bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Blue Pigment Produced by
Pantoea agglomerans
and Its Production Characteristics at Various Temperatures
Authors: Fujikawa Hiroshi , Akimoto Ryo 
Published: October 2010

ABSTRACT

A bacterium capable of producing a deep blue pigment was isolated from the environment and identified as
Pantoea agglomerans
. The pigment production characteristics of the bacterium under various conditions were studied. The optimal agar plate ingredients for pigment production by the bacterium were first studied: the optimal ingredients were 5 g/liter glucose, 10 g/liter tryptic soy broth, and 40 g/liter glycerol at pH 6.4. Bacterial cells grew on the agar plate during the incubation, while the pigment spread into the agar plate, meaning that it is water soluble. Pigment production was affected by the initial cell density. Namely, at higher initial cell densities ranging from 10
6.3
to 10
8.2
CFU/cm
2
on the agar plate, faster pigment production was observed, but no blue pigment was produced at a very high initial density of 10
9.1
CFU/cm
2
. Thus, the cell population of 10
8.2
CFU/cm
2
was used for subsequent study. Although the bacterium was capable of growing at temperatures above and below 10°C, it could produce the pigment only at temperatures of ≥10°C. Moreover, the pigment production was faster at higher temperatures in the range of 10 to 20°C. Pigment production at various temperature patterns was well described by a new logistic model. These results suggested that the bacterium could be used in the development of a microbial temperature indicator for the low-temperature-storage management of foods and clinical materials. To our knowledge, there is no other
P. agglomerans
strain capable of producing a blue pigment and the pigment is a new one of microbial origin.
Multiple UniqueCryptosporidiumIsolates from Three Species of Ground Squirrels (Spermophilus beecheyi,S. beldingi, andS. lateralis) in California
Authors: Pereira Maria das Graças Cabral , Li Xunde , McCowan Brenda , Phillips Ralph L. , Atwill Edward R. 
Published: October 2010

ABSTRACTPhylogenetic analyses of the 18S small-subunit (SSU) rRNA andCryptosporidiumoocyst wall protein (COWP) genes indicate that multiple uniqueCryptosporidiumisolates are shed by separate species ofSpermophilusground squirrels (S. beecheyi,S. beldingi, andS. lateralis) throughout California, despite some squirrel populations' being geographically isolated. The data support our assertion thatSpermophilussquirrels shed novelCryptosporidiumspecies.
Modulation of
Pseudomonas aeruginosa
Biofilm Dispersal by a Cyclic-Di-GMP Phosphodiesterase with a Putative Hypoxia-Sensing Domain
Authors: An Shuwen , Wu Ji'en , Zhang Lian-Hui 
Published: October 2010

ABSTRACT

Pseudomonas aeruginosa
encodes many enzymes that are potentially associated with the synthesis or degradation of the widely conserved second messenger cyclic-di-GMP (c-di-GMP). In this study, we show that mutation of
rbdA
, which encodes a fusion protein consisting of PAS-PAC-GGDEF-EAL multidomains, results in decreased biofilm dispersal. RbdA contains a highly conserved GGDEF domain and EAL domain, which are involved in the synthesis and degradation of c-di-GMP, respectively. However,
in vivo
and
in vitro
analyses show that the full-length RbdA protein only displays phosphodiesterase activity, causing c-di-GMP degradation. Further analysis reveals that the GGDEF domain of RbdA plays a role in activating the phosphodiesterase activity of the EAL domain in the presence of GTP. Moreover, we show that deletion of the PAS domain or substitution of the key residues implicated in sensing low-oxygen stress abrogates the functionality of RbdA. Subsequent study showed that RbdA is involved in positive regulation of bacterial motility and production of rhamnolipids, which are associated with biofilm dispersal, and in negative regulation of production of exopolysaccharides, which are required for biofilm formation. These data indicate that the c-di-GMP-degrading regulatory protein RbdA promotes biofilm dispersal through its two-pronged effects on biofilm development, i.e., downregulating biofilm formation and upregulating production of the factors associated with biofilm dispersal.
Effect of Sulfadiazine-Contaminated Pig Manure on the Abundances of Genes and Transcripts Involved in Nitrogen Transformation in the Root-Rhizosphere Complexes of Maize and Clover
Authors: Ollivier Julien , Kleineidam Kristina , Reichel Rüdiger , Thiele-Bruhn Sören , Kotzerke Anja , Kindler Reimo , Wilke Berndt-Michael , Schloter Michael 
Published: October 2010

