bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Correlation between Rates of Anaerobic Respiration and Levels of mRNA for Key Respiratory Genes in
Geobacter sulfurreducens
Authors: Chin Kuk-Jeong , Esteve-Núñez Abraham , Leang Ching , Lovley Derek R. 
Published: September 2004

ABSTRACT

The predominance of
Geobacter
species in environments in which Fe(III) reduction is important has suggested that Fe(III) reduction rates might be estimated in
Geobacter
-dominated environments by assessing in situ activity with molecular techniques. To determine whether mRNA levels of key respiratory genes might be correlated with respiration rates in
Geobacter sulfurreducens
, studies were conducted with fumarate as the electron acceptor and acetate as the limiting electron donor in anaerobic continuous cultures. Levels of mRNA for a fumarate reductase gene,
frdA
, quantified by real-time reverse transcription-PCR were directly correlated with fumarate reduction rates. In similar studies with Fe(III) as the electron acceptor, mRNA levels for
omcB
, a gene for an outer membrane
c
-type cytochrome involved in Fe(III) reduction, were positively correlated with Fe(III) reduction rates. Levels of mRNA for
frdA
and
omcB
were also positively correlated with fumarate and Fe(III) reduction rates, respectively, when growth was limited by the availability of fumarate or Fe(III), but mRNA levels were higher than in acetate-limited cultures. Levels of mRNA for
omcC
, which encodes a
c
-type cytochrome highly similar to OmcB but not necessary for Fe(III) reduction, followed patterns different than those of
omcB
. This agrees with the previous finding that OmcC is not involved in Fe(III) reduction and suggests that changes in mRNA levels of
omcB
are related to its role in Fe(III) reduction. These results demonstrate that mRNA levels for respiratory genes might be used to estimate in situ Fe(III) reduction rates in
Geobacter
-dominated environments but suggest that information on environmental conditions and/or the metabolic state of
Geobacter
species is also required for accurate rate estimates.
Cell Density-Dependent Gene Contributes to Efficient Seed Colonization by
Pseudomonas putida
KT2440
Authors: Espinosa-Urgel Manuel , Ramos Juan-Luis 
Published: September 2004

ABSTRACT

We have characterized the expression pattern of a gene,
ddcA
, involved in initial colonization of corn seeds by
Pseudomonas putida
KT2440. The
ddcA
gene codes for a putative membrane polypeptide belonging to a family of conserved proteins of unknown function. Members of this family are widespread among prokaryotes and include the products of a
Salmonella enterica
serovar Typhimurium gene expressed during invasion of macrophages and
psiE
, an
Escherichia coli
phosphate starvation-inducible gene. Although its specific role is undetermined, the presence of
ddcA
in multicopy restored the seed adhesion capacity of a KT2440
ddcA
mutant. Expression of
ddcA
is growth phase regulated, being maximal at the beginning of stationary phase. It is independent of RpoS, nutrient depletion, or phosphate starvation, and it is not the result of changes in the medium pH during growth. Expression of
ddcA
is directly dependent on cell density, being also stimulated by the addition of conditioned medium and of seed exudates. This is the first evidence suggesting the existence of a quorum-sensing system in
P. putida
KT2440. The potential implication of such a signaling process in seed adhesion and colonization by the bacterium is discussed.
Acidified Litter Benefits the Intestinal Flora Balance of Broiler Chickens
Authors: Garrido Margarita Novoa , Skjervheim Magne , Oppegaard Hanne , Sørum Henning 
Published: September 2004

