bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two
Bacteria
Phylotypes Are Predominant in the Suiyo Seamount Hydrothermal Plume
Authors: Sunamura Michinari , Higashi Yowsuke , Miyako Chiwaka , Ishibashi Jun-ichiro , Maruyama Akihiko 
Published: February 2004

ABSTRACT

Microbial diversity and populations in a hydrothermal plume that was present inside the caldera of the Suiyo Seamount, a submarine volcano on the Izu-Bonin Arc, were investigated by performing a phylogenetic analysis of the 16S rRNA gene and by using fluorescence in situ hybridization (FISH). Corresponding to transmissivity, an indicator of turbidity, the vertical total cell count as determined by 4′,6′-diamidino-2-phenylindole (DAPI) staining varied from 5.6 × 10
4
to 1.1 × 10
5
cells ml
−1
, and the apparent plume layer was assessed to be at a depth of 1,050 to 1,200 m inside the caldera and to contain 1.0 × 10
5
to 1.1 × 10
5
cells ml
−1
. From microbial samples collected in the plume by an in situ filtration system, the following two major phylogenetic groups, which were closely related to sulfur-oxidizing microbes, were obtained: the SUP05 group belonging to the gamma subclass of the
Proteobacteria
(13 of 20 clones) and the SUP01 group belonging to the epsilon subclass of the
Proteobacteria
(5 of 20 clones). Specific oligonucleotide probes for these groups (SUP05-187 and SUP01-63) were designed and were used with various water samples obtained from the Suiyo Seamount. In the apparent plume layer, up to 66% of the total counts of microbial cells were estimated to be
Bacteria
cells that hybridized to EUB338, and few cells were identified by the archaeal probe ARCH915. Almost all
Bacteria
cells were hard to identify with the known group-specific probes, such as ALF19, GAM42a, and CF319, while 88 to 90% of the
Bacteria
cells hybridized with SUP05-187 and >98% of them were considered members of the SUP05 and SUP01 populations. In a low-temperature vent fluid emitted from a bivalve-colonized mound, the SUP05 cells accounted for >99% of the
Bacteria
cells, suggesting that a portion of the plume cells originated on the surface of the seafloor at a depth of about 1,380 m. From further analysis of cell morphology (i.e., cell size and cell elongation index) we inferred that the SUP05 cells were active in the plume layer at a depth of 1,050 to 1,200 m compared to the activity in a near-bottom layer, while many elongated cells were found between these layers. These findings suggest that the morphology and distribution of SUP05 cells have complex relationships with hydrothermal activities and water circulation. Although growth and production rates remain to be defined, we concluded that this Suiyo Seamount caldera has functioned as a natural continuous incubator for these two phylotypes of
Bacteria
in an aphotic deep-sea environment.
Development of a Real-Time PCR Assay for Rapid Detection and Quantification ofAlexandrium minutum(a Dinoflagellate)
Authors: Galluzzi Luca , Penna Antonella , Bertozzini Elena , Vila Magda , Garcés Esther , Magnani Mauro 
Published: February 2004

