bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Specific Detection of a Novel
Pseudomonadaceae
Cluster Associated with Soils from Winter Wheat Plots of a Long-Term Agricultural Field Experiment
Authors: Pesaro Manuel , Widmer Franco 
Published: January 2006

ABSTRACT

The genus
Pseudomonas
(sensu stricto) represents a group of microorganisms directly involved in functions conferring plant health. We performed a study in the DOK long-term agricultural field experiment on the basis of previously published
Pseudomonas
-selective PCR primers in order to investigate the community structure of the microbial groups defined by the target range of these primers. Three different agricultural management systems, i.e., conventional, biodynamic, and bio-organic, along with mineral and unfertilized controls were investigated, with each system planted with either winter wheat or a grass-clover ley. Amplified small-subunit rRNA gene fragments were analyzed using the genetic profiling techniques restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE), revealing distinct differences between soils planted with winter wheat and grass clover but only minor differences between the management systems. Phylogenetic analyses of 59 clone sequences retrieved from bio-organic and unfertilized systems identified sequences related to
Pseudomonas fluorescens
and a novel cluster termed
Cellvibrio
-related
Pseudomonadaceae
(CRP). The CRP clones were exclusively isolated from winter wheat soil samples and were responsible for the crop-specific differences observed in RFLP and DGGE profiles. New primers were designed for the amplification of CRP targets directly from soil DNA, yielding strong signals exclusively for winter wheat soils. We concluded that crop-associated CRP exist in agricultural soils and that genetic profiling followed by specific probe design represents a valuable approach for identification as well as sensitive and rapid monitoring of novel microbial groups in the environment.
Introduction of Monochloramine into a Municipal Water System: Impact on Colonization of Buildings by
Legionella
spp
Authors: Moore Matthew R. , Pryor Marsha , Fields Barry , Lucas Claressa , Phelan Maureen , Besser Richard E. 
Published: January 2006

ABSTRACT

Legionnaires' disease (LD) outbreaks are often traced to colonized potable water systems. We collected water samples from potable water systems of 96 buildings in Pinellas County, Florida, between January and April 2002, during a time when chlorine was the primary residual disinfectant, and from the same buildings between June and September 2002, immediately after monochloramine was introduced into the municipal water system. Samples were cultured for legionellae and amoebae using standard methods. We determined predictors of
Legionella
colonization of individual buildings and of individual sampling sites. During the chlorine phase, 19 (19.8%) buildings were colonized with legionellae in at least one sampling site. During the monochloramine phase, six (6.2%) buildings were colonized. In the chlorine phase, predictors of
Legionella
colonization included water source (source B compared to all others, adjusted odds ratio [aOR], 6.7; 95% confidence interval [CI], 2.0 to 23) and the presence of a system with continuously circulating hot water (aOR, 9.8; 95% CI, 1.9 to 51). In the monochloramine phase, there were no predictors of individual building colonization, although we observed a trend toward greater effectiveness of monochloramine in hotels and single-family homes than in county government buildings. The presence of amoebae predicted
Legionella
colonization at individual sampling sites in both phases (OR ranged from 15 to 46, depending on the phase and sampling site). The routine introduction of monochloramine into a municipal drinking water system appears to have reduced colonization by
Legionella
spp. in buildings served by the system. Monochloramine may hold promise as community-wide intervention for the prevention of LD.
Isolation of Poly-3-Hydroxybutyrate Metabolism Genes from Complex Microbial Communities by Phenotypic Complementation of Bacterial Mutants
Authors: Wang Chunxia , Meek David J. , Panchal Priya , Boruvka Natalie , Archibald Frederick S. , Driscoll Brian T. , Charles Trevor C. 
Published: January 2006

ABSTRACT

The goal of this study was to initiate investigation of the genetics of bacterial poly-3-hydroxybutyrate (PHB) metabolism at the community level. We constructed metagenome libraries from activated sludge and soil microbial communities in the broad-host-range IncP cosmid pRK7813. Several unique clones were isolated from these libraries by functional heterologous complementation of a
Sinorhizobium meliloti bdhA
mutant, which is unable to grow on the PHB cycle intermediate
d
-3-hydroxybutyrate due to absence of the enzyme
d
-3-hydroxybutyrate dehydrogenase activity. Clones that conferred
d
-3-hydroxybutyrate utilization on
Escherichia coli
were also isolated. Although many of the
S. meliloti bdhA
mutant complementing clones restored
d
-3-hydroxybutyrate dehydrogenase activity to the mutant host, for some of the clones this activity was not detectable. This was also the case for almost all of the clones isolated in the
E. coli
selection. Further analysis was carried out on clones isolated in the
S. meliloti
complementation. Transposon mutagenesis to locate the complementing genes, followed by DNA sequence analysis of three of the genes, revealed coding sequences that were broadly divergent but lay within the diversity of known short-chain dehydrogenase/reductase encoding genes. In some cases, the amino acid sequence identity between pairs of deduced BdhA proteins was <35%, a level at which detection by nucleic acid hybridization based methods would probably not be successful.
Spirochaeta coccoides
sp. nov., a Novel Coccoid Spirochete from the Hindgut of the Termite
Neotermes castaneus
Authors: Dröge Stefan , Fröhlich Jürgen , Radek Renate , König Helmut 
Published: January 2006

