bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Diversity in Ultra-High-Pressure Rocks and Fluids from the Chinese Continental Scientific Drilling Project in China
Authors: Zhang Gengxin , Dong Hailiang , Xu Zhiqin , Zhao Donggao , Zhang Chuanlun 
Published: June 2005

ABSTRACTMicrobial communities in ultra-high-pressure (UHP) rocks and drilling fluids from the Chinese Continental Scientific Drilling Project were characterized. The rocks had a porosity of 1 to 3.5% and a permeability of ∼0.5 mDarcy. Abundant fluid and gas inclusions were present in the minerals. The rocks contained significant amounts of Fe2O3, FeO, P2O5, and nitrate (3 to 16 ppm). Acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the rocks and the fluids were 5.2 × 103to 2.4 × 104cells/g and 3.5 × 108to 4.2 × 109cells/g, respectively. Enrichment assays resulted in successful growth of thermophilic and alkaliphilic bacteria from the fluids, and some of these bacteria reduced Fe(III) to magnetite. 16S rRNA gene analyses indicated that the rocks were dominated by sequences similar to sequences ofProteobacteriaand that most organisms were related to nitrate reducers from a saline, alkaline, cold habitat; however, some phylotypes were either members of a novel lineage or closely related to uncultured clones. The bacterial communities in the fluids were more diverse and includedProteobacteria,Bacteroidetes, gram-positive bacteria,Planctomycetes, andCandidatustaxa. The archaeal diversity was lower, and most sequences were not related to any known cultivated species. Some archaeal sequences were 90 to 95% similar to sequences recovered from ocean sediments or other subsurface environments. Some archaeal sequences from the drilling fluids were >93% similar to sequences ofSulfolobus solfataricus, and the thermophilic nature was consistent with the in situ temperature. We inferred that the microbes in the UHP rocks reside in fluid and gas inclusions, whereas those in the drilling fluids may be derived from subsurface fluids.
Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries
Authors: Mills Heath J. , Martinez Robert J. , Story Sandra , Sobecky Patricia A. 
Published: June 2005

ABSTRACT

The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the
Bacteria
and
Archaea
communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible
Johnson Sea Link
(water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.
Influence of Glutamate on Growth, Sporulation, and Spore Properties ofBacillus cereusATCC 14579 in Defined Medium
Authors: de Vries Ynte P. , Atmadja Ratna D. , Hornstra Luc M. , de Vos Willem M. , Abee Tjakko 
Published: June 2005

ABSTRACTA chemically defined medium in combination with an airlift fermentor system was used to study the growth and sporulation ofBacillus cereusATCC 14579. The medium contained six amino acids and lactate as the main carbon sources. The amino acids were depleted during exponential growth, while lactate was metabolized mainly during stationary phase. Two concentrations of glutamate were used: high (20 mM; YLHG) and low (2.5 mM; YLLG). Under both conditions, sporulation was complete and synchronous. Sporulation started and was completed while significant amounts of carbon and nitrogen sources were still present in the medium, indicating that starvation was not the trigger for sporulation. Analysis of amino acids and NH4+in the culture supernatant showed that most of the nitrogen assimilated by the bacteria was taken up during sporulation. The consumption of glutamate depended on the initial concentration; in YLLG, all of the glutamate was used early during exponential growth, while in YLHG, almost all of the glutamate was used during sporulation. In YLLG, but not in YLHG, NH4+was taken up by the cells during sporulation. The total amount of nitrogen used by the bacteria in YLLG was less than that used by the bacteria in YLHG, although a significant amount of NH4+was present in the medium throughout sporulation. Despite these differences, growth and temporal expression of key sigma factors involved in sporulation were parallel, indicating that the genetic time frames of sporulation were similar under both conditions. Nevertheless, in YLHG, dipicolinic acid production started later and the spores were released from the mother cells much later than in YLLG. Notably, spores had a higher heat resistance when obtained after growth in YLHG than when obtained after growth in YLLG, and the spores germinated more rapidly and completely in response to inosine,l-alanine, and a combination of these two germinants.
Rational Design of a
Corynebacterium glutamicum
Pantothenate Production Strain and Its Characterization by Metabolic Flux Analysis and Genome-Wide Transcriptional Profiling
Authors: Hüser Andrea T. , Chassagnole Christophe , Lindley Nic D. , Merkamm Muriel , Guyonvarch Armel , Elišáková Veronika , Pátek Miroslav , Kalinowski Jörn , Brune Iris , Pühler Alfred , Tauch Andreas 
Published: June 2005