ABSTRACT

The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (
Zea mays
) and clover (
Trifolium alexandrinum
). At both the gene and transcript level, we performed real-time PCR using
nifH
,
amoA
(in both ammonia-oxidizing bacteria and archaea),
nirK
,
nirS
, and
nosZ
as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of
nifH
and clover, have been protected by the nodules.
Antimicrobial Resistance of
Campylobacter
Isolates from Retail Meat in the United States between 2002 and 2007
Authors: Zhao S. , Young S. R. , Tong E. , Abbott J. W. , Womack N. , Friedman S. L. , McDermott P. F. 
Published: October 2010

ABSTRACT

The emergence of antimicrobial resistance in
Campylobacter
spp. has been a growing public health concern globally. The objectives of this study were to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of
Campylobacter
spp. recovered by the National Antimicrobial Resistance Monitoring System (NARMS) retail meat program. Retail meat samples (
n
= 24,566) from 10 U.S. states collected between 2002 and 2007, consisting of 6,138 chicken breast, 6,109 ground turkey, 6,171 ground beef, and 6,148 pork chop samples, were analyzed. A total of 2,258
Campylobacter
jejuni
, 925
Campylobacter
coli
, and 7
Campylobacter
lari
isolates were identified. Chicken breast samples showed the highest contamination rate (49.9%), followed by ground turkey (1.6%), whereas both pork chops and ground beef had <0.5% contamination. The most common resistance was to doxycycline/tetracycline (46.6%), followed by nalidixic acid (18.5%), ciprofloxacin (17.4%), azithromycin and erythromycin (2.8%), telithromycin (2.4%), clindamycin (2.2%), and gentamicin (<0.1%). In a subset of isolates tested, no resistance to meropenem and florfenicol was seen.
C. coli
isolates showed higher resistance rates to antimicrobials, with the exception of doxycycline/tetracycline, than those seen for C
. jejuni
. Pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 1,226 PFGE profiles among the 2,318 isolates, with many clones being widely dispersed throughout the 6-year sampling period.
Phylogenetic, Microbiological, and Glycoside Hydrolase Diversities within the Extremely Thermophilic, Plant Biomass-Degrading Genus
Caldicellulosiruptor
Authors: Blumer-Schuette Sara E. , Lewis Derrick L. , Kelly Robert M. 
Published: October 2010

ABSTRACT

Phylogenetic, microbiological, and comparative genomic analyses were used to examine the diversity among members of the genus
Caldicellulosiruptor
, with an eye toward the capacity of these extremely thermophilic bacteria to degrade the complex carbohydrate content of plant biomass. Seven species from this genus (
C. saccharolyticus
,
C. bescii
,
C. hydrothermalis
,
C. owensensis
,
C. kronotskyensis
,
C. lactoaceticus
, and
C. kristjanssonii
) were compared on the basis of 16S rRNA gene phylogeny and cross-species DNA-DNA hybridization to a whole-genome
C. saccharolyticus
oligonucleotide microarray, revealing that
C. saccharolyticus
was the most divergent within this group. Growth physiology of the seven
Caldicellulosiruptor
species on a range of carbohydrates showed that, while all could be cultivated on acid-pretreated switchgrass, only
C. saccharolyticus
,
C. bescii
,
C. kronotskyensis
, and
C. lactoaceticus
were capable of hydrolyzing Whatman no. 1 filter paper. Two-dimensional gel electrophoresis of the secretomes from cells grown on microcrystalline cellulose revealed that the cellulolytic species also had diverse secretome fingerprints. The
C. saccharolyticus
secretome contained a prominent S-layer protein that appears in the cellulolytic
Caldicellulosiruptor
species, suggesting a possible role in cell-substrate interactions. Growth physiology also correlated with glycoside hydrolase (GH) and carbohydrate-binding module (CBM) inventories for the seven bacteria, as deduced from draft genome sequence information. These inventories indicated that the absence of a single GH and CBM family was responsible for diminished cellulolytic capacity. Overall, the genus
Caldicellulosiruptor
appears to contain more genomic and physiological diversity than previously reported, and this argues for continued efforts to isolate new members from high-temperature terrestrial biotopes.
Genetic Improvement of
Bacillus licheniformis
Strains for Efficient Deproteinization of Shrimp Shells and Production of High-Molecular-Mass Chitin and Chitosan
Authors: Hoffmann Kerstin , Daum Gabriele , Köster Marina , Kulicke Werner-Michael , Meyer-Rammes Heike , Bisping Bernward , Meinhardt Friedhelm 
Published: October 2010

