bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats
Authors: Liu Xueduan , Bagwell Christopher E. , Wu Liyou , Devol Allan H. , Zhou Jizhong 
Published: October 2003

ABSTRACT

This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (
dsrAB
) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class
Proteobacteria
(
Desulfobulbus propionicus
,
Desulfosarcina variabilis
) and the
Bacillus
-
Clostridium
(
Desulfotomaculum putei
) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability.
RpoS-Dependent Stress Response and Exoenzyme Production in
Vibrio vulnificus
Authors: Hülsmann A. , Rosche T. M. , Kong I.-S. , Hassan H. M. , Beam D. M. , Oliver J. D. 
Published: October 2003

ABSTRACT

Vibrio vulnificus
is an estuarine bacterium capable of causing rapidly fatal infections through both ingestion and wound infection. Like other opportunistic pathogens,
V. vulnificus
must adapt to potentially stressful environmental changes while living freely in seawater, upon colonization of the oyster gut, and upon infection of such diverse hosts as humans and eels. In order to begin to understand the ability of
V. vulnificus
to respond to such stresses, we examined the role of the alternate sigma factor RpoS, which is important in stress response and virulence in many pathogens. An
rpoS
mutant of
V. vulnificus
strain C7184o was constructed by homologous recombination. The mutant strain exhibited a decreased ability to survive diverse environmental stresses, including exposure to hydrogen peroxide, hyperosmolarity, and acidic conditions. The most striking difference was a high sensitivity of the mutant to hydrogen peroxide. Albuminase, caseinase, and elastase activity were detected in the wild type but not in the mutant strain, and an additional two hydrolytic activities (collagenase and gelatinase) were reduced in the mutant strain compared to the wild type. Additionally, the motility of the
rpoS
mutant was severely diminished. Overall, these studies suggest that
rpoS
in
V. vulnificus
is important for adaptation to environmental changes and may have a role in virulence.
Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures
Authors: Avrahami Sharon , Conrad Ralf 
Published: October 2003

ABSTRACTThe effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of theamoAgene, which codes for the α subunit of ammonia monooxygenase. AllamoAgene sequences found belonged to the genusNitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the differentNitrosospiraclusters, which was observed in moist soil and slurry incubations of GMS and OMS.NitrosospiraAmoA cluster 1 was mainly detected below 30°C, whileNitrosospiracluster 4 was predominant at 25°C.Nitrosospiraclusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a singleNitrosospiracluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively toNitrosospiracluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus,Nitrosospiracluster 1 was absent in OMS soil treated with less fertilizer, whileNitrosospiracluster 9 was only found in the sample given less fertilizer.
Immobilization of Arsenite and Ferric Iron by
Acidithiobacillus ferrooxidans
and Its Relevance to Acid Mine Drainage
Authors: Duquesne K. , Lebrun S. , Casiot C. , Bruneel O. , Personné J.-C. , Leblanc M. , Elbaz-Poulichet F. , Morin G. , Bonnefoy V. 
Published: October 2003

ABSTRACT

Weathering of the As-rich pyrite-rich tailings of the abandoned mining site of Carnoulès (southeastern France) results in the formation of acid waters heavily loaded with arsenic. Dissolved arsenic present in the seepage waters precipitates within a few meters from the bottom of the tailing dam in the presence of microorganisms. An
Acidithiobacillus ferrooxidans
strain, referred to as CC1, was isolated from the effluents. This strain was able to remove arsenic from a defined synthetic medium only when grown on ferrous iron. This
A. ferrooxidans
strain did not oxidize arsenite to arsenate directly or indirectly. Strain CC1 precipitated arsenic unexpectedly as arsenite but not arsenate, with ferric iron produced by its energy metabolism. Furthermore, arsenite was almost not found adsorbed on jarosite but associated with a poorly ordered schwertmannite. Arsenate is known to efficiently precipitate with ferric iron and sulfate in the form of more or less ordered schwertmannite, depending on the sulfur-to-arsenic ratio. Our data demonstrate that the coprecipitation of arsenite with schwertmannite also appears as a potential mechanism of arsenite removal in heavily contaminated acid waters. The removal of arsenite by coprecipitation with ferric iron appears to be a common property of the
A. ferrooxidans
species, as such a feature was observed with one private and three collection strains, one of which was the type strain.
Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments
Authors: Stach James E. M. , Maldonado Luis A. , Masson Douglas G. , Ward Alan C. , Goodfellow Michael , Bull Alan T. 
Published: October 2003

