bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of DNA Quantification To Measure Growth and Autolysis of
Lactococcus
and
Propionibacterium
spp. in Mixed Populations
Authors: Treimo Janneke , Vegarud Gerd , Langsrud Thor , Rudi Knut 
Published: September 2006

ABSTRACT

Autolysis is self-degradation of the bacterial cell wall that results in the release of enzymes and DNA. Autolysis of starter bacteria, such as lactococci and propionibacteria, is essential for cheese ripening, but our understanding of this important process is limited. This is mainly because the current tools for measuring autolysis cannot readily be used for analysis of bacteria in mixed populations. We have now addressed this problem by species-specific detection and quantification of free DNA released during autolysis. This was done by use of 16S rRNA gene single-nucleotide extension probes in combination with competitive PCR. We analyzed pure and mixed populations of
Lactococcus lactis
subsp.
lactis
and three different species of
Propionibacterium
. Results showed that
L. lactis
subsp.
lactis
INF L2 autolyzed first, followed by
Propionibacterium acidipropionici
ATCC 4965,
Propionibacterium freudenreichii
ISU P59, and then
Propionibacterium jensenii
INF P303. We also investigated the autolytic effect of rennet (commonly used in cheese production). We found that the effect was highly strain specific, with all the strains responding differently. Finally, autolysis of
L. lactis
subsp.
lactis
INF L2 and
P. freudenreichii
ISU P59 was analyzed in a liquid cheese model. Autolysis was detected later in this cheese model system than in broth media. A challenge with DNA, however, is DNA degradation. We addressed this challenge by using a DNA degradation marker. We obtained a good correlation between the degradation of the marker and the target in a model experiment. We conclude that our DNA approach will be a valuable tool for use in future analyses and for understanding autolysis in mixed bacterial populations.
Distinct Bacterial Communities Exist beneath a High Arctic Polythermal Glacier
Authors: Bhatia Maya , Sharp Martin , Foght Julia 
Published: September 2006

ABSTRACT
Bacterial communities reside in basal ice, sediment, and meltwater in the supra-, sub-, and proglacial environments of John Evans Glacier, Nunavut, Canada. We examined whether the subglacial bacterial community shares common members with the pro- and supraglacial communities, and by inference, whether it could be derived from communities in either of these environments (e.g., by ice overriding proglacial sediments or by in-wash of surface meltwaters). Terminal restriction fragment length polymorphism analysis of bacterial 16S rRNA genes amplified from these environments revealed that the subglacial water, basal ice, and sediment communities were distinct from those detected in supraglacial meltwater and proglacial sediments, with 60 of 142 unique terminal restriction fragments (T-RFs) detected exclusively in subglacial samples and only 8 T-RFs detected in all three environments. Supraglacial waters shared some T-RFs with subglacial water and ice, likely reflecting the seasonal flow of surface meltwater into the subglacial drainage system, whereas supraglacial and proglacial communities shared the fewest T-RFs. Thus, the subglacial community at John Evans Glacier appears to be predominantly autochthonous rather than allochthonous, and it may be adapted to subglacial conditions. Chemical analysis of water and melted ice also revealed differences between the supraglacial and proglacial environments, particularly regarding electrical conductivity and nitrate, sulfate, and dissolved organic carbon concentrations. Whereas the potential exists for common bacterial types to be broadly distributed throughout the glacial system, we have observed distinct bacterial communities in physically and chemically different glacial environments.
Effect of Natural Sunlight on Bacterial Activity and Differential Sensitivity of Natural Bacterioplankton Groups in Northwestern Mediterranean Coastal Waters
Authors: Alonso-Sáez Laura , Gasol Josep M. , Lefort Thomas , Hofer Julia , Sommaruga Ruben 
Published: September 2006

