bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Iron-Dependent Regulator Fur Controls Pheromone Signaling Systems and Luminescence in the Squid Symbiont Vibrio fischeri ES114
Authors: Septer Alecia N. , Lyell Noreen L. , Stabb Eric V. 
Published: January 2013

ABSTRACT

Bacteria often use pheromones to coordinate group behaviors in specific environments. While high cell density is required for pheromones to achieve stimulatory levels, environmental cues can also influence pheromone accumulation and signaling. For the squid symbiont
Vibrio fischeri
ES114, bioluminescence requires pheromone-mediated regulation, and this signaling is induced in the host to a greater extent than in culture, even at an equivalent cell density. Our goal is to better understand this environment-specific control over pheromone signaling and bioluminescence. Previous work with
V. fischeri
MJ1 showed that iron limitation induces luminescence, and we recently found that ES114 encounters a low-iron environment in its host. Here we show that ES114 induces luminescence at lower cell density and achieves brighter luminescence in low-iron media. This iron-dependent effect on luminescence required ferric uptake regulator (Fur), which we propose influences two pheromone signaling master regulators, LitR and LuxR. Genetic and bioinformatic analyses suggested that under low-iron conditions, Fur-mediated repression of
litR
is relieved, enabling more LitR to perform its established role as an activator of
luxR
. Interestingly, Fur may similarly control the LitR homolog SmcR of
Vibrio vulnificus
. These results reveal an intriguing regulatory link between low-iron conditions, which are often encountered in host tissues, and pheromone-dependent master regulators.
Isolation of a Substantial Proportion of Forest Soil Bacterial Communities Detected via Pyrotag Sequencing
Authors: VanInsberghe David , Hartmann Martin , Stewart Gordon R. , Mohn William W. 
Published: January 2013

ABSTRACT
We isolated 1,264 bacterial strains from forest soils previously surveyed via pyrosequencing of rRNA gene amplicons. Conventional culturing techniques recovered a substantial proportion of the community, with isolates representing 22% of 98,557 total pyrotags. Growth characteristics of isolates indicated that ecological traits were associated with relative abundances of corresponding pyrotag operational taxonomic units.
Increased Abundance and Transferability of Resistance Genes after Field Application of Manure from Sulfadiazine-Treated Pigs
Authors: Jechalke Sven , Kopmann Christoph , Rosendahl Ingrid , Groeneweg Joost , Weichelt Viola , Krögerrecklenfort Ellen , Brandes Nikola , Nordwig Mathias , Ding Guo-Chun , Siemens Jan , Heuer Holger , Smalla Kornelia 
Published: January 2013

ABSTRACT

Spreading manure containing antibiotics in agriculture is assumed to stimulate the dissemination of antibiotic resistance in soil bacterial populations. Plant roots influencing the soil environment and its microflora by exudation of growth substrates might considerably increase this effect. In this study, the effects of manure from pigs treated with sulfadiazine (SDZ), here called SDZ manure, on the abundance and transferability of sulfonamide resistance genes
sul1
and
sul2
in the rhizosphere of maize and grass were compared to the effects in bulk soil in a field experiment. In plots that repeatedly received SDZ manure, a significantly higher abundance of both
sul
genes was detected compared to that in plots where manure from untreated pigs was applied. Significantly lower abundances of
sul
genes relative to bacterial ribosomal genes were encountered in the rhizosphere than in bulk soil. However, in contrast to results for bulk soil, the
sul
gene abundance in the SDZ manure-treated rhizosphere constantly deviated from control treatments over a period of 6 weeks after manuring, suggesting ongoing antibiotic selection over this period. Transferability of sulfonamide resistance was analyzed by capturing resistance plasmids from soil communities into
Escherichia coli
. Increased rates of plasmid capture were observed in samples from SDZ manure-treated bulk soil and the rhizosphere of maize and grass. More than 97% of the captured plasmids belonged to the LowGC type (having low G+C content), giving further evidence for their important contribution to the environmental spread of antibiotic resistance. In conclusion, differences between bulk soil and rhizosphere need to be considered when assessing the risks associated with the spreading of antibiotic resistance.
Hydrologic and Vegetative Removal of Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii Surrogate Microspheres in Coastal Wetlands
Authors: Hogan Jennifer N. , Daniels Miles E. , Watson Fred G. , Oates Stori C. , Miller Melissa A. , Conrad Patricia A. , Shapiro Karen , Hardin Dane , Dominik Clare , Melli Ann , Jessup David A. , Miller Woutrina A. 
Published: January 2013