ABSTRACT

Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with ≥99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class
Actinobacteria.
Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/
D
) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (
P
= 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries.
F
ST
and phylogenetic grouping of taxa (P tests) were both significant (
P
< 0.00001 and
P
< 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.
Assessment of the Effects of Holding Time and Temperature on
Escherichia coli
Densities in Surface Water Samples
Authors: Pope Misty L. , Bussen Michelle , Feige Mary Ann , Shadix Lois , Gonder Sharon , Rodgers Crystal , Chambers Yildiz , Pulz Jessica , Miller Ken , Connell Kevin , Standridge Jon 
Published: October 2003

ABSTRACT

Escherichia coli
is a routinely used microbiological indicator of water quality. To determine whether holding time and storage conditions had an effect on
E. coli
densities in surface water, studies were conducted in three phases, encompassing 24 sites across the United States and four commonly used monitoring methods. During all three phases of the study,
E. coli
samples were analyzed at time 0 and at 8, 24, 30, and 48 h after sample collection. During phase 1, when 4°C samples were evaluated by Colilert or by placing a membrane onto mFC medium followed by transfer to nutrient agar containing 4-methylumbelliferyl-β-
d
-glucuronide (mFC/NA-MUG), three of four sites showed no significant differences throughout the 48-h study. During phase 2, five of seven sites showed no significant difference between time 0 and 24 h by membrane filtration (mFC/NA-MUG). When evaluated by the Colilert method, five of seven sites showed no significant difference in
E. coli
density between time 0 and 48 h. During phase 3, 8 of 13 sites showed no significant differences in
E. coli
densities between time 0 and the 48-h holding time, regardless of method. Based on the results of these studies, it appears that if samples are held below 10°C and are not allowed to freeze, most surface water
E. coli
samples analyzed by commonly used methods beyond 8 h after sample collection can generate
E. coli
data comparable to those generated within 8 h of sample collection. Notwithstanding this conclusion,
E. coli
samples collected from surface waters should always be analyzed as soon as possible.
Use of Bromodeoxyuridine Immunocapture To Identify Active Bacteria Associated with Arbuscular Mycorrhizal Hyphae
Authors: Artursson Veronica , Jansson Janet K. 
Published: October 2003

ABSTRACT

Arbuscular mycorrhizae are beneficial for crops grown under low-till management systems. Increasingly, it is becoming apparent that bacteria associated with mycorrhizae can enhance the beneficial relationship between mycorrhizae and plants. However, it has been difficult to study these relationships by conventional techniques. In this study actively growing bacteria were identified in soil from an undisturbed fallow field known to contain arbuscular mycorrhizae by using molecular tools to eliminate the need for cultivation. A thymidine analog, bromodeoxyuridine (BrdU), was added to the soil and incubated for 2 days. DNA was extracted, and the newly synthesized DNA was isolated by immunocapture of the BrdU-containing DNA. The active bacteria in the community were identified by 16S rRNA gene PCR amplification and DNA sequence analysis. Based on 16S rRNA gene sequence information, a selective medium was chosen to isolate the corresponding active bacteria.
Bacillus cereus
strain VA1, one of the bacteria identified by the BrdU method, was isolated from the soil and tagged with green fluorescent protein. By using confocal microscopy, this bacterium was shown to clearly attach to arbuscular mycorrhizal hyphae. This study was the first to use this combination of molecular and traditional approaches to isolate, identify, and visualize a specific bacterium that is active in fallow soil and associates with arbuscular mycorrhizal hyphae.
Nuclease Activity of
Saccharomyces cerevisiae
Mre11 Functions in Targeted Nucleotide Alteration
Authors: Liu Li , Usher Michael , Hu Yiling , Kmiec Eric B. 
Published: October 2003

ABSTRACT

Oligonucleotides can be used to direct site-specific changes in genomic DNA through a process in which mismatched base pairs in the oligonucleotide and the target DNA are created. The mechanism by which these complexes are developed and resolved is being studied by using
Saccharomyces cerevisiae
as a model system. Genetic analyses have revealed that in all likelihood the reaction occurs in two phases: DNA pairing and DNA repair. While the former phase involves strand assimilation, the latter phase likely involves an endonucleolytic processing step that leads to joint resolution. In this study, we established the importance of a functioning
MRE11
gene in the overall reaction, as yeast strains deficient in
MRE11
exhibited severely reduced activity. The activity could be rescued by complementation with wild-type
MRE11
genes but not with
MRE11
alleles lacking the nuclease function. Taken together, the data suggest that Mre11 provides nuclease activity for targeted nucleotide exchange, a process that could be used to reengineer yeast genes.
Prospecting for Novel Biocatalysts in a Soil Metagenome
Authors: Voget S. , Leggewie C. , Uesbeck A. , Raasch C. , Jaeger K.-E. , Streit W. R. 
Published: October 2003