ABSTRACT

A “second-generation” production strain was derived from a
Corynebacterium glutamicum
pantothenate producer by rational design to assess its potential to synthesize and accumulate the vitamin pantothenate by batch cultivation. The new pantothenate production strain carries a deletion of the
ilvA
gene to abolish isoleucine synthesis, the promoter down-mutation P-
ilvE
M3 to attenuate
ilvE
gene expression and thereby increase ketoisovalerate availability, and two compatible plasmids to overexpress the
ilvBNCD
genes and duplicated copies of the
panBC
operon. Production assays in shake flasks revealed that the P-
ilvE
M3 mutation and the duplication of the
panBC
operon had cumulative effects on pantothenate production. During pH-regulated batch cultivation, accumulation of 8 mM pantothenate was achieved, which is the highest value reported for
C. glutamicum
. Metabolic flux analysis during the fermentation demonstrated that the P-
ilvE
M3 mutation successfully reoriented the carbon flux towards pantothenate biosynthesis. Despite this repartition of the carbon flux, ketoisovalerate not converted to pantothenate was excreted by the cell and dissipated as by-products (ketoisocaproate,
dl
-2,3,-dihydroxy-isovalerate, ketopantoate, pantoate), which are indicative of saturation of the pantothenate biosynthetic pathway. Genome-wide expression analysis of the production strain during batch cultivation was performed by whole-genome DNA microarray hybridization and agglomerative hierarchical clustering, which detected the enhanced expression of genes involved in leucine biosynthesis, in serine and glycine formation, in regeneration of methylenetetrahydrofolate, in de novo synthesis of nicotinic acid mononucleotide, and in a complete pathway of acyl coenzyme A conversion. Our strategy not only successfully improved pantothenate production by genetically modified
C. glutamicum
strains but also revealed new constraints in attaining high productivity.
Novel Carotenoid Oxidase Involved in Biosynthesis of 4,4′-Diapolycopene Dialdehyde
Authors: Tao Luan , Schenzle Andreas , Odom J. Martin , Cheng Qiong 
Published: June 2005

ABSTRACT

Biosynthesis of C
30
carotenoids is relatively restricted in nature but has been described in
Staphylococcus
and in methylotrophic bacteria. We report here identification of a novel gene (
crtNb
) involved in conversion of 4,4′-diapolycopene to 4,4′-diapolycopene aldehyde. An aldehyde dehydrogenase gene (
ald
) responsible for the subsequent oxidation of 4,4′-diapolycopene aldehyde to 4,4′-diapolycopene acid was also identified in
Methylomonas
. CrtNb has significant sequence homology with diapophytoene desaturases (CrtN). However, data from knockout of
crtNb
and expression of
crtNb
in
Escherichia coli
indicated that CrtNb is not a desaturase but rather a novel carotenoid oxidase catalyzing oxidation of the terminal methyl group(s) of 4,4′-diaponeurosporene and 4,4′-diapolycopene to the corresponding terminal aldehyde. It has moderate to low activity on neurosporene and lycopene and no activity on β-carotene or ζ-carotene. Using a combination of C
30
carotenoid synthesis genes from
Staphylococcus
and
Methylomonas
, 4,4′-diapolycopene dialdehyde was produced in
E. coli
as the predominant carotenoid. This C
30
dialdehyde is a dark-reddish purple pigment that may have potential uses in foods and cosmetics.
Characteristics and Living Patterns of Marine Myxobacterial Isolates
Authors: Zhang Yu-qing , Li Yue-zhong , Wang Bing , Wu Zhi-hong , Zhang Cui-ying , Gong Xun , Qiu Zhi-jun , Zhang Yong 
Published: June 2005