ABSTRACT

By targeted deletion of the polyglutamate operon (
pga
) in
Bacillus licheniformis
F11, a derivative form, F11.1 (Δ
pga
), was obtained that, along with lacking polyglutamate (PGA) formation, displayed enhanced proteolytic activities. The phenotypic properties were maintained in a strain in which the
chiBA
operon was additionally deleted: F11.4 (Δ
chiBA
Δ
pga
). These genetically modified strains, carrying the Δ
pga
deletion either alone (F11.1) or together with the Δ
chiBA
(F11.4) deletion, were used in fermentations (20-liter scale) aiming at the deproteinization of shrimp shells in order to obtain long-chain chitin. After chemical deacetylation, the resulting chitosan samples were analyzed by nuclear magnetic resonance spectroscopy, size exclusion chromatography, and viscometry and compared to a chitosan preparation that was produced in parallel by chemical methods by a commercial chitosan supplier (GSRmbH). Though faint lipid impurities were present in the fermented polysaccharides, the viscosity of the material produced with the double-deletion mutant F11.4 (Δ
pga
Δ
chiBA
) was higher than that of the chemically produced and commercially available samples (Cognis GmbH). Thus, enhanced proteolytic activities and a lack of chitinase activity render the double mutant F11.4 a powerful tool for the production of long-chain chitosan.
Purification and Characterization of an Active
N
-Acetylglucosaminyltransferase Enzyme Complex from Streptococci
Authors: Wu Ren , Zhou Meixian , Wu Hui 
Published: October 2010

ABSTRACT

A new family of bacterial serine-rich repeat glycoproteins can function as adhesins required for biofilm formation and pathogenesis in streptococci and staphylococci. Biogenesis of these proteins depends on a gene cluster coding for glycosyltransferases and accessory secretion proteins. Previous studies show that Fap1, a member of this family from
Streptococcus parasanguinis
, can be glycosylated by a protein glycosylation complex in a recombinant heterogeneous host. Here we report a tandem affinity purification (TAP) approach used to isolate and study protein complexes from native streptococci. This method demonstrated that a putative glycosyltransferase (Gtf2), which is essential for Fap1 glycosylation, readily copurified with another glycosyltransferase (Gtf1) from native
S. parasanguinis
. This result and the similar isolation of a homologous two-protein complex from
Streptococcus pneumoniae
indicate the biological relevance of the complexes to the glycosylation in streptococci. Furthermore, novel
N
-acetylglucosaminyltransferase activity was discovered for the complexes. Optimal activity required heterodimer formation and appears to represent a novel type of glycosylation.
Growth and Virulence Properties of Biofilm-FormingSalmonellaentericaSerovar Typhimurium under Different Acidic Conditions
Authors: Xu Hua , Lee Hyeon-Yong , Ahn Juhee 
Published: October 2010