ABSTRACT

The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera
Pseudomonas
,
Agrobacterium
,
Xanthomonas
,
Microbulbifer
, and
Janthinobacterium.
Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (
amiA
), two cellulases (
gnuB
and
uvs080
), an α-amylase (
amyA
), a 1,4-α-glucan branching enzyme (
amyB
), and two pectate lyases (
pelA
and
uvs119
). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene
aguB
was overexpressed in
Escherichia coli
, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
A Novel Extracellular Multicopper Oxidase from
Phanerochaete chrysosporium
with Ferroxidase Activity
Authors: Larrondo Luis F. , Salas Loreto , Melo Francisco , Vicuña Rafael , Cullen Daniel 
Published: October 2003

ABSTRACT

Lignin degradation by the white rot basidiomycete
Phanerochaete chrysosporium
involves various extracellular oxidative enzymes, including lignin peroxidase, manganese peroxidase, and a peroxide-generating enzyme, glyoxal oxidase. Recent studies have suggested that laccases also may be produced by this fungus, but these conclusions have been controversial. We identified four sequences related to laccases and ferroxidases (Fet3) in a search of the publicly available
P. chrysosporium
database. One gene, designated
mco1
, has a typical eukaryotic secretion signal and is transcribed in defined media and in colonized wood. Structural analysis and multiple alignments identified residues common to laccase and Fet3 sequences. A recombinant MCO1 (rMCO1) protein expressed in
Aspergillus nidulans
had a molecular mass of 78 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the copper I-type center was confirmed by the UV-visible spectrum. rMCO1 oxidized various compounds, including 2,2′-azino(bis-3-ethylbenzthiazoline-6-sulfonate) (ABTS) and aromatic amines, although phenolic compounds were poor substrates. The best substrate was Fe
2+
, with a

K
m

close to 2 μM. Collectively, these results suggest that the
P. chrysosporium
genome does not encode a typical laccase but rather encodes a unique extracellular multicopper oxidase with strong ferroxidase activity.
An Alternative Efficient Procedure for Purification of the Obligate Intracellular Fish Bacterial Pathogen
Piscirickettsia salmonis
Authors: Henríquez Vitalia , Rojas María Verónica , Marshall Sergio H. 
Published: October 2003

ABSTRACT

Piscirickettsia salmonis
is an obligate intracellular bacterial pathogen of salmonid fish and the etiological agent of the aggressive disease salmonid rickettsial syndrome. Today, this disease, also known as piscirickettsiosis, is the cause of high mortality in net pen-reared salmonids in southern Chile. Although the bacteria can be grown in tissue culture cells, genetic analysis of the organism has been hindered because of the difficulty in obtaining
P. salmonis
DNA free from contaminating host cell DNA. In this report, we describe a novel procedure to purify in vitro-grown bacteria with iodixanol as the substrate to run differential centrifugation gradients which, combined with DNase I digestion, yield enough pure bacteria to do DNA analysis. The efficiency of the purification procedure relies on two main issues: semiquantitative synchrony of the
P. salmonis
-infected Chinook salmon embryo (CHSE-214) tissue culture cells and low osmolarity of iodixanol to better resolve bacteria from the membranous structures of the host cell. This method resulted in the isolation of intact piscirickettsia organisms and removed salmon and mitochondrial DNA effectively, with only 1.0% contamination with the latter.
Species-Specific Peptide Ligands for the Detection of
Bacillus anthracis
Spores
Authors: Williams David D. , Benedek Orsolya , Turnbough Charles L. 
Published: October 2003

