bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syntrophs Dominate Sequences Associated with the Mercury Methylation-Related Gene
hgcA
in the Water Conservation Areas of the Florida Everglades
Authors: Bae Hee-Sung , Dierberg Forrest E. , Ogram Andrew 
Published: August 2014

ABSTRACT

The mechanisms and rates of mercury methylation in the Florida Everglades are of great concern because of potential adverse impacts on human and wildlife health through mercury accumulation in aquatic food webs. We developed a new PCR primer set targeting
hgcA
, a gene encoding a corrinoid protein essential for Hg methylation across broad phylogenetic boundaries, and used this primer set to study the distribution of
hgcA
sequences in soils collected from three sites along a gradient in sulfate and nutrient concentrations in the northern Everglades. The sequences obtained were distributed in diverse phyla, including
Proteobacteria
,
Chloroflexi
,
Firmicutes
, and
Methanomicrobia
; however,
hgcA
clone libraries from all sites were dominated by sequences clustering within the order
Syntrophobacterales
of the
Deltaproteobacteria
(49 to 65% of total sequences).
dsrB
mRNA sequences, representing active sulfate-reducing prokaryotes at the time of sampling, obtained from these sites were also dominated by
Syntrophobacterales
(75 to 89%). Laboratory incubations with soils taken from the site low in sulfate concentrations also suggested that Hg methylation activities were primarily mediated by members of the order
Syntrophobacterales
, with some contribution by methanogens,
Chloroflexi
, iron-reducing
Geobacter
, and non-sulfate-reducing
Firmicutes
inhabiting the sites. This suggests that prokaryotes distributed within clades defined by syntrophs are the predominant group controlling methylation of Hg in low-sulfate areas of the Everglades. Any strategy for managing mercury methylation in the Everglades should consider that net mercury methylation is not limited to the action of sulfate reduction.
Molecular Basis of the Behavior of Hepatitis A Virus Exposed to High Hydrostatic Pressure
Authors: D'Andrea Lucía , Pérez-Rodríguez Francisco J. , Costafreda M. Isabel , Beguiristain Nerea , Fuentes Cristina , Aymerich Teresa , Guix Susana , Bosch Albert , Pintó Rosa M. 
Published: August 2014

ABSTRACT
Food-borne hepatitis A outbreaks may be prevented by subjecting foods at risk of virus contamination to moderate treatments of high hydrostatic pressure (HHP). A pretreatment promoting hepatitis A virus (HAV) capsid-folding changes enhances the virucidal effect of HHP, indicating that its efficacy depends on capsid conformation. HAV populations enriched in immature capsids (125S provirions) are more resistant to HHP, suggesting that mature capsids (150S virions) are more susceptible to this treatment. In addition, the monoclonal antibody (MAb) K24F2 epitope contained in the immunodominant site is a key factor for the resistance to HHP. Changes in capsid folding inducing a loss of recognition by MAb K24F2 render more susceptible conformations independently of the origin of such changes. Accordingly, codon usage-associated folding changes and changes stimulated by pH-dependent breathings, provided they confer a loss of recognition by MAb K24F2, induce a higher susceptibility to HHP. In conclusion, the resistance of HAV to HHP treatments may be explained by a low proportion of 150S particles combined with a good accessibility of the epitope contained in the immunodominant site close to the 5-fold axis.
Stress Response of Salmonella enterica Serovar Typhimurium to Acidified Nitrite
Authors: Mühlig Anna , Behr Jürgen , Scherer Siegfried , Müller-Herbst Stefanie 
Published: August 2014

ABSTRACTThe antimicrobial action of the curing agent sodium nitrite (NaNO2), which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we used RNA sequencing to analyze the acidified-NaNO2shock and adaptive responses ofSalmonella entericaserovar Typhimurium, a frequent contaminant in raw meat, considering parameters relevant for the production of raw-cured sausages. Upon a 10-min exposure to 150 mg/liter NaNO2in LB (pH 5.5) acidified with lactic acid, genes involved in nitrosative-stress protection, together with several other stress-related genes, were induced. In contrast, genes involved in translation, transcription, replication, and motility were downregulated. The induction of stress tolerance and the reduction of cell proliferation obviously promote survival under harsh acidified-NaNO2stress. The subsequent adaptive response was characterized by upregulation of NsrR-regulated genes and iron uptake systems and by downregulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite-mediated increase in the level of acid stress. Deletion ofcadA, which encodes lysine decarboxylase, resulted in increased sensitivity to acidified NaNO2. Intracellular pH measurements using a pH-sensitive green fluorescent protein (GFP) variant showed that the cytoplasmic pH ofS. Typhimurium in LB medium (pH 5.5) is decreased upon the addition of NaNO2. This study provides the first evidence that intracellular acidification is an additional antibacterial mode of action of acidified NaNO2.
Bdellovibrio and Like Organisms Enhanced Growth and Survival of Penaeus monodon and Altered Bacterial Community Structures in Its Rearing Water
Authors: Li Huanhuan , Chen Cheng , Sun Qiuping , Liu Renliang , Cai Junpeng 
Published: August 2014

