bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical Forms of Selenium in the Metal-Resistant Bacterium
Ralstonia metallidurans
CH34 Exposed to Selenite andSelenate
Authors: Sarret Géraldine , Avoscan Laure , Carrière Marie , Collins Richard , Geoffroy Nicolas , Carrot Francine , Covès Jacques , Gouget Barbara 
Published: May 2005

ABSTRACT

Ralstonia
metallidurans
CH34, a soil bacterium resistant to a
variety of metals, is known to reduce selenite to
intracellular granules of elemental selenium (Se
0
). We have
studied the kinetics of selenite (Se
IV
) and selenate
(Se
VI
) accumulation and used X-ray absorption spectroscopy
to identify the accumulated form of selenate, as well as possible
chemical intermediates during the transformation of these two
oxyanions. When introduced during the lag phase, the presence of
selenite increased the duration of this phase, as previously
observed. Selenite introduction was followed by a
period of slow uptake, during which the bacteria contained
Se
0
and alkyl selenide in equivalent proportions. This
suggests that two reactions with similar kinetics take place:
an assimilatory pathway leading to alkyl selenide and a slow
detoxification pathway leading to Se
0
. Subsequently,
selenite uptake strongly increased (up to 340 mg Se per g of proteins)
and Se
0
was the predominant transformation product,
suggesting an activation of selenite transport and reduction systems
after several hours of contact. Exposure to selenate did not induce an
increase in the lag phase duration, and the bacteria accumulated
approximately 25-fold less Se than when exposed to selenite.
Se
IV
was detected as a transient species in the first
12 h after selenate introduction, Se
0
also
occurred as a minor species, and the major accumulated form was alkyl
selenide. Thus, in the present experimental conditions, selenate mostly
follows an assimilatory pathway and the reduction
pathway is not activated upon selenate exposure. These results show
that
R. metallidurans
CH34 may be suitable for the
remediation of selenite-, but not selenate-, contaminated
environments.
LuxS-Based Signaling Affects
Streptococcus mutans
Biofilm Formation
Authors: Yoshida Akihiro , Ansai Toshihiro , Takehara Tadamichi , Kuramitsu Howard K. 
Published: May 2005

ABSTRACT

Streptococcus mutans
is implicated as a major etiological agent in human dental caries, and one of the important virulence properties of this organism is its ability to form biofilms (dental plaque) on tooth surfaces. We examined the role of autoinducer-2 (AI-2) on
S. mutans
biofilm formation by constructing a GS-5
luxS
-null mutant. Biofilm formation by the
luxS
mutant in 0.5% sucrose defined medium was found to be markedly attenuated compared to the wild type. Scanning electron microscopy also revealed that biofilms of the
luxS
mutant formed larger clumps in sucrose medium compared to the parental strain. Therefore, the expression of glucosyltransferase genes was examined and the
gtfB
and
gtfC
genes, but not the
gtfD
gene, in the
luxS
mutant were upregulated in the mid-log growth phase. Furthermore, we developed a novel two-compartment system to monitor AI-2 production by oral streptococci and periodontopathic bacteria. The biofilm defect of the
luxS
mutant was complemented by strains of
S. gordonii
,
S. sobrinus
, and
S. anginosus
; however, it was not complemented by
S. oralis
,
S. salivarius
, or
S. sanguinis
. Biofilm formation by the
luxS
mutant was also complemented by
Porphyromonas gingivalis
381 and
Actinobacillus actinomycetemcomitans
Y4 but not by a
P. gingivalis luxS
mutant. These results suggest that the regulation of the glucosyltransferase genes required for sucrose-dependent biofilm formation is regulated by AI-2. Furthermore, these results provide further confirmation of previous proposals that quorum sensing via AI-2 may play a significant role in oral biofilm formation.
Reduced Genetic Variation Occurs among Genes of the Highly Clonal Plant Pathogen
Xanthomonas axonopodis
pv. vesicatoria, Including the Effector Gene
avrBs2
Authors: Wichmann Gale , Ritchie David , Kousik C. S. , Bergelson Joy 
Published: May 2005

