bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, Abundance, and Activity of Archaeal Populations in Oil-Contaminated Groundwater Accumulated at the Bottom of an Underground Crude Oil Storage Cavity
Authors: Watanabe Kazuya , Kodama Yumiko , Hamamura Natsuko , Kaku Nobuo 
Published: October 2002

ABSTRACT

Fluorescence in situ hybridization has shown that cells labeled with an
Archaea
-specific probe (ARCH915) accounted for approximately 10% of the total cell count in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Although chemical analyses have revealed vigorous consumption of nitrate in cavity groundwater, the present study found that the methane production rate was higher than the nitrate consumption rate. To characterize the likely archaeal populations responsible for methane production in this system, fragments of 16S ribosomal DNA (rDNA) were amplified by PCR using eight different combinations of universal and
Archaea
-specific primers. Sequence analysis of 324 clones produced 23 different archaeal sequence types, all of which were affiliated with the kingdom
Euryarchaeota
. Among them, five sequence types (KuA1, KuA6, KuA12, KuA16, and KuA22) were obtained in abundance. KuA1 and KuA6 were closely related to the known methanogens
Methanosaeta concilii
(99% identical) and
Methanomethylovorans hollandica
(98%), respectively. Although no closely related organism was found for KuA12, it could be affiliated with the family
Methanomicrobiaceae
. KuA16 and KuA22 showed substantial homology only to some environmental clones. Both of these branched deeply in the
Euryarchaeota
, and may represent novel orders. Quantitative competitive PCR showed that KuA12 was the most abundant, accounting for ∼50% of the total archaeal rDNA copies detected. KuA1 and KuA16 also constituted significant proportions of the total archaeal rDNA copies (7 and 17%, respectively). These results suggest that limited species of novel archaea were enriched in the oil storage cavity. An estimate of specific methane production rates suggests that they were active methanogens.
The Peptidyl-Prolyl Isomerase Motif Is Lacking in PmpA, the PrsA-Like Protein Involved in the Secretion Machinery of
Lactococcus lactis
Authors: Drouault Sophie , Anba Jamila , Bonneau Sophie , Bolotin Alexander , Ehrlich S. Dusko , Renault Pierre 
Published: October 2002

ABSTRACT

The
prsA
-like gene from
Lactococcus lactis
encoding its single homologue to PrsA, an essential protein triggering the folding of secreted proteins in
Bacillus subtilis
, was characterized. This gene, annotated
pmpA
, encodes a lipoprotein of 309 residues whose expression is increased 7- to 10-fold when the source of nitrogen is limited. A slight increase in the expression of the PrsA-like protein (PLP) in
L. lactis
removed the degradation products previously observed with the
Staphylococcus hyicus
lipase used as a model secreted protein. This shows that PmpA either triggers the folding of the secreted lipase or activates its degradation by the cell surface protease HtrA. Unlike the case for
B. subtilis
, the inactivation of the gene encoding PmpA reduced only slightly the growth rate of
L. lactis
in standard conditions. However, it almost stopped its growth when the lipase was overexpressed in the presence of salt in the medium. Like PrsA of
B. subtilis
and PrtM of
L. lactis
, the
L. lactis
PmpA protein could thus have a foldase activity that facilitates protein secretion. These proteins belong to the third family of peptidyl-prolyl
cis
/
trans
-isomerases (PPIases) for which parvulin is the prototype. Almost all PLP from gram-positive bacteria contain a domain with the PPIase signature. An exception to this situation was found only in
Streptococcaceae
, the family to which
L. lactis
belongs. PLP from
Streptococcus pneumoniae
and
Enterococcus faecalis
possess this signature, but those of
L. lactis
,
Streptococcus pyogenes
, and
Streptococcus mutans
do not. However, secondary structure predictions suggest that the folding of PLP is conserved over the entire length of the proteins, including the unconserved signature region. The activity associated with the expression of PmpA in
L. lactis
and these genomic data show that either the PPIase motif is not necessary for PPIase activity or, more likely, PmpA foldase activity does not necessarily require PPIase activity.
Endotoxin Activity of
Moraxella osloensis
against the Grey Garden Slug,
Deroceras reticulatum
Authors: Tan Li , Grewal Parwinder S. 
Published: October 2002

