bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability of Related Human and Chicken
Campylobacter jejuni
Genotypes after Passage through Chick Intestine Studied by Pulsed-Field Gel Electrophoresis
Authors: Hänninen Marja-Liisa , Hakkinen Marjaana , Rautelin Hilpi 
Published: December 2019

ABSTRACT

The genomic stability of 12
Campylobacter jejuni
strains consisting of two groups of human and chicken isolates was studied by analysis of their PFGE (pulsed-field gel electrophoresis) patterns after passage through newly hatched chicks’ intestines. The patterns of
Sma
I,
Sal
I, and
Sac
II digests remained stable after intestinal passage, except for those of two strains. One originally human strain, FB 6371, changed its genotype from II/A (
Sma
I/
Sac
II) to I/B. Another strain, BTI, originally isolated from a chicken, changed its genotype from I/B to a new genotype. The genomic instability of the strains was further confirmed by
Sal
I digestion and ribotyping of the
Hae
III digests. In addition, heat-stable serotype 57 of strain FB 6371 changed to serotype 27 in all isolates with new genotypes but remained unchanged in an isolate with the original genotype. Serotype 27 of strain BTI remained stable. Our study suggests that during intestinal colonization, genomic rearrangement, as demonstrated by changed PFGE and ribopatterns, may occur.
Characterization of Two Subsurface H
2
-Utilizing Bacteria,
Desulfomicrobium hypogeium
sp. nov. and
Acetobacterium psammolithicum
sp. nov., and Their Ecological Roles
Authors: Krumholz Lee R. , Harris Steve H. , Tay Stephen T. , Suflita Joseph M. 
Published: December 2019

ABSTRACT

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H
2
consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named
Desulfomicrobium hypogeium
sp. nov. and
Acetobacterium psammolithicum
sp. nov. The steady-state H
2
concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H
2
between
D. hypogeium
and
A. psammolithicum
was examined, sulfate reduction was the dominant process.
Reductive Dechlorination of Tetrachloroethene to
cis
-1,2-Dichloroethene by a Thermophilic Anaerobic Enrichment Culture
Authors: Kengen Servé W. M. , Breidenbach Caroline G. , Felske Andreas , Stams Alfons J. M. , Schraa Gosse , de Vos Willem M. 
Published: December 2019

ABSTRACT

Thermophilic anaerobic biodegradation of tetrachloroethene (PCE) was investigated with various inocula from geothermal and nongeothermal areas. Only polluted harbor sediment resulted in a stable enrichment culture that converted PCE via trichloroethene to
cis
-1,2-dichloroethene at the optimum temperature of 60 to 65°C. After several transfers, methanogens were eliminated from the culture. Dechlorination was supported by lactate, pyruvate, fructose, fumarate, and malate as electron donor but not by H
2
, formate, or acetate. Fumarate and
l
-malate led to the highest dechlorination rate. In the absence of PCE, fumarate was fermented to acetate, H
2
, CO
2
, and succinate. With PCE, less H
2
was formed, suggesting that PCE competed for the reducing equivalents leading to H
2
. PCE dechlorination, apparently, was not outcompeted by fumarate as electron acceptor. At the optimum dissolved PCE concentration of ∼60 μM, a high dechlorination rate of 1.1 μmol h
−1
mg
−1
(dry weight) was found, which indicates that the dechlorination is not a cometabolic activity. Microscopic analysis of the fumarate-grown culture showed the dominance of a long thin rod. Molecular analysis, however, indicated the presence of two dominant species, both belonging to the low-G+C gram positives. The highest similarity was found with the genus
Dehalobacter
(90%), represented by the halorespiring organism
Dehalobacter restrictus
, and with the genus
Desulfotomaculum
(86%).
Chemoselective Nitro Group Reduction and Reductive Dechlorination Initiate Degradation of 2-Chloro-5-Nitrophenol by
Ralstonia eutropha
JMP134
Authors: Schenzle Andreas , Lenke Hiltrud , Spain Jim C. , Knackmuss Hans-Joachim 
Published: December 2019