ABSTRACT

The bacterial plant pathogen
Xanthomonas axonopodis
pv. vesicatoria, also known as
Xanthomonas campestris
pv. vesicatoria group A, is the causal agent of bacterial spot in pepper and tomato. In order to test different models that may explain the coevolution of
avrBs2
with its host plants, we sequenced
avrBs2
and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55
X. axonopodis
pv. vesicatoria strains collected from diseased peppers. We found an extreme lack of genetic variation among all
X. axonopodis
pv. vesicatoria genomic loci (average nucleotide diversity, π = 9.1 × 10
−5
), including
avrBs2
. This lack of diversity is consistent with
X. axonopodis
pv. vesicatoria having undergone a recent population bottleneck and/or selective sweep followed by population expansion. Coalescent analysis determined that approximately 1.4 × 10
4
to 7.16 × 10
4
bacterial generations have passed since the most recent common ancestor (MRCA) of the current
X. axonopodis
pv. vesicatoria population. Assuming a range of 50 to 500 bacterial generations per year, only 28 to 1,432 years have passed since the MRCA. This time frame coincides with human intervention with the pathogen's host plants, from domestication to modern agricultural practices. Examination of 19 mutated (loss-of-function)
avrBs2
alleles detected nine classes of mutations. All mutations affected protein coding, while no synonymous changes were found. The nature of at least one of the
avrBs2
mutations suggests that it may be possible to observe one stage of an evolutionary arms race as
X. axonopodis
pv. vesicatoria responds to selection pressure to alter
avrBs2
to escape host plant resistance.
Distribution of Genes for Synthesis of Trehalose and Mannosylglycerate in
Thermus
spp. and Direct Correlation of These Genes with Halotolerance
Authors: Alarico Susana , Empadinhas Nuno , Simões Catarina , Silva Zélia , Henne Anke , Mingote Ana , Santos Helena , da Costa Milton S. 
Published: May 2005

ABSTRACT

In this study we correlate the presence of genes leading to the synthesis of trehalose and mannosylglycerate (MG) in 17 strains of the genus
Thermus
with the ability of the strains to grow and accumulate these compatible solutes in a defined medium containing NaCl. The two sets of genes, namely,
otsA
/
otsB
for the synthesis of trehalose and
mpgS
/
mpgP
for the synthesis of MG, were necessary for the growth of
Thermus thermophilus
in a defined medium containing up to 6% NaCl. Strains lacking a complete
otsA
gene did not grow in defined medium containing >2% NaCl. One strain of
T. thermophilus
lacking the genes for the synthesis of MG did not grow in a medium with >1% NaCl. We did not identify any of these genes in the type strains of the other seven species of
Thermus
, and none of those strains grew in defined medium with 1% NaCl. The results strongly indicate that the combined accumulation of trehalose and MG is required for optimal osmotic adjustment.
Variation in Acid Resistance among Shiga Toxin-Producing Clones of Pathogenic
Escherichia coli
Authors: Large Teresa M. , Walk Seth T. , Whittam Thomas S. 
Published: May 2005

ABSTRACT

Pathogenic strains of
Escherichia coli
, such as
E. coli
O157:H7, have a low infectious dose and an ability to survive in acidic foods. These bacteria have evolved at least three distinct mechanisms of acid resistance (AR), including two amino acid decarboxylase-dependent systems (arginine and glutamate) and a glucose catabolite-repressed system. We quantified the survival rates for each AR mechanism separately in clinical isolates representing three groups of Shiga toxin-producing
E. coli
(STEC) clones (O157:H7, O26:H11/O111:H8, and O121:H19) and six commensal strains from ECOR group A. Members of the STEC clones were not significantly more acid resistant than the commensal strains when analyzed using any individual AR mechanism. The glutamate system provided the best protection in a highly acidic environment for all groups of isolates (<0.1 log reduction in CFU/ml per hour at pH 2.0). Under these conditions, there was notable variation in survival rates among the 30 O157:H7 strains, which depended in part on Mg
2+
concentration. The arginine system provided better protection at pH 2.5, with a range of 0.03 to 0.41 log reduction per hour, compared to the oxidative system, with a range of 0.13 to 0.64 log reduction per hour. The average survival rate for the O157:H7 clonal group was significantly less than that of the other STEC clones in the glutamate and arginine systems and significantly less than that of the O26/O111 clone in the oxidative system, indicating that this clonal group is not exceptionally acid resistant with these specific mechanisms.
Succession of Internal Sulfur Cycles and Sulfur-Oxidizing Bacterial Communities in Microaerophilic Wastewater Biofilms
Authors: Okabe Satoshi , Ito Tsukasa , Sugita Kenichi , Satoh Hisashi 
Published: May 2005

