bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybridization Analysis of Chesapeake Bay Virioplankton
Authors: Wommack K. Eric , Ravel Jacques , Hill Russell T. , Colwell Rita R. 
Published: December 2019

ABSTRACT

It has been hypothesized that, by specifically lysing numerically dominant host strains, the virioplankton may play a role in maintaining clonal diversity of heterotrophic bacteria and phytoplankton populations. If viruses selectively lyse only those host species that are numerically dominant, then the number of a specific virus within the virioplankton would be expected to change dramatically over time and space, in coordination with changes in abundance of the host. In this study, the abundances of specific viruses in Chesapeake Bay water samples were monitored, using nucleic acid probes and hybridization analysis. Total virioplankton in a water sample was separated by pulsed-field gel electrophoresis and hybridized with nucleic acid probes specific to either single viral strains or a group of viruses with similar genome sizes. The abundances of specific viruses were inferred from the intensity of the hybridization signal. By using this technique, a virus comprising 1/1,000 of the total virioplankton abundance (ca. 10
4
PFU/ml) could be detected. Titers of either a single virus species or a group of viruses changed over time, increasing to peak abundance and then declining to low or undetectable levels, and were geographically localized in the bay. Peak signal intensities, i.e., peak abundances of virus strains, were 10-fold greater than the low background level. Furthermore, virus species were found to be restricted to a particular depth, since probes specific to viruses from bottom water did not hybridize with virus genomes from surface water at the same geographical location. Overall, changes in abundances of specific viruses within the virioplankton were episodic, supporting the hypothesis that viral infection influences, if not controls, clonal diversity within heterotrophic bacteria and phytoplankton communities.
Polycyclic Aromatic Hydrocarbon Degradation by a New Marine Bacterium,
Neptunomonas naphthovorans
gen. nov., sp. nov
Authors: Hedlund Brian P. , Geiselbrecht Allison D. , Bair Timothy J. , Staley James T. 
Published: December 2019

ABSTRACT

Two strains of bacteria were isolated from creosote-contaminated Puget Sound sediment based on their ability to utilize naphthalene as a sole carbon and energy source. When incubated with a polycyclic aromatic hydrocarbon (PAH) compound in artificial seawater, each strain also degraded 2-methylnaphthalene and 1-methylnaphthalene; in addition, one strain, NAG-2N-113, degraded 2,6-dimethylnaphthalene and phenanthrene. Acenaphthene was not degraded when it was used as a sole carbon source but was degraded by both strains when it was incubated with a mixture of seven other PAHs. Degenerate primers and the PCR were used to isolate a portion of a naphthalene dioxygenase iron-sulfur protein (ISP) gene from each of the strains. A phylogenetic analysis of PAH dioxygenase ISP deduced amino acid sequences showed that the genes isolated in this study were distantly related to the genes encoding naphthalene dioxygenases of
Pseudomonas
and
Burkholderia
strains. Despite the differences in PAH degradation phenotype between the new strains, the dioxygenase ISP deduced amino acid fragments of these organisms were 97.6% identical. 16S ribosomal DNA-based phylogenetic analysis placed these bacteria in the gamma-3 subgroup of the
Proteobacteria
, most closely related to members of the genus
Oceanospirillum
. However, morphologic, physiologic, and genotypic differences between the new strains and the oceanospirilla justify the creation of a novel genus and species,
Neptunomonas naphthovorans
. The type strain of
N. naphthovorans
is strain NAG-2N-126.
Pleiotropic Effects of Adaptation to a Single Carbon Source for Growth on Alternative Substrates
Authors: Velicer Gregory J. 
Published: December 2019

ABSTRACT
It is frequently assumed that populations of genetically modified microorganisms will perform their intended function and then disappear from the environment due to inherent fitness disadvantages resulting from their genetic alteration. However, modified organisms used in bioremediation can be expected to adapt evolutionarily to growth on the anthropogenic substrate that they are intended to degrade. If such adaptation results in improved competitiveness for alternative, naturally occurring substrates, then this will increase the likelihood that the modified organisms will persist in the environment. In this study, bacteria capable of degrading the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) were used to test the effects of evolutionary adaptation to one substrate on fitness during growth on an alternative substrate. Twenty lineages of bacteria were allowed to evolve under abundant resource conditions on either 2,4-D or succinate as their sole carbon source. The competitiveness of each evolved line was then measured relative to that of its ancestor for growth on both substrates. Only three derived lines showed a clear drop in fitness on the alternative substrate after demonstrable adaptation to their selective substrate, while five derived lines showed significant simultaneous increases in fitness on both their selective and alternative substrates. These data demonstrate that adaptation to an anthropogenic substrate can pleiotropically increase competitiveness for an alternative natural substrate and therefore increase the likelihood that a genetically modified organism will persist in the environment.
Influence of Osmolarity and the Presence of an Osmoprotectant on
Lactococcus lactis
Growth and Bacteriocin Production
Authors: Uguen Patricia , Hamelin Jack , Le Pennec Jean-Paul , Blanco Carlos 
Published: December 2019

