling organism, was investigated at pressures ranging from 200 to 600 MPa. Surviving cells were characterized by determination of (i) cell viability and sublethal injury, (ii) membrane permeability to the fluorescent dyes propidium iodide (PI) and ethidium bromide (EB), (iii) metabolic activity with tetrazolium salts, and (iv) the activity of HorA, an ATP binding cassette-type multidrug resistance transporter conferring resistance to hop compounds. HP inactivation curves exhibited a shoulder, an exponential inactivation phase, and pronounced tailing caused by a barotolerant fraction of the population, about 1 in 10
6
cells. During exponential inactivation, more than 99.99% of cells were sublethally injured; however, no sublethal injury was detected in the barotolerant fraction of the culture. Sublethally injured cells were metabolically active, and loss of metabolic activity corresponded to the decrease of cell viability. Membrane damage measured by PI uptake occurred later than cell death, indicating that dye exclusion may be used as a fail-safe method for preliminary characterization of HP inactivation. An increase of membrane permeability to EB and a reduction of HorA activity were observed prior to the loss of cell viability, indicating loss of hop resistance of pressurized cells. Even mild HP treatments thus abolished the ability of cells to survive under adverse conditions.
Molecular Characterization of
Lactobacillus plantarum
Genes for β-Ketoacyl-Acyl Carrier Protein Synthase III (
fabH
) and Acetyl Coenzyme A Carboxylase (
accBCDA
), Which Are Essential for Fatty Acid Biosynthesis
Authors: Kiatpapan Pornpimon , Kobayashi Hajime , Sakaguchi Maki , Ono Hisayo , Yamashita Mitsuo , Kaneko Yoshinobu , Murooka Yoshikatsu 
Published: July 2002

ABSTRACT

Genes for subunits of acetyl coenzyme A carboxylase (ACC), which is the enzyme that catalyzes the first step in the synthesis of fatty acids in
Lactobacillus plantarum
L137, were cloned and characterized. We identified six potential open reading frames, namely,
manB
,
fabH
,
accB
,
accC
,
accD
, and
accA
, in that order. Nucleotide sequence analysis suggested that
fabH
encoded β-ketoacyl-acyl carrier protein synthase III, that the
accB
,
accC
,
accD
, and
accA
genes encoded biotin carboxyl carrier protein, biotin carboxylase, and the β and α subunits of carboxyltransferase, respectively, and that these genes were clustered. The organization of
acc
genes was different from that reported for
Escherichia coli
, for
Bacillus subtilis
, and for
Pseudomonas aeruginosa. E. coli accB
and
accD
mutations were complemented by the
L. plantarum accB
and
accD
genes, respectively. The predicted products of all five genes were confirmed by using the T7 expression system in
E. coli
. The gene product of
accB
was biotinylated in
E. coli
. Northern and primer extension analyses demonstrated that the five genes in
L. plantarum
were regulated polycistronically in an
acc
operon.
Characterization of a Highly Thermostable Alkaline Phosphatase from the EuryarchaeonPyrococcus abyssi
Authors: Zappa Sébastien , Rolland Jean-Luc , Flament Didier , Gueguen Yannick , Boudrant Joseph , Dietrich Jacques 
Published: July 2002

ABSTRACTThis work reports the first isolation and characterization of an alkaline phosphatase (AP) from a hyperthermophilic archaeon. An AP gene fromPyrococcus abyssi, a euryarchaeon isolated from a deep-sea hydrothermal vent, was cloned and the enzyme expressed inEscherichia coli. Analysis of the sequence showed conservation of the active site and structural elements of theE. coliAP. The recombinant AP was purified and characterized. Monomeric and homodimeric active forms were detected, with a monomer molecular mass of 54 kDa. Apparent optimum pH and temperature were estimated at 11.0 and 70°C, respectively. Thus far,P. abyssiAP has been demonstrated to be the most thermostable AP, with half-lives at 100 and 105°C of 18 and 5 h, respectively. Enzyme activity was found to be dependent on divalent cations: metal ion chelators inhibited activity, whereas the addition of exogenous Mg(II), Zn(II), and Co(II) increased activity. The enzyme was inhibited by inorganic phosphate, but not by molybdate and vanadate. Strong inhibitory effects were observed in the presence of thiol-reducing agents, although cysteine residues of theP. abyssiAP were not found to be incorporated within intra- or interchain disulfide bonds. In addition,P. abyssiAP was demonstrated to dephosphorylate linear DNA fragments with dephosphorylation efficiencies of 93.8 and 84.1% with regard to cohesive and blunt ends, respectively.
Diversity of
Geotrichum candidum
Strains Isolated from Traditional Cheesemaking Fabrications in France
Authors: Marcellino N. , Beuvier E. , Grappin R. , Guéguen M. , Benson D. R. 
Published: July 2002