ABSTRACT

The succession of sulfur-oxidizing bacterial (SOB) community structure and the complex internal sulfur cycle occurring in wastewater biofilms growing under microaerophilic conditions was analyzed by using a polyphasic approach that employed 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization, microelectrode measurements, and standard batch and reactor experiments. A complete sulfur cycle was established via S
0
accumulation within 80 days in the biofilms in replicate. This development was generally split into two phases, (i) a sulfur-accumulating phase and (ii) a sulfate-producing phase. In the first phase (until about 40 days), since the sulfide production rate (sulfate-reducing activity) exceeded the maximum sulfide-oxidizing capacity of SOB in the biofilms, H
2
S was only partially oxidized to S
0
by mainly
Thiomicrospira denitirificans
with NO
3
−
as an electron acceptor, leading to significant accumulation of S
0
in the biofilms. In the second phase, the SOB populations developed further and diversified with time. In particular, S
0
accumulation promoted the growth of a novel strain, strain SO07, which predominantly carried out the oxidation of S
0
to SO
4
2−
under oxic conditions, and
Thiothrix
sp. strain CT3. In situ hybridization analysis revealed that the dense populations of
Thiothrix
(ca. 10
9
cells cm
−3
) and strain SO07 (ca. 10
8
cells cm
−3
) were found at the sulfur-rich surface (100 μm), while the population of
Thiomicrospira denitirificans
was distributed throughout the biofilms with a density of ca. 10
7
to 10
8
cells cm
−3
. Microelectrode measurements revealed that active sulfide-oxidizing zones overlapped the spatial distributions of different phylogenetic SOB groups in the biofilms. As a consequence, the sulfide-oxidizing capacities of the biofilms became high enough to completely oxidize all H
2
S produced by SRB to SO
4
2−
in the second phase, indicating establishment of the complete sulfur cycle in the biofilms.
New Resistance Mechanism in
Helicoverpa armigera
Threatens Transgenic Crops Expressing
Bacillus thuringiensis
Cry1Ac Toxin
Authors: Gunning Robin V. , Dang Ho T. , Kemp Fred C. , Nicholson Ian C. , Moores Graham D. 
Published: May 2005

ABSTRACT

In Australia, the cotton bollworm,
Helicoverpa armigera
, has a long history of resistance to conventional insecticides. Transgenic cotton (expressing the
Bacillus thuringiensis
toxin Cry1Ac) has been grown for
H. armigera
control since 1996. It is demonstrated here that a population of Australian
H. armigera
has developed resistance to Cry1Ac toxin (275-fold). Some 70% of resistant
H. armigera
larvae were able to survive on Cry1Ac transgenic cotton (Ingard) The resistance phenotype is inherited as an autosomal semidominant trait. Resistance was associated with elevated esterase levels, which cosegregated with resistance. In vitro studies employing surface plasmon resonance technology and other biochemical techniques demonstrated that resistant strain esterase could bind to Cry1Ac protoxin and activated toxin. In vivo studies showed that Cry1Ac-resistant larvae fed Cy1Ac transgenic cotton or Cry1Ac-treated artificial diet had lower esterase activity than non-Cry1Ac-fed larvae. A resistance mechanism in which esterase sequesters Cry1Ac is proposed.
Quantitative Analysis of Group II Intron Expression and Splicing inLactococcus lactis
Authors: Chen Yuqing , Klein Joanna R. , McKay Larry L. , Dunny Gary M. 
Published: May 2005