ABSTRACT

We studied the effects of natural sunlight on heterotrophic marine bacterioplankton in short-term experiments. We used a single-cell level approach involving flow cytometry combined with physiological probes and microautoradiography to determine sunlight effects on the activity and integrity of the cells. After 4 h of sunlight exposure, most bacterial cells maintained membrane integrity and viability as assessed by the simultaneous staining with propidium iodide and SYBR green I. In contrast, a significant inhibition of heterotrophic bacterial activity was detected, measured by 5-cyano-2,3 ditolyl tetrazolium chloride reduction and leucine incorporation. We applied microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization to test the sensitivity of the different bacterial groups naturally occurring in the Northwestern Mediterranean to sunlight. Members of the
Gammaproteobacteria
and
Bacteroidetes
groups appeared to be highly resistant to solar radiation, with small changes in activity after exposure. On the contrary,
Alphaproteobacteria
bacteria were more sensitive to radiation as measured by the cell-specific incorporation of labeled amino acids, leucine, and ATP. Within
Alphaproteobacteria
, bacteria belonging to the
Roseobacter
group showed higher resistance than members of the SAR11 cluster. The activity of
Roseobacter
was stimulated by exposure to photosynthetic available radiation compared to the dark treatment. Our results suggest that UV radiation can significantly affect the in situ single-cell activity of bacterioplankton and that naturally dominating phylogenetic bacterial groups have different sensitivity to natural levels of incident solar radiation.
Attachment of and Biofilm Formation by
Enterobacter sakazakii
on Stainless Steel and Enteral Feeding Tubes
Authors: Kim Hoikyung , Ryu Jee-Hoon , Beuchat Larry R. 
Published: September 2006

ABSTRACT

Enterobacter sakazakii
has been reported to form biofilms, but environmental conditions affecting attachment to and biofilm formation on abiotic surfaces have not been described. We did a study to determine the effects of temperature and nutrient availability on attachment and biofilm formation by
E. sakazakii
on stainless steel and enteral feeding tubes. Five strains grown to stationary phase in tryptic soy broth (TSB), infant formula broth (IFB), or lettuce juice broth (LJB) at 12 and 25°C were examined for the extent to which they attach to these materials. Higher populations attached at 25°C than at 12°C. Stainless steel coupons and enteral feeding tubes were immersed for 24 h at 4°C in phosphate-buffered saline suspensions (7 log CFU/ml) to facilitate the attachment of 5.33 to 5.51 and 5.03 to 5.12 log CFU/cm
2
, respectively, before they were immersed in TSB, IFB, or LJB, followed by incubation at 12 or 25°C for up to 10 days. Biofilms were not produced at 12°C. The number of cells of test strains increased by 1.42 to 1.67 log CFU/cm
2
and 1.16 to 1.31 log CFU/cm
2
in biofilms formed on stainless steel and feeding tubes, respectively, immersed in IFB at 25°C; biofilms were not formed on TSB and LJB at 25°C, indicating that nutrient availability plays a major role in processes leading to biofilm formation on the surfaces of these inert materials. These observations emphasize the importance of temperature control in reconstituted infant formula preparation and storage areas in preventing attachment and biofilm formation by
E. sakazakii
.
Cloning of a Heavy-Metal-Binding Protein Derived from Activated-Sludge Microorganisms
Authors: Sano Daisuke , Myojo Ken , Omura Tatsuo 
Published: September 2006

ABSTRACT

A gene of the heavy-metal-binding protein (HMBP) was newly isolated from a genetic DNA library of activated-sludge microorganisms. HMBP was produced by transformed
Escherichia coli
, and the copper-binding ability of HMBP was confirmed. HMBP derived from activated sludge could be available as heavy metal adsorbents in water and wastewater treatments.
Microbially Mediated Biodegradation of Hexahydro-1,3,5-Trinitro-1,3,5- Triazine by Extracellular Electron Shuttling Compounds
Authors: Kwon Man Jae , Finneran Kevin T. 
Published: September 2006

