bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substantial Rise in the Prevalence of Lyme Borreliosis Spirochetes in a Region of Western Germany over a 10-Year Period
Authors: Kampen Helge , Rötzel Diana C. , Kurtenbach Klaus , Maier Walter A. , Seitz Hanns M. 
Published: March 2004

ABSTRACT

More than a decade after a study on the transmission cycle of
Borrelia burgdorferi
sensu lato in the Siebengebirge, a nature reserve near Bonn, Germany, questing nymphal and adult
Ixodes ricinus
ticks were collected again in three selected areas of the same low mountain range and examined for infection with
B. burgdorferi
sensu lato. Between May and October 2001, a total of 1,754 ticks were collected by blanket dragging; 374 ticks were analyzed for
B. burgdorferi
sensu lato by both an immunofluorescence assay (IFA) and at least two different PCR tests, whereas 171 ticks were analyzed by PCR only. By combining all assays, an average of 14% of the ticks tested positive for
B. burgdorferi
sensu lato, 5.5, 15.8, and 21.8% in the three collection areas. Of the nymphs and adults examined, 12.9 and 21.1%, respectively, were found to be spirochete infected. A lower total infection prevalence was obtained by IFA (14.4%) than by a nested PCR approach (16.5%), but both were higher than that obtained by a simple PCR approach (11.9%). Compared with data collected over a decade ago, the mean infection prevalence of
B. burgdorferi
sensu lato in the ticks was significantly higher for all three biotopes, whereas a similar pattern of habitat-specific infection prevalence was observed. Genotyping of
B. burgdorferi
sensu lato revealed high relative prevalences of
B. valaisiana
(identified in 43.1% of infected ticks) and
B. garinii
(32.3%), whereas
B. afzelii
(12.3%) and
B. burgdorferi
sensu stricto (1.5%) were relatively rare. We conclude that
B. burgdorferi
sensu lato infection has increased in this region over the last 15 years due to presently unknown changes in ecological conditions, perhaps related to climate change or wildlife management.
High-Throughput Metabolic Fingerprinting of Legume Silage Fermentations via Fourier Transform Infrared Spectroscopy and Chemometrics
Authors: Johnson Helen E. , Broadhurst David , Kell Douglas B. , Theodorou Michael K. , Merry Roger J. , Griffith Gareth W. 
Published: March 2004

ABSTRACT

Silage quality is typically assessed by the measurement of several individual parameters, including pH, lactic acid, acetic acid, bacterial numbers, and protein content. The objective of this study was to use a holistic metabolic fingerprinting approach, combining a high-throughput microtiter plate-based fermentation system with Fourier transform infrared (FT-IR) spectroscopy, to obtain a snapshot of the sample metabolome (typically low-molecular-weight compounds) at a given time. The aim was to study the dynamics of red clover or grass silage fermentations in response to various inoculants incorporating lactic acid bacteria (LAB). The hyperspectral multivariate datasets generated by FT-IR spectroscopy are difficult to interpret visually, so chemometrics methods were used to deconvolute the data. Two-phase principal component-discriminant function analysis allowed discrimination between herbage types and different LAB inoculants and modeling of fermentation dynamics over time. Further analysis of FT-IR spectra by the use of genetic algorithms to identify the underlying biochemical differences between treatments revealed that the amide I and amide II regions (wavenumbers of 1,550 to 1,750 cm
−1
) of the spectra were most frequently selected (reflecting changes in proteins and free amino acids) in comparisons between control and inoculant-treated fermentations. This corresponds to the known importance of rapid fermentation for the efficient conservation of forage proteins.
Impact of Violacein-Producing Bacteria on Survival and Feeding of Bacterivorous Nanoflagellates
Authors: Matz Carsten , Deines Peter , Boenigk Jens , Arndt Hartmut , Eberl Leo , Kjelleberg Staffan , Jürgens Klaus 
Published: March 2004