ABSTRACTThe group II intron Ll.ltrB is found within theltrBrelaxase gene of the conjugative element pRS01 inLactococcus lactis. Precise splicing of the intron is essential for pRS01 transfer. The transcription regulation and in vivo splicing activity of Ll.ltrB have not been investigated thoroughly inL. lactisin the natural pRS01 context. We developed absolute quantitative real-time reverse transcription-PCR assays to quantify RNA levels of the 5′ exon (ltrBE1) and the spliced relaxase (ltrB) and intron-encoded protein (ltrA) genes, as well as Ll.ltrB splicing activity under different physiological conditions. The mRNA levels for the ATP-binding protein OppD were assayed for comparison to theltrBtranscripts. TheoppDmRNA ranged from 10- to 10,000-fold higher thanltrBregion genes.ltrBE1expression was growth-phase dependent. The mRNA level ofltrAwas almost constant during all growth phases and in all media tested. Ll.ltrB in vivo splicing activity ranged from (6.5 ± 2.1)% to (22.1 ± 8.0)%. Acid challenge significantly decreased bothltrBregion mRNA levels and intron splicing activity. The presence of recipient cells, different mating environments, and temperature stress had no significant effects on expression and splicing. Western blotting showed that the level of LtrB protein expressed from an intronlessltrBgene was much higher (about 20-fold) than the level of protein expressed from an intron-containing construct. Interestingly, LtrB protein showed a tendency to function incison itsoriTtarget. The low level ofltrBtranscript and relatively inefficient splicing of the intron may limit Ll.ltrB mobility and dissemination in nature.
Architecture of a Nascent
Sphingomonas
sp. Biofilm under Varied Hydrodynamic Conditions
Authors: Venugopalan V. P. , Kuehn M. , Hausner M. , Springael D. , Wilderer P. A. , Wuertz S. 
Published: May 2005

ABSTRACT

The architecture of a
Sphingomonas
biofilm was studied during early phases of its formation, using strain L138, a
gfp
-tagged derivative of
Sphingomonas
sp. strain LB126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. Spatial and temporal distribution of cells and exopolymer secretions (EPS) within the biofilm, development of microcolonies under flow conditions representing varied Reynolds numbers, and changes in diffusion length with reference to EPS production were studied by sequential sacrificing of biofilms grown in multichannel flow cells and by time-lapse confocal imaging. The area of biofilm in terms of microscopic images required to ensure representative sampling varied by an order of magnitude when area of cell coverage (2 × 10
5
μm
2
) or microcolony size (1 × 10
6
μm
2
) was the biofilm parameter under investigation. Hence, it is necessary to establish the inherent variability of any biofilm metric one is attempting to quantify.
Sphingomonas
sp. strain L138 biofilm architecture consisted of microcolonies and extensive water channels. Biomass and EPS distribution were maximal at 8 to 9 μm above the substratum, with a high void fraction near the substratum. Time-lapse confocal imaging and digital image analysis showed that growth of the microcolonies was not uniform: adjacently located colonies registered significant growth or no growth at all. Microcolonies in the biofilm had the ability to move across the attachment surface as a unit, irrespective of fluid flow direction, indicating that movement of microcolonies is an inherent property of the biofilm. Width of water channels decreased as EPS production increased, resulting in increased diffusion distances in the biofilm. Changing hydrodynamic conditions (Reynolds numbers of 0.07, 52, and 87) had no discernible influence on the characteristics of microcolonies (size, shape, or orientation with respect to flow) during the first 24 h of biofilm development. Inherent factors appear to have overriding influence, vis-à-vis environmental factors, on early stages of microcolony development under these laminar flow conditions.
Distribution and Stability of Sulfate-Reducing Prokaryotic and Hydrogenotrophic Methanogenic Assemblages in Nutrient-Impacted Regions of the Florida Everglades
Authors: Castro Hector , Newman Susan , Reddy K. R. , Ogram Andrew 
Published: May 2005

