bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of Listeria Species in Urban and Natural Environments
Authors: Sauders Brian D. , Overdevest Jon , Fortes Esther , Windham Katy , Schukken Ynte , Lembo Arthur , Wiedmann Martin 
Published: April 2012

ABSTRACT

A total of 442
Listeria
isolates, including 234
Listeria seeligeri
, 80
L. monocytogenes
, 74
L. welshimeri
, 50
L. innocua
, and 4
L. marthii
isolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments.
Listeria
spp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. While
L. seeligeri
and
L. welshimeri
were significantly associated with natural environments (
P
≤ 0.0001),
L. innocua
and
L. monocytogenes
were significantly associated with urban environments (
P
≤ 0.0001). Sequencing of
sigB
for all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. Some
Listeria
spp. and
sigB
allelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certain
Listeria
spp. and
sigB
allelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genus
Listeria
not only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates that
Listeria
species and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed for
Listeria
and (ii) that detection of some
Listeria
species may not be a good indicator for
L. monocytogenes
.
High-Throughput Screening for Streptomyces Antibiotic Biosynthesis Activators
Authors: Chen Li , Wang Yemin , Guo Hang , Xu Min , Deng Zixin , Tao Meifeng 
Published: April 2012

ABSTRACT

A genomic cosmid library of
Streptomyces clavuligerus
was constructed and transferred efficiently by conjugation to
Streptomyces lividans
, and 12 distinct groups of overlapping cosmid clones that activated the silent actinorhodin biosynthesis gene cluster were identified. This generally applicable high-throughput screening procedure greatly facilitates the identification of antibiotic biosynthesis activators.
Increase in Furfural Tolerance in Ethanologenic Escherichia coli LY180 by Plasmid-Based Expression of
thyA
Authors: Zheng Huabao , Wang Xuan , Yomano Lorraine P. , Shanmugam Keelnatham T. , Ingram Lonnie O. 
Published: April 2012

ABSTRACT

Furfural is an inhibitory side product formed during the depolymerization of hemicellulose by mineral acids. Genomic libraries from three different bacteria (
Bacillus subtilis
YB886,
Escherichia coli
NC3, and
Zymomonas mobilis
CP4) were screened for genes that conferred furfural resistance on plates. Beneficial plasmids containing the
thyA
gene (coding for thymidylate synthase) were recovered from all three organisms. Expression of this key gene in the
de novo
pathway for dTMP biosynthesis improved furfural resistance on plates and during fermentation. A similar benefit was observed by supplementation with thymine, thymidine, or the combination of tetrahydrofolate and serine (precursors for 5,10-methylenetetrahydrofolate, the methyl donor for ThyA). Supplementation with deoxyuridine provided a small benefit, and deoxyribose was of no benefit for furfural tolerance. A combination of thymidine and plasmid expression of
thyA
was no more effective than either alone. Together, these results demonstrate that furfural tolerance is increased by approaches that increase the supply of pyrimidine deoxyribonucleotides. However, ThyA activity was not directly affected by the addition of furfural. Furfural has been previously shown to damage DNA in
E. coli
and to activate a cellular response to oxidative damage in yeast. The added burden of repairing furfural-damaged DNA in
E. coli
would be expected to increase the cellular requirement for dTMP. Increased expression of
thyA
(
E. coli
,
B. subtilis
, or
Z. mobilis
), supplementation of cultures with thymidine, and supplementation with precursors for 5,10-methylenetetrahydrofolate (methyl donor) are each proposed to increase furfural tolerance by increasing the availability of dTMP for DNA repair.
Dioxygenation of the Biphenyl Dioxygenation Product
Authors: Overwin Heike , González Myriam , Méndez Valentina , Seeger Michael , Wray Victor , Hofer Bernd 
Published: April 2012

ABSTRACT

Two biphenyl dioxygenases (BphAs) were shown to catalyze dioxygenation of biphenyldienediol in the nonoxidized ring to form the respective symmetrical biphenyl-bis-dienediol. This novel metabolite served as a growth substrate for both BphA source strains. Its catabolism through the upper
bph
pathway of
Burkholderia xenovorans
LB400 was analyzed.
Insights into the Maturation of Hyperthermophilic Pyrolysin and the Roles of Its N-Terminal Propeptide and Long C-Terminal Extension
Authors: Dai Zheng , Fu Heting , Zhang Yufeng , Zeng Jing , Tang Bing , Tang Xiao-Feng 
Published: April 2012