ABSTRACT

The growth, morphology, and life cycle of two marine myxobacterial isolates, halotolerant
Myxococcus fulvus
strain HW-1 and halophilic
Haliangium ochraceum
strain SMP-2, were studied as models to determine the living patterns of myxobacteria in the ocean. The growth, morphology, and development of halotolerant strain HW-1 shifted in response to salinity. The optimal seawater concentration for growth of HW-1 was 0 to 80% (salinity, 0.1 to 2.9%), and the strain grew poorly in media with a salinity of more than 4%. The cells became shorter as the seawater concentration increased. The fruiting body structure was complete only on agar prepared with low concentrations of seawater or salts (less than 60% seawater; salinity, 2.1%), and rudimentary structures or even simple cell mounds appeared as the seawater concentration increased. In contrast, the halophilic strain SMP-2 was unable to grow without NaCl. The cell length and the morphology of the fruiting body-like structure did not change in response to salts. In seawater liquid medium, the cells of both strains were confirmed to be able to form myxospores directly from vegetative cells, but they could not do so in medium containing a low seawater concentration (10% or less). HW-1 cells from medium containing a high concentration of seawater grew independent of cell density, while cells from medium containing a low concentration of seawater (10% or less) showed density-dependent growth. SMP-2 cells showed density-dependent growth under all salinity conditions. The results suggest that the halotolerant myxobacteria are the result of degenerative adaptation of soil myxobacteria to the marine environment, while the halophilic myxobacteria form a different evolutionary group that is indigenous to the ocean.
Surface Display of Recombinant Proteins on
Bacillus thuringiensis
Spores
Authors: Du Cheng , Chan Wing C. , McKeithan Timothy W. , Nickerson Kenneth W. 
Published: June 2005

ABSTRACT

The insecticidal protoxin from
Bacillus thuringiensis
has been shown to be a major component of the spore coat. We have developed a novel surface display system using
B. thuringiensis
spores in which the N-terminal portion of the protoxin is replaced with a heterologous protein. The expression vector with a sporulation-specific promoter was successfully used to display green fluorescent protein and a single-chain antibody (scFv) gene that encodes anti-4-ethoxymethylene-2-phenyl-2-oxazolin-5-one (anti-phOx) antibody. The spores that carry the anti-phOx antibody can bind to phOx specifically.
Genomic DNA Amplification from a Single Bacterium
Authors: Raghunathan Arumugham , Ferguson Harley R. , Bornarth Carole J. , Song Wanmin , Driscoll Mark , Lasken Roger S. 
Published: June 2005

ABSTRACT
Genomic DNA was amplified about 5 billion-fold from single, flow-sorted bacterial cells by the multiple displacement amplification (MDA) reaction, using φ 29 DNA polymerase. A 662-bp segment of the 16S rRNA gene could be accurately sequenced from the amplified DNA. MDA methods enable new strategies for studying nonculturable microorganisms.
Occurrence of Drug-Resistant Bacteria in Two European Eel Farms
Authors: Alcaide Elena , Blasco María-Dolores , Esteve Consuelo 
Published: June 2005

ABSTRACT
The occurrence of strains that are resistant to oxolinic acid, oxytetracycline, sulfamethoxazole-trimethoprim, and nitrofurantoin among heterotrophic bacteria, including human and fish pathogens, in two freshwater eel farms was investigated. High levels of individual- and multiple-drug-resistant bacteria were detected, although sampling events were not correlated with clinical outbreaks and drug therapy.
Evaluation of Agar Plates for Direct Enumeration of
Campylobacter
spp. from Poultry Carcass Rinses
Authors: Oyarzabal Omar A. , Macklin Kenneth S. , Barbaree James M. , Miller Robert S. 
Published: June 2005

ABSTRACT

Campy-Cefex, a modification of Campy-Cefex, modified charcoal cefoperazone deoxycholate (mCCDA), Karmali, CAMPY, and Campy-Line agars were evaluated for their efficiency to isolate and enumerate
Campylobacter
spp. from poultry carcass rinses. Campy-Cefex and its modification produced the best results but were statistically similar to CAMPY, mCCDA, and Karmali.
Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and
o
-Xylene in Sediment-Free Iron-Reducing Enrichment Cultures
Authors: Jahn Michael K. , Haderlein Stefan B. , Meckenstock Rainer U. 
Published: June 2005

