bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chthoniobacter flavus
gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two,
Spartobacteria
classis nov., of the Phylum
Verrucomicrobia
Authors: Sangwan Parveen , Chen Xiaolei , Hugenholtz Philip , Janssen Peter H. 
Published: October 2004

ABSTRACT

The phylum
Verrucomicrobia
is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the
Verrucomicrobia
are resolved by comparative analysis of 16S rRNA genes, mostly obtained directly from environmental samples. To date, only two of these subdivisions (1 and 4) have characterized pure-culture representatives. We have isolated and characterized the first known pure-culture representative of subdivision 2. Strain Ellin428 is an aerobic heterotrophic bacterium that is able to grow with many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate. Cells are yellow, rod-shaped, nonmotile, and gram-stain negative, and they contain peptidoglycan with direct cross-linkages of the A1γ
meso
-Dpm type. The isolate grows well at 25°C on a variety of standard biological media, including some used in the routine cultivation of bacteria from soil. The pH range for growth is 4.0 to 7.0. Low levels of menaquinones MK-10 and MK-11 were detected. The major cellular fatty acids are C
14:0
, a-C
15:0
, C
16:1ω7c
, and/or 2OH i-C
15:0
, and C
16:0
. The G+C content of the genomic DNA is 61 mol%. We propose a new genus and species,
Chthoniobacter flavus
gen. nov., sp. nov., with isolate Ellin428 as the type strain, and a new class for the subdivision to which it belongs,
Spartobacteria
classis nov. Environmental sequences indicate that the class
Spartobacteria
is largely represented by globally distributed, abundant, and active soil bacteria.
Expression of an Exogenous 1-Aminocyclopropane-1-Carboxylate Deaminase Gene in
Sinorhizobium meliloti
Increases Its Ability To Nodulate Alfalfa
Authors: Ma Wenbo , Charles Trevor C. , Glick Bernard R. 
Published: October 2004

ABSTRACT

1-Aminocyclopropane-1-carboxylate (ACC) deaminase has been found in various plant growth-promoting rhizobacteria, including rhizobia. This enzyme degrades ACC, the immediate precursor of ethylene, and thus decreases the biosynthesis of ethylene in higher plants. The ACC deaminase of
Rhizobium leguminosarum
bv.
viciae
128C53K was previously reported to be able to enhance nodulation of peas. The ACC deaminase structural gene (
acdS
) and its upstream regulatory gene, a leucine-responsive regulatory protein (LRP)-like gene (
lrpL
), from
R. leguminosarum
bv.
viciae
128C53K were introduced into
Sinorhizobium meliloti
, which does not produce this enzyme, in two different ways: through a plasmid vector and by in situ transposon replacement. The resulting ACC deaminase-producing
S. meliloti
strains showed 35 to 40% greater efficiency in nodulating
Medicago sativa
(alfalfa), likely by reducing ethylene production in the host plants. Furthermore, the ACC deaminase-producing
S. meliloti
strain was more competitive in nodulation than the wild-type strain. We postulate that the increased competitiveness might be related to utilization of ACC as a nutrient within the infection threads.
Pathogenic
Aeromonas hydrophila
Serogroup O:14 and O:81 Strains with an S Layer
Authors: Esteve Consuelo , Alcaide Elena , Canals Rocío , Merino Susana , Blasco Dolores , Figueras Maria José , Tomás Juan M. 
Published: October 2004

ABSTRACT

Five autoagglutinating
Aeromonas hydrophila
isolates recovered from eels and humans were assigned to serogroups O:14 and O:81 of the Sakazaki and Shimada (National Institutes of Health) scheme. They had the following properties in common: positive precipitation after boiling, moderate surface hydrophobicity (salt-aggregation-test value around 1.2), pathogenicity for fish and mice (50% lethal dose, 10
4.61
to 10
7.11
), lipopolysaccharides that contained O-polysaccharide chains of homogeneous chain length, and an external S layer peripheral to the cell wall observed by electron microscopy. A strong cross-reactivity was detected by immunoblotting between the homogeneous O-polysaccharide fraction of O:14 and O:81 strains but not between them and the lipopolysaccharide of
A. hydrophila
TF7 (O:11 reference strain). Outer membrane fractions of these strains contained a predominant 53- to 54-kDa protein which was glycine extractable under low-pH (pH 2.8) conditions and was identified as the surface array protein. The S-layer proteins of the O:14 and O:81
A. hydrophila
strains seemed to be primarily different from those previously purified from strains
A. hydrophila
TF7 and
Aeromonas salmonicida
A450 on the basis of colony hybridizations with both the structural genes
vapA
and
ahsA
. This is the first report of the presence of an S layer in mesophilic
Aeromonas
strains not belonging to serogroup O:11.
New Method for Estimating Bacterial Cell Abundances in Natural Samples by Use of Sublimation
Authors: Glavin Daniel P. , Cleaves H. James , Schubert Michael , Aubrey Andrew , Bada Jeffrey L. 
Published: October 2004