ABSTRACT

A novel spirochete strain, SPN1, was isolated from the hindgut contents of the termite
Neotermes castaneus
. The highest similarities (about 90%) of the strain SPN1 16S rRNA gene sequence are with spirochetes belonging to the genus
Spirochaeta
, and thus, the isolate could not be assigned to the so-called termite clusters of the treponemes or to a known species of the genus
Spirochaeta
. Therefore, it represents a novel species, which was named
Spirochaeta coccoides
. In contrast to all other known validly described spirochete species, strain SPN1 shows a coccoid morphology and is immotile. The isolated strain is obligately anaerobic and ferments different mono-, di-, and oligosaccharides by forming formate, acetate, and ethanol as the main fermentation end products. Furthermore, strain SPN1 is able to grow anaerobically with yeast extract as the sole carbon and energy source. The fastest growth was obtained at 30°C, the temperature at which the termites were also grown. The cells possess different enzymatic activities that are involved in the degradation of lignocellulose in the termite hindgut, such as β-
d
-glucosidase, α-
l
-arabinosidase, and β-
d
-xylosidase. Therefore, they may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut.
Extensive Variation in Intracellular Symbiont Community Composition among Members of a Single Population of the Wood-Boring BivalveLyrodus pedicellatus(Bivalvia: Teredinidae)
Authors: Luyten Yvette A. , Thompson Janelle R. , Morrill Wendy , Polz Martin F. , Distel Daniel L. 
Published: January 2006

ABSTRACTShipworms (wood-boring bivalves of the familyTeredinidae) harbor in their gills intracellular bacterial symbionts thought to produce enzymes that enable the host to consume cellulose as its primary carbon source. Recently, it was demonstrated that multiple genetically distinct symbiont populations coexist within one shipworm species,Lyrodus pedicellatus. Here we explore the extent to which symbiont communities vary among individuals of this species by quantitatively examining the diversity, abundance, and pattern of occurrence of symbiont ribotypes (unique 16S rRNA sequence types) among specimens drawn from a single laboratory-reared population. A total of 18 ribotypes were identified in two clone libraries generated from gill tissue of (i) a single specimen and (ii) four pooled specimens. Phylogenetic analysis assigned all of the ribotypes to a unique clade within the γ subgroup of proteobacteria which contained at least five well-supported internal clades (phylotypes). By competitive quantitative PCR and constant denaturant capillary electrophoresis, we estimated the number and abundance of symbiont phylotypes in gill samples of 13 individual shipworm specimens. Phylotype composition varied greatly; however, in all specimens the numerically dominant symbiont belonged to one of two nearly mutually exclusive phylotypes, each of which was detected with similar frequencies among specimens. A third phylotype, containing the culturable symbiontTeredinibacter turnerae, was identified in nearly all specimens, and two additional phylotypes were observed more sporadically. Such extensive variation in ribotype and phylotype composition among host specimens adds to a growing body of evidence that microbial endosymbiont populations may be both complex and dynamic and suggests that such genetic variation should be evaluated with regard to physiological and ecological differentiation.
Characterization of PhlG, a Hydrolase That Specifically Degrades the Antifungal Compound 2,4-Diacetylphloroglucinol in the Biocontrol Agent
Pseudomonas fluorescens
CHA0
Authors: Bottiglieri Mélanie , Keel Christoph 
Published: January 2006