ABSTRACTThe marine dinoflagellate genusAlexandriumincludes a number of species which produce neurotoxins responsible for paralytic shellfish poisoning (PSP), which in humans may cause muscular paralysis, neurological symptoms, and, in extreme cases, death.A. minutumis the most widespread toxic PSP species in the western Mediterranean basin. The monitoring of coastal waters for the presence of harmful algae also normally involves microscopic examinations of phytoplankton populations. These procedures are time consuming and require a great deal of taxonomic experience, thus limiting the number of specimens that can be analyzed. Because of the genetic diversity of different genera and species, molecular tools may also help to detect the presence of target microorganisms in marine field samples. In this study, we developed a real-time PCR-based assay for rapid detection of all toxic species of theAlexandriumgenus in both fixative-preserved environmental samples and cultures. Moreover, we developed a real-time quantitative PCR assay for the quantification ofA. minutumcells in seawater samples.Alexandriumgenus-specific primers were designed on the 5.8S rDNA region. Primer specificity was confirmed by using BLAST and by amplification of a representative sample of the DNA of other dinoflagellates and diatoms. Using a standard curve constructed with a plasmid containing the ITS1-5.8S-ITS2A. minutumsequence and culturedA. minutumcells, we determined the absolute number of 5.8S rDNA copies per cell. Consequently, after quantification of 5.8S rDNA copies in samples containingA. minutumcells, we were also able to estimate the number of cells. Several fixedA. minutumbloom sea samples from Arenys Harbor (Catalan Coast, Spain) were analyzed using this method, and quantification results were compared with standard microscopy counting methods. The two methods gave comparable results, confirming that real-time PCR could be a valid, fast alternative procedure for the detection and quantification of target phytoplankton species during coastal water monitoring.
Metamorphosis of a Scleractinian Coral in Response to Microbial Biofilms
Authors: Webster Nicole S. , Smith Luke D. , Heyward Andrew J. , Watts Joy E. M. , Webb Richard I. , Blackall Linda L. , Negri Andrew P. 
Published: February 2004

ABSTRACT

Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the
Alphaproteobacteria
,
Betaproteobacteria
,
Gammaproteobacteria
, and
Cytophaga
-
Flavobacterium
of
Bacteroidetes
had the largest influence on overall community composition. A low abundance of
Archaea
was detected in almost all biofilms, providing the first report of
Archaea
associated with coral reef biofilms. No differences in the relative densities of each subdivision of
Proteobacteria
were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no difference was detected in banding profiles between biofilms which induced larval metamorphosis and those where no metamorphosis occurred. This investigation demonstrates that complex microbial communities can induce coral metamorphosis in the absence of CCA.
Effects of Temperature and Pressure on Sulfate Reduction and Anaerobic Oxidation of Methane in Hydrothermal Sediments of Guaymas Basin
Authors: Kallmeyer Jens , Boetius Antje 
Published: February 2004

ABSTRACT

Rates of sulfate reduction (SR) and anaerobic oxidation of methane (AOM) in hydrothermal deep-sea sediments from Guaymas Basin were measured at temperatures of 5 to 200°C and pressures of 1 × 10
5
, 2.2 × 10
7
, and 4.5 × 10
7
Pa. A maximum SR of several micromoles per cubic centimeter per day was found at between 60 and 95°C and 2.2 × 10
7
and 4.5 × 10
7
Pa. Maximal AOM was observed at 35 to 90°C but generally accounted for less than 5% of SR.
New Approach for Specific Determination of Antibiotics by Use of Luminescent
Escherichia coli
and Immune Serum
Authors: Vlasova Irina I. , Asrieli Tatyana V. , Gavrilova Elisaveta M. , Danilov Vadim S. 
Published: February 2004

ABSTRACT

This paper describes a possible application of luminescent
Escherichia coli
activated by blood serum for high-sensitivity and high-specificity assays of antibiotics in solutions. Antibiotics inhibited luminescence of a genetically engineered
E. coli
strain; the system sensitivity to some antibiotics grew notably after the cells had been preactivated by blood serum. The highest level of sensitivity (2.8 ± 0.6 ng/ml) of luminescent cells was obtained for aminoglycoside antibiotics (gentamicin and streptomycin). It is feasible to create the specific biosensor for antibiotics on the basis of bioluminescent
E. coli
strains by applying sera containing antibodies against the antibiotic under assay. The presence of antibodies specific for gentamicin in serum affects inhibition of luminescent cells by gentamicin but not inhibition by other antibiotics.
Diversity of Phage Types among Archived Cultures of the Demerec Collection of
Salmonella enterica
serovar Typhimurium Strains
Authors: Rabsch Wolfgang , Helm R. Allen , Eisenstark Abraham 
Published: February 2004