ABSTRACT

Currently available detectors for spores of
Bacillus anthracis
, the causative agent of anthrax, are inadequate for frontline use and general monitoring. There is a critical need for simple, rugged, and inexpensive detectors capable of accurate and direct identification of
B. anthracis
spores. Necessary components in such detectors are stable ligands that bind tightly and specifically to target spores. By screening a phage display peptide library, we identified a family of peptides, with the consensus sequence TYPXPXR, that bind selectively to
B. anthracis
spores. We extended this work by identifying a peptide variant, ATYPLPIR, with enhanced ability to bind to
B. anthracis
spores and an additional peptide, SLLPGLP, that preferentially binds to spores of species phylogenetically similar to, but distinct from,
B. anthracis
. These two peptides were used in tandem in simple assays to rapidly and unambiguously identify
B. anthracis
spores. We envision that these peptides can be used as sensors in economical and portable
B. anthracis
spore detectors that are essentially free of false-positive signals due to other environmental
Bacillus
spores.
Development of a
mariner
-Based Transposon for Use in
Sorangium cellulosum
Authors: Julien Bryan , Fehd Ruby 
Published: October 2003

ABSTRACT

In order to generate marked insertions in the myxobacterium
Sorangium cellulosum
, a transposon based on the eukaryotic
mariner
transposon was developed. The transposition frequency was increased with the use of a mutated
tnp
gene. The transposon randomly inserts into the chromosome, as demonstrated by targeted mutagenesis of the
epoK
gene.
Effects of Minerals on Resistance of
Bacillus subtilis
Spores to Heat and Hydrostatic Pressure
Authors: Igura Noriyuki , Kamimura Yuya , Islam M. Shahidul , Shimoda Mitsuya , Hayakawa Isao 
Published: October 2003

ABSTRACT

Among
Bacillus subtilis
IFO13722 spores sporulated at 30, 37, and 44°C, those sporulated at 30°C had the highest resistance to treatments with high hydrostatic pressure (100 to 300 MPa, 55°C, 30 min). Pressure resistance increased after demineralization of the spores and decreased after remineralization of the spores with Ca
2+
or Mg
2+
, whereas the resistance did not change when spores were remineralized with Mn
2+
or K
+
, suggesting that former two divalent ions were involved in the activation of cortex-lytic enzymes during germination.
Teschoviruses as Indicators of Porcine Fecal Contamination of Surface Water
Authors: Jiménez-Clavero Miguel Angel , Fernández Carlos , Ortiz José Antonio , Pro Javier , Carbonell Gregoria , Tarazona José Vicente , Roblas Neftalí , Ley Victoria 
Published: October 2003

ABSTRACT

Teschoviruses specifically infect pigs and are shed in pig feces. Hence, their presence in water should indicate contamination with pig fecal residues. To assess this hypothesis, we have developed a real-time reverse transcriptase PCR (RT-PCR) method that allows the quantitative detection of pig teschovirus (PTV) RNA. The method is able to detect 92 fg of PTV RNA per ml of sample. Using this method, we have detected the presence of PTV RNA in water and fecal samples from all pig farms examined (
n
= 5). Feces from other animal species (cattle, sheep, and goats) were negative in this test. To compare the PTV RNA detection method with conventional chemical determinations currently in use for evaluation of water contamination, we analyzed water samples collected downstream from a pig slurry spillage site. We have found a positive correlation within both types of determinations. The sensitivity of the PTV detection assay was similar to that achieved by unspecific organic matter determination and superior to all other conventional chemical analyses performed. Furthermore, the new method is highly specific, revealing the porcine origin of the contamination, a feature that is lacking in currently available methods for the assessment of water contamination.
Comparison of
Campylobacter
Isolates from Poultry and Humans: Association between In Vitro Virulence Properties, Biotypes, and Pulsed-Field Gel Electrophoresis Clusters
Authors: Nadeau Éric , Messier Serge , Quessy Sylvain 
Published: October 2003

ABSTRACT

The in vitro virulence properties of 197 temporally and geographically related
Campylobacter
isolates from chicken broilers and humans were compared. Comparisons of the virulence properties associated with genotypes and biotypes were made. All isolates adhered to, and 63% invaded, INT-407 cells, whereas 13% were cytotoxic for CHO cells. CHO cell-cytotoxic extracts were also cytotoxic for INT-407 cells, but the sensitivity for Vero cells was variable. The proportion of isolates demonstrating a high invasiveness potential (>1,000 CFU ml
−1
) or Vero cell cytotoxicity was significantly higher for human than for poultry isolates. Invasiveness was associated with
Campylobacter jejuni
isolates of biotypes 1 and 2, whereas CHO and INT-407 cell cytotoxicity was associated with
C. jejuni
isolates of biotypes 3 and 4. Cytotoxic isolates were also clustered according to pulsed-field gel electrophoresis profiles.