ABSTRACT

We studied the role of bacterial secondary metabolites in the context of grazing protection against protozoans. A model system was used to examine the impact of violacein-producing bacteria on feeding rates, growth, and survival of three common bacterivorous nanoflagellates. Freshwater isolates of
Janthinobacterium lividum
and
Chromobacterium violaceum
produced the purple pigment violacein and exhibited acute toxicity to the nanoflagellates tested. High-resolution video microscopy revealed that these bacteria were ingested by the flagellates at high rates. The uptake of less than three bacteria resulted in rapid flagellate cell death after about 20 min and cell lysis within 1 to 2 h. In selectivity experiments with nontoxic
Pseudomonas putida
MM1, flagellates did not discriminate against pigmented strains. Purified violacein from cell extracts of
C. violaceum
showed high toxicity to nanoflagellates. In addition, antiprotozoal activity was found to positively correlate with the violacein content of the bacterial strains. Pigment synthesis in
C. violaceum
is regulated by an
N
-acylhomoserine lactone (AHL)-dependent quorum-sensing system. An AHL-deficient, nonpigmented mutant provided high flagellate growth rates, while the addition of the natural
C. violaceum
AHL could restore toxicity. Moreover, it was shown that the presence of violacein-producing bacteria in an otherwise nontoxic bacterial diet considerably inhibited flagellate population growth. Our results suggest that violacein-producing bacteria possess a highly effective survival mechanism which may exemplify the potential of some bacterial secondary metabolites to undermine protozoan grazing pressure and population dynamics.
Influence of Lipoteichoic Acid
d
-Alanylation on Protein Secretion in
Lactococcus lactis
as Revealed by Random Mutagenesis
Authors: Nouaille S. , Commissaire J. , Gratadoux J. J. , Ravn P. , Bolotin A. , Gruss A. , Le Loir Y. , Langella P. 
Published: March 2004

ABSTRACT

Lactococcus lactis
, a food-grade nonpathogenic lactic acid bacterium, is a good candidate for the production of heterologous proteins of therapeutic interest. We examined host factors that affect secretion of heterologous proteins in
L. lactis
. Random insertional mutagenesis was performed with
L. lactis
strain MG1363 carrying a staphylococcal nuclease (Nuc) reporter cassette in its chromosome. This cassette encodes a fusion protein between the signal peptide of the Usp45 lactococcal protein and the mature moiety of a truncated form of Nuc (NucT). The Nuc secretion efficiency (secreted NucT versus total NucT) from this construct is low in
L. lactis
(∼40%). Twenty mutants affected in NucT production and/or in secretion capacity were selected and identified. In these mutants, several independent insertions mapped in the
dltA
gene (involved in
d
-alanine transfer in lipoteichoic acids) and resulted in a NucT secretion defect. Characterization of the
dltA
mutant phenotype with respect to NucT secretion revealed that it is involved in a late secretion stage by causing mature NucT entrapment at the cell surface.
Salinity Responses of Benthic Microbial Communities in a Solar Saltern (Eilat, Israel)
Authors: Sørensen Ketil Bernt , Canfield Donald E. , Oren Aharon 
Published: March 2004

ABSTRACT
The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries. The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120‰, and sulfate reduction was strongly inhibited at an in situ salinity of 215‰. Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget. Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust. In slurries with a salinity of 180‰ or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria. Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120‰.
Identification and Isolation of Anaerobic, Syntrophic Phthalate Isomer-Degrading Microbes from Methanogenic Sludges Treating Wastewater from Terephthalate Manufacturing
Authors: Qiu Yan-Ling , Sekiguchi Yuji , Imachi Hiroyuki , Kamagata Yoichi , Tseng I-Cheng , Cheng Sheng-Shung , Ohashi Akiyoshi , Harada Hideki 
Published: March 2004

