bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Rates of Sulfate Reduction in a Low-Sulfate Hot Spring Microbial Mat Are Driven by a Low Level of Diversity of Sulfate-Respiring Microorganisms
Authors: Dillon Jesse G. , Fishbain Susan , Miller Scott R. , Bebout Brad M. , Habicht Kirsten S. , Webb Samuel M. , Stahl David A. 
Published: June 2007

ABSTRACT

The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this mat community was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and were associated with a
Thermodesulfovibrio
-like population. Reduced activity at greater depths was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation.
A Cyclic AMP Receptor Protein-Regulated Cell-Cell Communication System Mediates Expression of a FecA Homologue in
Stenotrophomonas maltophilia
Authors: Huang Tzu-Pi , Wong Amy C. Lee 
Published: June 2007

ABSTRACT

Stenotrophomonas maltophilia
WR-C possesses an
rpf
/diffusible signal factor (DSF) cell-cell communication system. It produces
cis
-Δ2-11-methyl-dodecenoic acid, a DSF, and seven structural derivatives, which require
rpfF
and
rpfB
for synthesis. Acquisition of iron from the environment is important for bacterial growth as well as the expression of virulence genes. We identified a gene homologous to
fecA
, which encodes a ferric citrate receptor that transports exogenous siderophore ferric citrate from the environment into the bacterial periplasm. Western blot analysis with anti-FecA-His
6
antibody showed that the FecA homologue was induced in the iron-depleted medium supplemented with a low concentration of ferric citrate. Deletion of
rpfF
or
rpfB
resulted in reduced FecA expression compared to the wild type. Synthetic DSF restored FecA expression by the Δ
rpfF
mutant to the wild-type level. Reverse transcription-PCR showed that the
fecA
transcript was decreased in the Δ
rpfF
mutant compared to the wild type. These data suggest that DSF affected the level of
fecA
mRNA. Transposon inactivation of
crp
, which encodes cyclic AMP (cAMP) receptor protein (CRP) resulted in reduced FecA expression and
rpfF
transcript level. Putative CRP binding sites were located upstream of the
rpfF
promoter, indicating that the effect of CRP on FecA is through the
rpf
/DSF pathway and by directly controlling
rpfF
. We propose that CRP may serve as a checkpoint for iron uptake, protease activity, and hemolysis in response to environmental changes such as changes in concentrations of glucose, cAMP, iron, or DSF.
Growth and Mycorrhizal Community Structure ofPinus sylvestrisSeedlings following the Addition of Forest Litter
Authors: Aučina Algis , Rudawska Maria , Leski Tomasz , Skridaila Audrius , Riepšas Edvardas , Iwanski Michal 
Published: June 2007

ABSTRACTWe report the effects of pine and oak litter on species composition and diversity of mycorrhizal fungi colonizing 2-year-oldPinus sylvestrisL. seedlings grown in a bare-root nursery in Lithuania. A layer of pine or oak litter was placed on the surface of the nursery bed soil to mimic natural litter cover. Oak litter amendment appeared to be most favorable for seedling survival, with a 73% survival rate, in contrast to the untreated mineral bed soil (44%). The concentrations of total N, P, K, Ca, and Mg were higher in oak growth medium than in pine growth medium. Relative to the control (pH 6.1), the pH was lower in pine growth medium (5.8) and higher in oak growth medium (6.3). There were also twofold and threefold increases in the C content of growth medium with the addition of pine and oak litter, respectively. Among seven mycorrhizal morphotypes, eight different mycorrhizal taxa were identified:Suillus luteus,Suillus variegatus,Wilcoxina mikolae, aTubersp., aTomentellasp.,Cenococcum geophilum,Amphinema byssoides, and one unidentified ectomycorrhizal symbiont. Forest litter addition affected the relative abundance of mycorrhizal symbionts more than their overall representation. This was more pronounced for pine litter than for oak litter, with 40% and 25% increases in the abundance of suilloid mycorrhizae, respectively. Our findings provide preliminary evidence that changes in the supply of organic matter through litter manipulation may have far-reaching effects on the chemistry of soil, thus influencing the growth and survival of Scots pine seedlings and their mycorrhizal communities.
Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria
Authors: Singh Brajesh K. , Tate Kevin R. , Kolipaka Gokul , Hedley Carolyn B. , Macdonald Catriona A. , Millard Peter , Murrell J. Colin 
Published: June 2007