ABSTRACT

Ralstonia eutropha
JMP134 utilizes 2-chloro-5-nitrophenol as a sole source of nitrogen, carbon, and energy. The initial steps for degradation of 2-chloro-5-nitrophenol are analogous to those of 3-nitrophenol degradation in
R. eutropha
JMP134. 2-Chloro-5-nitrophenol is initially reduced to 2-chloro-5-hydroxylaminophenol, which is subject to an enzymatic Bamberger rearrangement yielding 2-amino-5-chlorohydroquinone. The chlorine of 2-amino-5-chlorohydroquinone is removed by a reductive mechanism, and aminohydroquinone is formed. 2-Chloro-5-nitrophenol and 3-nitrophenol induce the expression of 3-nitrophenol nitroreductase, of 3-hydroxylaminophenol mutase, and of the dechlorinating activity. 3-Nitrophenol nitroreductase catalyzes chemoselective reduction of aromatic nitro groups to hydroxylamino groups in the presence of NADPH. 3-Nitrophenol nitroreductase is active with a variety of mono-, di-, and trinitroaromatic compounds, demonstrating a relaxed substrate specificity of the enzyme. Nitrosobenzene serves as a substrate for the enzyme and is converted faster than nitrobenzene.
A Pyruvated Mannose-Specific Xanthan Lyase Involved in Xanthan Degradation by
Paenibacillus alginolyticus
XL-1
Authors: Ruijssenaars Harald J. , de Bont Jan A. M. , Hartmans Sybe 
Published: December 2019

ABSTRACT

The xanthan-degrading bacterium
Paenibacillus alginolyticus
XL-1, isolated from soil, degrades approximately 28% of the xanthan molecule and appears to leave the backbone intact. Several xanthan-degrading enzymes were excreted during growth on xanthan, including xanthan lyase. Xanthan lyase production was induced by xanthan and inhibited by glucose and low-molecular-weight enzymatic degradation products from xanthan. A xanthan lyase with a molecular mass of 85 kDa and a pI of 7.9 was purified and characterized. The enzyme is specific for pyruvated mannosyl side chain residues and optimally active at pH 6.0 and 55°C.
Aggregation of
Bacillus thuringiensis
Cry1A Toxins upon Binding to Target Insect Larval Midgut Vesicles
Authors: Aronson Arthur I. , Geng Chaoxian , Wu Lan 
Published: December 2019

ABSTRACT

During sporulation,
Bacillus thuringiensis
produces crystalline inclusions comprised of a mixture of δ-endotoxins. Following ingestion by insect larvae, these inclusion proteins are solubilized, and the protoxins are converted to toxins. These bind specifically to receptors on the surfaces of midgut apical cells and are then incorporated into the membrane to form ion channels. The steps required for toxin insertion into the membrane and possible oligomerization to form a channel have been examined. When bound to vesicles from the midguts of
Manduca sexta
larvae, the Cry1Ac toxin was largely resistant to digestion with protease K. Only about 60 amino acids were removed from the Cry1Ac amino terminus, which included primarily helix α1. Following incubation of the Cry1Ab or Cry1Ac toxins with vesicles, the preparations were solubilized by relatively mild conditions, and the toxin antigens were analyzed by immunoblotting. In both cases, most of the toxin formed a large, antigenic aggregate of ca. 200 kDa. These toxin aggregates did not include the toxin receptor aminopeptidase N, but interactions with other vesicle components were not excluded. No oligomerization occurred when inactive toxins with mutations in amphipathic helices (α5) and known to insert into the membrane were tested. Active toxins with other mutations in this helix did form oligomers. There was one exception; a very active helix α5 mutant toxin bound very well to membranes, but no oligomers were detected. Toxins with mutations in the loop connecting helices α2 and α3, which affected the irreversible binding to vesicles, also did not oligomerize. There was a greater extent of oligomerization of the Cry1Ac toxin with vesicles from the
Heliothis virescens
midgut than with those from the
M. sexta
midgut, which correlated with observed differences in toxicity. Tight binding of virtually the entire toxin molecule to the membrane and the subsequent oligomerization are both important steps in toxicity.
Microbial Control of the Culture ofArtemiaJuveniles through Preemptive Colonization by Selected Bacterial Strains
Authors: Verschuere Laurent , Rombaut Geert , Huys Geert , Dhont Jean , Sorgeloos Patrick , Verstraete Willy 
Published: December 2019

