bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a
Authors: Luo Quan , Hiessl Sebastian , Poehlein Anja , Daniel Rolf , Steinbüchel Alexander 
Published: April 2014

ABSTRACTThe complete genome sequence ofNocardia novaSH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based onin silicoanalyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include,inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid–AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genusNocardiaregarding metabolic diversity.
Use of Silicate Minerals for pH Control during Reductive Dechlorination of Chloroethenes in Batch Cultures of Different Microbial Consortia
Authors: Lacroix Elsa , Brovelli Alessandro , Barry D. A. , Holliger Christof 
Published: April 2014

ABSTRACT

In chloroethene-contaminated sites undergoing
in situ
bioremediation, groundwater acidification is a frequent problem in the source zone, and buffering strategies have to be implemented to maintain the pH in the neutral range. An alternative to conventional soluble buffers is silicate mineral particles as a long-term source of alkalinity. In previous studies, the buffering potentials of these minerals have been evaluated based on abiotic dissolution tests and geochemical modeling. In the present study, the buffering potentials of four silicate minerals (andradite, diopside, fayalite, and forsterite) were tested in batch cultures amended with tetrachloroethene (PCE) and inoculated with different organohalide-respiring consortia. Another objective of this study was to determine the influence of pH on the different steps of PCE dechlorination. The consortia showed significant differences in sensitivities toward acidic pH for the different dechlorination steps. Molecular analysis indicated that
Dehalococcoides
spp. that were present in all consortia were the most pH-sensitive organohalide-respiring guild members compared to
Sulfurospirillum
spp. and
Dehalobacter
spp. In batch cultures with silicate mineral particles as pH-buffering agents, all four minerals tested were able to maintain the pH in the appropriate range for reductive dechlorination of chloroethenes. However, complete dechlorination to ethene was observed only with forsterite, diopside, and fayalite. Dissolution of andradite increased the redox potential and did not allow dechlorination. With forsterite, diopside, and fayalite, dechlorination to ethene was observed but at much lower rates for the last two dechlorination steps than with the positive control. This indicated an inhibition effect of silicate minerals and/or their dissolution products on reductive dechlorination of
cis
-dichloroethene and vinyl chloride. Hence, despite the proven pH-buffering potential of silicate minerals, compatibility with the bacterial community involved in
in situ
bioremediation has to be carefully evaluated prior to their use for pH control at a specific site.
Microscopy, Culture, and Quantitative Real-Time PCR Examination Confirm Internalization of Mycobacteria in Plants
Authors: Kaevska M. , Lvoncik S. , Slana I. , Kulich P. , Kralik P. 
Published: April 2014

ABSTRACT

The environment is a reservoir of nontuberculous mycobacteria and is considered a source of infection for animals and humans. Mycobacteria can persist in different types of environments for a relatively long time. We have studied their possible internalization into plant tissue through intact, as well as damaged, root systems of different types of plants grown
in vitro
and under field conditions. The substrate into which plants were seeded was previously contaminated with different strains of
Mycobacterium avium
(10
8
to 10
10
cells/g of soil) and feces from animals with paratuberculosis. We detected
M. avium
subsp.
avium
,
hominissuis
, and
paratuberculosis
in the stems and leaves of the plants by both culture and real-time quantitative PCR. The presence of mycobacteria in the plant tissues was confirmed by microscopy. The concentration of mycobacteria found inside plant tissue was several orders of magnitude lower (up to 10
4
cells/g of tissue) than the initial concentration of mycobacteria present in the culture medium or substrate. These findings led us to the hypothesis that plants may play a role in the spread and transmission of mycobacteria to other organisms in the environment.
Diversity and Transport of Microorganisms in Intertidal Sands of the California Coast
Authors: Boehm Alexandria B. , Yamahara Kevan M. , Sassoubre Lauren M. 
Published: April 2014