ABSTRACT

Although the influence of phosphorus loading on the Everglades ecosystem has received a great deal of attention, most research has targeted macro indicators, such as those based on vegetation or fauna, or chemical and physical parameters involved in biogeochemical cycles. Fewer studies have addressed the role of microorganisms, and these have mainly targeted gross informative parameters such as microbial biomass, enzymatic activities, and microbial enumerations. The objectives of this study were to characterize the dynamics of sulfate-reducing and methanogenic assemblages using terminal restriction fragment length polymorphism (T-RFLP) targeting the dissimilatory sulfite reductase (
dsrA
) and methyl coenzyme M reductase (
mcrA
) genes, respectively, and assess the impact of nutrient enrichment on microbial assemblages in the northern Everglades. T-RFLP combined with principal component analysis was a powerful technique to discriminate between soils from sites with eutrophic, transitional, and oligotrophic nutrient concentrations.
dsrA
T-RFLP provided a higher level of discrimination between the three sites.
mcrA
was a relatively weaker system to distinguish between sites, since it could not categorically discriminate between eutrophic and transition soil samples, but may be useful as an early indicator of phosphorus loading which is altering hydrogenotrophic methanogenic community in the transition zones, making them more similar to eutrophic zones. Clearly, targeting a combination of different microbial communities provides greater insight into the functioning of this ecosystem and provides useful information for understanding the relationship between eutrophication effects and microbial assemblages.
Combined Approach for Characterization of Uncultivated Magnetotactic Bacteria from Various Aquatic Environments
Authors: Flies Christine B. , Peplies Jörg , Schüler Dirk 
Published: May 2005

ABSTRACT

Both magnetic collection and “race track” purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the
Alphaproteobacteria
. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the
Nitrospira
phylum, displaying 91% 16S rRNA sequence similarity to “
Magnetobacterium bavaricum
.” In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus
Magnetospirillum
which had not routinely been isolated in pure culture before were obtained.
Sensitivity of Planktonic and Biofilm-Associated
Salmonella
spp. to Ionizing Radiation
Authors: Niemira Brendan A. , Solomon Ethan B. 
Published: May 2005

ABSTRACT

Salmonella enterica
forms biofilms that are relatively resistant to chemical sanitizing treatments. Ionizing radiation has been used to inactivate
Salmonella
on a variety of foods and contact surfaces, but the relative efficacy of the process against biofilm-associated cells versus free-living planktonic cells is not well documented. The radiation sensitivity of planktonic or biofilm-associated cells was determined for three food-borne-illness-associated isolates of
Salmonella
. Biofilms were formed on sterile glass slides in a coincubation apparatus, using inoculated tryptic soy broth, incubated at 37°C for 48 h. Resulting biofilms were 18 to 24 μm in height as determined by confocal scanning laser microscopy. The planktonic and biofilm cultures were gamma irradiated to doses of 0.0 (control), 0.5, 1.0, 1.5, 2.0 and 2.5 kGy. The
D
10
value (the dose of radiation required to reduce a population by 1 log
10
, or 90%) was calculated for each isolate-culture based on surviving populations at each radiation dose. The
D
10
values of
S. enterica
serovar Anatum were not significantly (
P
< 0.05) different for biofilm-associated (0.645 kGy) and planktonic (0.677 kGy) cells. In contrast, the biofilm-associated cells of
S. enterica
serovar Stanley were significantly more sensitive to ionizing radiation than the respective planktonic cells, with
D
10
values of 0.531 and 0.591 kGy, respectively.
D
10
values of
S. enterica
serovar Enteritidis were similarly reduced for biofilm-associated (0.436 kGy) versus planktonic (0.535 kGy) cells. The antimicrobial efficacy of ionizing radiation is therefore preserved or enhanced in treatment of biofilm-associated bacteria.
Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes
Authors: Hobel Cédric F. V. , Marteinsson Viggó T. , Hreggvidsson Gudmundur Ó. , Kristjánsson Jakob K. 
Published: May 2005

ABSTRACT
The microbial diversity of intertidal hot springs on the seashore of northwest Iceland was examined by combining directed in situ enrichments, artificial support colonization, and mat sampling. Analysis of 16S rRNA genes revealed the presence of clones related to both marine and terrestrial, thermophilic, mesophilic, and psychrophilic microorganisms scattered among 11 bacterial divisions. No archaea were found. The species composition of the enrichments was affected by the length of the hot periods experienced at low tide and was very different from those found in the biomass. A total of 36 chitinase genes were detected by molecular screening of the samples with degenerate primers for glycoside hydrolase family 18. The chitinase gene diversity was at least twofold higher in the enrichment samples than in the controls, indicating that a much higher diversity of hydrolytic genes can be accessed with this approach.