ABSTRACT

The existence of several thousand
Salmonella enterica
serovar Typhimurium LT2 and LT7 cultures originally collected by M. Demerec and sealed in agar stab vials for 33 to 46 years is a resource for evolutionary and mutational studies. Cultures from 74 of these vials, descendants of cells sealed and stored in nutrient agar stabs several decades ago, were phage typed by the Callow and Felix, Lilleengen, and Anderson systems. Among 53 LT2 archived strains, 16 had the same phage type as the nonarchival sequenced LT2 strain. The other 37 archived cultures differed in phage typing pattern from the sequenced strain. These 37 strains were divided into 10 different phage types. Among the 19 LT7 strains, only one was similar to the parent by phage typing, while 18 were different. These 18 strains fell into eight different phage types. The typing systems were developed to track epidemics from source to consumer, as well as geographic spread. The value of phage typing is dependent upon the stability of the phage type of any given strain throughout the course of the investigation. Thus, the variation over time observed in these archived cultures is particularly surprising. Possible mechanisms for such striking diversity may include loss of prophages, prophage mosaics as a result of recombination events, changes in phage receptor sites on the bacterial cell surface, or mutations in restriction-modification systems.
Permanent Colonization by
Lactobacillus casei
Is Hindered by the Low Rate of Cell Division in Mouse Gut
Authors: Lee Y. K. , Ho P. S. , Low C. S. , Arvilommi H. , Salminen S. 
Published: February 2004

ABSTRACT

Long residence times of probiotics in the intestinal tract would prolong their potential beneficial health effects and assist colonization. This study investigated the colonization potential of
Lactobacillus casei
Shirota in mouse intestine by using 5 (and 6)-carboxyfluorescein diacetate, succinimidyl ester (cFDA-SE) for assessment of doubling times in different parts of the intestine. The amounts of intestinal water overlying the surfaces of the duodenum, jejunum, ileum, and colon in BALB/c mice were 34.4 ± 2.9, 58.8 ± 6.8, 21.6 ± 2.2, and 8.0 ± 1.0 mg, respectively. Based on the residual concentrations of cFDA-SE-labeled lactobacilli on intestinal mucosal surfaces, the average half times for the wash-out of lactobacilli fed were estimated at 3.98, 1.55, 1.34, and 2.48 days in the duodenum, jejunum, ileum, and colon, respectively. The average doubling times of the lactobacilli, estimated from the residual fluorescent levels of surface-adhered cells, were 4.10, 4.78, 4.56, and 5.59 days in the duodenum, jejunum, ileum, and colon, respectively. It is estimated that the lactobacilli would have to achieve an average doubling time of 1.03 to 2.04 days to colonize the various sections of the mouse intestinal tract more permanently.
Expression, Secretion, and Glycosylation of the 45- and 47-kDa Glycoprotein of
Mycobacterium tuberculosis
in
Streptomyces lividans
Authors: Lara Martha , Servín-González Luis , Singh Mahavir , Moreno Carlos , Cohen Ingrid , Nimtz Manfred , Espitia Clara 
Published: February 2004

ABSTRACT

The gene encoding the 45/47 kDa glycoprotein (Rv1860) of
Mycobacterium tuberculosis
was expressed in
Streptomyces lividans
under its own promoter and under the thiostrepton-inducible
Streptomyces
promoter

P
tipA

. The recombinant protein was released into the culture medium and, like the native protein, migrated as a double band at 45 and 47 kDa in sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) gels. However, in contrast to the native protein, only the 47-kDa recombinant protein could be labeled with concanavalin A (ConA). Carbohydrate digestion with jack bean α-
d
-mannosidase resulted in a reduction in the molecular mass of the recombinant protein upper band and completely eliminated ConA binding. Two-dimensional gel electrophoresis revealed only one isoelectric point for the recombinant protein. Comparative fingerprinting analysis of the individually purified upper and lower recombinant protein bands, treated under the same conditions with specific proteases, resulted in similar peptide patterns, and the peptides had the same N-terminal sequence, suggesting that migration of the recombinant protein as two bands in SDS-PAGE gels could be due to differences in glycosylation. Mass spectrometry analysis of the recombinant protein indicated that as in native protein, both the N-terminal and C-terminal domains of the recombinant protein are glycosylated. Furthermore, it was determined that antibodies of human tuberculosis patients reacted mainly against the carbohydrate residues of the glycoprotein. Altogether, these observations show that expression of genes for mycobacterial antigens in
S. lividans
is very useful for elucidation of the functional role and molecular mechanisms of glycosylation in bacteria.
Modular Broad-Host-Range Expression Vectors for Single-Protein and Protein Complex Purification
Authors: Fodor Barna D. , Kovács Ákos T. , Csáki Róbert , Hunyadi-Gulyás Éva , Klement Éva , Maróti Gergely , Mészáros Lívia S. , Medzihradszky Katalin F. , Rákhely Gábor , Kovács Kornél L. 
Published: February 2004