ABSTRACTThe microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the manufacturing of terephthalic acid. Primary enrichments were made with each of three phthalate isomers (ortho-, iso-, and terephthalate) as the sole energy source at 37°C with two sources of anaerobic sludge (both had been used to treat wastewater containing high concentrations of phthalate isomers) as the inoculum. Six methanogenic enrichment cultures were obtained which not only degraded the isomer used for the enrichment but also had the potential to degrade part of other phthalate isomers as well as benzoate with concomitant production of methane, presumably involving strictly syntrophic substrate degradation. Our 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that the predominant bacteria in the enrichment cultures were affiliated with a recently recognized non-sulfate-reducing subcluster (subcluster Ih) in the group ‘Desulfotomaculumlineage I' or a clone cluster (group TA) in the class delta-Proteobacteria. Several attempts were made to isolate these microbes, resulting in the isolation of a terephthalate-degrading bacterium, designated strain JT, in pure culture. A coculture of the strain with the hydrogenotrophic methanogenMethanospirillum hungateiconverted terephthalate to acetate and methane within 3 months of incubation, whereas strain JT could not degrade terephthalate in pure culture. During the degradation of terephthalate, a small amount of benzoate was transiently accumulated as an intermediate, indicative of decarboxylation of terephthalate to benzoate as the initial step of the degradation. 16S rRNA gene sequence analysis revealed that the strain was a member of subcluster Ih of the group ‘Desulfotomaculumlineage I', but it was only distantly related to other known species.
Direct Observation of Microbial Inhibition of Calcite Dissolution
Authors: Lüttge Andreas , Conrad Pamela G. 
Published: March 2004

ABSTRACT

Vertical scanning interferometry (VSI) provides a method for quantification of surface topography at the angstrom to nanometer level. Time-dependent VSI measurements can be used to study the surface-normal retreat across crystal and other solid surfaces during dissolution or corrosion processes. Therefore, VSI can be used to directly and nondestructively measure mineral dissolution rates with high precision. We have used this method to compare the abiotic dissolution behavior of a representative calcite (CaCO
3
) cleavage face with that observed upon addition of an environmental microbe,
Shewanella oneidensis
MR-1, to the crystal surface. From our direct observations, we have concluded that the presence of the microbes results in a significant inhibition of the rate of calcite dissolution. This inhibition appears to be a 2nd-order effect that is related to the formation of etch pits. The opening of etch pits was greatly inhibited in the presence of added bacteria, suggesting that the bacterial cells exert their effect by inhibiting the formation of etch pits at high-energy sites at the crystal surface caused by lattice defects, e.g., screw or point dislocations. The experimental methodology thus provides a nondestructive, directly quantifiable, and easily visualized view of the interactions of microbes and minerals during weathering (or corrosion) processes or during mineral precipitation.
Phage Community Dynamics in Hot Springs
Authors: Breitbart Mya , Wegley Linda , Leeds Steven , Schoenfeld Tom , Rohwer Forest 
Published: March 2004

ABSTRACT
In extreme thermal environments such as hot springs, phages are the only known microbial predators. Here we present the first study of prokaryotic and phage community dynamics in these environments. Phages were abundant in hot springs, reaching concentrations of a million viruses per milliliter. Hot spring phage particles were resistant to shifts to lower temperatures, possibly facilitating DNA transfer out of these extreme environments. The phages were actively produced, with a population turnover time of 1 to 2 days. Phage-mediated microbial mortality was significant, making phage lysis an important component of hot spring microbial food webs. Together, these results show that phages exert an important influence on microbial community structure and energy flow in extreme thermal environments.
Ecophysiological Interaction between Nitrifying Bacteria and Heterotrophic Bacteria in Autotrophic Nitrifying Biofilms as Determined by Microautoradiography-Fluorescence In Situ Hybridization
Authors: Kindaichi Tomonori , Ito Tsukasa , Okabe Satoshi 
Published: March 2004