ABSTRACT

Constructed wetland systems are used to reduce pollutants and pathogens in wastewater effluent, but comparatively little is known about pathogen transport through natural wetland habitats. Fecal protozoans, including
Cryptosporidium parvum
,
Giardia lamblia
, and
Toxoplasma gondii
, are waterborne pathogens of humans and animals, which are carried by surface waters from land-based sources into coastal waters. This study evaluated key factors of coastal wetlands for the reduction of protozoal parasites in surface waters using settling column and recirculating mesocosm tank experiments. Settling column experiments evaluated the effects of salinity, temperature, and water type (“pure” versus “environmental”) on the vertical settling velocities of
C. parvum
,
G. lamblia
, and
T. gondii
surrogates, with salinity and water type found to significantly affect settling of the parasites. The mesocosm tank experiments evaluated the effects of salinity, flow rate, and vegetation parameters on parasite and surrogate counts, with increased salinity and the presence of vegetation found to be significant factors for removal of parasites in a unidirectional transport wetland system. Overall, this study highlights the importance of water type, salinity, and vegetation parameters for pathogen transport within wetland systems, with implications for wetland management, restoration efforts, and coastal water quality.
Isolation of a Bifidogenic Peptide from the Pepsin Hydrolysate of Bovine Lactoferrin
Authors: Oda Hirotsugu , Wakabayashi Hiroyuki , Yamauchi Koji , Sato Takumi , Xiao Jin-Zhong , Abe Fumiaki , Iwatsuki Keiji 
Published: January 2013

ABSTRACT

Lactoferrin is an iron-binding glycoprotein found in the milk of most mammals for which various biological functions have been reported, such as antimicrobial activity and bifidogenic activity. In this study, we compared the bifidogenic activity of bovine lactoferrin (bLF) and pepsin hydrolysate of bLF (bLFH), isolated bifidogenic peptide from bLFH, and investigated the bifidogenic spectra of bLF, bLFH, and its active peptide against 42 bifidobacterial strains comprising nine species. Against
Bifidobacterium breve
ATCC 15700
T
, minimal effective concentrations of bLF and bLFH were 300 and 10 μg/ml. Against
Bifidobacterium longum
subsp.
infantis
ATCC 15697
T
, the minimal effective concentration of bLFH was 30 μg/ml, and bLF did not show bifidogenic activity within 300 μg/ml. As an active peptide, a heterodimer of A
1
-W
16
and L
43
-A
48
linked by a disulfide bond was isolated. Previously, this peptide was identified as having antibacterial activity. An amino acid mixture with the same composition as this peptide showed no bifidogenic activity. The strains of each species whose growth was highly promoted (>150%) by this peptide at 3.75 μM were as follows:
B. breve
(7 out of 7 strains [7/7]),
B. longum
subsp.
infantis
(5/5),
Bifidobacterium bifidum
(2/5),
B. longum
subsp.
longum
(1/3),
Bifidobacterium adolescentis
(3/6),
Bifidobacterium catenulatum
(1/4),
Bifidobacterium pseudocatenulatum
(0/4),
Bifidobacterium dentium
(0/5), and
Bifidobacterium angulatum
(0/3). Growth of none of the strains was highly promoted by bLF at 3.75 μM. We demonstrated that bLFH showed stronger bifidogenic activity than natural bLF, especially against infant-representative species,
B. breve
and
B. longum
subsp.
infantis
; furthermore, we isolated its active peptide. This is the first report about a bifidogenic peptide derived from bLF.
Monitoring the Single-Cell Stress Response of the Diatom Thalassiosira pseudonana by Quantitative Real-Time Reverse Transcription-PCR
Authors: Shi Xu , Gao Weimin , Chao Shih-hui , Zhang Weiwen , Meldrum Deirdre R. 
Published: January 2013