ABSTRACT

In this study, a 96-h laboratory reduction test was conducted with strain BDHSH06 (GenBank accession no.
EF011103
) as the test strain for
Bdellovibrio
and like organisms (BALOs) and 20 susceptible marine bacterial strains forming microcosms as the targets. The results showed that BDHSH06 reduced the levels of approximately 50% of prey bacterial strains within 96 h in the seawater microcosms. An 85-day black tiger shrimp (
Penaeus monodon
) rearing experiment was performed. The shrimp survival rate, body length, and weight in the test tanks were 48.1% ± 1.2%, 99.8 ± 10.0 mm, and 6.36 ± 1.50 g, respectively, which were values significantly (
P
< 0.05) higher than those for the control,
viz
., 31.0% ± 2.1%, 86.0 ± 11.1 mm, and 4.21 ± 1.56 g, respectively. With the addition of BDHSH06, total bacterial and
Vibrio
numbers were significantly reduced (
P
< 0.05) by 1.3 to 4.5 log CFU · ml
−1
and CFU · g
−1
in both water and shrimp intestines, respectively, compared to those in the control. The effect of BDHSH06 on bacterial community structures in the rearing water was also examined using PCR amplification of the 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE). The DGGE profiles of rearing water samples from the control and test tanks revealed that the amounts of 44% of the bacterial species were reduced when BDHSH06 was added to the rearing water over the 85-day rearing period, and among these, approximately 57.1% were nonculturable. The results of this study demonstrated that BDHSH06 can be used as a biocontrol/probiotic agent in
P. monodon
culture.
Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine
Authors: Tseng Marion , Fratamico Pina M. , Bagi Lori , Delannoy Sabine , Fach Patrick , Manning Shannon D. , Funk Julie A. 
Published: August 2014

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) infections are a critical public health concern because they can cause severe clinical outcomes, such as hemolytic uremic syndrome, in humans. Determining the presence or absence of virulence genes is essential in assessing the potential pathogenicity of STEC strains. Currently, there is limited information about the virulence genes carried by swine STEC strains; therefore, this study was conducted to examine the presence and absence of 69 virulence genes in STEC strains recovered previously from finishing swine in a longitudinal study. A subset of STEC strains was analyzed by pulsed-field gel electrophoresis (PFGE) to examine their genetic relatedness. Swine STEC strains (
n
= 150) were analyzed by the use of a high-throughput real-time PCR array system, which included 69 virulence gene targets. Three major pathotypes consisted of 16 different combinations of virulence gene profiles, and serotypes were determined in the swine STEC strains. The majority of the swine STEC strains (
n
= 120) belonged to serotype O59:H21 and carried the same virulence gene profile, which consisted of 9 virulence genes:
stx
2e
,
iha
,
ecs1763
,
lpfA
O113
,
estIa
(
STa
),
ehaA
,
paa
,
terE
, and
ureD
. The
eae
,
nleF
, and
nleH1-2
genes were detected in one swine STEC strain (O49:H21). Other genes encoding adhesins, including
iha
, were identified (
n
= 149). The PFGE results demonstrated that swine STEC strains from pigs raised in the same finishing barn were closely related. Our results revealed diverse virulence gene contents among the members of the swine STEC population and enhance understanding of the dynamics of transmission of STEC strains among pigs housed in the same barn.
An ArsR/SmtB Family Member Is Involved in the Regulation by Arsenic of the Arsenite Oxidase Operon in Thiomonas arsenitoxydans
Authors: Moinier Danielle , Slyemi Djamila , Byrne Deborah , Lignon Sabrina , Lebrun Régine , Talla Emmanuel , Bonnefoy Violaine 
Published: August 2014