ABSTRACT

Pyrolysin-like proteases from hyperthermophiles are characterized by large insertions and long C-terminal extensions (CTEs). However, little is known about the roles of these extra structural elements or the maturation of these enzymes. Here, the recombinant proform of
Pyrococcus furiosus
pyrolysin (Pls) and several N- and C-terminal deletion mutants were successfully expressed in
Escherichia coli
. Pls was converted to mature enzyme (mPls) at high temperatures via autoprocessing of both the N-terminal propeptide and the C-terminal portion of the long CTE, indicating that the long CTE actually consists of the C-terminal propeptide and the C-terminal extension (CTEm), which remains attached to the catalytic domain in the mature enzyme. Although the N-terminal propeptide deletion mutant PlsΔN displayed weak activity, this mutant was highly susceptible to autoproteolysis and/or thermogenic hydrolysis. The N-terminal propeptide acts as an intramolecular chaperone to assist the folding of pyrolysin into its thermostable conformation. In contrast, the C-terminal propeptide deletion mutant PlsΔC199 was converted to a mature form (mPlsΔC199), which is the same size as but less stable than mPls, suggesting that the C-terminal propeptide is not essential for folding but is important for pyrolysin hyperthermostability. Characterization of the full-length (mPls) and CTEm deletion (mPlsΔC740) mature forms demonstrated that CTEm not only confers additional stability to the enzyme but also improves its catalytic efficiency for both proteineous and small synthetic peptide substrates. Our results may provide important clues about the roles of propeptides and CTEs in the adaptation of hyperthermophilic proteases to hyperthermal environments.
Identification of the Promoter in the Intergenic Region between
orf1
and
cry8Ea1
Controlled by Sigma H Factor
Authors: Du Lixin , Qiu Lili , Peng Qi , Lereclus Didier , Zhang Jie , Song Fuping , Huang Dafang 
Published: April 2012

ABSTRACT

Bacillus thuringiensis
Cry8Ea toxin is specifically toxic to larvae of the Asian cockchafer,
Holotrichia parallela
. Here we investigated the mechanism of transcriptional regulation of the
cry8Ea1
gene. Reverse transcription-PCR (RT-PCR) results indicated that
cry8Ea1
and an upstream gene (
orf1
) were cotranscribed. Transcriptional fusions with the
lacZ
gene demonstrated that transcription of the
cry8Ea1
gene started from two promoters: P

orf1

, which is located upstream of the
orf1
gene, and P

cry8E

, located in the intergenic region mapping between
orf1
and
cry8Ea1
. Of the known, similar
orf1-cry
operons, this is the first report of the existence of a promoter in the intergenic region between the
orf1
and
cry
genes. The transcriptional activity of P

orf1

was found during sporulation in
B. thuringiensis
subsp.
kurstaki
HD-73 and was almost abolished in the
sigE
mutant, while the transcriptional activity of P

cry8E

was detected after the end of the exponential phase in HD-73 and was considerably lower in the
sigH
mutant. The transcription start sites generated by the two
cry8Ea1
promoters were determined by the 5′ -SMARTer rapid amplification of cDNA ends (RACE) method. The −35 and −10 regions of P

orf1

and P

cry8E

showed high sequence similarity with the σ
E
and σ
H
promoters, respectively. These results indicated that P

orf1

is controlled by the σ
E
factor and P

cry8E

by the σ
H
factor.
Complete Sequence Analysis of Two Methanotroph-Specific
repABC
-Containing Plasmids from Methylocystis sp. Strain SC2
Authors: Dam Bomba , Kube Michael , Dam Somasri , Reinhardt Richard , Liesack Werner 
Published: April 2012

ABSTRACT

The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium
Methylocystis
sp. strain SC2. The physical existence of the two plasmids in strain SC2 was confirmed by pulsed-field gel electrophoresis followed by Southern hybridization. Both plasmids have a conserved replication module of the
repABC
system and carry genes involved in their faithful maintenance and conjugation. In addition, they contain genes that might be involved in essential metabolic processes. These include several heavy metal resistance genes and copper transport genes in pBSC2-1 and a complete nitrous oxide reductase operon and a
pmoC
singleton in pBSC2-2, the latter encoding the PmoC subunit of particulate methane monooxygenase.
Novel Clade of Alphaproteobacterial Endosymbionts Associated with Stinkbugs and Other Arthropods
Authors: Matsuura Yu , Kikuchi Yoshitomo , Meng Xian Ying , Koga Ryuichi , Fukatsu Takema 
Published: April 2012