ABSTRACT

The diversity of French fungus-ripened cheeses is due partly to the succession of fungi that colonize the cheese during ripening.
Geotrichum candidum
appears in the early stages of ripening on soft cheeses such as Camembert and semihard cheeses such as St. Nectaire and Reblochon. Its lipases and proteases promote flavor development, and its aminopeptidases reduce bitterness imparted by low-molecular-weight peptides in cheese. We assessed the genetic diversity of
G. candidum
strains by using random amplification of polymorphic DNA (RAPD)-PCR correlated with phenotypic tests for carbon assimilation and salt tolerance. Strains were isolated from milk, curd, and cheese collected in seven major cheesemaking regions of France. Sixty-four isolates were characterized. We found high genetic diversity of
G. candidum
even within the same cheesemaking regions. Strains did not group according to region. All of the strains from the Haute-Savoie were able to assimilate lactate as the sole source of carbon, while lactate assimilation varied among strains from the Auvergne. Strains varied in
d
-mannitol assimilation, and none used citrate as the sole source of carbon. Yeast-like colony morphology predominated in Reblochon, while all of the strains isolated from St. Nectaire were filamentous. The RAPD-PCR technique readily differentiated
Geotrichum fragrans
isolated from milk and curd in a St. Nectaire cheesemaking facility. This study reveals an enormous diversity of
G. candidum
that has been empirically selected through the centuries by the cheesemakers of France.
Variation of Microbial Communities in Soil, Rhizosphere, and Rhizoplane in Response to Crop Species, Soil Type, and Crop Development
Authors: Wieland Gabriele , Neumann Regine , Backhaus Horst 
Published: July 2002

ABSTRACT
We investigated the influence of plant species, soil type, and plant development time on the shaping of microbial communities in soil and in association with roots. The sample group consisted of a total of 32 microcosms in three habitats: soil, rhizosphere, and rhizoplane. Communities were represented by the patterns of a sequence-specific separation of rRNA target sequences. Effects of experimental parameters were classified by a cluster analysis of pattern similarities. The type of plant species (clover, bean, or alfalfa) had the greatest effect in plant-associated habitats and also affected soil patterns. Plant development had a minor habitat-dependent effect that was partly obscured by replicate variation. The results stress the applicability of biased community representations in an analysis of induced variation.
Impact of Dilution on Microbial Community Structure and Functional Potential: Comparison of Numerical Simulations and Batch Culture Experiments
Authors: Franklin Rima B. , Garland Jay L. , Bolster Carl H. , Mills Aaron L. 
Published: July 2002

ABSTRACT

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted–low-dilution communities and the communities regrown from the very dilute (more than 10
−4
) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10
−1
) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.
Cell Cycle Regulation by Light in
Prochlorococcus
Strains
Authors: Jacquet Stéphan , Partensky Frédéric , Marie Dominique , Casotti Raffaella , Vaulot Daniel 
Published: July 2002

ABSTRACT

The effect of light on the synchronization of cell cycling was investigated in several strains of the oceanic photosynthetic prokaryote
Prochlorococcus
using flow cytometry. When exposed to a light-dark (L-D) cycle with an irradiance of 25 μmol of quanta · m
−2
s
−1
, the low-light-adapted strain SS 120 appeared to be better synchronized than the high-light-adapted strain PCC 9511. Submitting L-D-entrained populations to shifts (advances or delays) in the timing of the “light on” signal translated to corresponding shifts in the initiation of the S phase, suggesting that this signal is a key parameter for the synchronization of population cell cycles. Cultures that were shifted from an L-D cycle to continuous irradiance showed persistent diel oscillations of flow-cytometric signals (light scatter and chlorophyll fluorescence) but with significantly reduced amplitudes and a phase shift. Complete darkness arrested most of the cells in the G
1
phase of the cell cycle, indicating that light is required to trigger the initiation of DNA replication and cell division. However, some cells also arrested in the S phase, suggesting that cell cycle controls in
Prochlorococcus
spp. are not as strict as in marine
Synechococcus
spp. Shifting
Prochlorococcus
cells from low to high irradiance translated quasi-instantaneously into an increase of cells in both the S and G
2
phases of the cell cycle and then into faster growth, whereas the inverse shift induced rapid slowing of the population growth rate. These data suggest a close coupling between irradiance levels and cell cycling in
Prochlorococcus
spp.
In Situ Accessibility of
Escherichia coli
23S rRNA to Fluorescently Labeled Oligonucleotide Probes
Authors: Fuchs Bernhard M. , Syutsubo Kazuaki , Ludwig Wolfgang , Amann Rudolf 
Published: July 2002