ABSTRACT
Forced by tides and waves, large volumes of seawater are flushed through the beach daily. Organic material and nutrients in seawater are remineralized and cycled as they pass through the beach. Microorganisms are responsible for most of the biogeochemical cycling in the beach; however, few studies have characterized their diversity in intertidal sands, and little work has characterized the extent to which microbes are transported between different compartments of the beach. The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands. Nearly 1,000 unique taxa were identified in sands from 10 or more unique beaches, suggesting the existence of a group of “cosmopolitan” sand microorganisms. A biogeographical analysis identified a taxon-distance relationship among the beaches. In addition, sands with similar grain size, organic carbon content, exposed to a similar wave climate, and having the same degree of anthropogenic influence tended to have similar microbial communities. Column experiments identified microbes readily mobilized by seawater infiltrating through unsaturated intertidal sands. The ease with which microbes were mobilized suggests that intertidal sands may represent a reservoir of bacteria that seed the beach aquifer where they may partake in biogeochemical cycling.
High Genetic Diversity among Strains of the Unindustrialized Lactic Acid Bacterium Carnobacterium maltaromaticum in Dairy Products as Revealed by Multilocus Sequence Typing
Authors: Rahman Abdur , Cailliez-Grimal Catherine , Bontemps Cyril , Payot Sophie , Chaillou Stéphane , Revol-Junelles Anne-Marie , Borges Frédéric 
Published: April 2014

ABSTRACT

Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter.
Carnobacterium maltaromaticum
is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes
C. maltaromaticum
an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes
dapE
,
ddlA
,
glpQ
,
ilvE
,
pyc
,
pyrE
, and
leuS
was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.
Differing Populations of Endemic Bacteriophages in Cattle Shedding High and Low Numbers of Escherichia coli O157:H7 Bacteria in Feces
Authors: Hallewell J. , Niu Y. D. , Munns K. , McAllister T. A. , Johnson R. P. , Ackermann H.-W. , Thomas J. E. , Stanford K. 
Published: April 2014

ABSTRACT

The objectives of this study were to identify endemic bacteriophages (phages) in the feedlot environment and determine relationships of these phages to
Escherichia coli
O157:H7 from cattle shedding high and low numbers of naturally occurring
E. coli
O157:H7. Angus crossbred steers were purchased from a southern Alberta (Canada) feedlot where cattle excreting ≥10
4
CFU · g
−1
of
E. coli
O157:H7 in feces at a single time point were identified as supershedders (SS;
n
= 6), and cattle excreting <10
4
CFU · g
−1
of feces were identified as low shedders (LS;
n
= 5). Fecal pats or fecal grabs were collected daily from individual cattle for 5 weeks.
E. coli
O157:H7 in feces was detected by immunomagnetic separation and enumerated by direct plating, and phages were isolated using short- and overnight-enrichment methods. The total prevalence of
E. coli
O157:H7 isolated from feces was 14.4% and did not differ between LS and SS (
P
= 0.972). The total prevalence of phages was higher in the LS group (20.9%) than in the SS group (8.3%;
P
= 0.01). Based on genome size estimated by pulsed-field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of
Myoviridae
and T1-like phage of
Siphoviridae
were isolated. Compared to T1- and O1-like phages, T4-like phages exhibited a broad host range and strong lytic capability when targeting
E. coli
O157:H7. Moreover, the T4-like phages were more frequently isolated from feces of LS than SS, suggesting that endemic phages may impact the shedding dynamics of
E. coli
O157:H7 in cattle.
Reconstruction of
mreB
Expression in Staphylococcus aureus via a Collection of New Integrative Plasmids
Authors: Yepes Ana , Koch Gudrun , Waldvogel Andrea , Garcia-Betancur Juan-Carlos , Lopez Daniel 
Published: April 2014