ABSTRACTDirectly monitoring the stress response of microbes to their environments could be one way to inspect the health of microorganisms themselves, as well as the environments in which the microorganisms live. The ultimate resolution for such an endeavor could be down to a single-cell level. In this study, using the diatomThalassiosira pseudonanaas a model species, we aimed to measure gene expression responses of this organism to various stresses at a single-cell level. We developed a single-cell quantitative real-time reverse transcription-PCR (RT-qPCR) protocol and applied it to determine the expression levels of multiple selected genes under nitrogen, phosphate, and iron depletion stress conditions. The results, for the first time, provided a quantitative measurement of gene expression at single-cell levels inT. pseudonanaand demonstrated that significant gene expression heterogeneity was present within the cell population. In addition, different expression patterns between single-cell- and bulk-cell-based analyses were also observed for all genes assayed in this study, suggesting that cell response heterogeneity needs to be taken into consideration in order to obtain accurate information that indicates the environmental stress condition.
Effects of DNA Size on Transformation and Recombination Efficiencies in Xylella fastidiosa
Authors: Kung Stephanie H. , Retchless Adam C. , Kwan Jessica Y. , Almeida Rodrigo P. P. 
Published: January 2013

ABSTRACT

Horizontally transferred DNA acquired through transformation and recombination has the potential to contribute to the diversity and evolution of naturally competent bacteria. However, many different factors affect the efficiency with which DNA can be transformed and recombined. In this study, we determined how the size of both homologous and nonhomologous regions affects transformation and recombination efficiencies in
Xylella fastidiosa
, a naturally competent generalist pathogen responsible for many emerging plant diseases. Our experimental data indicate that 96 bp of flanking homology is sufficient to initiate recombination, with recombination efficiencies increasing exponentially with the size of the homologous flanking region up to 1 kb. Recombination efficiencies also decreased with the size of the nonhomologous insert, with no recombination detected when 6 kb of nonhomologous DNA was flanked on either side by 1 kb of homologous sequences. Upon analyzing sequenced
X. fastidiosa
subsp.
fastidiosa
genomes for evidence of allele conversion, we estimated the mean size of recombination events to be 1,906 bp, with each event modifying, on average, 1.79% of the nucleotides in the recombined region. There is increasing evidence that horizontally acquired genes significantly affect the genetic diversity of
X. fastidiosa
, and DNA acquired through natural transformation could be a prominent mode of this horizontal transfer.
Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers
Authors: Drury Bradley , Rosi-Marshall Emma , Kelly John J. 
Published: January 2013

ABSTRACT

In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of
Deltaproteobacteria
,
Desulfococcus
,
Dechloromonas
, and
Chloroflexi
sequences and increases in abundances of
Nitrospirae
and
Sphingobacteriales
sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization.
Caffeate Respiration in the Acetogenic Bacterium Acetobacterium woodii: a Coenzyme A Loop Saves Energy for Caffeate Activation
Authors: Hess Verena , Gonzï¿½lez Josï¿½ M. , Parthasarathy Anutthaman , Buckel Wolfgang , Mï¿½ller Volker 
Published: January 2013

ABSTRACT

The anaerobic acetogenic bacterium
Acetobacterium woodii
couples reduction of caffeate with electrons derived from molecular hydrogen to the synthesis of ATP by a chemiosmotic mechanism with sodium ions as coupling ions. Caffeate is activated to caffeyl coenzyme A (caffeyl-CoA) prior to its reduction, and the caffeate reduction operon encodes an ATP-dependent caffeyl-CoA synthetase that is thought to catalyze the initial caffeate activation. The operon also encodes a potential CoA transferase, the product of
carA
, which was thought to be involved in subsequent ATP-independent caffeate activation. To prove the proposed function of
carA
, we overproduced its protein in
Escherichia coli
and then purified it. Purified CarA drives the formation of caffeyl-CoA from caffeate with hydrocaffeyl-CoA as the CoA donor. The dependence of the reaction on caffeate and hydrocaffeyl-CoA followed Michaelis-Menten kinetics, with apparent