ABSTRACT

The genetic organization of the
aioBA
operon, encoding the arsenite oxidase of the moderately acidophilic and facultative chemoautotrophic bacterium
Thiomonas arsenitoxydans
, is different from that of the
aioBA
operon in the other arsenite oxidizers, in that it encodes AioF, a metalloprotein belonging to the ArsR/SmtB family. AioF is stabilized by arsenite, arsenate, or antimonite but not molybdate. Arsenic is tightly attached to AioF, likely by cysteine residues. When loaded with arsenite or arsenate, AioF is able to bind specifically to the regulatory region of the
aio
operon at two distinct positions. In
Thiomonas arsenitoxydans
, the promoters of
aioX
and
aioB
are convergent, suggesting that transcriptional interference occurs. These results indicate that the regulation of the
aioBA
operon is more complex in
Thiomonas arsenitoxydans
than in the other
aioBA
containing arsenite oxidizers and that the arsenic binding protein AioF is involved in this regulation. On the basis of these data, a model to explain the tight control of
aioBA
expression by arsenic in
Thiomonas arsenitoxydans
is proposed.
Different Effects of Transgenic Maize and Nontransgenic Maize on Nitrogen-Transforming Archaea and Bacteria in Tropical Soils
Authors: Cotta Simone Raposo , Dias Armando Cavalcante Franco , Marriel Ivanildo Evódio , Andreote Fernando Dini , Seldin Lucy , van Elsas Jan Dirk 
Published: August 2014

ABSTRACT
The composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants.
Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria
Authors: Soro Valeria , Dutton Lindsay C. , Sprague Susan V. , Nobbs Angela H. , Ireland Anthony J. , Sandy Jonathan R. , Jepson Mark A. , Micaroni Massimo , Splatt Peter R. , Dymock David , Jenkinson Howard F. 
Published: August 2014

ABSTRACT

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with
Actinomyces oris
or
Fusobacterium nucleatum
. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with
Porphyromonas gingivalis
,
Prevotella intermedia
,
Parvimonas micra
, or
Streptococcus gordonii
, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium.
Enhanced Inactivation of Food-Borne Pathogens in Ready-To-Eat Sliced Ham by Near-Infrared Heating Combined with UV-C Irradiation and Mechanism of the Synergistic Bactericidal Action
Authors: Ha Jae-Won , Kang Dong-Hyun 
Published: August 2014

ABSTRACT

The objective of the study described in this article was, first, to investigate the effect of the simultaneous application of near-infrared (NIR) heating and UV irradiation on inactivation of
Escherichia coli
O157:H7,
Salmonella enterica
serovar Typhimurium, and
Listeria monocytogenes
in ready-to-eat (RTE) sliced ham and as well as its effect on product quality and, second, to elucidate the underlying mechanisms of the synergistic bactericidal action of NIR heating and UV irradiation. With the inoculation amounts used, simultaneous NIR-UV combined treatment for 70 s achieved 3.62, 4.17, and 3.43 log CFU reductions of
E. coli
O157:H7,
S
. Typhimurium, and
L. monocytogenes
, respectively. For all three pathogens, the simultaneous application of both technologies resulted in an additional log unit reduction as a result of their synergism compared to the sum of the reductions obtained after the individual treatments. To investigate the mechanisms of NIR-UV synergistic injury for a particular microorganism in a food base, we evaluated the effect of four types of metabolic inhibitors using the overlay method and confirmed that damage to cellular membranes and the inability of cells to repair these structures due to ribosomal damage were the primary factors related to the synergistic lethal effect. Additionally, NIR-UV combined treatment for a maximum of 70 s did not alter the color values or texture parameters of ham slices significantly (
P
> 0.05). These results suggest that a NIR-UV combined process could be an innovative antimicrobial intervention for RTE meat products.
Transcriptome Analysis of the Entomopathogenic Oomycete Lagenidium giganteum Reveals Putative Virulence Factors
Authors: Quiroz Velasquez Paula F. , Abiff Sumayyah K. , Fins Katrina C. , Conway Quincy B. , Salazar Norma C. , Delgado Ana Paula , Dawes Jhanelle K. , Douma Lauren G. , Tartar Aurélien 
Published: August 2014

ABSTRACT

A combination of 454 pyrosequencing and Sanger sequencing was used to sample and characterize the transcriptome of the entomopathogenic oomycete
Lagenidium giganteum
. More than 50,000 high-throughput reads were annotated through homology searches. Several selected reads served as seeds for the amplification and sequencing of full-length transcripts. Phylogenetic analyses inferred from full-length cellulose synthase alignments revealed that
L giganteum
is nested within the peronosporalean galaxy and as such appears to have evolved from a phytopathogenic ancestor. In agreement with the phylogeny reconstructions, full-length
L. giganteum
oomycete effector orthologs, corresponding to the cellulose-binding elicitor lectin (CBEL), crinkler (CRN), and elicitin proteins, were characterized by domain organizations similar to those of pathogenicity factors of plant-pathogenic oomycetes. Importantly, the
L. giganteum
effectors provide a basis for detailing the roles of canonical CRN, CBEL, and elicitin proteins in the infectious process of an oomycete known principally as an animal pathogen. Finally, phylogenetic analyses and genome mining identified members of glycoside hydrolase family 5 subfamily 27 (GH5_27) as putative virulence factors active on the host insect cuticle, based in part on the fact that GH5_27 genes are shared by entomopathogenic oomycetes and fungi but are underrepresented in nonentomopathogenic genomes. The genomic resources gathered from the
L. giganteum
transcriptome analysis strongly suggest that filamentous entomopathogens (oomycetes and fungi) exhibit convergent evolution: they have evolved independently from plant-associated microbes, have retained genes indicative of plant associations, and may share similar cores of virulence factors, such as GH5_27 enzymes, that are absent from the genomes of their plant-pathogenic relatives.
Diversity and Antimicrobial Resistance of Salmonella enterica Isolates from Surface Water in Southeastern United States
Authors: Li Baoguang , Vellidis George , Liu Huanli , Jay-Russell Michele , Zhao Shaohua , Hu Zonglin , Wright Anita , Elkins Christopher A. 
Published: August 2014