ABSTRACT

One of the main causes of failure of fluorescence in situ hybridization with rRNA-targeted oligonucleotides, besides low cellular ribosome content and impermeability of cell walls, is the inaccessibility of probe target sites due to higher-order structure of the ribosome. Analogous to a study on the 16S rRNA (B. M. Fuchs, G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann, Appl. Environ. Microbiol. 64:4973–4982, 1998), the accessibility of the 23S rRNA of
Escherichia coli
DSM 30083
T
was studied in detail with a set of 184 CY3-labeled oligonucleotide probes. The probe-conferred fluorescence was quantified flow cytometrically. The brightest signal resulted from probe 23S-2018, complementary to positions 2018 to 2035. The distribution of probe-conferred cell fluorescence in six arbitrarily set brightness classes (classes I to VI, 100 to 81%, 80 to 61%, 60 to 41%, 40 to 21%, 20 to 6%, and 5 to 0% of the brightness of 23S-2018, respectively) was as follows: class I, 3%; class II, 21%; class III, 35%; class IV, 18%; class V, 16%; and class VI, 7%. A fine-resolution analysis of selected areas confirmed steep changes in accessibility on the 23S RNA to oligonucleotide probes. This is similar to the situation for the 16S rRNA. Indeed, no significant differences were found between the hybridization of oligonucleotide probes to 16S and 23S rRNA. Interestingly, indications were obtained of an effect of the type of fluorescent dye coupled to a probe on in situ accessibility. The results were translated into an accessibility map for the 23S rRNA of
E. coli
, which may be extrapolated to other bacteria. Thereby, it may contribute to a better exploitation of the high potential of the 23S rRNA for identification of bacteria in the future.
Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm
Authors: Gieseke Armin , Purkhold Ulrike , Wagner Michael , Amann Rudolf , Schramm Andreas 
Published: July 2002

ABSTRACT

The microbial community structure and activity dynamics of a phosphate-removing biofilm from a sequencing batch biofilm reactor were investigated with special focus on the nitrifying community. O
2
, NO
2
−
, and NO
3
−
profiles in the biofilm were measured with microsensors at various times during the nonaerated-aerated reactor cycle. In the aeration period, nitrification was oxygen limited and restricted to the first 200 μm at the biofilm surface. Additionally, a delayed onset of nitrification after the start of the aeration was observed. Nitrate accumulating in the biofilm in this period was denitrified during the nonaeration period of the next reactor cycle. Fluorescence in situ hybridization (FISH) revealed three distinct ammonia-oxidizing populations, related to the
Nitrosomonas europaea, Nitrosomonas oligotropha,
and
Nitrosomonas communis
lineages. This was confirmed by analysis of the genes coding for 16S rRNA and for ammonia monooxygenase (
amoA
). Based upon these results, a new 16S rRNA-targeted oligonucleotide probe specific for the
Nitrosomonas oligotropha
lineage was designed. FISH analysis revealed that the first 100 μm at the biofilm surface was dominated by members of the
N. europaea
and the
N. oligotropha
lineages, with a minor fraction related to
N. communis
. In deeper biofilm layers, exclusively members of the
N. oligotropha
lineage were found. This separation in space and a potential separation of activities in time are suggested as mechanisms that allow coexistence of the different ammonia-oxidizing populations. Nitrite-oxidizing bacteria belonged exclusively to the genus
Nitrospira
and could be assigned to a 16S rRNA sequence cluster also found in other sequencing batch systems.
Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments
Authors: Orphan V. J. , Hinrichs K.-U. , Ussler W. , Paull C. K. , Taylor L. T. , Sylva S. P. , Hayes J. M. , Delong E. F. 
Published: July 2002

ABSTRACT

The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order
Methanosarcinales
, were consistently associated with methane seep marine sediments. The same sediments contained abundant
13
C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia.
13
C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of δ-proteobacteria, in particular, close relatives of
Desulfosarcina variabilis
. Biomarker analyses of the same sediments showed bacterial fatty acids with strong
13
C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing
Desulfosarcina
and
Desulfococcus
species. Additionally, the presence of abundant
13
C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order
Desulfosarcinales
, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the
Desulfosarcinales
and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.