ABSTRACT

The potent antimicrobial compound 2,4-diacetylphloroglucinol (DAPG) is a major determinant of biocontrol activity of plant-beneficial
Pseudomonas fluorescens
CHA0 against root diseases caused by fungal pathogens. The DAPG biosynthetic locus harbors the
phlG
gene, the function of which has not been elucidated thus far. The
phlG
gene is located upstream of the
phlACBD
biosynthetic operon, between the
phlF
and
phlH
genes which encode pathway-specific regulators. In this study, we assigned a function to PhlG as a hydrolase specifically degrades DAPG to equimolar amounts of mildly toxic monoacetylphloroglucinol (MAPG) and acetate. DAPG added to cultures of a DAPG-negative Δ
phlA
mutant of strain CHA0 was completely degraded, and MAPG was temporarily accumulated. In contrast, DAPG was not degraded in cultures of a Δ
phlA
Δ
phlG
double mutant. To confirm the enzymatic nature of PhlG in vitro, the protein was histidine tagged, overexpressed in
Escherichia coli
, and purified by affinity chromatography. Purified PhlG had a molecular mass of about 40 kDa and catalyzed the degradation of DAPG to MAPG. The enzyme had a
k
cat
of 33 s
−1
and a

K
m

of 140 μM at 30°C and pH 7. The PhlG enzyme did not degrade other compounds with structures similar to DAPG, such as MAPG and triacetylphloroglucinol, suggesting strict substrate specificity. Interestingly, PhlG activity was strongly reduced by pyoluteorin, a further antifungal compound produced by the bacterium. Expression of
phlG
was not influenced by the substrate DAPG or the degradation product MAPG but was subject to positive control by the GacS/GacA two-component system and to negative control by the pathway-specific regulators PhlF and PhlH.
Use of
Bacillus thuringiensis
Toxins for Control of the Cotton Pest
Earias insulana
(Boisd.) (Lepidoptera: Noctuidae)
Authors: Ibargutxi María A. , Estela Anna , Ferré Juan , Caballero Primitivo 
Published: January 2006

ABSTRACT

Thirteen of the most common lepidopteran-specific Cry proteins of
Bacillus thuringiensis
have been tested for their efficacy against newly hatched larvae of two populations of the spiny bollworm,
Earias insulana
. At a concentration of 100 μg of toxin per milliliter of artificial diet, six Cry toxins (Cry1Ca, Cry1Ea, Cry1Fa, Cry1Ja, Cry2Aa, and Cry2Ab) were not toxic at all. Cry1Aa, Cry1Ja, and Cry2Aa did not cause mortality but caused significant inhibition of growth. The other Cry toxins (Cry1Ab, Cry1Ac, Cry1Ba, Cry1Da, Cry1Ia, and Cry9Ca) were toxic to
E. insulana
larvae. The 50% lethal concentration values of these toxins ranged from 0.39 to 21.13 μg/ml (for Cry9Ca and Cry1Ia, respectively) for an
E. insulana
laboratory colony originating from Egypt and from 0.20 to 4.25 μg/ml (for Cry9Ca and Cry1Da, respectively) for a laboratory colony originating from Spain. The relative potencies of the toxins in the population from Egypt were highest for Cry9Ca and Cry1Ab, and they were both significantly more toxic than Cry1Ac and Cry1Ba, followed by Cry1Da and finally Cry1Ia. In the population from Spain, Cry9Ca was the most toxic, followed in decreasing order by Cry1Ac and Cry1Ba, and the least toxic was Cry1Da. Binding experiments were performed to test whether the toxic Cry proteins shared binding sites in this insect.
125
I-labeled Cry1Ac and Cry1Ab and biotinylated Cry1Ba, Cry1Ia, and Cry9Ca showed specific binding to the brush border membrane vesicles from
E. insulana
. Competition binding experiments among these toxins showed that only Cry1Ab and Cry1Ac competed for the same binding sites, indicating a high possibility that this insect may develop cross-resistance to Cry1Ab upon exposure to Cry1Ac transgenic cotton but not to the other toxins tested.
Characterization of Germination Receptors of
Bacillus cereus
ATCC 14579
Authors: Hornstra Luc M. , de Vries Ynte P. , Wells-Bennik Marjon H. J. , de Vos Willem M. , Abee Tjakko 
Published: January 2006