K
m

values of 75 ï¿½ 5 μM for caffeate and 8 ï¿½ 2 μM for hydrocaffeyl-CoA. The enzyme activity had broad ranges of pH and temperature optima. In addition to being able to use caffeate, CarA could use
p
-coumarate and ferulate but not cinnamate, sinapate, or
p
-hydroxybenzoate as a CoA acceptor. Neither acetyl-CoA nor butyryl-CoA served as the CoA donor for CarA. The enzyme uses a ping-pong mechanism for CoA transfer and is the first classified member of a new subclass of family I CoA transferases that has two catalytic domains on one polypeptide chain. Apparently, CarA catalyzes an energy-saving CoA loop for caffeate activation in the steady state of caffeate respiration.
New Type of Outer Membrane Vesicle Produced by the Gram-Negative Bacterium Shewanella vesiculosa M7
T
: Implications for DNA Content
Authors: P�rez-Cruz Carla , Carri�n Ornella , Delgado Lidia , Martinez Gemma , L�pez-Iglesias Carmen , Mercade Elena 
Published: January 2013

ABSTRACT

Outer membrane vesicles (OMVs) from Gram-negative bacteria are known to be involved in lateral DNA transfer, but the presence of DNA in these vesicles has remained difficult to explain. An ultrastructural study of the Antarctic psychrotolerant bacterium
Shewanella vesiculosa
M7
T
has revealed that this Gram-negative bacterium naturally releases conventional one-bilayer OMVs through a process in which the outer membrane is exfoliated and only the periplasm is entrapped, together with a more complex type of OMV, previously undescribed, which on formation drag along inner membrane and cytoplasmic content and can therefore also entrap DNA. These vesicles, with a double-bilayer structure and containing electron-dense material, were visualized by transmission electron microscopy (TEM) after high-pressure freezing and freeze-substitution (HPF-FS), and their DNA content was fluorometrically quantified as 1.8 � 0.24 ng DNA/μg OMV protein. The new double-bilayer OMVs were estimated by cryo-TEM to represent 0.1% of total vesicles. The presence of DNA inside the vesicles was confirmed by gold DNA immunolabeling with a specific monoclonal IgM against double-stranded DNA. In addition, a proteomic study of purified membrane vesicles confirmed the presence of plasma membrane and cytoplasmic proteins in OMVs from this strain. Our data demonstrate the existence of a previously unobserved type of double-bilayer OMV in the Gram-negative bacterium
Shewanella vesiculosa
M7
T
that can incorporate DNA, for which we propose the name outer-inner membrane vesicle (O-IMV).
Identification and Characterization of Spontaneous Deletions within the Sp11-Sp12 Prophage Region of Escherichia coli O157:H7 Sakai
Authors: Chen Chun , Lewis Carrie R. , Goswami Kakolie , Roberts Elisabeth L. , DebRoy Chitrita , Dudley Edward G. 
Published: January 2013

ABSTRACT

Prophages make up 12% of the enterohemorrhagic
Escherichia coli
genome and play prominent roles in the evolution and virulence of this food-borne pathogen. Acquisition and loss of and rearrangements within prophage regions are the primary causes of differences in pulsed-field gel electrophoresis (PFGE) patterns among strains of
E. coli
O157:H7. Sp11 and Sp12 are two tandemly integrated and putatively defective prophages carried by
E. coli
O157:H7 strain Sakai. In this study, we identified 3 classes of deletions that occur within the Sp11-Sp12 region, at a frequency of ca. 7.74 ï¿½ 10
−4
. One deletion resulted in a precise excision of Sp11, and the other two spanned the junction of Sp11 and Sp12. All deletions resulted in shifts in the XbaI fragment pattern observed by PFGE. We sequenced the inducible prophage pool of Sakai but did not identify any mature phage particles corresponding to either Sp11 or Sp12. Deletions containing
pchB
and
psrC
, which are Sp11-carried genes encoding proteins known or suspected to regulate type III secretion, did not affect the secretion levels of the EspA or EspB effector. Alignment of the Sp11-Sp12 DNA sequence with its corresponding regions in other
E. coli
O157:H7 and O55:H7 strains suggested that homologous recombination rather than integrase-mediated excision is the mechanism behind these deletions. Therefore, this study provides a mechanism behind the previously observed genetic instability of this genomic region of
E. coli
O157:H7.
Development of a New Generation of Vectors for Gene Expression, Gene Replacement, and Protein-Protein Interaction Studies in Mycobacteria
Authors: Parikh Amit , Kumar Devanand , Chawla Yogesh , Kurthkoti Krishna , Khan Shazia , Varshney Umesh , Nandicoori Vinay K. 
Published: January 2013