ABSTRACT

A set of modular broad-host-range expression vectors with various affinity tags (six-His-tag, FLAG-tag, Strep-tag II, T7-tag) was created. The complete nucleotide sequences of the vectors are known, and these small vectors can be mobilized by conjugation. They are useful in the purification of proteins and protein complexes from gram-negative bacterial species. The plasmids were easily customized for
Thiocapsa roseopersicina
,
Rhodobacter capsulatus
, and
Methylococcus capsulatus
by inserting an appropriate promoter. These examples demonstrate the versatility and flexibility of the vectors. The constructs harbor the T7 promoter for easy overproduction of the desired protein in an appropriate
Escherichia coli
host. The vectors were useful in purifying different proteins from
T. roseopersicina
. The FLAG-tag-Strep-tag II combination was utilized for isolation of the HynL-HypC
2
protein complex involved in hydrogenase maturation. These tools should be useful for protein purification and for studying protein-protein interactions in a range of bacterial species.
Cyanobacterial-Type, Heteropentameric, NAD
+
-Reducing NiFe Hydrogenase in the Purple Sulfur Photosynthetic Bacterium
Thiocapsa roseopersicina
Authors: Rákhely Gábor , Kovács Ákos T. , Maróti Gergely , Fodor Barna D. , Csanádi Gyula , Latinovics Dóra , Kovács Kornél L. 
Published: February 2004

ABSTRACT

Structural genes coding for two membrane-associated NiFe hydrogenases in the phototrophic purple sulfur bacterium
Thiocapsa roseopersicina
(
hupSL
and
hynSL
) have recently been isolated and characterized. Deletion of both hydrogenase structural genes did not eliminate hydrogenase activity in the cells, and considerable hydrogenase activity was detected in the soluble fraction. The enzyme responsible for this activity was partially purified, and the gene cluster coding for a cytoplasmic, NAD
+
-reducing NiFe hydrogenase was identified and sequenced. The deduced gene products exhibited the highest similarity to the corresponding subunits of the cyanobacterial bidirectional soluble hydrogenases (HoxEFUYH). The five genes were localized on a single transcript according to reverse transcription-PCR experiments. A σ
54
-type promoter preceded the gene cluster, suggesting that there was inducible expression of the operon. The Hox hydrogenase was proven to function as a truly bidirectional hydrogenase; it produced H
2
under nitrogenase-repressed conditions, and it recycled the hydrogen produced by the nitrogenase in cells fixing N
2
. In-frame deletion of the
hoxE
gene eliminated hydrogen evolution derived from the Hox enzyme in vivo, although it had no effect on the hydrogenase activity in vitro. This suggests that HoxE has a hydrogenase-related role; it likely participates in the electron transfer processes. This is the first example of the presence of a cyanobacterial-type, NAD
+
-reducing hydrogenase in a phototrophic bacterium that is not a cyanobacterium. The potential physiological implications are discussed.
Effect of Tetracycline on Transfer and Establishment of the Tetracycline-Inducible Conjugative Transposon Tn
916
in the Guts of Gnotobiotic Rats
Authors: Bahl Martin Iain , Sørensen Søren J. , Hansen Lars Hestbjerg , Licht Tine Rask 
Published: February 2004