ABSTRACT

Moraxella osloensis
is a gram-negative bacterium associated with
Phasmarhabditis hermaphrodita
, a slug-parasitic nematode that has prospects for biological control of mollusk pests, especially the grey garden slug,
Deroceras reticulatum
. This bacterium-feeding nematode acts as a vector that transports
M. osloensis
into the shell cavity of the slug, and the bacterium is the killing agent in the nematode-bacterium complex. We discovered that
M. osloensis
produces an endotoxin(s), which is tolerant to heat and protease treatments and kills the slug after injection into the shell cavity. Washed or broken cells treated with penicillin and streptomycin from 3-day
M. osloensis
cultures were more pathogenic than similar cells from 2-day
M. osloensis
cultures. However, heat and protease treatments and 2 days of storage at 22°C increased the endotoxin activity of the young broken cells but not the endotoxin activity of the young washed cells treated with the antibiotics. This suggests that there may be a proteinaceous substance(s) that is structurally associated with the endotoxin(s) and masks its toxicity in the young bacterial cells. Moreover, 2 days of storage of the young washed bacterial cells at 22°C enhanced their endotoxin activity if they were not treated with the antibiotics. Furthermore, purified lipopolysaccharide (LPS) from the 3-day
M. osloensis
cultures was toxic to slugs, with an estimated 50% lethal dose of 48 μg per slug, thus demonstrating that the LPS of
M. osloensis
is an endotoxin that is active against
D. reticulatum
. This appears to be the first report of a biological toxin that is active against mollusks.
Molecular Cloning and Characterization of the Gene Coding for the Aerobic Azoreductase from
Xenophilus azovorans
KF46F
Authors: Blümel Silke , Knackmuss Hans-Joachim , Stolz Andreas 
Published: October 2002

ABSTRACT

The gene coding for an aerobic azoreductase was cloned from
Xenophilus azovorans
KF46F (formerly
Pseudomonas
sp. strain KF46F), which was previously shown to grow with the carboxylated azo compound 1-(4′-carboxyphenylazo)-2-naphthol (carboxy-Orange II) as the sole source of carbon and energy. The deduced amino acid sequence encoded a protein with a molecular weight of 30,278 and showed no significant homology to amino acid sequences currently deposited at the relevant data bases. A presumed NAD(P)H-binding site was identified in the amino-terminal region of the azoreductase. The enzyme was heterologously expressed in
Escherichia coli
and the azoreductase activities of resting cells and cell extracts were compared. The results suggested that whole cells of the recombinant
E. coli
strains were unable to take up sulfonated azo dyes and therefore did not show in vivo azoreductase activity. The turnover of several industrially relevant azo dyes by cell extracts from the recombinant
E. coli
strain was demonstrated.
Life at the Energetic Edge: Kinetics of Circumneutral Iron Oxidation by Lithotrophic Iron-Oxidizing Bacteria Isolated from the Wetland-Plant Rhizosphere
Authors: Neubauer Scott C. , Emerson David , Megonigal J. Patrick 
Published: October 2002

ABSTRACT

Batch cultures of a lithotrophic Fe(II)-oxidizing bacterium, strain BrT, isolated from the rhizosphere of a wetland plant, were grown in bioreactors and used to determine the significance of microbial Fe(II) oxidation at circumneutral pH and to identify abiotic variables that affect the partitioning between microbial oxidation and chemical oxidation. Strain BrT grew only in the presence of an Fe(II) source, with an average doubling time of 25 h. In one set of experiments, Fe(II) oxidation rates were measured before and after the cells were poisoned with sodium azide. These experiments indicated that strain BrT accounted for 18 to 53% of the total iron oxidation, and the average cellular growth yield was 0.70 g of CH
2
O per mol of Fe(II) oxidized. In a second set of experiments, Fe(II) was constantly added to bioreactors inoculated with live cells, killed cells, or no cells. A statistical model fitted to the experimental data demonstrated that metabolic Fe(II) oxidation accounted for up to 62% of the total oxidation. The total Fe(II) oxidation rates in these experiments were strongly limited by the rate of Fe(II) delivery to the system and were also influenced by O
2
and total iron concentrations. Additionally, the model suggested that the microbes inhibited rates of abiotic Fe(II) oxidation, perhaps by binding Fe(II) to bacterial exopolymers. The net effect of strain BrT was to accelerate total oxidation rates by up to 18% compared to rates obtained with cell-free treatments. The results suggest that neutrophilic Fe(II)-oxidizing bacteria may compete for limited O
2
in the rhizosphere and therefore influence other wetland biogeochemical cycles.
Mechanisms and Rates of Bacterial Colonization of Sinking Aggregates
Authors: Kiørboe Thomas , Grossart Hans-Peter , Ploug Helle , Tang Kam 
Published: October 2002