ABSTRACTThis study was designed to characterize the viability and potential virulence of bofilm-formingSalmonellaentericaserovar Typhimurium under different pH levels, ranging from 5 to 7. The plate count method and real-time reverse transcription-PCR (RT-PCR) were used to evaluate the survival ofS.Typhimurium grown in Trypticase soy broth (TSB) adjusted to pH 5, 6, and 7 (TSB-5, TSB-6, and TSB-7, respectively) at 37°C for 10 days. In TSB-5 and TSB-6, the numbers of viable cells estimated by using the real-time RT-PCR were greater than the culturable counts enumerated by the plate count method. Reflectance micro-Fourier transform infrared (micro-FTIR) spectroscopy was used to evaluate the biochemical changes in biofilm cells. Considerable changes in chemical components were observed in the biofilm cells grown in TSB-5 and TSB-6 when compared to the cells grown in TSB-7. The enterotoxin production and invasive ability of planktonic and biofilmS.Typhimurium cells were inferred by the relative levels of expression ofstnandinvA. The levels of expression ofstnandinvAwere significantly increased in biofilmS.Typhimurium cells grown in TSB-5 (1.9-fold and 3.2-fold) and TSB-6 (2.1-fold and 22.3-fold) after 10 days of incubation. These results suggest that the biofilm-formingS. Typhimurium under different pH levels might change the virulence production and stress response mechanisms.
Distribution of Antimicrobial Resistance and Virulence Genes inEnterococcusspp. and Characterization of Isolates from Broiler Chickens
Authors: Diarra Moussa S. , Rempel Heidi , Champagne Julie , Masson Luke , Pritchard Jane , Topp Edward 
Published: October 2010

ABSTRACTEnterococci are now frequent causative agents of nosocomial infections. In this study, we analyzed the frequency and distribution of antibiotic resistance and virulence genotypes ofEnterococcusisolates from broiler chickens. Fecal and cecal samples from nine commercial poultry farms were collected to quantify total enterococci. Sixty-nine presumptive enterococci were isolated and identified by API 20 Strep, and their susceptibilities to antibiotics were determined. Genotypes were assessed through the use of a novel DNA microarray carrying 70 taxonomic, 17 virulence, and 174 antibiotic resistance gene probes. Total enterococcal counts were different from farm to farm and between sample sources (P< 0.01). Fifty-one (74%) of the isolates were identified asE. faecium, whereas nine (13%), seven (10%), and two (3%) isolates were identified asE. hirae,E. faecalis, andE. gallinarum, respectively. Multiple-antibiotic resistance was evident inE. faeciumandE. faecalisisolates. The most common multiple-antibiotic resistance phenotype was Bac Ery Tyl Lin Str Gen Tet Cip. Genes conferring resistance to aminoglycoside (aac,aacA-aphD,aadB,aphA,sat4), macrolide (ermA,ermB,ermAM,msrC), tetracycline (tetL,tetM,tetO), streptogramin (satG_vatE8), bacitracin (bcrR), and lincosamide (linB) antibiotics were detected in corresponding phenotypes. A range of 9 to 12 different virulence genes was found inE. faecalis, includingace,agg,agrBEfs(agrBgene ofE. faecalis),cad1, the cAM373 and cCF10 genes,cob,cpd1,cylAB,efaAEfs, andgelE. All sevenE. faecalisisolates were found to carry thegelEgene and to hydrolize gelatin and bile salts. Results from this study showed the presence of enterococci of public and environmental health concerns in broiler chicken farms and demonstrated the utility of a microarray to quickly and reliably analyze resistance and virulence genotypes ofEnterococcusspp.
Genotypic Diversity ofBorrelia burgdorferiStrains Detected inIxodes scapularisLarvae Collected from North American Songbirds
Authors: Brinkerhoff R. Jory , Bent Stephen J. , Folsom-O'Keefe Corrine M. , Tsao Kimberly , Hoen Anne Gatewood , Barbour Alan G. , Diuk-Wasser Maria A. 
Published: October 2010

ABSTRACTWe genotypedBorrelia burgdorferistrains detected in larvae ofIxodes scapularisremoved from songbirds and compared them with those found in host-seekingI. scapularisnymphs sampled throughout the eastern United States. Birds are capable of transmitting most known genotypes, albeit at different frequencies than expected based on genotypes found among host-seeking nymphs.
Influence of the Composition of the Cellulolytic Flora on the Development of Hydrogenotrophic Microorganisms, Hydrogen Utilization, and Methane Production in the Rumens of Gnotobiotically Reared Lambs
Authors: Chaucheyras-Durand Frédérique , Masséglia Sébastien , Fonty Gérard , Forano Evelyne 
Published: October 2010