ABSTRACTThe use of juvenileArtemiaas feed in aquaculture and in the pet shop industry has been getting more attention during the last decade. In this study, the use of selected bacterial strains to improve the nutritional value of dry food forArtemiajuveniles and to obtain control of the associated microbial community was examined. Nine bacterial strains were selected based on their positive effects on survival and/or growth ofArtemiajuveniles under monoxenic culture conditions, while other strains caused no significant effect, significantly lower rates of survival and/or growth, or even total mortality of theArtemia. The nine selected strains were used to preemptively colonize the culture water ofArtemiajuveniles. Xenic culture ofArtemiaunder suboptimal conditions yielded better survival and/or growth rates when they were grown in the preemptively colonized culture medium than when grown in autoclaved seawater. The preemptive colonization of the culture water had a drastic influence on the microbial communities that developed in the culture water or that were associated with theArtemia, as determined with Biolog GN community-level physiological profiles. Chemotaxonomical characterization based on fatty acid methyl ester analysis of bacterial isolates recovered from the culture tanks was performed, and a comparison with the initially introduced strains was made. Finally, several modes of action for the beneficial effect of the bacterial strains are proposed.
Chitinases from Uncultured Marine Microorganisms
Authors: Cottrell Matthew T. , Moore Jessica A. , Kirchman David L. 
Published: December 2019

ABSTRACT

Our understanding of the degradation of organic matter will benefit from a greater appreciation for the genes encoding enzymes involved in the hydrolysis of biopolymers such as chitin, one of the most abundant polymers in nature. To isolate representative and abundant chitinase genes from uncultivated marine bacteria, we constructed libraries of genomic DNA isolated from coastal and estuarine waters. The libraries were screened for genes encoding proteins that hydrolyze a fluorogenic analogue of chitin, 4-methylumbelliferyl β-
d
-
N
,
N
′-diacetylchitobioside (MUF-diNAG). The abundance of clones capable of MUF-diNAG hydrolysis was higher in the library constructed with DNA from the estuary than in that constructed with DNA from coastal waters, although the abundance of positive clones was also dependent on the method used to screen the library. Plaque assays revealed nine MUF-diNAG-positive clones of 75,000 screened for the estuarine sample and two clones of 750,000 for the coastal sample. A microtiter plate assay revealed approximately 1 positive clone for every 500 clones screened in the coastal library. The number of clones detected with the plaque assay was consistent with estimates of the portion of culturable bacteria that degrade chitin. Our results suggest that culture-dependent methods do not greatly underestimate the portion of marine bacterial communities capable of chitin degradation.
Effect of Organic Solvents on the Yield of Solvent-Tolerant
Pseudomonas putida
S12
Authors: Isken Sonja , Derks Antoine , Wolffs Petra F. G. , de Bont Jan A. M. 
Published: December 2019

ABSTRACT

Solvent-tolerant microorganisms are useful in biotransformations with whole cells in two-phase solvent-water systems. The results presented here describe the effects that organic solvents have on the growth of these organisms. The maximal growth rate of
Pseudomonas putida
S12, 0.8 h
−1
, was not affected by toluene in batch cultures, but in chemostat cultures the solvent decreased the maximal growth rate by nearly 50%. Toluene, ethylbenzene, propylbenzene, xylene, hexane, and cyclohexane reduced the biomass yield, and this effect depended on the concentration of the solvent in the bacterial membrane and not on its chemical structure. The dose response to solvents in terms of yield was linear up to an approximately 200 mM concentration of solvent in the bacterial membrane, both in the wild type and in a mutant lacking an active efflux system for toluene. Above this critical concentration the yield of the wild type remained constant at 0.2 g of protein/g of glucose with increasing concentrations of toluene. The reduction of the yield in the presence of solvents is due to a maintenance higher by a factor of three or four as well as to a decrease of the maximum growth yield by 33%. Therefore, energy-consuming adaptation processes as well as the uncoupling effect of the solvents reduce the yield of the tolerant cells.
cis/trans
Isomerase of Unsaturated Fatty Acids of
Pseudomonas putida
P8: Evidence for a Heme Protein of the Cytochrome
c
Type
Authors: Holtwick Rita , Keweloh Heribert , Meinhardt Friedhelm 
Published: December 2019