ABSTRACT

We have developed a new method based on the sublimation of adenine from
Escherichia coli
to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500°C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from ∼10
5
to 10
9
E. coli
cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.
Improved Stress Tolerance of GroESL-OverproducingLactococcus lactisand ProbioticLactobacillus paracaseiNFBC 338
Authors: Desmond C. , Fitzgerald G. F. , Stanton C. , Ross R. P. 
Published: October 2004

ABSTRACTThe bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes. Two-dimensional polyacrylamide gel electrophoresis revealed that GroEL expression in probioticLactobacillus paracaseiNFBC 338 was increased under heat adaptation conditions (52°C for 15 min). Subsequently, thegroESLoperon ofL. paracaseiNFBC 338 was PCR amplified, and by using the nisin-inducible expression system, two plasmids, pGRO1 and pGRO2, were constructed on the basis of vectors pNZ8048 and pMSP3535, respectively. These vectors were transferred intoLactococcus lactis(pGRO1) andL. paracasei(pGRO2), and after induction with nisin, overexpressed GroEL represented 15 and 20% of the total cellular protein in each strain, respectively. Following heat shock treatment of lactococci (at 54°C) and lactobacilli (at 60°C), the heat-adapted cultures maintained the highest level of viability (5-log-unit increase, approximately) in each case, while it was found that the GroESL-overproducing strains performed only moderately better (1-log-unit increase) than the controls. On the other hand, the salt tolerance of both GroESL-overproducing strains (in 5 M NaCl) was similar to that of the parent cultures. Interestingly, both strains overproducing GroESL exhibited increased solvent tolerance, most notably, the ability to grow in the presence of butanol (0.5% [vol/vol]) for 5 h, while the viability of the parent strain declined. These results confirm the integral role of GroESL in solvent tolerance, and to a lesser extent, thermotolerance of lactic acid bacteria. Furthermore, this study demonstrates that technologically sensitive cultures, including certain probiotic lactobacilli, can potentially be manipulated to become more robust for survival under harsh conditions, such as food product development and gastrointestinal transit.
Bacterial Community Associated with Black Band Disease in Corals
Authors: Frias-Lopez Jorge , Klaus James S. , Bonheyo George T. , Fouke Bruce W. 
Published: October 2004

ABSTRACT

Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division
Firmicutes
, two species of the
Cytophaga-Flexibacter-Bacteroides
(CFB) group, and one species of δ-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of
Firmicutes
were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a
Beggiatoa
species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.
Genome-Wide Transposon Mutagenesis of
Borrelia burgdorferi
for Identification of Phenotypic Mutants
Authors: Stewart Philip E. , Hoff Jessica , Fischer Elizabeth , Krum Jonathan G. , Rosa Patricia A. 
Published: October 2004

ABSTRACT

The spirochete
Borrelia burgdorferi
is the causative agent of Lyme disease, the leading vector-borne illness in the United States. Many of the genetic factors affecting spirochete morphology and physiology are unknown due to the limited genetic tools available and the large number of open reading frames with unknown functions. By adapting a
mariner
transposon to function in
B. burgdorferi
, we have developed a random mutagenesis system that tags the mutated locus for rapid identification. Transposition occurs at saturating levels in
B. burgdorferi
and appears to be random, targeting both linear and circular replicons. By combining the transposon system with a screen for factors affecting growth rate, mutations were readily identified in genes putatively involved in cell division and chemotaxis and a hypothetical open reading frame involved in outer membrane integrity. The successful adaptation of a
mariner
transposon to function in
B. burgdorferi
should aid in identifying virulence factors and novel gene products related to spirochete physiology.
Unexpectedly Diverse
Mesorhizobium
Strains and
Rhizobium leguminosarum
Nodulate Native Legume Genera of New Zealand, while Introduced Legume Weeds Are Nodulated by
Bradyrhizobium
Species
Authors: Weir Bevan S. , Turner Susan J. , Silvester Warwick B. , Park Duck-Chul , Young John M. 
Published: October 2004