ABSTRACT

We have investigated the transfer of Tn
916
among strains of
Enterococcus faecalis
OG1 colonizing in the intestines of gnotobiotic rats. This animal model allows a low limit of detection and efficient colonization of the chosen bacteria. The animals continuously received tetracycline in drinking water. A tetracycline-sensitive recipient strain was allowed to colonize the animals before the resistant donor was introduced. The numbers of donors, recipients, and transconjugants in fecal samples and intestinal segments were estimated. The bioavailable amounts of tetracycline in fecal samples and intestinal segments were monitored by using bacterial biosensors carrying a transcriptional fusion of a tetracycline-regulated promoter and a
lacZ
reporter gene. Chromosomal locations of Tn
916
in transconjugants isolated either from the same animal or from different animals were compared by Southern blot analysis. Our results indicated that selection for the resistant phenotype was the major factor causing higher numbers of transconjugants in the presence of tetracycline. Tetracycline-sensitive
E. faecalis
cells colonized the intestine even when the concentrations of tetracycline in feces and intestinal luminal contents exceeded growth-inhibitory concentrations. This suggests the existence of tetracycline-depleted microhabitats in the intestinal environment.
N
2
Fixation by Unicellular Bacterioplankton from the Atlantic and Pacific Oceans: Phylogeny and In Situ Rates
Authors: Falcón Luisa I. , Carpenter Edward J. , Cipriano Frank , Bergman Birgitta , Capone Douglas G. 
Published: February 2004

ABSTRACT

N
2
-fixing proteobacteria (α and γ) and unicellular cyanobacteria are common in both the tropical North Atlantic and Pacific oceans. In near-surface waters proteobacterial
nifH
transcripts were present during both night and day while unicellular cyanobacterial
nifH
transcripts were present during the nighttime only, suggesting separation of N
2
fixation and photosynthesis by unicellular cyanobacteria. Phylogenetic relationships among unicellular cyanobacteria from both oceans were determined after sequencing of a conserved region of 16S ribosomal DNA (rDNA) of cyanobacteria, and results showed that they clustered together, regardless of the ocean of origin. However, sequencing of
nifH
transcripts of unicellular cyanobacteria from both oceans showed that they clustered separately. This suggests that unicellular cyanobacteria from the tropical North Atlantic and subtropical North Pacific share a common ancestry (16S rDNA) and that potential unicellular N
2
fixers have diverged (
nifH
). N
2
fixation rates for unicellular bacterioplankton (including small cyanobacteria) from both oceans were determined in situ according to the acetylene reduction and
15
N
2
protocols. The results showed that rates of fixation by bacterioplankton can be almost as high as those of fixation by the colonial N
2
-fixing marine cyanobacteria
Trichodesmium
spp. in the tropical North Atlantic but that rates are much lower in the subtropical North Pacific.
Determination of Cu Environments in the CyanobacteriumAnabaena flos-aquaeby X-Ray Absorption Spectroscopy
Authors: Kretschmer X. C. , Meitzner G. , Gardea-Torresdey J. L. , Webb R. 
Published: February 2004

ABSTRACTWhole cells and peptidoglycan isolated from cell walls of the cyanobacteriumAnabaena flos-aquaewere lyophilized and used at pH 2 and pH 5 in Cu(II) binding studies. X-ray absorption spectra measured at the Cu K-edge were used to determine the oxidation states and chemical environments of Cu species in the whole-cell and peptidoglycan samples. In the whole-cell samples, most of the Cu retained at both pH values was coordinated by phosphate ligands. The whole-cell fractions contained significant concentrations of Cu(I) as well as Cu(II). An X-ray absorption near-edge spectrum analysis suggested that Cu(I) was coordinated by amine and thiol ligands. An analysis of the peptidoglycan fractions found that more Cu was adsorbed by the peptidoglycan fraction prepared at pH 5, due to increased chelation by amine and carboxyl ligands. The peptidoglycan fractions, also referred to as the cell wall fractions, contained little or no Cu(I). The Cu loading level was 30 times higher in the cell wall sample prepared at pH 5 than in the sample prepared at pH 2. Amine and bidentate carboxyl ligands had similar relative levels of importance in cell wall peptidoglycan samples prepared at both pH values, but phosphate coordination was insignificant.