ABSTRACT

The alterations in the balance of the normal intestinal bacterial flora of chickens exposed to acidified wood-derived litter were analyzed and compared to those of a control group exposed to nonacidified litter. A total of 1,728 broilers were divided into two groups, with six replicates in each. One group was exposed to dry wood-derived litter, and the other was exposed to dry wood-derived litter sprayed with a mixture of sodium lignosulfonate, formic acid, and propionic acid. At five different times, five chickens from each pen were killed and the intestinal contents from ileum and caeca were collected. The samples were diluted and plated onto selective media to identify coliforms,
Lactobacillus
spp.,
Clostridium perfringens
, and
Enterococcus
spp. Covariance analysis of bacterial counts showed significantly lower counts for
C. perfringens
in the caeca and the ileum and for
Enterococcus
spp. and
Lactobacillus
spp. in the ileum in chickens exposed to the acidified litter.
Lactobacillus
spp. showed significantly higher counts in the caeca in chickens exposed to acidified litter. There was no difference between the two litters with regard to coliforms in the ileum and the caeca or to
Enterococcus
spp. in the caeca. The study shows that exposing the chickens to acidified litter lowers the intestinal bacterial number, especially in the ileum, without negative consequences for the chicken's health or performance. Of special interest are the lower counts of
C. perfringens
and
Enterococcus
spp. that might reduce the risk of developing clinical or subclinical necrotic enteritis and growth depression.
Nonmarine Crenarchaeol in Nevada Hot Springs
Authors: Pearson A. , Huang Z. , Ingalls A. E. , Romanek C. S. , Wiegel J. , Freeman K. H. , Smittenberg R. H. , Zhang C. L. 
Published: September 2004

ABSTRACT

Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids of the
Crenarchaeota
. The structurally unusual GDGT crenarchaeol has been proposed as a taxonomically specific biomarker for the marine planktonic group I archaea. It is found ubiquitously in the marine water column and in sediments. In this work, samples of microbial community biomass were obtained from several alkaline and neutral-pH hot springs in Nevada, United States. Lipid extracts of these samples were analyzed by high-performance liquid chromatography-mass spectrometry and by gas chromatography-mass spectrometry. Each sample contained GDGTs, and among these compounds was crenarchaeol. The distribution of archaeal lipids in Nevada hot springs did not appear to correlate with temperature, as has been observed in the marine environment. Instead, a significant correlation with the concentration of bicarbonate was observed. Archaeal DNA was analyzed by denaturing gradient gel electrophoresis. All samples contained 16S rRNA gene sequences which were more strongly related to thermophilic crenarchaeota than to
Cenarchaeum symbiosum
, a marine nonthermophilic crenarchaeon. The occurrence of crenarchaeol in environments containing sequences affiliated with thermophilic crenarchaeota suggests a wide phenotypic distribution of this compound. The results also indicate that crenarchaeol can no longer be considered an exclusive biomarker for marine species.
Molecular Characterization of CcpA and Involvement of This Protein in Transcriptional Regulation of Lactate Dehydrogenase and Pyruvate Formate-Lyase in the Ruminal Bacterium
Streptococcus bovis
Authors: Asanuma Narito , Yoshii Takahiro , Hino Tsuneo 
Published: September 2004

ABSTRACT

A
ccpA
gene that encodes global catabolite control protein A (CcpA) in
Streptococcus bovis
was identified and characterized, and the involvement of CcpA in transcriptional control of a gene (
ldh
) encoding lactate dehydrogenase (LDH) and a gene (
pfl
) encoding pyruvate formate-lyase (PFL) was examined. The
ccpA
gene was shown to be transcribed as a monocistronic operon. A catabolite-responsive element (
cre
) was found in the promoter region of
ccpA
, suggesting that
ccpA
transcription in
S. bovis
is autogenously regulated. CcpA required HPr that was phosphorylated at the serine residue at position 46 (HPr-[Ser-P]) for binding to the
cre
site, but glucose 6-phosphate, fructose 1,6-bisphosphate, and NADP had no effect on binding. Diauxic growth was observed when
S. bovis
was grown in a medium containing glucose and lactose, but it disappeared when
ccpA
was disrupted, which indicates that CcpA is involved in catabolite repression in
S. bovis
. The level of
ccpA
mRNA was higher when cells were grown on glucose than when they were grown on lactose, which was in line with the level of
ldh
mRNA. When cells were grown on glucose, the
ldh
mRNA level was lower but the
pfl
mRNA level was higher in a
ccpA
-disrupted mutant than in the parent strain, which suggests that
ldh
transcription is enhanced and
pfl
transcription is suppressed by CcpA. The
ccpA
-disrupted mutant produced less lactate and more formate than the parent, probably because the mutant had reduced LDH activity and elevated PFL activity. In the upper region of both
ldh
and
pfl
, a
cre
-like sequence was found, suggesting that the complex consisting of CcpA and HPr-[Ser-P] binds to the possible
cre
sites. Thus, CcpA appears to be involved in the global regulation of sugar utilization in
S. bovis
.
Combined Use of Cultivation-Dependent and Cultivation-Independent Methods Indicates that Members of Most Haloarchaeal Groups in an Australian Crystallizer Pond Are Cultivable
Authors: Burns D. G. , Camakaris H. M. , Janssen P. H. , Dyall-Smith M. L. 
Published: September 2004