ABSTRACT

Protein localization has been traditionally explored in unicellular organisms, whose ease of genetic manipulation facilitates molecular characterization. The two rod-shaped bacterial models
Escherichia coli
and
Bacillus subtilis
have been prominently used for this purpose and have displaced other bacteria whose challenges for genetic manipulation have complicated any study of cell biology. Among these bacteria is the spherical pathogenic bacterium
Staphylococcus aureus
. In this report, we present a new molecular toolbox that facilitates gene deletion in staphylococci in a 1-step recombination process and additional vectors that facilitate the insertion of diverse reporter fusions into newly identified neutral loci of the
S. aureus
chromosome. Insertion of the reporters does not add any antibiotic resistance genes to the chromosomes of the resultant strains, thereby making them amenable for further genetic manipulations. We used this toolbox to reconstitute the expression of
mreB
in
S. aureus
, a gene that encodes an actin-like cytoskeletal protein which is absent in coccal cells and is presumably lost during the course of speciation. We observed that in
S. aureus
, MreB is organized in discrete structures in association with the membrane, leading to an unusual redistribution of the cell wall material. The production of MreB also caused cell enlargement, but it did not revert staphylococcal shape. We present interactions of MreB with key staphylococcal cell wall-related proteins. This work facilitates the use
S. aureus
as a model system in exploring diverse aspects of cellular microbiology.
In Situ
Evaluation of Paenibacillus alvei in Reducing Carriage of Salmonella enterica Serovar Newport on Whole Tomato Plants
Authors: Allard Sarah , Enurah Alexander , Strain Errol , Millner Patricia , Rideout Steven L. , Brown Eric W. , Zheng Jie 
Published: April 2014

ABSTRACT

Recently, tomatoes have been implicated as a primary vehicle in food-borne outbreaks of
Salmonella enterica
serovar Newport and other
Salmonella
serovars. Long-term intervention measures to reduce
Salmonella
prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as
Paenibacillus alvei
was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. After initial antimicrobial activity screening against
Salmonella
and 10 other bacterial pathogens associated with the human food supply, strain TS-15 was further used to challenge an attenuated strain of
S
. Newport on inoculated fruits, leaves, and blossoms of tomato plants in an insect-screened high tunnel with a split-plot design. Survival of
Salmonella
after inoculation was measured for groups with and those without the antagonist at days 0, 1, 2, and 3 and either day 5 for blossoms or day 6 for fruits and leaves. Strain TS-15 exhibited broad-range antimicrobial activity against both major food-borne pathogens and major bacterial phytopathogens of tomato. After
P. alvei
strain TS-15 was applied onto the fruits, leaves, and blossoms of tomato plants, the concentration of
S
. Newport declined significantly (
P
≤ 0.05) compared with controls. Astonishingly, >90% of the plants had no detectable levels of
Salmonella
by day 5 for blossoms. The naturally occurring antagonist strain TS-15 is highly effective in reducing the carriage of
Salmonella
Newport on whole tomato plants. The application of
P. alvei
strain TS-15 is a promising approach for reducing the risk of
Salmonella
contamination during tomato production.
Triggering Respirofermentative Metabolism in the Crabtree-Negative Yeast Pichia guilliermondii by Disrupting the
CAT8
Gene
Authors: Qi Kai , Zhong Jian-Jiang , Xia Xiao-Xia 
Published: April 2014