ABSTRACT

Escherichia coli
-mycobacterium shuttle vectors are important tools for gene expression and gene replacement in mycobacteria. However, most of the currently available vectors are limited in their use because of the lack of extended multiple cloning sites (MCSs) and convenience of appending an epitope tag(s) to the cloned open reading frames (ORFs). Here we report a new series of vectors that allow for the constitutive and regulatable expression of proteins, appended with peptide tag sequences at their N and C termini, respectively. The applicability of these vectors is demonstrated by the constitutive and induced expression of the
Mycobacterium tuberculosis pknK
gene, coding for protein kinase K, a serine-threonine protein kinase. Furthermore, a suicide plasmid with expanded MCS for creating gene replacements, a plasmid for chromosomal integrations at the commonly used L5
attB
site, and a hypoxia-responsive vector, for expression of a gene(s) under hypoxic conditions that mimic latency, have also been created. Additionally, we have created a vector for the coexpression of two proteins controlled by two independent promoters, with each protein being in fusion with a different tag. The shuttle vectors developed in the present study are excellent tools for the analysis of gene function in mycobacteria and are a valuable addition to the existing repertoire of vectors for mycobacterial research.
Characterization of an Acid-Inducible Sulfatase in Salmonella enterica Serovar Typhimurium
Authors: Das Seema , Singh Swati , McClelland Michael , Forst Steven , Gyaneshwar Prasad 
Published: January 2013

ABSTRACT

Sulfatases of enteric bacteria can provide access to heavily sulfated mucosal glycans. In this study, we show that
aslA
(STM0084) of
Salmonella enterica
serovar Typhimurium LT2 encodes a sulfatase that requires mildly acidic pH for its expression and activity. AslA is not regulated by sulfur compounds or tyramine but requires the EnvZ-OmpR and PhoPQ regulatory systems, which play an important role in pathogenesis.
Antifungal Hydroxy Fatty Acids Produced during Sourdough Fermentation: Microbial and Enzymatic Pathways, and Antifungal Activity in Bread
Authors: Black Brenna A. , Zannini Emanuele , Curtis Jonathan M. , Gï¿½nzle Michael G. 
Published: January 2013

ABSTRACT

Lactobacilli convert linoleic acid to hydroxy fatty acids; however, this conversion has not been demonstrated in food fermentations and it remains unknown whether hydroxy fatty acids produced by lactobacilli have antifungal activity. This study aimed to determine whether lactobacilli convert linoleic acid to metabolites with antifungal activity and to assess whether this conversion can be employed to delay fungal growth on bread. Aqueous and organic extracts from seven strains of lactobacilli grown in modified De Man Rogosa Sharpe medium or sourdough were assayed for antifungal activity.
Lactobacillus hammesii
exhibited increased antifungal activity upon the addition of linoleic acid as a substrate. Bioassay-guided fractionation attributed the antifungal activity of
L. hammesii
to a monohydroxy C
18:1
fatty acid. Comparison of its antifungal activity to those of other hydroxy fatty acids revealed that the monohydroxy fraction from
L. hammesii
and coriolic (13-hydroxy-9,11-octadecadienoic) acid were the most active, with MICs of 0.1 to 0.7 g liter
−1
. Ricinoleic (12-hydroxy-9-octadecenoic) acid was active at a MIC of 2.4 g liter
−1
.
L. hammesii
accumulated the monohydroxy C
18:1
fatty acid in sourdough to a concentration of 0.73 ï¿½ 0.03 g liter
−1
(mean ï¿½ standard deviation). Generation of hydroxy fatty acids in sourdough also occurred through enzymatic oxidation of linoleic acid to coriolic acid. The use of 20% sourdough fermented with
L. hammesii
or the use of 0.15% coriolic acid in bread making increased the mold-free shelf life by 2 to 3 days or from 2 to more than 6 days, respectively. In conclusion,
L. hammesii
converts linoleic acid in sourdough and the resulting monohydroxy octadecenoic acid exerts antifungal activity in bread.