ABSTRACT

Haloarchaea are the dominant microbial flora in hypersaline waters with near-saturating salt levels. The haloarchaeal diversity of an Australian saltern crystallizer pond was examined by use of a library of PCR-amplified 16S rRNA genes and by cultivation. High viable counts (10
6
CFU/ml) were obtained on solid media. Long incubation times (≥8 weeks) appeared to be more important than the medium composition for maximizing viable counts and diversity. Of 66 isolates examined, all belonged to the family
Halobacteriaceae
, including members related to species of the genera
Haloferax
,
Halorubrum
, and
Natronomonas
. In addition, isolates belonging to a novel group (the ADL group), previously detected only as 16S rRNA genes in an Antarctic hypersaline lake (Deep Lake), were cultivated for the first time. The 16S rRNA gene library identified the following five main groups:
Halorubrum
groups 1 and 2 (49%), the SHOW (square haloarchaea of Walsby) group (33%), the ADL group (16%), and the
Natronomonas
group (2%). There were two significant differences between the organisms detected in cultivation and 16S rRNA sequence results. Firstly,
Haloferax
spp. were frequently isolated on plates (15% of all isolates) but were not detected in the 16S rRNA sequences. Control experiments indicated that a bias against
Haloferax
sequences in the generation of the 16S rRNA gene library was unlikely, suggesting that
Haloferax
spp. readily form colonies, even though they were not a dominant group. Secondly, while the 16S rRNA gene library identified the SHOW group as a major component of the microbial community, no isolates of this group were obtained. This inability to culture members of the SHOW group remains an outstanding problem in studying the ecology of hypersaline environments.
Role of Hexose Transport in Control of Glycolytic Flux in
Saccharomyces cerevisiae
Authors: Elbing Karin , Larsson Christer , Bill Roslyn M. , Albers Eva , Snoep Jacky L. , Boles Eckhard , Hohmann Stefan , Gustafsson Lena 
Published: September 2004

ABSTRACT

The yeast
Saccharomyces cerevisiae
predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type
S. cerevisiae
does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in
S. cerevisiae
and will provide new tools for the control of industrial fermentations.
Comparison of Fluorescence Microscopy and Solid-Phase Cytometry Methods for Counting Bacteria in Water
Authors: Lisle John T. , Hamilton Martin A. , Willse Alan R. , McFeters Gordon A. 
Published: September 2004

ABSTRACT

Total direct counts of bacterial abundance are central in assessing the biomass and bacteriological quality of water in ecological and industrial applications. Several factors have been identified that contribute to the variability in bacterial abundance counts when using fluorescent microscopy, the most significant of which is retaining an adequate number of cells per filter to ensure an acceptable level of statistical confidence in the resulting data. Previous studies that have assessed the components of total-direct-count methods that contribute to this variance have attempted to maintain a bacterial cell abundance value per filter of approximately 10
6
cells filter
−1
. In this study we have established the lower limit for the number of bacterial cells per filter at which the statistical reliability of the abundance estimate is no longer acceptable. Our results indicate that when the numbers of bacterial cells per filter were progressively reduced below 10
5
, the microscopic methods increasingly overestimated the true bacterial abundance (range, 15.0 to 99.3%). The solid-phase cytometer only slightly overestimated the true bacterial abundances and was more consistent over the same range of bacterial abundances per filter (range, 8.9 to 12.5%). The solid-phase cytometer method for conducting total direct counts of bacteria was less biased and performed significantly better than any of the microscope methods. It was also found that microscopic count data from counting 5 fields on three separate filters were statistically equivalent to data from counting 20 fields on a single filter.
Heads or Tails: Host-Parasite Interactions in the
Drosophila-Wolbachia
System
Authors: Veneti Zoe , Clark Michael E. , Karr Timothy L. , Savakis Charalambos , Bourtzis Kostas 
Published: September 2004