ABSTRACT

We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (
Pinus radiata
) forests and one shrubland (mainly
Kunzea ericoides
var.
ericoides
) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C
18
PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C
16
PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (
pmoA
) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to
Methylococcus capsulatus
) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.
Impact of Alginate Conditioning Film on Deposition Kinetics of Motile and Nonmotile
Pseudomonas aeruginosa
Strains
Authors: de Kerchove Alexis J. , Elimelech Menachem 
Published: June 2007

ABSTRACT

The initial deposition of bacteria in most aquatic systems is affected by the presence of a conditioning film adsorbed at the liquid-solid interface. Due to the inherent complexity of such films, their impact on bacterial deposition remains poorly defined. The aim of this study was to gain a better understanding of the effect of a conditioning film on the deposition of motile and nonmotile
Pseudomonas aeruginosa
cells in a radial stagnation point flow system. A well-defined alginate film was used as a model conditioning film because of its polysaccharide and polyelectrolyte nature. Deposition experiments under favorable (nonrepulsive) conditions demonstrated the importance of swimming motility for cell transport towards the substrate. The impact of the flagella of motile cells on deposition is dependent on the presence of the conditioning film. We showed that on a clean substrate surface, electrostatic repulsion governs bacterial deposition and the presence of flagella increases cell deposition. However, our results suggest that steric interactions between flagella and extended polyelectrolytes of the conditioning film hinder cell deposition. At a high ionic strength (100 mM), active swimming motility and changes in alginate film structure suppressed the steric barrier and allowed conditions favorable for deposition. We demonstrated that bacterial deposition is highly influenced by cell motility and the structure of the conditioning film, which are both dependent on ionic strength.
Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds
Authors: Fall Saliou , Hamelin Jérôme , Ndiaye Farma , Assigbetse Komi , Aragno Michel , Chotte Jean Luc , Brauman Alain 
Published: June 2007

ABSTRACTIn tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by theActinobacteriaphylum, whereas theFirmicutesandProteobacteriaphyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering ofActinobacteriaphylotypes between the mound and the surrounding soil. TheActinobacteriaclones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by theNocardioidaceaefamily. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.
Cloning of a Novel Aldo-Keto Reductase Gene from
Klebsiella
sp. Strain F51-1-2 and Its Functional Expression in
Escherichia coli
Authors: Jiang Hong , Yang Chao , Qu Hong , Liu Zheng , Fu Q. S. , Qiao Chuanling 
Published: June 2007

ABSTRACT

A soil bacterium capable of metabolizing organophosphorus compounds by reducing the P═S group in the molecules was taxonomically identified as
Klebsiella
sp. strain F51-1-2. The gene involved in the reduction of organophosphorus compounds was cloned from this strain by the shotgun technique, and the deduced protein (named AKR5F1) showed homology to members of the aldo-keto reductase (AKR) superfamily. The intact coding region for AKR5F1 was subcloned into vector pET28a and overexpressed in
Escherichia coli
BL21(DE3). Recombinant His
6
-tagged AKR5F1 was purified in one step using Ni-nitrilotriacetic acid affinity chromatography. Assays for cofactor specificity indicated that reductive transformation of organophosphorus compounds by the recombinant AKR5F1 specifically required NADH. The kinetic constants of the purified recombinant AKR5F1 toward six thion organophosphorus compounds were determined. For example, the

K
m

and
k
cat
values of reductive transformation of malathion by the purified recombinant AKR5F1 are 269.5 ± 47.0 μΜ and 25.7 ± 1.7 min
−1
, respectively. Furthermore, the reductive transformation of organophosphorus compounds can be largely explained by structural modeling.
Frataxin, a Conserved Mitochondrial Protein, in the Hydrogenosome of
Trichomonas vaginalis
Authors: Dolezal Pavel , Dancis Andrew , Lesuisse Emmanuel , Sutak Róbert , Hrdý Ivan , Embley T. Martin , Tachezy Jan 
Published: June 2007