ABSTRACT

Specific amino acids, purine ribonucleosides, or a combination of the two is required for efficient germination of endospores of
Bacillus cereus
ATCC 14579. A survey including 20 different amino acids showed that
l
-alanine,
l
-cysteine,
l
-threonine, and
l
-glutamine are capable of initiating the germination of endospores of
B. cereus
ATCC 14579. In addition, the purine ribonucleosides inosine and adenosine can trigger germination of the spores. Advanced annotation of the
B. cereus
ATCC 14579 genome revealed the presence of seven putative germination (
ger
) operons, termed
gerG
,
gerI
,
gerK
,
gerL
,
gerQ
,
gerR
, and
gerS
. To determine the role of the encoded putative receptors in nutrient-induced germination, disruption mutants were constructed by the insertion of pMUTIN4 into each of the seven operons. Four of the seven mutants were affected in the germination response to amino acids or purine ribonucleosides, whereas no phenotype could be attributed to the mutants with disrupted
gerK
,
gerL
, and
gerS
loci. The strain with a disrupted
gerR
operon was severely hampered in the ability to germinate: germination occurred in response to
l
-glutamine but not in the presence of any of the other amino acids tested. The
gerG
mutant showed significantly reduced
l
-glutamine-induced germination, which points to a role of this receptor in the
l
-glutamine germination signaling pathway.
gerR
,
gerI
, and
gerQ
mutants showed reduced germination rates in the presence of inosine, suggesting a role for these operons in ribonucleoside signaling. Efficient germination by the combination of
l
-glutamine and inosine was shown to involve the
gerG
and
gerI
operons, since the germination of mutants lacking either one of these receptors was significantly reduced. Germination triggered by the combination of
l
-phenylalanine and inosine was lost in the
gerI
mutant, indicating that both molecules are effective at the GerI receptor.
Antimicrobial Drug Resistance Genes Do Not Convey a Secondary Fitness Advantage to Calf-Adapted
Escherichia coli
Authors: Khachatryan Artashes R. , Hancock Dale D. , Besser Thomas E. , Call Douglas R. 
Published: January 2006

ABSTRACT

Maintenance of antimicrobial drug resistance in bacteria can be influenced by factors unrelated to direct selection pressure such as close linkage to other selectively advantageous genes and secondary advantage conveyed by antimicrobial resistance genes in the absence of drug selection. Our previous trials at a dairy showed that the maintenance of the antimicrobial resistance genes is not influenced by specific antimicrobial selection and that the most prevalent antimicrobial resistance phenotype of
Escherichia coli
is specifically selected for in young calves. In this paper we examine the role of secondary advantages conveyed by antimicrobial resistance genes. We tested antimicrobial-susceptible null mutant strains for their ability to compete with their progenitor strains in vitro and in vivo. The null mutant strains were generated by selection for spontaneous loss of resistance genes in broth supplemented with fusaric acid or nickel chloride. On average, the null mutant strains were as competitive as the progenitor strains in vitro and in newborn calves (in vivo). Inoculation of newborn calves at the dairy with antimicrobial-susceptible strains of
E. coli
did not impact the prevalence of antimicrobial-resistant
E. coli
. Our results demonstrate that the antimicrobial resistance genes are not responsible for the greater fitness advantage of antimicrobial-resistant
E. coli
in calves, but the farm environment and the diet clearly exert critical selective pressures responsible for the maintenance of antimicrobial resistance genes. Our current hypothesis is that the antimicrobial resistance genes are linked to other genes responsible for differential fitness in dairy calves.
Mercury Methylation from Unexpected Sources: Molybdate-Inhibited Freshwater Sediments and an Iron-Reducing Bacterium
Authors: Fleming Emily J. , Mack E. Erin , Green Peter G. , Nelson Douglas C. 
Published: January 2006

ABSTRACT

Methylmercury has been thought to be produced predominantly by sulfate-reducing bacteria in anoxic sediments. Here we show that in circumneutral pH sediments (Clear Lake, CA) application of a specific inhibitor of sulfate-reducing bacteria at appropriate concentrations typically inhibited less than one-half of all anaerobic methylation of added divalent mercury. This suggests that one or more additional groups of microbes are active methylators in these sediments impacted by a nearby abandoned mercury mine. From Clear Lake sediments, we isolated the iron-reducing bacterium
Geobacter
sp. strain CLFeRB, which can methylate mercury at a rate comparable to
Desulfobulbus propionicus
strain 1pr3, a sulfate-reducing bacterium known to be an active methylator. This is the first time that an iron-reducing bacterium has been shown to methylate mercury at environmentally significant rates. We suggest that mercury methylation by iron-reducing bacteria represents a previously unidentified and potentially significant source of this environmental toxin in iron-rich freshwater sediments.
Efficient and Stable Display of Functional Proteins on Bacterial Magnetic Particles Using Mms13 as a Novel Anchor Molecule
Authors: Yoshino Tomoko , Matsunaga Tadashi 
Published: January 2006