ABSTRACT

Wolbachia
strains are endosymbiotic bacteria typically found in the reproductive tracts of arthropods. These bacteria manipulate host reproduction to ensure maternal transmission. They are usually transmitted vertically, so it has been predicted that they have evolved a mechanism to target the host's germ cells during development. Through cytological analysis we found that
Wolbachia
strains display various affinities for the germ line of
Drosophila
. Different
Wolbachia
strains show posterior, anterior, or cortical localization in
Drosophila
embryos, and this localization is congruent with the classification of the organisms based on the
wsp
(
Wolbachia
surface protein) gene sequence. This embryonic distribution pattern is established during early oogenesis and does not change until late stages of embryogenesis. The posterior and anterior localization of
Wolbachia
resembles that of
oskar
and
bicoid
mRNAs, respectively, which define the anterior-posterior axis in the
Drosophila
oocyte. By comparing the properties of a single
Wolbachia
strain in different host backgrounds and the properties of different
Wolbachia
strains in the same host background, we concluded that bacterial factors determine distribution, while bacterial density seems to be limited by the host. Possible implications concerning cytoplasmic incompatibility and evolution of strains are discussed.
Microautoradiographic Study of
Rhodocyclus
-Related Polyphosphate-Accumulating Bacteria in Full-Scale Enhanced Biological Phosphorus Removal Plants
Authors: Kong Yunhong , Nielsen Jeppe Lund , Nielsen Per Halkjær 
Published: September 2004

ABSTRACT

The ecophysiology of uncultured
Rhodocyclus
-related polyphosphate-accumulating organisms (PAO) present in three full-scale enhanced biological phosphorus removal (EBPR) activated sludge plants was studied by using microautoradiography combined with fluorescence in situ hybridization. The investigations showed that these organisms were present in all plants examined and constituted 5 to 10, 10 to 15, and 17 to 22% of the community biomass. The behavior of these bacteria generally was consistent with the biochemical models proposed for PAO, based on studies of lab-scale investigations of enriched and often unknown PAO cultures.
Rhodocyclus
-related PAO were able to accumulate short-chain substrates, including acetate, propionate, and pyruvate, under anaerobic conditions, but they could not assimilate many other low-molecular-weight compounds, such as ethanol and butyrate. They were able to assimilate two substrates (e.g., acetate and propionate) simultaneously. Leucine and thymidine could not be assimilated as sole substrates and could only be assimilated as cosubstrates with acetate, perhaps serving as N sources. Glucose could not be assimilated by the
Rhodocyclus
-related PAO, but it was easily fermented in the sludge to products that were subsequently consumed. Glycolysis, and not the tricarboxylic acid cycle, was the source that provided the reducing power needed by the
Rhodocyclus
-related PAO to form the intracellular polyhydroxyalkanoate storage compounds during anaerobic substrate assimilation. The
Rhodocyclus
-related PAO were able to take up orthophosphate and accumulate polyphosphate when oxygen, nitrate, or nitrite was present as an electron acceptor. Furthermore, in the presence of acetate growth was sustained by using oxygen, as well as nitrate or nitrite, as an electron acceptor. This strongly indicates that
Rhodocyclus
-related PAO were able to denitrify and thus played a role in the denitrification occurring in full-scale EBPR plants.
Construction of a Xylan-Fermenting Yeast Strain through Codisplay of Xylanolytic Enzymes on the Surface of Xylose-Utilizing
Saccharomyces cerevisiae
Cells
Authors: Katahira Satoshi , Fujita Yasuya , Mizuike Atsuko , Fukuda Hideki , Kondo Akihiko 
Published: September 2004