ABSTRACT

Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and xylene (BTEX) are widespread contaminants in groundwater. We examined the anaerobic degradation of BTEX compounds with amorphous ferric oxide as electron acceptor. Successful enrichment cultures were obtained for all BTEX substrates both in the presence and absence of AQDS (9,10-anthraquinone-2,6-disulfonic acid). The electron balances showed a complete anaerobic oxidation of the aromatic compounds to CO
2
. This is the first report on the anaerobic degradation of
o
-xylene and ethylbenzene in sediment-free iron-reducing enrichment cultures.
Environmental Contamination with Vancomycin-Resistant Enterococci from Hospital Sewage in Portugal
Authors: Novais Carla , Coque Teresa M. , Ferreira Helena , Sousa João Carlos , Peixe Luisa 
Published: June 2005

ABSTRACT

Vancomycin-resistant enterococci (VRE) were detected in samples of sewage obtained downstream of hospitals of the Porto area in Portugal, and in samples from the Douro Estuary. Clonal analysis, Tn
1546
typing, and presence of putative virulence traits indicate the clinical origin of these isolates. This observation highlights the importance of hospital sewage in the VRE contamination of the environment.
Large-Scale Engineering of the
Corynebacterium glutamicum
Genome
Authors: Suzuki Nobuaki , Okayama Satoshi , Nonaka Hiroshi , Tsuge Yota , Inui Masayuki , Yukawa Hideaki 
Published: June 2005

ABSTRACT

The engineering of
Corynebacterium glutamicum
is important for enhanced production of biochemicals. To construct an improved
C. glutamicum
genome, we developed a precise genome excision method based on the Cre/
loxP
recombination system and successfully deleted 11 distinct genomic regions identified by comparative analysis of
C. glutamicum
genomes. Despite the loss of several predicted open reading frames, the mutant cells exhibited normal growth under standard laboratory conditions. With a total of 250 kb (7.5% of the genome), the 11 genomic regions were loaded with cryptic prophages, transposons, and genes of unknown function which were dispensable for cell growth, indicating recent horizontal acquisitions to the genome. This provides an interesting background for functional genomic studies and can be used in the improvement of cell traits.
Bacteriocin from Honeybee Beebread
Enterococcus
avium
, Active against
Listeria
monocytogenes
Authors: Audisio M. Carina , Terzolo Horacio R. , Apella María C. 
Published: June 2005

ABSTRACT

Enterococcus
avium
isolated from
Apis
mellifera
beebread produces a thermoresistant bacteriocin with a strain-dependent inhibitory effect on
Listeria
and without effect on gram-negative bacteria. The bacteriocin appeared to be a polypeptide of about 6 kDa. Genetic analyses revealed no extrachromosomal material in
E. avium
.
Glutamine Synthesis Is Essential for Growth of
Streptococcus thermophilus
in Milk and Is Linked to Urea Catabolism
Authors: Monnet Christophe , Mora Diego , Corrieu Georges 
Published: June 2005

ABSTRACT

Growth of a glutamine synthetase-deficient mutant of
Streptococcus thermophilus
was compared to that of the parent strain in milk that was not supplemented or was supplemented with ammonium chloride, glutamine, or the urease inhibitor flurofamide. It was concluded that one of the functions of urease is to supply ammonia for the synthesis of glutamine.
Nitrate and Phosphate Affect Cultivability of Cyanobacteria from Environments with Low Nutrient Levels
Authors: Ernst Anneliese , Deicher Manfred , Herman Peter M. J. , Wollenzien Ute I. A. 
Published: June 2005