ABSTRACT

The New Zealand native legume flora are represented by four genera,
Sophora
,
Carmichaelia
,
Clianthus
, and
Montigena
. The adventive flora of New Zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. Until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in New Zealand. The success of the introduced species may be due, at least in part, to the nature of their rhizobial symbioses. This study set out to address this issue by identifying rhizobial strains isolated from species of the four native legume genera and from the introduced weeds:
Acacia
spp. (wattles),
Cytisus scoparius
(broom), and
Ulex europaeus
(gorse). The identities of the isolates and their relationship to known rhizobia were established by comparative analysis of 16S ribosomal DNA,
atpD
,
glnII
, and
recA
gene sequences. Maximum-likelihood analysis of the resultant data partitioned the bacteria into three genera. Most isolates from native legumes aligned with the genus
Mesorhizobium
, either as members of named species or as putative novel species. The widespread distribution of strains from individual native legume genera across
Mesorhizobium
spp. contrasts with previous reports implying that bacterial species are specific to limited numbers of legume genera. In addition, four isolates were identified as
Rhizobium leguminosarum
. In contrast, all sequences from isolates from introduced weeds aligned with
Bradyrhizobium
species but formed clusters distinct from existing named species. These results show that native legume genera and these introduced legume genera do not have the same rhizobial populations.
Multiple-Antibiotic Resistance of
Enterococcus
spp. Isolated from Commercial Poultry Production Environments
Authors: Hayes Joshua R. , English Linda L. , Carr Lewis E. , Wagner David D. , Joseph Sam W. 
Published: October 2004

ABSTRACT

The potential impact of food animals in the production environment on the bacterial population as a result of antimicrobial drug use for growth enhancement continues to be a cause for concern. Enterococci from 82 farms within a poultry production region on the eastern seaboard were isolated to establish a baseline of susceptibility profiles for a number of antimicrobials used in production as well as clinical environments. Of the 541 isolates recovered,
Enterococcus faecalis
(53%) and
E. faecium
(31%) were the predominant species, while multiresistant antimicrobial phenotypes were observed among all species. The prevalence of resistance among isolates of
E. faecalis
was comparatively higher among lincosamide, macrolide, and tetracycline antimicrobials, while isolates of
E. faecium
were observed to be more frequently resistant to fluoroquinolones and penicillins. Notably, 63% of the
E. faecium
isolates were resistant to the streptogramin quinupristin-dalfopristin, while high-level gentamicin resistance was observed only among the
E. faecalis
population, of which 7% of the isolates were resistant. The primary observations are that enterococci can be frequently isolated from the poultry production environment and can be multiresistant to antimicrobials used in human medicine. The high frequency with which resistant enterococci are isolated from this environment suggests that these organisms might be useful as sentinels to monitor the development of resistance resulting from the usage of antimicrobial agents in animal production.
Nanoscale Investigation of Pathogenic Microbial Adhesion to a Biomaterial
Authors: Emerson Ray J. , Camesano Terri A. 
Published: October 2004

ABSTRACT

Microbial infections of medical implants occur in more than 2 million surgical cases each year in the United States alone. These increase patient morbidity and mortality, as well as patient cost and recovery time. Many treatments are available, but none are guaranteed to remove the infection. In many cases, the device infections are caused by the adhesion of microbes to the implant, ensuing growth, pathogenesis, and dissemination. The purpose of this work is to examine the initial events in microbial adhesion by simulating the approach and contact between a planktonic cell, immobilized on an atomic force microscope (AFM) cantilever, and a biomaterial or biofilm substrate. The two model microbes used in this study,
Candida parapsilosis
(ATCC 90018) and
Pseudomonas aeruginosa
(ATCC 10145), were chosen for both their clinical relevance and their ease of acquisition and handling in the laboratory setting. Attractive interactions exist between
C. parapsilosis
and both unmodified silicone rubber and
P. aeruginosa
biofilms. Using
C. parapsilosis
cells immobilized on AFM cantilevers with a silicone substrate, we have measured attractive forces of 4.3 ± 0.25 nN in the approach portion of the force cycle. On
P. aeruginosa
biofilms, the magnitude of the attractive force decreases to 2.0 ± 0.40 nN and is preceded by a 2.0-nN repulsion at approximately 75 nm from the cell surface. These data suggest that
C. parapsilosis
may adhere to both silicone rubber and
P. aeruginosa
biofilms, possibly contributing to patient morbidity and mortality. Characterization of cell-biomaterial and cell-cell interactions allows for a quantitative link between the physicomechanical and physicochemical properties of implant materials and the nanoscale interactions leading to microbial colonization and infection.
Accelerated Biodegradation of Cement by Sulfur-Oxidizing Bacteria as a Bioassay for Evaluating Immobilization of Low-Level Radioactive Waste
Authors: Aviam Orli , Bar-Nes Gabi , Zeiri Yehuda , Sivan Alex 
Published: October 2004