ABSTRACT

Hemicellulose is one of the major forms of biomass in lignocellulose, and its essential component is xylan. We used a cell surface engineering system based on α-agglutinin to construct a
Saccharomyces cerevisiae
yeast strain codisplaying two types of xylan-degrading enzymes, namely, xylanase II (XYNII) from
Trichoderma reesei
QM9414 and β-xylosidase (XylA) from
Aspergillus oryzae
NiaD300, on the cell surface. In a high-performance liquid chromatography analysis, xylose was detected as the main product of the yeast strain codisplaying XYNII and XylA, while xylobiose and xylotriose were detected as the main products of a yeast strain displaying XYNII on the cell surface. These results indicate that xylan is sequentially hydrolyzed to xylose by the codisplayed XYNII and XylA. In a further step toward achieving the simultaneous saccharification and fermentation of xylan, a xylan-utilizing
S. cerevisiae
strain was constructed by codisplaying XYNII and XylA and introducing genes for xylose utilization, namely, those encoding xylose reductase and xylitol dehydrogenase from
Pichia stipitis
and xylulokinase from
S. cerevisiae
. After 62 h of fermentation, 7.1 g of ethanol per liter was directly produced from birchwood xylan, and the yield in terms of grams of ethanol per gram of carbohydrate consumed was 0.30 g/g. These results demonstrate that the direct conversion of xylan to ethanol is accomplished by the xylan-utilizing
S. cerevisiae
strain.
Shewanella oneidensis
MR-1 Restores Menaquinone Synthesis to a Menaquinone-Negative Mutant
Authors: Myers Charles R. , Myers Judith M. 
Published: September 2004

ABSTRACT

The mechanisms underlying the use of insoluble electron acceptors by metal-reducing bacteria, such as
Shewanella oneidensis
MR-1, are currently under intensive study. Current models for shuttling electrons across the outer membrane (OM) of MR-1 include roles for OM cytochromes and the possible excretion of a redox shuttle. While MR-1 is able to release a substance that restores the ability of a menaquinone (MK)-negative mutant, CMA-1, to reduce the humic acid analog anthraquinone-2,6-disulfonate (AQDS), cross-feeding experiments conducted here showed that the substance released by MR-1 restores the growth of CMA-1 on several soluble electron acceptors. Various strains derived from MR-1 also release this substance; these include mutants lacking the OM cytochromes OmcA and OmcB and the OM protein MtrB. Even though strains lacking OmcB and MtrB cannot reduce Fe(III) or AQDS, they still release a substance that restores the ability of CMA-1 to use MK-dependent electron acceptors, including AQDS and Fe(III). Quinone analysis showed that this released substance restores MK synthesis in CMA-1. This ability to restore MK synthesis in CMA-1 explains the cross-feeding results and challenges the previous hypothesis that this substance represents a redox shuttle that facilitates metal respiration.
Comparison of Atomic Force Microscopy Interaction Forces between Bacteria and Silicon Nitride Substrata for Three Commonly Used Immobilization Methods
Authors: Vadillo-Rodríguez Virginia , Busscher Henk J. , Norde Willem , de Vries Joop , Dijkstra René J. B. , Stokroos Ietse , van der Mei Henny C. 
Published: September 2004

ABSTRACT

Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanometer scale. For AFM, bacterial cells need to be firmly anchored to a substratum surface in order to withstand the friction forces from the silicon nitride tip. Different strategies for the immobilization of bacteria have been described in the literature. This paper compares AFM interaction forces obtained between
Klebsiella terrigena
and silicon nitride for three commonly used immobilization methods, i.e., mechanical trapping of bacteria in membrane filters, physical adsorption of negatively charged bacteria to a positively charged surface, and glutaraldehyde fixation of bacteria to the tip of the microscope. We have shown that different sample preparation techniques give rise to dissimilar interaction forces. Indeed, the physical adsorption of bacterial cells on modified substrata may promote structural rearrangements in bacterial cell surface structures, while glutaraldehyde treatment was shown to induce physicochemical and mechanical changes on bacterial cell surface properties. In general, mechanical trapping of single bacterial cells in filters appears to be the most reliable method for immobilization.