ABSTRACT

Pichia guilliermondii
is a Crabtree-negative yeast that does not normally exhibit respirofermentative metabolism under aerobic conditions, and methods to trigger this metabolism may have applications for physiological study and industrial applications. In the present study,
CAT8
, which encodes a putative global transcriptional activator, was disrupted in
P. guilliermondii
. This yeast's ethanol titer increased by >20-fold compared to the wild type (WT) during aerobic fermentation using glucose. A comparative transcriptional analysis indicated that the expression of genes in the tricarboxylic acid cycle and respiratory chain was repressed in the
CAT8
-disrupted (Δ
CAT8
) strain, while the fermentative pathway genes were significantly upregulated. The respiratory activities in the Δ
CAT8
strain, indicated by the specific oxygen uptake rate and respiratory state value, decreased to one-half and one-third of the WT values, respectively. In addition, the expression of
HAP4
, a transcriptional respiratory activator, was significantly repressed in the Δ
CAT8
strain. Through disruption of
HAP4
, the ethanol production of
P. guilliermondii
was also increased, but the yield and titer were lower than that in the Δ
CAT8
strain. A further transcriptional comparison between Δ
CAT8
and Δ
HAP4
strains suggested a more comprehensive reprogramming function of
Cat8
in the central metabolic pathways. These results indicated the important role of
CAT8
in regulating the glucose metabolism of
P. guilliermondii
and that the regulation was partially mediated by repressing
HAP4
. The strategy proposed here might be applicable to improve the aerobic fermentation capacity of other Crabtree-negative yeasts.
Cryptococcus neoformans Dual GDP-Mannose Transporters and Their Role in Biology and Virulence
Authors: Wang Zhuo A. , Griffith Cara L. , Skowyra Michael L. , Salinas Nichole , Williams Matthew , Maier Ezekiel J. , Gish Stacey R. , Liu Hong , Brent Michael R. , Doering Tamara L. 
Published: April 2014

ABSTRACT

Cryptococcus neoformans
is an opportunistic yeast responsible for lethal meningoencephalitis in humans. This pathogen elaborates a polysaccharide capsule, which is its major virulence factor. Mannose constitutes over one-half of the capsule mass and is also extensively utilized in cell wall synthesis and in glycosylation of proteins and lipids. The activated mannose donor for most biosynthetic reactions, GDP-mannose, is made in the cytosol, although it is primarily consumed in secretory organelles. This compartmentalization necessitates specific transmembrane transporters to make the donor available for glycan synthesis. We previously identified two cryptococcal GDP-mannose transporters, Gmt1 and Gmt2. Biochemical studies of each protein expressed in
Saccharomyces cerevisiae
showed that both are functional, with similar kinetics and substrate specificities
in vitro
. We have now examined these proteins
in vivo
and demonstrate that cells lacking Gmt1 show significant phenotypic differences from those lacking Gmt2 in terms of growth, colony morphology, protein glycosylation, and capsule phenotypes. Some of these observations may be explained by differential expression of the two genes, but others suggest that the two proteins play overlapping but nonidentical roles in cryptococcal biology. Furthermore,
gmt1 gmt2
double mutant cells, which are unexpectedly viable, exhibit severe defects in capsule synthesis and protein glycosylation and are avirulent in mouse models of cryptococcosis.
Trypanosoma cruzi Bromodomain Factor 3 Binds Acetylated α-Tubulin and Concentrates in the Flagellum during Metacyclogenesis
Authors: Alonso Victoria Lucia , Villanova Gabriela Vanina , Ritagliati Carla , Machado Motta María Cristina , Cribb Pamela , Serra Esteban Carlos 
Published: April 2014

ABSTRACT

Bromodomains are highly conserved acetyl-lysine binding domains found mainly in proteins associated with chromatin and nuclear acetyltransferases. The
Trypanosoma cruzi
genome encodes at least four bromodomain factors (
Tc
BDFs). We describe here bromodomain factor 3 (
Tc
BDF3), a bromodomain-containing protein localized in the cytoplasm.
Tc
BDF3 cytolocalization was determined, using purified antibodies, by Western blot and immunofluorescence analyses in all life cycle stages of
T. cruzi
. In epimastigotes and amastigotes, it was detected in the cytoplasm, the flagellum, and the flagellar pocket, and in trypomastigotes only in the flagellum. Subcellular localization of
Tc
BDF3 was also determined by digitonin extraction, ultrastructural immunocytochemistry, and expression of
Tc
BDF3 fused to cyan fluorescent protein (CFP). Tubulin can acquire different posttranslational modifications, which modulate microtubule functions. Acetylated α-tubulin has been found in the axonemes of flagella and cilia, as well as in the subpellicular microtubules of trypanosomatids.
Tc
BDF3 and acetylated α-tubulin partially colocalized in isolated cytoskeletons and flagella from
T. cruzi
epimastigotes and trypomastigotes. Interaction between the two proteins was confirmed by coimmunoprecipitation and far-Western blot assays with synthetic acetylated α-tubulin peptides and recombinant
Tc
BDF3.
Construction and Characterization of a Borrelia burgdorferi Strain with Conditional Expression of the Essential Telomere Resolvase, ResT
Authors: Bandy Nicholas J. , Salman-Dilgimen Aydan , Chaconas George 
Published: April 2014