ABSTRACT

Growth inhibition of
Lactococcus lactis
provoked by increasing osmolarity is reversed when glycine betaine (GB) or its analogs are added to a defined medium. Lacticin 481 production increased sharply with growth medium osmolarity in the absence of osmoprotectant but remained unaffected when GB was supplied in media of increasing osmolarity.
2-Bromoethanesulfonate, Sulfate, Molybdate, and Ethanesulfonate Inhibit Anaerobic Dechlorination of Polychlorobiphenyls by Pasteurized Microorganisms
Authors: Ye Dingyi , Quensen John F. , Tiedje James M. , Boyd Stephen A. 
Published: December 2019

ABSTRACT
Dechlorination of Aroclor 1242 by pasteurized microorganisms was inhibited by 2-bromoethanesulfonate (BES), sulfate, molybdate, and ethanesulfonate. Consumption of these anions and production of sulfide from BES were detected. The inhibition could not be relieved by hydrogen. Taken together these results suggest that pattern M dechlorination is mediated by spore-forming sulfidogenic bacteria. These results also suggest that BES may inhibit anaerobic dechlorination by nonmethanogens by more than one mechanism.
Highly Sensitive Protein Translation Assay for Trichothecene Toxicity in Airborne Particulates: Comparison with Cytotoxicity Assays
Authors: Yike Iwona , Allan Terry , Sorenson William G. , Dearborn Dorr G. 
Published: December 2019

ABSTRACT
Screening assays for environmental mycotoxins in bulk samples currently use cytotoxicity in cell cultures, but their application to air particulate samples often lacks sensitivity and specificity for fungal spores. An assay based on inhibition of protein synthesis using translation of firefly luciferase in a rabbit reticulocyte system has been developed for the detection of trichothecene mycotoxins found in the spores of toxigenic fungi. Ethanol extracts of air particulates trapped on polycarbonate filters are ultrafiltered and applied at several dilutions to a translation reaction mixture. The activity of translated luciferase is measured directly in a luminometer, eliminating the need for radioisotopes and time-consuming sample processing. Parallel standard curves using a commercially available trichothecene provide for expression of the results in T-2 toxin equivalents per cubic meter of air. The assay can be completed in 2 h and is readily applicable to multiple samples. Comparison to the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cytotoxicity assay indicates a 400-fold increase in sensitivity of trichothecene detection in addition to a much higher specificity for these toxins. Initial field testing indicates a strong correlation between the measured level of toxicity and the presence of toxigenic fungi detected with microbiological methods. In conclusion, this luciferase translation assay offers a rapid and highly sensitive and specific method for quantitative detection of trichothecene mycotoxin activity in air particulate samples.
The Outer Membrane of Gram-Negative Bacteria Inhibits Antibacterial Activity of Brochocin-C
Authors: Gao Yan , van Belkum Marco J. , Stiles Michael E. 
Published: December 2019

ABSTRACT

Brochocin-C is a two-peptide bacteriocin produced by
Brochothrix campestris
ATCC 43754 that has a broad activity spectrum comparable to that of nisin. Brochocin-C has an inhibitory effect on EDTA-treated gram-negative bacteria,
Salmonella enterica
serovar Typhimurium lipopolysaccharide mutants, and spheroplasts of Typhimurium strains LT2 and SL3600. Brochocin-C treatment of cells and spheroplasts of strains of LT2 and SL3600 resulted in hydrolysis of ATP. The outer membrane of gram-negative bacteria protects the cytoplasmic membrane from the action of brochocin-C. It appears that brochocin-C is similar to nisin and possibly does not require a membrane receptor for its function; however, the difference in effect of the two bacteriocins on intracellular ATP indicates that they cause different pore sizes in the cytoplasmic membrane.
Possible Role of Xanthobaccins Produced by
Stenotrophomonas
sp. Strain SB-K88 in Suppression of Sugar Beet Damping-Off Disease
Authors: Nakayama Takato , Homma Yoshihisa , Hashidoko Yasuyuki , Mizutani Junya , Tahara Satoshi 
Published: December 2019