ABSTRACT

Quantifying the rate at which bacteria colonize aggregates is a key to understanding microbial turnover of aggregates. We used encounter models based on random walk and advection-diffusion considerations to predict colonization rates from the bacteria's motility patterns (swimming speed, tumbling frequency, and turn angles) and the hydrodynamic environment (stationary versus sinking aggregates). We then experimentally tested the models with 10 strains of bacteria isolated from marine particles: two strains were nonmotile; the rest were swimming at 20 to 60 μm s
−1
with different tumbling frequency (0 to 2 s
−1
). The rates at which these bacteria colonized artificial aggregates (stationary and sinking) largely agreed with model predictions. We report several findings. (i) Motile bacteria rapidly colonize aggregates, whereas nonmotile bacteria do not. (ii) Flow enhances colonization rates. (iii) Tumbling strains colonize aggregates enriched with organic substrates faster than unenriched aggregates, while a nontumbling strain did not. (iv) Once on the aggregates, the bacteria may detach and typical residence time is about 3 h. Thus, there is a rapid exchange between attached and free bacteria. (v) With the motility patterns observed, freely swimming bacteria will encounter an aggregate in <1 day at typical upper-ocean aggregate concentrations. This is faster than even starving bacteria burn up their reserves, and bacteria may therefore rely solely on aggregates for food. (vi) The net result of colonization and detachment leads to a predicted equilibrium abundance of attached bacteria as a function of aggregate size, which is markedly different from field observations. This discrepancy suggests that inter- and intraspecific interactions among bacteria and between bacteria and their predators may be more important than colonization in governing the population dynamics of bacteria on natural aggregates.
Cloning and Inactivation of a Branched-Chain-Amino-Acid Aminotransferase Gene from
Staphylococcus carnosus
and Characterization of the Enzyme
Authors: Madsen Søren M. , Beck Hans Christian , Ravn Peter , Vrang Astrid , Hansen Anne Maria , Israelsen Hans 
Published: October 2002

ABSTRACT

Staphylococcus carnosus
and
Staphylococcus xylosus
are widely used as aroma producers in the manufacture of dried fermented sausages. Catabolism of branched-chain amino acids (BCAAs) by these strains contributes to aroma formation by production of methyl-branched aldehydes and carboxy acids. The first step in the catabolism is most likely a transamination reaction catalyzed by BCAA aminotransferases (IlvE proteins). In this study, we cloned the
ilvE
gene from
S. carnosus
by using degenerate oligonucleotides and PCR. We found that the deduced amino acid sequence was 80% identical to that of the corresponding enzyme in
Staphylococcus aureus
and that the
ilvE
gene was constitutively expressed as a monocistronic transcript. To study the influence of
ilvE
on BCAA catabolism, we constructed an
ilvE
deletion mutant by gene replacement. The IlvE protein from
S. carnosus
was shown mainly to catalyze the transamination of isoleucine, valine, leucine, and, to some extent, methionine using pyridoxal 5′-phosphate as a coenzyme. The
ilvE
mutant degraded less than 5% of the BCAAs, while the wild-type strain degraded 75 to 95%. Furthermore, the mutant strain produced approximately 100-fold less of the methyl-branched carboxy acids, 2-methylpropanoic acid, 2-methylbutanoic acid, and 3-methylbutanoic acid, which derived from the BCAA catabolism, clearly emphasizing the role of IlvE in aroma formation. In contrast to previous reports, we found that IlvE was the only enzyme that catalyzed the deamination of BCAAs in
S. carnosus
. The
ilvE
mutant strain showed remarkably lower growth rate and biomass yield compared to those of the wild-type strain when grown in rich medium. Normal growth rate and biomass yield were restored by addition of the three BCAA-derived α-keto acids, showing that degradation products of BCAAs were essential for optimal cell growth.
Transfer of Microorganisms, Including
Listeria monocytogenes
, from Various Materials to Beef
Authors: Midelet Graziella , Carpentier Brigitte 
Published: October 2002