ABSTRACT

Borrelia
species are unique in the bacterial world in possessing segmented genomes which sometimes contain over 20 genetic elements. Most elements are linear and contain covalently closed hairpin ends requiring a specialized process, telomere resolution, for their generation. Hairpin telomere resolution is mediated by the telomere resolvase, ResT. Although the process has been studied extensively
in vitro
, the essential nature of the
resT
gene has precluded biological studies to further probe the role of ResT. In this work, we have generated a
B. burgdorferi
strain that carries an isopropyl-β-
d
-thiogalactopyranoside (IPTG)-inducible
resT
gene controlled by a tightly regulated promoter. ResT is expressed in this strain at ∼14,000 monomers per cell, similar to the ∼15,000 monomers observed for the parental strain. We demonstrate ResT depletion with a half-life of 16 h upon IPTG washout. ResT depletion resulted in arrested growth 48 h after washout. Interestingly, not all spirochetes died after ResT washout, and at least 15% remained quiescent and could be resuscitated even at 2 weeks postwashout. Significant levels of DNA synthesis were not observed upon growth arrest, suggesting that ResT might interact directly or indirectly with factors controlling the initiation or elongation of DNA synthesis. Analysis of the linear plasmids lp17 and lp28-2 showed that the linear forms of these plasmids began to disappear and be replaced by higher-molecular-weight forms by 24 h post-IPTG washout. Treatment of DNA from the ResT-depleted strain with ResT
in vitro
revealed the presence of replicated telomeres expected in replication intermediates.
Streptococcus mutans Extracellular DNA Is Upregulated during Growth in Biofilms, Actively Released via Membrane Vesicles, and Influenced by Components of the Protein Secretion Machinery
Authors: Liao Sumei , Klein Marlise I. , Heim Kyle P. , Fan Yuwei , Bitoun Jacob P. , Ahn San-Joon , Burne Robert A. , Koo Hyun , Brady L. Jeannine , Wen Zezhang T. 
Published: April 2014

ABSTRACT

Streptococcus mutans
, a major etiological agent of human dental caries, lives primarily on the tooth surface in biofilms. Limited information is available concerning the extracellular DNA (eDNA) as a scaffolding matrix in
S. mutans
biofilms. This study demonstrates that
S. mutans
produces eDNA by multiple avenues, including lysis-independent membrane vesicles. Unlike eDNAs from cell lysis that were abundant and mainly concentrated around broken cells or cell debris with floating open ends, eDNAs produced via the lysis-independent pathway appeared scattered but in a structured network under scanning electron microscopy. Compared to eDNA production of planktonic cultures, eDNA production in 5- and 24-h biofilms was increased by >3- and >1.6-fold, respectively. The addition of DNase I to growth medium significantly reduced biofilm formation. In an
in vitro
adherence assay, added chromosomal DNA alone had a limited effect on
S. mutans
adherence to saliva-coated hydroxylapatite beads, but in conjunction with glucans synthesized using purified glucosyltransferase B, the adherence was significantly enhanced. Deletion of sortase A, the transpeptidase that covalently couples multiple surface-associated proteins to the cell wall peptidoglycan, significantly reduced eDNA in both planktonic and biofilm cultures. Sortase A deficiency did not have a significant effect on membrane vesicle production; however, the protein profile of the mutant membrane vesicles was significantly altered, including reduction of adhesin P1 and glucan-binding proteins B and C. Relative to the wild type, deficiency of protein secretion and membrane protein insertion machinery components, including Ffh, YidC1, and YidC2, also caused significant reductions in eDNA.