ABSTRACT

From a pool of 600 temperature-sensitive transposon mutants of
Pseudomonas putida
P8, 1 strain was isolated that carries a mini-Tn
5
insertion within the cytochrome
c
operon. As a result, genes involved in the attachment of heme to cytochrome
c
-type proteins are turned off. Accordingly, cytochrome
c
could not be detected spectrophotometrically. The mutant also exhibited a remarkable reduction of
cis-trans
isomerization capability for unsaturated fatty acids. Consistent with the genetic and physiological data is the detection of a cytochrome
c
-type heme-binding motif close to the N terminus of the predicted polypeptide of the
cis/trans
isomerase (
cti
) gene (
C
VA
CH
; conserved amino acids in italics). The functional significance of this motif was proven by site-directed mutagenesis. A possible mechanism of heme-catalyzed
cis-trans
isomerization of unsaturated fatty acids is discussed.
PCR-Based Genotyping of Epidemic and Preepidemic
Trichoderma
Isolates Associated with Green Mold of
Agaricus bisporus
Authors: Chen X. , Romaine C. P. , Tan Q. , Schlagnhaufer B. , Ospina-Giraldo M. D. , Royse D. J. , Huff D. R. 
Published: December 2019

ABSTRACT

We used randomly amplified polymorphic DNA (RAPD)-PCR to estimate genetic variation among isolates of
Trichoderma
associated with green mold on the cultivated mushroom
Agaricus bisporus
. Of 83 isolates examined, 66 were sampled during the recent green mold epidemic, while the remaining 17 isolates were collected just prior to the epidemic and date back to the 1950s.
Trichoderma harzianum
biotype 4 was identified by RAPD analysis as the cause of almost 90% of the epidemic-related episodes of green mold occurring in the major commercial mushroom-growing region in North America. Biotype 4 was more closely allied to
T. harzianum
biotype 2, the predominant pathogenic genotype in Europe, than to the less pathogenic biotype 1 and
Trichoderma atroviride
(formerly
T. harzianum
biotype 3). No variation in the RAPD patterns was observed among the isolates within biotype 2 or 4, suggesting that the two pathogenic biotypes were populations containing single clones. Considerable genetic variation, however, was noted among isolates of biotype 1 and
T. atroviride
from Europe. Biotype 4 was not represented by the preepidemic isolates of
Trichoderma
as determined by RAPD markers and PCR amplification of an arbitrary DNA sequence unique to the genomes of biotypes 2 and 4. Our findings suggest that the onset of the green mold epidemic in North America resulted from the recent introduction of a highly virulent genotype of the pathogen into cultivated mushrooms.
Increase in Alfalfa Nodulation, Nitrogen Fixation, and Plant Growth by Specific DNA Amplification in
Sinorhizobium meliloti
Authors: Castillo Marcela , Flores Margarita , Mavingui Patrick , Martínez-Romero Esperanza , Palacios Rafael , Hernández Georgina 
Published: December 2019

ABSTRACT

To improve symbiotic nitrogen fixation on alfalfa plants,
Sinorhizobium meliloti
strains containing different average copy numbers of a symbiotic DNA region were constructed by specific DNA amplification (SDA). A DNA fragment containing a regulatory gene (
nodD1
), the common nodulation genes (
nodABC
), and an operon essential for nitrogen fixation (
nifN
) from the
nod
regulon region of the symbiotic plasmid pSyma of
S. meliloti
was cloned into a plasmid unable to replicate in this organism. The plasmid then was integrated into the homologous DNA region of
S. meliloti
strains 41 and 1021, which resulted in a duplication of the symbiotic region.
Sinorhizobium
derivatives carrying further amplification were selected by growing the bacteria in increased concentrations of an antibiotic marker present in the integrated vector. Derivatives of strain 41 containing averages of 3 and 6 copies and a derivative of strain 1021 containing an average of 2.5 copies of the symbiotic region were obtained. In addition, the same region was introduced into both strains as a multicopy plasmid, yielding derivatives with an average of seven copies per cell. Nodulation, nitrogenase activity, plant nitrogen content, and plant growth were analyzed in alfalfa plants inoculated with the different strains. The copy number of the symbiotic region was critical in determining the plant phenotype. In the case of the strains with a moderate increase in copy number, symbiotic properties were improved significantly. The inoculation of alfalfa with these strains resulted in an enhancement of plant growth.
Iron-Oxidizing Bacteria Are Associated with Ferric Hydroxide Precipitates (Fe-Plaque) on the Roots of Wetland Plants
Authors: Emerson David , Weiss Johanna V. , Megonigal J. Patrick 
Published: December 2019