ABSTRACTEcophysiological interactions between the community members (i.e., nitrifiers and heterotrophic bacteria) in a carbon-limited autotrophic nitrifying biofilm fed only NH4+as an energy source were investigated by using a full-cycle 16S rRNA approach followed by microautoradiography (MAR)-fluorescence in situ hybridization (FISH). Phylogenetic differentiation (identification) of heterotrophic bacteria was performed by 16S rRNA gene sequence analysis, and FISH probes were designed to determine the community structure and the spatial organization (i.e., niche differentiation) in the biofilm. FISH analysis showed that this autotrophic nitrifying biofilm was composed of 50% nitrifying bacteria (ammonia-oxidizing bacteria [AOB] and nitrite-oxidizing bacteria [NOB]) and 50% heterotrophic bacteria, and the distribution was as follows: members of the alpha subclass of the classProteobacteria(α-Proteobacteria), 23%; γ-Proteobacteria, 13%; green nonsulfur bacteria (GNSB), 9%;Cytophaga-Flavobacterium-Bacteroides(CFB) division, 2%; and unidentified (organisms that could not be hybridized with any probe except EUB338), 3%. These results indicated that a pair of nitrifiers (AOB and NOB) supported a heterotrophic bacterium via production of soluble microbial products (SMP). MAR-FISH revealed that the heterotrophic bacterial community was composed of bacteria that were phylogenetically and metabolically diverse and to some extent metabolically redundant, which ensured the stability of the ecosystem as a biofilm. α- and γ-Proteobacteriadominated the utilization of [14C]acetic acid and14C-amino acids in this biofilm. Despite their low abundance (ca. 2%) in the biofilm community, members of the CFB cluster accounted for the largest fraction (ca. 64%) of the bacterial community consumingN-acetyl-d-[1-14C]glucosamine (NAG). The GNSB accounted for 9% of the14C-amino acid-consuming bacteria and 27% of the [14C]NAG-consuming bacteria but did not utilize [14C]acetic acid. Bacteria classified in the unidentified group accounted for 6% of the total heterotrophic bacteria and could utilize all organic substrates, including NAG. This showed that there was an efficient food web (carbon metabolism) in the autotrophic nitrifying biofilm community, which ensured maximum utilization of SMP produced by nitrifiers and prevented buildup of metabolites or waste materials of nitrifiers to significant levels.
Rapid Detection and Enumeration of
Legionella pneumophila
in Hot Water Systems by Solid-Phase Cytometry
Authors: Aurell Helena , Catala Philippe , Farge Pierre , Wallet France , Le Brun Matthieu , Helbig Jürgen H. , Jarraud Sophie , Lebaron Philippe 
Published: March 2004

ABSTRACT

A new method for the rapid and sensitive detection of
Legionella pneumophila
in hot water systems has been developed. The method is based on an IF assay combined with detection by solid-phase cytometry. This method allowed the enumeration of
L. pneumophila
serogroup 1 and
L. pneumophila
serogroups 2 to 6, 8 to 10, and 12 to 15 in tap water samples within 3 to 4 h. The sensitivity of the method was between 10 and 100 bacteria per liter and was principally limited by the filtration capacity of membranes. The specificity of the antibody was evaluated against 15 non-
Legionella
strains, and no cross-reactivity was observed. When the method was applied to natural waters, direct counts of
L. pneumophila
were compared with the number of CFU obtained by the standard culture method. Direct counts were always higher than culturable counts, and the ratio between the two methods ranged from 1.4 to 325. Solid-phase cytometry offers a fast and sensitive alternative to the culture method for
L. pneumophila
screening in hot water systems.
Diverse Organization of Genes of the β-Ketoadipate Pathway in Members of the Marine
Roseobacter
Lineage
Authors: Buchan Alison , Neidle Ellen L. , Moran Mary Ann 
Published: March 2004