ABSTRACT

We investigated the influence of the composition of the fibrolytic microbial community on the development and activities of hydrogen-utilizing microorganisms in the rumens of gnotobiotically reared lambs. Two groups of lambs were reared. The first group was inoculated with
Fibrobacter succinogenes
, a non-H
2
-producing species, as the main cellulolytic organism, and the second group was inoculated with
Ruminococcus albus
,
Ruminococcus flavefaciens
, and anaerobic fungi that produce hydrogen. The development of hydrogenotrophic bacterial communities, i.e., acetogens, fumarate and sulfate reducers, was monitored in the absence of methanogens and after inoculation of methanogens. Hydrogen production and utilization and methane production were measured in rumen content samples incubated
in vitro
in the presence of exogenous hydrogen (supplemented with fumarate or not supplemented with fumarate) or in the presence of ground alfalfa hay as a degradable substrate. Our results show that methane production was clearly reduced when the dominant fibrolytic species was a non-H
2
-producing species, such as
Fibrobacter succinogenes
, without significantly impairing fiber degradation and fermentations in the rumen. The addition of fumarate to the rumen contents stimulated H
2
utilization only by the ruminal microbiota inoculated with
F. succinogenes
, suggesting that these communities could play an important role in fumarate reduction
in vivo
.
Formation of Isobutene from 3-Hydroxy-3-Methylbutyrate by Diphosphomevalonate Decarboxylase
Authors: Gogerty David S. , Bobik Thomas A. 
Published: October 2010

ABSTRACT

Isobutene is an important commercial chemical used for the synthesis of butyl rubber, terephthalic acid, specialty chemicals, and a gasoline performance additive known as alkylate. Currently, isobutene is produced from petroleum and hence is nonrenewable. Here, we report that the
Saccharomyces cerevisiae
mevalonate diphosphate decarboxylase (
Sc
MDD) can convert 3-hydroxy-3-methylbutyrate (3-HMB) to isobutene. Whole cells of
Escherichia coli
producing
Sc
MDD with an N-terminal 6×His tag (His
6
-
Sc
MDD) formed isobutene from 3-HMB at a rate of 154 pmol h
−1
g cells
−1
. In contrast, no isobutene was detected from control cells lacking
Sc
MDD. His
6
-
Sc
MDD was purified by nickel affinity chromatography and shown to produce isobutene from 3-HMB at a rate of 1.33 pmol min
−1
mg
−1
protein. Controls showed that both His
6
-
Sc
MDD and 3-HMB were required for detectable isobutene formation. Isobutene was identified by gas chromatography (GC) with flame ionization detection as well as by GC-mass spectrometry (MS).
Sc
MDD was subjected to error-prone PCR, and two improved variants were characterized,
Sc
MDD1 (I145F) and
Sc
MDD2 (R74H). Whole cells of
E. coli
producing
Sc
MDD1 and
Sc
MDD2 produced isobutene from 3-HMB at rates of 3,000 and 5,888 pmol h
−1
g cells
−1
, which are 19- and 38-fold increases compared to rates for cells producing His
6
-
Sc
MDD. This showed that genetic modifications can be used to increase the rate at which
Sc
MDD converts 3-HMB to isobutene. Because 3-HMB can be produced from
l
-leucine,
Sc
MDD has a potential application for the production of renewable isobutene. Moreover, isobutene is a gas, which might simplify its purification from a fermentation medium, substantially reducing production costs.
Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments
Authors: Lu Shipeng , Gischkat Stefan , Reiche Marco , Akob Denise M. , Hallberg Kevin B. , Küsel Kirsten 
Published: October 2010

ABSTRACT

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their
in situ
functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the
Gammaproteobacteria
(an unknown
Dyella-
like genus and
Acidithiobacillus
-related strains) were obtained from the top acidic sediment zones (pH 2.8).
Firmicutes
strains (related to
Bacillus
and
Alicyclobacillus
) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the
Alphaproteobacteria
,
Acidocella
-related strains were only isolated from acidic zones, whereas
Acidiphilium
-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns.
Geobacter
-related clone sequences were only obtained from deep sediment zones, and
Geobacter
-specific quantitative PCR yielded 8 × 10
5
gene copy numbers. Isolates related to the
Acidobacterium
,
Acidocella
, and
Alicyclobacillus
genera and to the unknown
Dyella
-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.