ABSTRACT

The potential for humic substances to stimulate the reduction of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was investigated. This study describes a novel approach for the remediation of RDX-contaminated environments using microbially mediated electron shuttling. Incubations without cells demonstrated that reduced AQDS transfers electrons directly to RDX, which was reduced without significant accumulation of the nitroso intermediates. Three times as much reduced AQDS (molar basis) was needed to completely reduce RDX. The rate and extent of RDX reduction differed greatly among electron shuttle/acceptor amendments for resting cell suspensions of
Geobacter metallireducens
and
G. sulfurreducens
with acetate as the sole electron donor. AQDS and purified humic substances stimulated the fastest rate of RDX reduction. The nitroso metabolites did not significantly accumulate in the presence of AQDS or humic substances. RDX reduction in the presence of poorly crystalline Fe(III) was relatively slow and metabolites transiently accumulated. However, adding humic substances or AQDS to Fe(III)-containing incubations increased the reduction rates. Cells of
G. metallireducens
alone reduced RDX; however, the rate of RDX reduction was slow relative to AQDS-amended incubations. These data suggest that extracellular electron shuttle-mediated RDX transformation is not organism specific but rather is catalyzed by multiple Fe(III)- and humic-reducing species. Electron shuttle-mediated RDX reduction may eventually become a rapid and effective cleanup strategy in both Fe(III)-rich and Fe(III)-poor environments.
Diversity of Telomere Palindromic Sequences and Replication Genes among
Streptomyces
Linear Plasmids
Authors: Zhang Ran , Yang Yong , Fang Ping , Jiang Chenglin , Xu Lihua , Zhu Yingmin , Shen Meijuan , Xia Haiyang , Zhao Jianfu , Chen Tongbin , Qin Zhongjun 
Published: September 2006

ABSTRACT

Streptomyces
sp. linear plasmids and linear chromosomes usually contain
conserved terminal palindromic sequences bound by the conserved
telomeric proteins Tap and Tp, encoded by the
tap
and
tpg
genes, respectively, as well as plasmid loci required for
DNA replication in circular mode when the telomeres are deleted. These
consist of iterons and an adjacent
rep
gene. By using PCR, we
found that 8 of 17 newly detected linear plasmids in
Streptomyces
strains lack typical telomeric
tap
and
tpg
sequences. Instead, two novel telomeres in plasmids pRL1
and pRL2 from the eight strains and one conserved telomere in pFRL1
from the other strains were identified, while multiple short
palindromes were also found in the plasmids. The complete nucleotide
sequence of pRL2 revealed a gene encoding a protein containing two
domains, resembling Tap of
Streptomyces
and a helicase of
Thiobacillus
, and an adjacent gene encoding a protein similar
to Tpg of
Streptomyces
and a portion of the telomere terminal
protein pTP of adenoviruses. No typical iterons-
rep
loci were
found in the three plasmids. These results indicate an unexpected
diversity of telomere palindromic sequences and replication genes among
Streptomyces
linear
plasmids.
Halotolerant Cyanobacterium
Aphanothece halophytica
Contains a Betaine Transporter Active at Alkaline pH and High Salinity
Authors: Laloknam Surasak , Tanaka Kimihiro , Buaboocha Teerapong , Waditee Rungaroon , Incharoensakdi Aran , Hibino Takashi , Tanaka Yoshito , Takabe Teruhiro 
Published: September 2006

ABSTRACT

Aphanothece halophytica
is a halotolerant alkaliphilic cyanobacterium which can grow in media of up to 3.0 M NaCl and pH 11. This cyanobacterium can synthesize betaine from glycine by three-step methylation using
S
-adenosylmethionine as a methyl donor. To unveil the mechanism of betaine uptake and efflux in this alkaliphile, we isolated and characterized a betaine transporter. A gene encoding a protein (BetT

A. halophytica

) that belongs to the betaine-choline-carnitine transporter (BCCT) family was isolated. Although the predicted isoelectric pH of a typical BCCT family transporter, OpuD of
Bacillus subtilis
, is basic, 9.54, that of BetT

A. halophytica

is acidic, 4.58. BetT

A. halophytica

specifically catalyzed the transport of betaine. Choline, γ-aminobutyric acid, betaine aldehyde, sarcosine, dimethylglycine, and amino acids such as proline did not compete for the uptake of betaine by BetT

A. halophytica

. Sodium markedly enhanced betaine uptake rates, whereas potassium and other cations showed no effect, suggesting that BetT

A. halophytica

is a Na
+
-betaine symporter. Betaine uptake activities of BetT

A. halophytica

were high at alkaline pH values, with the optimum pH around 9.0. Freshwater
Synechococcus
cells overexpressing BetT

A. halophytica

showed NaCl-activated betaine uptake activities with enhanced salt tolerance, allowing growth in seawater supplemented with betaine. Kinetic properties of betaine uptake in
Synechococcus
cells overexpressing BetT

A. halophytica

were similar to those in
A. halophytica
cells. These findings indicate that
A. halophytica
contains a Na
+
-betaine symporter that contributes to the salt stress tolerance at alkaline pH. BetT