ABSTRACT

Here we report a novel clade of secondary endosymbionts associated with insects and other arthropods. Seed bugs of the genus
Nysius
(Hemiptera: Lygaeidae) harbor the primary gammaproteobacterial symbiont
Schneideria nysicola
within a pair of bacteriomes in the abdomen. Our survey of
Nysius
species for their facultative bacterial associates consistently yielded a novel type of alphaproteobacterial 16S rRNA gene sequence in addition to those of
Wolbachia
. Diagnostic PCR survey of 343 individuals representing 24 populations of four
Nysius
species revealed overall detection rates of the alphaproteobacteria at 77.6% in
Nysius plebeius
, 87.7% in
Nysius
sp. 1, 81.0% in
Nysius
sp. 2, and 100% in
Nysius expressus
. Further survey of diverse stinkbugs representing 24 families, 191 species, and 582 individuals detected the alphaproteobacteria from an additional 12 species representing six families. Molecular phylogenetic analysis showed that the alphaproteobacteria from the stinkbugs form a distinct and coherent monophyletic group in the order
Rickettsiales
together with several uncharacterized endosymbionts from fleas and ticks. The alphaproteobacterial symbiont clade was allied to bacterial clades such as the endosymbionts of acanthamoebae, the endosymbionts of cnidarians, and
Midichloria
spp., the mitochondrion-associated endosymbionts of ticks.
In situ
hybridization and electron microscopy identified small filamentous bacterial cells in various tissues of
N. plebeius
, including the bacteriome and ovary. The concentrated localization of the symbiont cells at the anterior pole of oocytes indicated its vertical transmission route through host insect generations. The designation “
Candidatus
Lariskella arthropodarum” is proposed for the endosymbiont clade.
Prevalence of Clostridium difficile in Uncooked Ground Meat Products from Pittsburgh, Pennsylvania
Authors: Curry Scott R. , Marsh Jane W. , Schlackman Jessica L. , Harrison Lee H. 
Published: April 2012

ABSTRACT

The prevalence of
Clostridium difficile
in retail meat samples has varied widely. The food supply may be a source for
C. difficile
infections. A total of 102 ground meat and sausage samples from 3 grocers in Pittsburgh, PA, were cultured for
C. difficile
. Brand A pork sausages were resampled between May 2011 and January 2012. Two out of 102 (2.0%) meat products initially sampled were positive for
C. difficile
; both were pork sausage from brand A from the same processing facility (facility A). On subsequent sampling of brand A products, 10/19 samples from processing facility A and 1/10 samples from 3 other facilities were positive for
C. difficile
. The isolates recovered were inferred ribotype 078, comprising 6 genotypes. The prevalence of
C. difficile
in retail meat may not be as high as previously reported in North America. When contamination occurs, it may be related to events at processing facilities.
Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes
Authors: Collins Andrew J. , LaBarre Brenna A. , Wong Won Brian S. , Shah Monica V. , Heng Steven , Choudhury Momena H. , Haydar Shahela A. , Santiago Jose , Nyholm Spencer V. 
Published: April 2012

ABSTRACT

Microbial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid,
Euprymna scolopes
, a well-studied model organism for symbiosis research. Transmission electron microscopy (TEM) analysis of the ANG revealed dense bacterial assemblages of rod- and coccus-shaped cells segregated by morphology into separate, epithelium-lined tubules. The host epithelium was morphologically heterogeneous, containing ciliated and nonciliated cells with various brush border thicknesses. Hemocytes of the host's innate immune system were also found in close proximity to the bacteria within the tubules. A census of 16S rRNA genes suggested that
Rhodobacterales, Rhizobiales
, and
Verrucomicrobia
bacteria were prevalent, with members of the genus
Phaeobacter
dominating the consortium. Analysis of 454-shotgun sequencing data confirmed the presence of members of these taxa and revealed members of a fourth,
Flavobacteria
of the
Bacteroidetes
phylum. 16S rRNA fluorescent
in situ
hybridization (FISH) revealed that many ANG tubules were dominated by members of specific taxa, namely,
Rhodobacterales
,
Verrucomicrobia
, or
Cytophaga-Flavobacteria-Bacteroidetes
, suggesting symbiont partitioning to specific host tubules. In addition, FISH revealed that bacteria, including
Phaeobacter
species from the ANG, are likely deposited into the jelly coat of freshly laid eggs. This report establishes the ANG of the invertebrate
E. scolopes
as a model to examine interactions between a bacterial consortium and its host.
Abundance, Distribution, and Activity of Fe(II)-Oxidizing and Fe(III)-Reducing Microorganisms in Hypersaline Sediments of Lake Kasin, Southern Russia
Authors: Emmerich Maren , Bhansali Ankita , Lösekann-Behrens Tina , Schröder Christian , Kappler Andreas , Behrens Sebastian 
Published: April 2012