ABSTRACT

Disposal of low-level radioactive waste by immobilization in cement is being evaluated worldwide. The stability of cement in the environment may be impaired by sulfur-oxidizing bacteria that corrode the cement by producing sulfuric acid. Since this process is so slow that it is not possible to perform studies of the degradation kinetics and to test cement mixtures with increased durability, procedures that accelerate the biodegradation are required. Semicontinuous cultures of
Halothiobacillus neapolitanus
and
Thiomonas intermedia
containing thiosulfate as the sole energy source were employed to accelerate the biodegradation of cement samples. This resulted in a weight loss of up to 16% after 39 days, compared with a weight loss of 0.8% in noninoculated controls. Scanning electron microscopy of the degraded cement samples revealed deep cracks, which could be associated with the formation of low-density corrosion products in the interior of the cement. Accelerated biodegradation was also evident from the leaching rates of Ca
2+
and Si
2+
, the major constituents of the cement matrix, and Ca exhibited the highest rate (up to 20 times greater than the control rate) due to the reaction between free lime and the biogenic sulfuric acid. Leaching of Sr
2+
and Cs
+
, which were added to the cement to simulate immobilization of the corresponding radioisotopes, was also monitored. In contrast to the linear leaching kinetics of calcium, silicon, and strontium, the leaching pattern of cesium produced a saturation curve similar to the control curve. Presumably, the leaching of cesium is governed by the diffusion process, whereas the leaching kinetics of the other three ions seems to governed by dissolution of the cement.
Galactose Metabolism by
Streptococcus mutans
Authors: Abranches Jacqueline , Chen Yi-Ywan M. , Burne Robert A. 
Published: October 2004

ABSTRACT

The
galK
gene, encoding galactokinase of the Leloir pathway, was insertionally inactivated in
Streptococcus mutans
UA159. The
galK
knockout strain displayed only marginal growth on galactose, but growth on glucose or lactose was not affected. In strain UA159, the sugar phosphotransferase system (PTS) for lactose and the PTS for galactose were induced by growth in lactose and galactose, although galactose PTS activity was very low, suggesting that
S. mutans
does not have a galactose-specific PTS and that the lactose PTS may transport galactose, albeit poorly. To determine if the galactose growth defect of the
galK
mutant could be overcome by enhancing lactose PTS activity, the gene encoding a putative repressor of the operon for lactose PTS and phospho-β-galactosidase,
lacR
, was insertionally inactivated. A
galK
and
lacR
mutant still could not grow on galactose, although the strain had constitutively elevated lactose PTS activity. The glucose PTS activity of
lacR
mutants grown in glucose was lower than in the wild-type strain, revealing an influence of LacR or the lactose PTS on the regulation of the glucose PTS. Mutation of the
lacA
gene of the tagatose pathway caused impaired growth in lactose and galactose, suggesting that galactose can only be efficiently utilized when both the Leloir and tagatose pathways are functional. A mutation of the permease in the multiple sugar metabolism operon did not affect growth on galactose. Thus, the galactose permease of
S. mutans
is not present in the
gal
,
lac
, or
msm
operons.
Reduction of
Escherichia coli
O157:H7 Populations in Cattle by Addition of Colicin E7-Producing
E. coli
to Feed
Authors: Schamberger Gerry P. , Phillips Ronald L. , Jacobs Jennifer L. , Diez-Gonzalez Francisco 
Published: October 2004

ABSTRACT

A cattle trial using artificially inoculated calves was conducted to determine the effect of the addition of colicinogenic
Escherichia coli
strains capable of producing colicin E7 (a 61-kDa DNase) to feed on the fecal shedding of serotype O157:H7. The experiment was divided into three periods. In period 1, which lasted 24 days, six calves were used as controls, and eight calves received 10
7
CFU of
E. coli
(a mixture of eight colicinogenic
E. coli
strains) per g of feed. Both groups were orally inoculated with nalidixic acid-resistant
E. coli
O157:H7 strains 7 days after the treatment started. In periods 2 and 3, the treatment and control groups were switched, and the colicinogenic
E. coli
dose was increased 10-fold. During period 3, which lasted as long as period 1, both groups were reinoculated with
E. coli
O157:H7. The numbers of
E. coli
O157:H7 were consistently greater in the control groups during the three periods, but comparisons within each time period determined a statistically significant (
P
< 0.05) difference only at day 21 of period 1. However, when the daily average counts were compared between the period 1 control group and the period 3 treatment group that included the same six animals, an overall reduction of 1.1 log
10
CFU/g was observed, with a maximum decrease of 1.8 log
10
CFU/g at day 21 (overall statistical significance,
P
= 0.001). Serotype O157:H7 was detected in 44% of the treatment group's intestinal tissue samples and in 64% of those from the control group (
P
< 0.04). These results indicated that the daily addition of 10
8
CFU of colicin E7-producing
E. coli
per gram of feed could reduce the fecal shedding of serotype O157:H7.