ABSTRACT

Recent data suggest that frataxin plays a key role in eukaryote cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (FeS) cluster biosynthesis. We have now identified a frataxin homologue (
T. vaginalis
frataxin) from the human parasite
Trichomonas vaginalis
. Instead of mitochondria, this unicellular eukaryote possesses hydrogenosomes, peculiar organelles that produce hydrogen but nevertheless share common ancestry with mitochondria.
T. vaginalis
frataxin contains conserved residues implicated in iron binding, and in silico, it is predicted to form a typical α-β sandwich motif. The short N-terminal extension of
T. vaginalis
frataxin resembles presequences that target proteins to hydrogenosomes, a prediction confirmed by the results of overexpression of
T. vaginalis
frataxin in
T. vaginalis
. When expressed in the mitochondria of a frataxin-deficient
Saccharomyces cerevisiae
strain,
T. vaginalis
frataxin partially restored defects in heme and FeS cluster biosynthesis. Although components of heme synthesis or heme-containing proteins have not been found in
T. vaginalis
to date,
T. vaginalis
frataxin was also shown to interact with
S. cerevisiae
ferrochelatase by using a Biacore assay. The discovery of conserved iron-metabolizing pathways in mitochondria and hydrogenosomes provides additional evidence not only of their common evolutionary history, but also of the fundamental importance of this pathway for eukaryotes.
Self-Aggregation of
Cryptococcus neoformans
Capsular Glucuronoxylomannan Is Dependent on Divalent Cations
Authors: Nimrichter Leonardo , Frases Susana , Cinelli Leonardo P. , Viana Nathan B. , Nakouzi Antonio , Travassos Luiz R. , Casadevall Arturo , Rodrigues Marcio L. 
Published: June 2007

ABSTRACT

The capsular components of the human pathogen
Cryptococcus neoformans
are transported to the extracellular space and then used for capsule enlargement by distal growth. It is not clear, however, how the glucuronoxylomannan (GXM) fibers are incorporated into the capsule. In the present study, we show that concentration of
C. neoformans
culture supernatants by ultrafiltration results in the formation of highly viscous films containing pure polysaccharide, providing a novel, nondenaturing, and extremely rapid method to isolate extracellular GXM. The weight-averaged molecular mass of GXM in the film, determined using multiangle laser light scattering, was ninefold smaller than that of GXM purified from culture supernatants by differential precipitation with cetyl trimethyl ammonium bromide (CTAB). Polysaccharides obtained either by ultrafiltration or by CTAB-mediated precipitation showed different reactivities with GXM-specific monoclonal antibodies. Viscosity analysis associated with inductively coupled plasma mass spectrometry and measurements of zeta potential in the presence of different ions implied that polysaccharide aggregation was a consequence of the interaction between the carboxyl groups of glucuronic acid and divalent cations. Consistent with this observation, capsule enlargement in living
C. neoformans
cells was influenced by Ca
2+
in the culture medium. These results suggest that capsular assembly in
C. neoformans
results from divalent cation-mediated self-aggregation of extracellularly accumulated GXM molecules.
Differential Regulation of Two Oligogalacturonate Outer Membrane Channels, KdgN and KdgM, ofDickeya dadantii(Erwinia chrysanthemi)
Authors: Condemine Guy , Ghazi Alexandre 
Published: June 2007

ABSTRACTThe entry of oligogalacturonates intoDickeya dadantiioccurs through the specific channel KdgM. The genome of the bacterium encodes a second member of this family of outer membrane proteins, KdgN. We showed that this protein is also involved in the uptake of oligogalacturonates. When KdgN was reconstituted in proteoliposomes, it formed channels with a conductance of about 450 pS at a positive potential. These channels had weak anionic selectivity. The regulation ofkdgNis complex, and five genes controlling the expression ofkdgNhave been identified:kdgR,pecS,ompR,hns, andcrp. Moreover,kdgNwas regulated by growth phase but only when bacteria were grown in rich medium. Most of these regulators ofkdgNalso controlkdgMexpression, but some of them regulatekdgMin the opposite manner: while PecS and OmpR are repressors ofkdgM, they are activators ofkdgN. This pattern resembles the regulation of theEscherichia coligeneral porins OmpF and OmpC, but such opposite regulation of two specific outer membrane channels has never been described before. KdgN may allow the bacteria to collect oligogalacturonates under saprophytic conditions, when virulence genes, includingkdgM, are not expressed.
Identification of Genes in
Xanthomonas campestris
pv. vesicatoria Induced during Its Interaction with Tomato
Authors: Tamir-Ariel Dafna , Navon Naama , Burdman Saul 
Published: June 2007