ABSTRACT

The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing
Bacteria
and
Archaea
in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter
−1
) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for
Bacteria
and
Archaea
revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 × 10
2
to 8.32 × 10
3
iron(II)-oxidizing
Bacteria
and 4.16 × 10
2
to 2.13 × 10
3
iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total
Bacteria
, total
Archaea
, and species dominating the iron(III)-reducing enrichment cultures (relatives of
Halobaculum gomorrense
,
Desulfosporosinus lacus
, and members of the
Bacilli
) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.
Styrene Oxide Isomerase of Rhodococcus opacus 1CP, a Highly Stable and Considerably Active Enzyme
Authors: Oelschlägel Michel , Gröning Janosch A. D. , Tischler Dirk , Kaschabek Stefan R. , Schlömann Michael 
Published: April 2012

ABSTRACT

Styrene oxide isomerase (SOI) is involved in peripheral styrene catabolism of bacteria and converts styrene oxide to phenylacetaldehyde. Here, we report on the identification, enrichment, and biochemical characterization of a novel representative from the actinobacterium
Rhodococcus opacus
1CP. The enzyme, which is strongly induced during growth on styrene, was shown to be membrane integrated, and a convenient procedure was developed to highly enrich the protein in active form from the wild-type host. A specific activity of about 370 U mg
−1
represents the highest activity reported for this enzyme class so far. This, in combination with a wide pH and temperature tolerance, the independence from cofactors, and the ability to convert a spectrum of substituted styrene oxides, makes a biocatalytic application imaginable. First, semipreparative conversions were performed from which up to 760 μmol of the pure phenylacetaldehyde could be obtained from 130 U of enriched SOI. Product concentrations of up to 76 mM were achieved. However, due to the high chemical reactivity of the aldehyde function, SOI was shown to be the subject of an irreversible product inhibition. A half-life of 15 min was determined at a phenylacetaldehyde concentration of about 55 mM, indicating substantial limitations of applicability and the need to modify the process.
Distribution of Genetic Marker Concentrations for Fecal Indicator Bacteria in Sewage and Animal Feces
Authors: Kelty Catherine A. , Varma Manju , Sivaganesan Mano , Haugland Richard A. , Shanks Orin C. 
Published: April 2012

ABSTRACT

Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including
Clostridium
spp.,
Escherichia coli
, enterococci, and
Bacteroidales
, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (
P
> 0.05). In addition, large differences (up to 5 log
10
copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications.
Overexpression of Genes Encoding Glycolytic Enzymes in Corynebacterium glutamicum Enhances Glucose Metabolism and Alanine Production under Oxygen Deprivation Conditions
Authors: Yamamoto Shogo , Gunji Wataru , Suzuki Hiroaki , Toda Hiroshi , Suda Masako , Jojima Toru , Inui Masayuki , Yukawa Hideaki 
Published: April 2012

ABSTRACT

We previously reported that
Corynebacterium glutamicum
strain Δ
ldhA
Δ
ppc
+
alaD
+
gapA
, overexpressing glyceraldehyde-3-phosphate dehydrogenase-encoding
gapA
, shows significantly improved glucose consumption and alanine formation under oxygen deprivation conditions (T. Jojima, M. Fujii, E. Mori, M. Inui, and H. Yukawa, Appl. Microbiol. Biotechnol. 87:159–165, 2010). In this study, we employ stepwise overexpression and chromosomal integration of a total of four genes encoding glycolytic enzymes (herein referred to as glycolytic genes) to demonstrate further successive improvements in
C. glutamicum
glucose metabolism under oxygen deprivation. In addition to
gapA
, overexpressing pyruvate kinase-encoding
pyk
and phosphofructokinase-encoding
pfk
enabled strain GLY2/pCRD500 to realize respective 13% and 20% improved rates of glucose consumption and alanine formation compared to GLY1/pCRD500. Subsequent overexpression of glucose-6-phosphate isomerase-encoding
gpi
in strain GLY3/pCRD500 further improved its glucose metabolism. Notably, both alanine productivity and yield increased after each overexpression step. After 48 h of incubation, GLY3/pCRD500 produced 2,430 mM alanine at a yield of 91.8%. This was 6.4-fold higher productivity than that of the wild-type strain. Intracellular metabolite analysis showed that
gapA
overexpression led to a decreased concentration of metabolites upstream of glyceraldehyde-3-phosphate dehydrogenase, suggesting that the overexpression resolved a bottleneck in glycolysis. Changing ratios of the extracellular metabolites by overexpression of glycolytic genes resulted in reduction of the intracellular NADH/NAD
+
ratio, which also plays an important role on the improvement of glucose consumption. Enhanced alanine dehydrogenase activity using a high-copy-number plasmid further accelerated the overall alanine productivity. Increase in glycolytic enzyme activities is a promising approach to make drastic progress in growth-arrested bioprocesses.