A. halophytica

is the first identified transporter for compatible solutes in cyanobacteria.
Persistence of Nontuberculous Mycobacteria in a Drinking Water System after Addition of Filtration Treatment
Authors: Hilborn Elizabeth D. , Covert Terry C. , Yakrus Mitchell A. , Harris Stephanie I. , Donnelly Sandra F. , Rice Eugene W. , Toney Sean , Bailey Stephanie A. , Stelma Gerard N. 
Published: September 2006

ABSTRACTThere is evidence that drinking water may be a source of infections with pathogenic nontuberculous mycobacteria (NTM) in humans. One method by which NTM are believed to enter drinking water distribution systems is by their intracellular colonization of protozoa. Our goal was to determine whether we could detect a reduction in the prevalence of NTM recovered from an unfiltered surface drinking water system after the addition of ozonation and filtration treatment and to characterize NTM isolates by using molecular methods. We sampled water from two initially unfiltered surface drinking water treatment plants over a 29-month period. One plant received the addition of filtration and ozonation after 6 months of sampling. Sample sites included those at treatment plant effluents, distributed water, and cold water taps (point-of-use [POU] sites) in public or commercial buildings located within each distribution system. NTM were recovered from 27% of the sites. POU sites yielded the majority of NTM, with >50% recovery despite the addition of ozonation and filtration. Closely related electrophoretic groups ofMycobacterium aviumwere found to persist at POU sites for up to 26 months. Water collected from POU cold water outlets was persistently colonized with NTM despite the addition of ozonation and filtration to a drinking water system. This suggests that cold water POU outlets need to be considered as a potential source of chronic human exposure to NTM.
Biotyping of Enterotoxigenic
Staphylococcus aureus
by Enterotoxin Gene Cluster (
egc
) Polymorphism and
spa
Typing Analyses
Authors: Blaiotta Giuseppe , Fusco Vincenzina , von Eiff Christof , Villani Francesco , Becker Karsten 
Published: September 2006

ABSTRACT

Thirty-five
Staphylococcus aureus
strains, including 10 reference strains and 25 strains recovered from clinical specimens and food samples, were analyzed by PCR REA (restriction endonucleases analysis) of the
egc
operon and
spa
typing. Nineteen
spa
types and seven different
egc
operons, including four putative new
egc
variants, were revealed. In 13 strains, allelic variants of
sei
and/or
seg
were found. By an analysis of their nucleotide sequence identities, a new homogeneous cluster of a
sei
variant, called the
sei
variant, was detected in six strains. In addition, the prototype
sei
was shown to be more polymorphic than assumed so far. Seven strains possessed the recently described
seg
variant, also exhibiting several nucleotide exchanges.
spa
typing was more effective than REA
egc
grouping as a typing technique. Since, in some cases, the REA typing method was able to discriminate strains showing the same
spa
type, it must be considered for PCR approaches involved in diagnostic procedures and may be useful for epidemiological studies. Hence, the polyphasic approach used in this study can be reliably and advantageously applied for typing
egc
-positive
S. aureus
strains.
Global Molecular and Morphological Effects of 24-Hour Chromium(VI) Exposure on
Shewanella oneidensis
MR-1
Authors: Chourey Karuna , Thompson Melissa R. , Morrell-Falvey Jennifer , VerBerkmoes Nathan C. , Brown Steven D. , Shah Manesh , Zhou Jizhong , Doktycz Mitchel , Hettich Robert L. , Thompson Dorothea K. 
Published: September 2006