ABSTRACTNitrate and phosphate concentrations higher than those found in the natural environment slowed down growth of two strains of non-bloom-forming, phycoerythrin-richSynechococcusspp. isolated from mesotrophic subalpine lakes. The results make clear why isolation of these picocyanobacteria in standard cultivation media was difficult. At low concentrations, closely related strains exhibited distinct growth characteristics with respect to these two nutrients, possibly explaining differences in their seasonal appearance in the natural environment.
Evaluation of Five Antibody Detection Tests for Diagnosis of Bovine Paratuberculosis
Authors: Collins Michael T. , Wells Scott J. , Petrini Kristine R. , Collins James E. , Schultz Ronald D. , Whitlock Robert H. 
Published: June 2005

ABSTRACT

Five diagnostic tests based on enzyme-linked immunosorbent assay (ELISA) technology for bovine paratuberculosis were evaluated by using individual serum or milk samples from 359 dairy cattle in seven paratuberculosis-free herds and 2,094 dairy cattle in seven
Mycobacterium paratuberculosis
-infected dairy herds. Three independent laboratories using three different culture procedures completed fecal cultures for
M. paratuberculosis
on these cattle and found 417 cows to be shedding
M. paratuberculosis
in their feces. An animal that was fecal culture positive for
M. paratuberculosis
by any of the three laboratories was considered a confirmed case of infection. The specificity of three ELISAs (two on serum and one on milk) was ≥99.8%. The specificity of the remaining two ELISAs, both done on serum, was 94.9 and 84.7%. Four of the five ELISAs evaluated produced similar sensitivity in detecting fecal culture-positive cattle (27.8 to 28.9%). Serum ELISA “D” had the lowest specificity (84.7%) and the highest sensitivity (44.5%), but if the cutoff value defining a positive test was changed from 125 to 250% (of the positive control) the sensitivity and specificity, 31.8 and 97.5%, respectively, were comparable to those of the other four assays. If the case definition for
M. paratuberculosis
infection was based on the culture results of a single laboratory instead of the combined results of three laboratories, ELISA sensitivity estimates were 45.7 to 50.0%. With the exception of ELISA D, assay agreement was high (kappa 0.66 to 0.85) for categorical assay interpretations (positive or negative), but linear regression of quantitative results showed low correlation coefficients (
r
2
= 0.40 to 0.68) due to the fact that ELISA results for some cows were high in one assay but low in another assay. Likelihood ratio analysis showed a direct relationship between the magnitude of ELISA result and the odds of a cow shedding
M. paratuberculosis
in its feces. If used judiciously and interpreted quantitatively, these ELISAs are useful tools in support of paratuberculosis control programs in dairy herds.
Lipopolysaccharide-Based Enzyme-Linked Immunosorbent Assay for Experimental Use in Detection of Antibodies toLawsonia intracellularisin Pigs
Authors: Kroll J. J. , Eichmeyer M. A. , Schaeffer M. L. , McOrist S. , Harris D. L. , Roof M. B. 
Published: June 2005

ABSTRACTAn enzyme-linked immunosorbent assay (ELISA) forLawsonia intracellulariswas developed and compared with a whole-cell antigen-based immunofluorescence antibody test (IFAT). The antigen-containing lipopolysaccharide (LPS) was derived from Percoll gradient purified cultures ofL. intracellularisby using a modification of the Westphal hot phenol procedure. The antigen was bound directly to polystyrene 96-well microtiter plates, and the assay was performed in an indirect ELISA format. Specificity and sensitivity values based on 80 known positive and 80 known negative serum samples from controlled experimental trials were 93.7% and 88.7%, respectively. Serological results from a controlledL. intracellularischallenge exposure study confirmed the high specificity and sensitivity of this assay (100% and 99.5%, respectively). Comparisons between the LPS ELISA and the IFAT in detecting anti-Lawsoniaantibodies in this controlled study revealed significantly more LPS ELISA-positive pigs than IFAT-positive pigs on days 21, 28, 35, and 42 (P= 0.003, 0.030, 0.002, and 0.006, respectively). This indirect ELISA (LPS ELISA) test is an improved method of detecting antibodies in pigs soon after exposure toL. intracellularis, regardless of isolate type (vaccine or wild type) in experimental studies. The LPS ELISA may be used as a tool to support future research trials on vaccine efficacy and to further understand the immune response induced byL. intracellularis.