ABSTRACT

Members of the
Roseobacter
lineage, an ecologically important marine clade within the class α-
Proteobacteria
, harbor genes for the protocatechuate branch of the β-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. The genes of this pathway are typically clustered, although gene order varies among organisms. Here we characterize genes linked to
pcaH
and
-G
, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the
Roseobacter
lineage (pairwise 16S rRNA gene sequence identities, 92 to 99%). Sequence analysis of genomic fragments revealed five unique
pca
gene arrangements. Identical gene organization was found for isolates demonstrating species-level identity (i.e., >99% 16S rRNA gene similarity). In one isolate, six functionally related genes were clustered:
pcaQ
,
pobA
,
pcaD
,
pcaC
,
pcaH
, and
pcaG
. The remaining seven isolates lacked at least one of these genes in their clusters, although the relative order of the remaining genes was preserved. Three genes (
pcaC
, -
H
, and -
G
) were physically linked in all isolates. A highly conserved open reading frame (ORF) was found immediately downstream of
pcaG
in all eight isolates. Reverse transcription-PCR analysis of RNA from one isolate,
Silicibacter pomeroyi
DSS-3, provides evidence that this ORF is coexpressed with upstream
pca
genes. The absence of this ORF in similar bacterial
pca
gene clusters from diverse microbes suggests a niche-specific role for its protein product in
Roseobacter
group members. Collectively, these comparisons of bacterial
pca
gene organization illuminate a complex evolutionary history and underscore the widespread ecological importance of the encoded β-ketoadipate pathway.
pbp2229
-Mediated Nisin Resistance Mechanism in
Listeria monocytogenes
Confers Cross-Protection to Class IIa Bacteriocins and Affects Virulence Gene Expression
Authors: Gravesen Anne , Kallipolitis Birgitte , Holmstrøm Kim , Høiby Poul Erik , Ramnath Manilduth , Knøchel Susanne 
Published: March 2004

ABSTRACT

It was previously shown that enhanced nisin resistance in some mutants was associated with increased expression of three genes,
pbp2229
,
hpk1021
, and
lmo2487
, encoding a penicillin-binding protein, a histidine kinase, and a protein of unknown function, respectively. In the present work, we determined the direct role of the three genes in nisin resistance. Interruption of
pbp2229
and
hpk1021
eliminated the nisin resistance phenotype. Interruption of
hpk1021
additionally abolished the increase in
pbp2229
expression. The results indicate that this nisin resistance mechanism is caused directly by the increase in
pbp2229
expression, which in turn is brought about by the increase in
hpk1021
expression. We also found a degree of cross-protection between nisin and class IIa bacteriocins and investigated possible mechanisms. The expression of virulence genes in one nisin-resistant mutant and two class IIa bacteriocin-resistant mutants of the same wild-type strain was analyzed, and each mutant consistently showed either an increase or a decrease in the expression of virulence genes (
prfA
-regulated as well as
prfA
-independent genes). Although the changes mostly were moderate, the consistency indicates that a mutant-specific change in virulence may occur concomitantly with bacteriocin resistance development.
Application of a Vital Fluorescent Staining Method for Simultaneous, Near-Real-Time Concentration Monitoring of Two Bacterial Strains in an Atlantic Coastal Plain Aquifer in Oyster, Virginia
Authors: Fuller Mark E. , Mailloux Brian J. , Streger Sheryl H. , Hall James A. , Zhang Pengfei , Kovacik William P. , Vainberg Simon , Johnson William P. , Onstott Tullis C. , DeFlaun Mary F. 
Published: March 2004

ABSTRACT

Two differentially labeled bacterial strains were monitored in near-real time during two field-scale bacterial transport experiments in a shallow aquifer in July 2000 and July 2001.
Comamonas
sp. strain DA001 and
Acidovorax
sp. strain OY-107 were grown and labeled with the vital fluorescent stain TAMRA/SE (5 [and -6]-carboxytetramethylrhodamine, succinimidyl ester) or CFDA/SE (5 [and -6]-carboxyfluorescein diacetate, succinimidyl ester). Fluorescently labeled cells and a conservative bromide tracer were introduced into a suboxic superficial aquifer, followed by groundwater collection from down-gradient multilevel samplers. Cells were enumerated in the field by microplate spectrofluorometry, with confirmatory analyses for selected samples done in the laboratory by epifluorescence microscopy, flow cytometry, and ferrographic capture. There was general agreement in the results from all of the vital-stain-based enumeration methods, with differences ranging from <10% up to 40% for the analysis of identical samples between different tracking methods. Field analysis by microplate spectrofluorometry was robust and efficient, allowing thousands of samples to be analyzed in quadruplicate for both of the injected strains. The near-real-time data acquisition allowed adjustments to the predetermined sampling schedule to be made. The microplate spectrofluorometry data sets for the July 2000 and July 2001 experiments allowed the transport of the injected cells to be related to the site hydrogeology and injection conditions and enabled the assessment of differences in the transport of the two strains. This near-real-time method should prove effective for a number of microbial ecology applications.