ABSTRACT

The biological impact of 24-h (“chronic”) chromium(VI)
[Cr(VI) or chromate] exposure on
Shewanella oneidensis
MR-1
was assessed by analyzing cellular morphology as well as genome-wide
differential gene and protein expression profiles. Cells challenged
aerobically with an initial chromate concentration of 0.3 mM in complex
growth medium were compared to untreated control cells grown in the
absence of chromate. At the 24-h time point at which cells were
harvested for transcriptome and proteome analyses, no residual Cr(VI)
was detected in the culture supernatant, thus suggesting the complete
uptake and/or reduction of this metal by cells. In contrast to the
untreated control cells, Cr(VI)-exposed cells formed apparently
aseptate, nonmotile filaments that tended to aggregate. Transcriptome
profiling and mass spectrometry-based proteomic characterization
revealed that the principal molecular response to 24-h Cr(VI) exposure
was the induction of prophage-related genes and their encoded products
as well as a number of functionally undefined hypothetical genes that
were located within the integrated phage regions of the MR-1 genome. In
addition, genes with annotated functions in DNA metabolism, cell
division, biosynthesis and degradation of the murein (peptidoglycan)
sacculus, membrane response, and general environmental stress
protection were upregulated, while genes encoding chemotaxis, motility,
and transport/binding proteins were largely repressed under conditions
of 24-h chromate
treatment.
Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased
Siderastrea siderea
Authors: Sekar Raju , Mills DeEtta K. , Remily Elizabeth R. , Voss Joshua D. , Richardson Laurie L. 
Published: September 2006

ABSTRACT

Microbial community profiles and species composition associated with two black band-diseased colonies of the coral
Siderastrea siderea
were studied by 16S rRNA-targeted gene cloning, sequencing, and amplicon-length heterogeneity PCR (LH-PCR). Bacterial communities associated with the surface mucopolysaccharide layer (SML) of apparently healthy tissues of the infected colonies, together with samples of the black band disease (BBD) infections, were analyzed using the same techniques for comparison. Gene sequences, ranging from 424 to 1,537 bp, were retrieved from all positive clones (
n
= 43 to 48) in each of the four clone libraries generated and used for comparative sequence analysis. In addition to LH-PCR community profiling, all of the clone sequences were aligned with LH-PCR primer sequences, and the theoretical lengths of the amplicons were determined. Results revealed that the community profiles were significantly different between BBD and SML samples. The SML samples were dominated by γ-proteobacteria (53 to 64%), followed by β-proteobacteria (18 to 21%) and α-proteobacteria (5 to 11%). In contrast, both BBD clone libraries were dominated by α-proteobacteria (58 to 87%), followed by verrucomicrobia (2 to 10%) and 0 to 6% each of δ-proteobacteria, bacteroidetes, firmicutes, and cyanobacteria. Alphaproteobacterial sequence types related to the bacteria associated with toxin-producing dinoflagellates were observed in BBD clone libraries but were not found in the SML libraries. Similarly, sequences affiliated with the family
Desulfobacteraceae
and toxin-producing cyanobacteria, both believed to be involved in BBD pathogenesis, were found only in BBD libraries. These data provide evidence for an association of numerous toxin-producing heterotrophic microorganisms with BBD of corals.
Environmental Influences onVibrioPopulations in Northern Temperate and Boreal Coastal Waters (Baltic and Skagerrak Seas)
Authors: Eiler Alexander , Johansson Mona , Bertilsson Stefan 
Published: September 2006

ABSTRACTEven if manyVibriospp. are endemic to coastal waters, their distribution in northern temperate and boreal waters is poorly studied. To identify environmental factors regulatingVibriopopulations in a salinity gradient along the Swedish coastline, we combinedVibrio-specific quantitative competitive PCR with denaturant gradient gel electrophoresis-based genotyping. The totalVibrioabundance ranged from 4 × 103to 9.6 × 104cells liter−1, with the highest abundances in the more saline waters of the Skagerrak Sea. SeveralVibriopopulations were present throughout the salinity gradient, with abundances of single populations ranging from 5 × 102to 7 × 104cells liter−1. Clear differences were observed along the salinity gradient, where three populations dominated the more saline waters of the Skagerrak Sea and two populations containing mainly representatives ofV. anguillarumandV. aestuarianusgenotypes were abundant in the brackish waters of the Baltic Sea. Our results suggest that this apparent niche separation within the genusVibriomay also be influenced by alternate factors such as nutrient levels and high abundances of dinoflagellates. AV. cholerae/V. mimicuspopulation was detected in more than 50% of the samples, with abundances exceeding 103cells liter−1, even in the cold (annual average water temperature of around 5°C) and low-salinity (2 to 4‰) samples from the Bothnian Bay (latitude, 65°N). The unsuspected and widespread occurrence of this population in temperate and boreal coastal waters suggests that potentialVibriopathogens may also be endemic to cold and brackish waters and hence may represent a previously overlooked health hazard.