ABSTRACT

A study of prevalence, diversity, and antimicrobial resistance of
Salmonella enterica
in surface water in the southeastern United States was conducted. A new scheme was developed for recovery of
Salmonella
from irrigation pond water and compared with the FDA's
Bacteriological Analytical Manual
(8th ed., 2014) (BAM) method. Fifty-one isolates were recovered from 10 irrigation ponds in produce farms over a 2-year period; nine
Salmonella
serovars were identified by pulsed-field gel electrophoresis analysis, and the major serovar was
Salmonella enterica
serovar Newport (
S
. Newport,
n
= 29), followed by
S. enterica
serovar Enteritidis (
n
= 6),
S. enterica
serovar Muenchen (
n
= 4),
S. enterica
serovar Javiana (
n
= 3),
S. enterica
serovar Thompson (
n
= 2), and other serovars. It is noteworthy that the PulseNet patterns of some of the isolates were identical to those of the strains that were associated with the
S
. Thompson outbreaks in 2010, 2012, and 2013,
S
. Enteritidis outbreaks in 2011 and 2013, and an
S
. Javiana outbreak in 2012. Antimicrobial susceptibility testing confirmed 16
S
. Newport isolates of the multidrug resistant-AmpC (MDR-AmpC) phenotype, which exhibited resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT), and to the 1st, 2nd, and 3rd generations of cephalosporins (cephalothin, amoxicillin-clavulanic acid, and ceftriaxone). Moreover, the
S
. Newport MDR-AmpC isolates had a PFGE pattern indistinguishable from the patterns of the isolates from clinical settings. These findings suggest that the irrigation water may be a potential source of contamination of
Salmonella
in fresh produce. The new
Salmonella
isolation scheme significantly increased recovery efficiency from 21.2 (36/170) to 29.4% (50/170) (
P
= 0.0002) and streamlined the turnaround time from 5 to 9 days with the BAM method to 4 days and thus may facilitate microbiological analysis of environmental water.
Distinct Immunomodulation of Bone Marrow-Derived Dendritic Cell Responses to Lactobacillus plantarum WCFS1 by Two Different Polysaccharides Isolated from Lactobacillus rhamnosus LOCK 0900
Authors: Górska Sabina , Schwarzer Martin , Jachymek Wojciech , Srutkova Dagmar , Brzozowska Ewa , Kozakova Hana , Gamian Andrzej 
Published: August 2014

ABSTRACT

The structures of polysaccharides (PS) isolated from
Lactobacillus rhamnosus
LOCK 0900 and results from stimulation of mouse bone marrow-derived dendritic cells (BM-DC) and human embryonal kidney (HEK293) cells stably transfected with Toll-like receptors (TLR) upon exposure to these antigens were studied.
L. rhamnosus
LOCK 0900 produces PS that differ greatly in their structure. The polymer L900/2, with a high average molecular mass of 830 kDa, is a branched heteropolysaccharide with a unique repeating unit consisting of seven sugar residues and pyruvic acid, whereas L900/3 has a low average molecular mass of 18 kDa and contains a pentasaccharide repeating unit and phosphorus. Furthermore, we found that both described PS neither induce cytokine production and maturation of mouse BM-DC nor induce signaling through TLR2/TLR4 receptors. However, they differ profoundly in their abilities to modulate the BM-DC immune response to the well-characterized human isolate
Lactobacillus plantarum
WCFS1. Exposure to L900/2 enhanced interleukin-10 (IL-10) production induced by
L. plantarum
WCFS1, while in contrast, L900/3 enhanced the production of IL-12p70. We conclude that PS, probably due to their chemical features, are able to modulate the immune responses to third-party antigens. The ability to induce regulatory IL-10 by L900/2 opens up the possibility to use this PS in therapy of inflammatory conditions, such as inflammatory bowel disease, whereas L900/3 might be useful in reverting the antigen-dependent Th2-skewed immune responses in allergies.