ABSTRACT

Magnetic particles are increasingly used for various biomedical applications because they are easy to handle and separate from biological samples. In this work, a novel anchor molecule was used for targeted protein display onto magnetic nanoparticles. The magnetic bacterium
Magnetospirillum magneticum
AMB-1 synthesizes intracellular bacterial magnetic particles (BMPs) covered with a lipid bilayer membrane. In our recent research, an integral BMP membrane protein, Mms13, was isolated and used as an anchor molecule to display functional proteins onto BMPs. The anchoring properties of Mms13 were confirmed by luciferase fusion studies. The C terminus of Mms13 was shown to be expressed on the surface of BMPs, and Mms13 was bound to magnetite directly and tightly permitting stable localization of a large protein, luciferase (61 kDa), on BMPs. Consequently, luminescence intensity obtained from BMPs using Mms13 as an anchor molecule was >400 or 1,000 times higher than Mms16 or MagA, which previously were used as anchor molecules. Furthermore, the immunoglobulin G-binding domain of protein A (ZZ) was displayed uniformly on BMPs using Mms13, and antigen was detected by transmission electron microscopy using antibody-labeled gold nanoparticles on a single BMP displaying the ZZ-antibody complex. The results of this study demonstrated the utility of Mms13 as a molecular anchor, which will facilitate the assembly of other functional proteins onto BMPs in the near feature.
Aerobic Biodegradation of 2,2′-Dithiodibenzoic Acid Produced from Dibenzothiophene Metabolites
Authors: Young Rozlyn F. , Cheng Stephanie M. , Fedorak Phillip M. 
Published: January 2006

ABSTRACT

Dibenzothiophene is a sulfur heterocycle found in crude oils and coal. The biodegradation of dibenzothiophene through the Kodama pathway by
Pseudomonas
sp. strain BT1d leads to the formation of three disulfides: 2-oxo-2-(2-thiophenyl)ethanoic acid disulfide, 2-oxo-2-(2-thiophenyl)ethanoic acid-2-benzoic acid disulfide, and 2,2′-dithiodibenzoic acid. When provided as the carbon and sulfur source in liquid medium, 2,2′-dithiodibenzoic acid was degraded by soil enrichment cultures. Two bacterial isolates, designated strains RM1 and RM6, degraded 2,2′-dithiodibenzoic acid when combined in the medium. Isolate RM6 was found to have an absolute requirement for vitamin B
12
, and it degraded 2,2′-dithiodibenzoic acid in pure culture when the medium was supplemented with this vitamin. Isolate RM6 also degraded 2,2′-dithiodibenzoic acid in medium containing sterilized supernatants from cultures of isolate RM1 grown on glucose or benzoate. Isolate RM6 was identified as a member of the genus
Variovorax
using the Biolog system and 16S rRNA gene analysis. Although the mechanism of disulfide metabolism could not be determined, benzoic acid was detected as a transient metabolite of 2,2′-dithiodibenzoic acid biodegradation by
Variovorax
sp. strain RM6. In pure culture, this isolate mineralized 2,2′-dithiodibenzoic acid, releasing 59% of the carbon as carbon dioxide and 88% of the sulfur as sulfate.
Putative ABC Transporter Responsible for Acetic Acid Resistance in
Acetobacter aceti
Authors: Nakano Shigeru , Fukaya Masahiro , Horinouchi Sueharu 
Published: January 2006

ABSTRACT

Two-dimensional gel electrophoretic analysis of the membrane fraction of
Acetobacter aceti
revealed the presence of several proteins that were produced in response to acetic acid. A 60-kDa protein, named AatA, which was mostly induced by acetic acid, was prepared;
aatA
was cloned on the basis of its NH
2
-terminal amino acid sequence. AatA, consisting of 591 amino acids and containing ATP-binding cassette (ABC) sequences and ABC signature sequences, belonged to the ABC transporter superfamily. The
aatA
mutation with an insertion of the neomycin resistance gene within the
aatA
coding region showed reduced resistance to acetic acid, formic acid, propionic acid, and lactic acid, whereas the
aatA
mutation exerted no effects on resistance to various drugs, growth at low pH (adjusted with HCl), assimilation of acetic acid, or resistance to citric acid. Introduction of plasmid pABC101 containing
aatA
under the control of the
Escherichia coli lac
promoter into the
aatA
mutant restored the defect in acetic acid resistance. In addition, pABC101 conferred acetic acid resistance on
E. coli
. These findings showed that AatA was a putative ABC transporter conferring acetic acid resistance on the host cell. Southern blot analysis and subsequent nucleotide sequencing predicted the presence of
aatA
orthologues in a variety of acetic acid bacteria belonging to the genera
Acetobacter
and
Gluconacetobacter
. The fermentation with
A. aceti
containing
aatA
on a multicopy plasmid resulted in an increase in the final yield of acetic acid.