ABSTRACT

The quantity of microorganisms that may be transferred to a food that comes into contact with a contaminated surface depends on the density of microorganisms on the surface and on the attachment strengths of the microorganisms on the materials. We made repeated contacts between pieces of meat and various surfaces (stainless steel and conveyor belt materials [polyvinyl chloride and polyurethane]), which were conditioned with meat exudate and then were contaminated with
Listeria monocytogenes
,
Staphylococcus sciuri
,
Pseudomonas putida
, or
Comamonas
sp. Attachment strengths were assessed by the slopes of the two-phase curves obtained by plotting the logarithm of the number of microorganisms transferred against the order number of the contact. These curves were also used to estimate the microbial population on the surface by using the equation of A. Veulemans, E. Jacqmain, and D. Jacqmain (Rev. Ferment. Ind. Aliment. 25:58-65, 1970). The biofilms were characterized according to their physicochemical surface properties and structures. Their exopolysaccharide-producing capacities were assessed from biofilms grown on polystyrene. The
L. monocytogenes
biofilms attached more strongly to polymers than did the other strains, and attachment strength proved to be weaker on stainless steel than on the two polymers. However, in most cases, it was the population of the biofilms that had the strongest influence on the total number of CFU detached. Although attachment strengths were weaker on stainless steel, this material, carrying a smaller population of bacteria, had a weaker contaminating capacity. In most cases the equation of Veulemans et al. revealed more bacteria than did swabbing the biofilms, and it provided a better assessment of the contaminating potential of the polymeric materials studied here.
Molecular Breeding of Transgenic Rice Plants Expressing a Bacterial Chlorocatechol Dioxygenase Gene
Authors: Shimizu Masami , Kimura Tetsuya , Koyama Takayoshi , Suzuki Katsuhisa , Ogawa Naoto , Miyashita Kiyotaka , Sakka Kazuo , Ohmiya Kunio 
Published: October 2002

ABSTRACT

The
cbnA
gene encoding the chlorocatechol dioxygenase gene from
Ralstonia eutropha
NH9 was introduced into rice plants. The
cbnA
gene was expressed in transgenic rice plants under the control of a modified cauliflower mosaic virus 35S promoter. Western blot analysis using anti-CbnA protein indicated that the
cbnA
gene was expressed in leaf tissue, roots, culms, and seeds. Transgenic rice calluses expressing the
cbnA
gene converted 3-chlorocatechol to 2-chloromucote efficiently. Growth and morphology of the transgenic rice plants expressing the
cbnA
gene were not distinguished from those of control rice plants harboring only a Ti binary vector. It is thus possible to breed transgenic plants that degrade chloroaromatic compounds in soil and surface water.
Chlorxanthomycin, a Fluorescent, Chlorinated, Pentacyclic Pyrene from a
Bacillus
sp
Authors: Magyarosy Andrew , Ho Jonathan Z. , Rapoport Henry , Dawson Scott , Hancock Joe , Keasling Jay D. 
Published: October 2002

ABSTRACT

A gram-positive
Bacillus
sp. that fluoresces yellow under long-wavelength UV light on several common culture media was isolated from soil samples. On the basis of carbon source utilization studies, fatty acid methyl ester analysis, and 16S ribosomal DNA analysis, this bacterium was most similar to
Bacillus megaterium
. Chemical extraction yielded a yellow-orange fluorescent pigment, which was characterized by X-ray crystallography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The fluorescent compound, chlorxanthomycin, is a pentacyclic, chlorinated molecule with the molecular formula C
22
H
15
O
6
Cl and a molecular weight of 409.7865. Chlorxanthomycin appears to be located in the cytoplasm, does not diffuse out of the cells into the culture medium, and has selective antibiotic activity.
Possible Quorum Sensing in Marine Snow Bacteria: Production of Acylated Homoserine Lactones by
Roseobacter
Strains Isolated from Marine Snow
Authors: Gram Lone , Grossart Hans-Peter , Schlingloff Andrea , Kiørboe Thomas 
Published: October 2002