ABSTRACT

The presence of Fe-oxidizing bacteria in the rhizosphere of four different species of wetland plants was investigated in a diverse wetland environment that had Fe(II) concentrations ranging from tens to hundreds of micromoles per liter and a pH range of 3.5 to 6.8. Enrichments for neutrophilic, putatively lithotrophic Fe-oxidizing bacteria were successful on roots from all four species; acidophilic Fe-oxidizing bacteria were enriched only on roots from plants whose root systems were exposed to soil solutions with a pH of <4. In
Sagittaria australis
there was a positive correlation (
P
< 0.01) between cell numbers and the total amount of Fe present; the same correlation was not found for
Leersia oryzoides
. These results present the first evidence for culturable Fe-oxidizing bacteria associated with Fe-plaque in the rhizosphere.
Virus Passage through Track-Etch Membranes Modified by Salinity and a Nonionic Surfactant
Authors: Lytle C. David , Routson Licia B. , Jain Nisha B. , Myers Matthew R. , Green Barbara L. 
Published: December 2019

ABSTRACT

Why do viruses sometimes not pass through larger pores in track-etch filters? Increasing the salinity (0.8 to 160 mM Na
+
) decreased φX174 and PRD1 passage through track-etch polycarbonate membranes (sodium dodecyl sulfate coated but not polyvinylpyrrolidone coated) and PRD1 passage through polyester membranes. Undiminished passage when 0.1% Tween 80 was added implied that nonionic virus adsorption occurred and indicated that high levels of salinity decreased virus passage by decreasing electrostatic repulsion that prevented adsorption.
Mechanism of Alanine Hyperproduction by
Arthrobacter oxydans
HAP-1: Metabolic Shift to Fermentation under Nongrowth Aerobic Conditions
Authors: Hashimoto Shin-ichi , Katsumata Ryoichi 
Published: December 2019

ABSTRACT

Arthrobacter oxydans
HAP-1 hyperproduces
dl
-alanine in a non-growth-associated manner. We found that decreased activities of pyruvate dehydrogenase and of the enzyme catalyzing NADH oxidation in the stationary phase are paralleled by a shift of pyruvate metabolism to alanine synthesis by
l
-alanine dehydrogenase. We propose that this enzyme functions as an electron sink even under aerobic conditions.
High-Efficiency Transformation of
Rhizobium leguminosarum
by Electroporation
Authors: Garg Bindu , Dogra Romesh C. , Sharma Parveen K. 
Published: December 2019

ABSTRACT

Electrotransformation of
Rhizobium leguminosarum
was successfully carried out with a 15.1-kb plasmid, pMP154 (Cm
r
), containing a
nodABC-lacZ
fusion by electroporation. The maximum transformation efficiency, 10
8
transformants/μg of DNA, was achieved at a field strength of 14 kV/cm with a pulse of 7.3 ms (186 Ω). The number of transformants was found to increase with increasing cell density, with no sign of saturation. In relation to DNA dosage, the maximum transformation efficiency (5.8 × 10
8
transformants/μg of DNA) was obtained with 0.5 μg of DNA/ml of cell suspension, and a further increase in the DNA concentration resulted in a decline in transformation efficiency.
Quantification of Chemotaxis to Naphthalene by
Pseudomonas putida
G7
Authors: Marx Randall B. , Aitken Michael D. 
Published: December 2019

ABSTRACT

The capillary assay was used to quantify the chemotactic response of
Pseudomonas putida
G7 to naphthalene. Experiments were conducted in which the cell concentration in the assay chamber, the naphthalene concentration in the capillary, or the incubation time was varied. Data from these experiments were evaluated with a model that accounted for the effect of diffusion on the distribution of substrate and the transport of cells from the chamber through the capillary orifice. By fitting a numerical solution of this model to the data, it was possible to determine the chemotactic sensitivity coefficient, χ
0
. The mean of the best-fit values for χ
0
from the three types of experiments was 7.2 × 10
−5
cm
2
/s. A less computationally intensive model based on earlier approaches that ignore cell transport in the chamber resulted in χ
0
values that were approximately three times higher. The models evaluated in the present study could simulate the results of capillary assays only at low chamber cell concentrations, for which the effect of consumption on the distribution of substrate was negligible. Results from this work suggest that it is possible to use the capillary assay to quantify taxis towards environmentally relevant chemoeffectors that have low aqueous solubility.