ABSTRACT

Xanthomonas campestris
pv. vesicatoria is the causal agent of bacterial spot disease of tomato and pepper. The disease process is interactive and very intricate and involves a plethora of genes in the pathogen and in the host. In the pathogen, different genes are activated in response to the changing environment to enable it to survive, adapt, evade host defenses, propagate, and damage the host. To understand the disease process, it is imperative to broaden our understanding of the gene machinery that participates in it, and the most reliable way is to identify these genes in vivo. Here, we have adapted a recombinase-based in vivo expression technology (RIVET) to study the genes activated in
X. campestris
pv. vesicatoria during its interaction with one of its hosts, tomato. This is the first study that demonstrates the feasibility of this approach for identifying in vivo induced genes in a plant pathogen. RIVET revealed 61 unique
X. campestris
pv. vesicatoria genes or operons that delineate a picture of the different processes involved in the pathogen-host interaction. To further explore the role of some of these genes, we generated knockout mutants for 13 genes and characterized their ability to grow in planta and to cause disease symptoms. This analysis revealed several genes that may be important for the interaction of the pathogen with its host, including a
citH
homologue gene, encoding a citrate transporter, which was shown to be required for wild-type levels of virulence.
Molecular Characterization of Class 3 Integrons fromDelftiaspp
Authors: Xu Hai , Davies Julian , Miao Vivian 
Published: June 2007

ABSTRACTTwo environmental strains,Delftia acidovoransC17 andDelftia tsuruhatensisA90, were found to carry class 3 integrons, which have seldom been reported and then only from pathogens in which they are associated with antibiotic resistance genes. TheDelftiaintegrons comprised a highly conserved class 3 integrase gene, upstream and oppositely oriented from a set of three or four gene cassettes that encoded unidentified functions. The A90 integron had one more gene cassette than the C17 integron, but the two were otherwise the same; furthermore, they were located within regions of sequence identity in both strains and linked to chromosomal genes. A screen of otherDelftiaand related strains did not reveal the presence of additional class 3 integrons. The observations suggest that these integrons were horizontally transferred toDelftiaas part of a larger region and reside as chromosomal elements that probably predate transposon dissemination, as has been proposed for certain class 1 integrons.
A Second Large Plasmid Encodes Conjugative Transfer and Antimicrobial Resistance in O119:H2 and Some Typical O111 Enteropathogenic
Escherichia coli
Strains
Authors: Nwaneshiudu Adaobi I. , Mucci Tania , Pickard Derek J. , Okeke Iruka N. 
Published: June 2007

ABSTRACT

A novel and functional conjugative transfer system identified in O119:H2 enteropathogenic
Escherichia coli
(EPEC) strain MB80 by subtractive hybridization is encoded on a large multidrug resistance plasmid, distinct from the well-described EPEC adherence factor (EAF) plasmid. Variants of the MB80 conjugative resistance plasmid were identified in other EPEC strains, including the prototypical O111:NM strain B171, from which the EAF plasmid has been sequenced. This separate large plasmid and the selective advantage that it confers in the antibiotic era have been overlooked because it comigrates with the virulence plasmid on conventional gels.
Pseudomonas aeruginosa
Type IV Pilus Expression in
Neisseria gonorrhoeae
: Effects of Pilin Subunit Composition on Function and Organelle Dynamics
Authors: Winther-Larsen Hanne C. , Wolfgang Matthew C. , van Putten Jos P. M. , Roos Norbert , Aas Finn Erik , Egge-Jacobsen Wolfgang M. , Maier Berenike , Koomey Michael 
Published: June 2007

ABSTRACT

Type IV pili (TFP) play central roles in the expression of many phenotypes including motility, multicellular behavior, sensitivity to bacteriophages, natural genetic transformation, and adherence. In
Neisseria gonorrhoeae
, these properties require ancillary proteins that act in conjunction with TFP expression and influence organelle dynamics. Here, the intrinsic contributions of the pilin protein itself to TFP dynamics and associated phenotypes were examined by expressing the
Pseudomonas aeruginosa
PilA
PAK
pilin subunit in
N. gonorrhoeae
. We show here that, although PilA
PAK
pilin can be readily assembled into TFP in this background, steady-state levels of purifiable fibers are dramatically reduced relative those of endogenous pili. This defect is due to aberrant TFP dynamics as it is suppressed in the absence of the PilT pilus retraction ATPase. Functionally, PilA
PAK
pilin complements gonococcal adherence for human epithelial cells but only in a
pilT
background, and this property remains dependent on the coexpression of both the PilC adhesin and the PilV pilin-like protein. Since
P. aeruginosa
pilin only moderately supports neisserial sequence-specific transformation despite its assembly proficiency, these results together suggest that PilA
PAK
pilin functions suboptimally in this environment. This appears to be due to diminished compatibility with resident proteins essential for TFP function and dynamics. Despite this, PilA
PAK
pili support retractile force generation in this background equivalent to that reported for endogenous pili. Furthermore, PilA
PAK
pili are both necessary and sufficient for bacteriophage PO4 binding, although the strain remains phage resistant. Together, these findings have significant implications for TFP biology in both
N. gonorrhoeae
and
P. aeruginosa
.