ABSTRACT

We report here, for the first time, that bacteria associated with marine snow produce communication signals involved in quorum sensing in gram-negative bacteria. Four of 43 marine microorganisms isolated from marine snow were found to produce acylated homoserine lactones (AHLs) in well diffusion and thin-layer chromatographic assays based on the
Agrobacterium tumefaciens
reporter system. Three of the AHL-producing strains were identified by 16S ribosomal DNA gene sequence analysis as
Roseobacter
spp., and this is the first report of AHL production by these α-
Proteobacteria
. It is likely that AHLs in
Roseobacter
species and other marine snow bacteria govern phenotypic traits (biofilm formation, exoenzyme production, and antibiotic production) which are required mainly when the population reaches high densities, e.g., in the marine snow community.
Horizontal Transmission of Shiga Toxin-ProducingEscherichia coliwithin Groups of Dairy Calves
Authors: Cobbold R. , Desmarchelier P. 
Published: October 2002

ABSTRACTTo examine the dissemination of Shiga-toxigenicEscherichia coli(STEC) within cattle groups, dairy calves on two farms utilizing different calf-rearing practices were exposed to a traceable STEC strain. Test strain dissemination differed significantly between farms, with a higher prevalence being associated with group penning. Pen floors and calf hides may be the main environmental mechanisms of transmission. Dairy calf husbandry represents a control point for reducing on-farm STEC prevalence.
Role of the
htrA
Gene in
Klebsiella pneumoniae
Virulence
Authors: Cortés Guadalupe , de Astorza Beatriz , Benedí Vicente J. , Albertí Sebastián 
Published: October 2002

ABSTRACT

We recently described the use of mini-Tn
5
to generate complement-sensitive mutants derived from a complement-resistant
Klebsiella pneumoniae
clinical isolate deficient in the lipopolysaccharide O side chain. One mutant with a reduced capacity to survive in nonimmune human sera carried the transposon inserted in the
htrA
gene. We cloned and sequenced the gene and predicted from the deduced amino acid sequence that the putative HtrA homolog contains structural features similar to those of previously described HtrA proteins. To investigate the biological functions and the role of the
htrA
gene in the virulence of
K. pneumoniae
, we constructed an isogenic mutant by insertion-duplication mutagenesis. Characterization of the mutant showed that it had greater sensitivity to temperature (50°C) and oxidative stress (H
2
O
2
) than the parent strain. Furthermore, the
htrA
mutant produced less capsule, bound more molecules of complement component C3, and was more sensitive to complement and whole-blood killing than was the parent strain. Finally, disruption of the
htrA
gene in a virulent
K. pneumoniae
strain caused a reduction of its virulence in a mice model. Our results indicate that the
htrA
gene plays an important role in the virulence of
K. pneumoniae
.
Immune Cell-Mediated Protection against Vaginal Candidiasis: Evidence for a Major Role of Vaginal CD4+T Cells and Possible Participation of Other Local Lymphocyte Effectors
Authors: Santoni Giorgio , Boccanera Maria , Adriani Daniela , Lucciarini Roberta , Amantini Consuelo , Morrone Stefania , Cassone Antonio , De Bernardis Flavia 
Published: October 2002

ABSTRACTThe protective roles of different lymphocyte subsets were investigated in a rat vaginal candidiasis model by adoptive transfer of vaginal lymphocytes (VL) or sorted, purified CD3+T cells, CD4+or CD8+T cells, or CD3−CD5+B cells from the vaginas of naïve or immune rats following three rounds ofCandida albicansinfection. The adoptive transfer of total VL from nonimmune animals did not alter the course of vaginal candidiasis of the recipient rats. In contrast, the animals receiving total VL or CD3+T cells from immune rats showed a highly significant acceleration of fungus clearance compared with animals which received nonimmune VL. The animals with vaginal CD3−CD5+B cells transferred from immune rats also had fewerCandidaCFU than the controls, but fungal clearance was significantly retarded with respect to the animals administered immune T cells. Sorted, purified CD4+and CD8+vaginal T cells from immune rats were also adoptively transferred to naïve animals. Although both populations were seen to accelerate the clearance of the fungus from the vagina, CD4+T cells were much more effective than CD8+T cells. Overall, there was no difference between the antifungal effects of immune vaginal CD4+T cells and those achievable with the transfer of whole, immune VL. Histological observations of the vaginal tissues of rats with adoptively transferred immune T cells demonstrated a remarkable accumulation of lymphocytes in the subepithelial lamina propria and also infiltrating the mucosal epithelium. These results strongly suggest that distinct vaginal lymphocyte subsets participate in the adaptive anti-Candidaimmunity at the vaginal level, with the vaginal CD4+T cells probably playing a major role.