ABSTRACT

Three antifungal compounds, designated xanthobaccins A, B, and C, were isolated from the culture fluid of
Stenotrophomonas
sp. strain SB-K88, a rhizobacterium of sugar beet that suppresses damping-off disease. Production of xanthobaccin A in culture media was compared with the disease suppression activities of strain SB-K88 and less suppressive strains that were obtained by subculturing. Strain SB-K88 was applied to sugar beet seeds, and production of xanthobaccin A in the rhizosphere of seedlings was confirmed by using a test tube culture system under hydroponic culture conditions; 3 μg of xanthobaccin A was detected in the rhizosphere on a per-plant basis. Direct application of purified xanthobaccin A to seeds suppressed damping-off disease in soil naturally infested by
Pythium
spp. We suggest that xanthobaccin A produced by strain SB-K88 plays a key role in suppression of sugar beet damping-off disease.
Two Cellobiohydrolase-Encoding Genes from
Aspergillus niger
Require
d
-Xylose and the Xylanolytic Transcriptional Activator XlnR for Their Expression
Authors: Gielkens Marco M. C. , Dekkers Ester , Visser Jaap , de Graaff Leo H. 
Published: December 2019

ABSTRACT

Two cellobiohydrolase-encoding genes,
cbhA
and
cbhB
, have been isolated from the filamentous fungus
Aspergillus niger
. The deduced amino acid sequence shows that CbhB has a modular structure consisting of a fungus-type cellulose-binding domain (CBD) and a catalytic domain separated by a Pro/Ser/Thr-rich linker peptide. CbhA consists only of a catalytic domain and lacks a CBD and linker peptide. Both proteins are homologous to fungal cellobiohydrolases in family 7 of the glycosyl hydrolases. Northern blot analysis showed that the transcription of the
cbhA
and
cbhB
genes is induced by
d
-xylose but not by sophorose and, in addition, requires the xylanolytic transcriptional activator XlnR.
Use of PCR-Based Methods for Rapid Differentiation of
Lactobacillus delbrueckii
subsp.
bulgaricus
and
L. delbrueckii
subsp.
lactis
Authors: Torriani Sandra , Zapparoli Giacomo , Dellaglio Franco 
Published: December 2019

ABSTRACT

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of
Lactobacillus delbrueckii
subsp.
bulgaricus
and
L. delbrueckii
subsp.
lactis
. PCR with a single combination of primers which targeted the proline iminopeptidase (
pepIP
) gene of
L. delbrueckii
subsp.
bulgaricus
allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except
L. delbrueckii
subsp.
delbrueckii
LMG 6412
T
, which clustered with
L. delbrueckii
subsp.
lactis
strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual
L. delbrueckii
strains.
High-Level Production of Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) by Fed-Batch Culture of Recombinant
Escherichia coli
Authors: Choi Jong-il , Lee Sang Yup 
Published: December 2019

ABSTRACT

Fermentation strategies for production of high concentrations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] with different 3-hydroxyvalerate (3HV) fractions by recombinant
Escherichia coli
harboring the
Alcaligenes latus
polyhydroxyalkanoate biosynthesis genes were developed. Fed-batch cultures of recombinant
E. coli
with the pH-stat feeding strategy facilitated production of high concentrations and high contents of P(3HB-co-3HV) in a chemically defined medium. When a feeding solution was added in order to increase the glucose and propionic acid concentrations to 20 g/liter and 20 mM, respectively, after each feeding, a cell dry weight of 120.3 g/liter and a relatively low P(3HB-co-3HV) content, 42.5 wt%, were obtained. Accumulation of a high residual concentration of propionic acid in the medium was the reason for the low P(3HB-co-3HV) content. An acetic acid induction strategy was used to stimulate the uptake and utilization of propionic acid. When a fed-batch culture and this strategy were used, we obtained a cell concentration, a P(3HB-co-3HV) concentration, a P(3HB-co-3HV) content, and a 3HV fraction of 141.9 g/liter, 88.1 g/liter, 62.1 wt%, and 15.3 mol%, respectively. When an improved nutrient feeding strategy, acetic acid induction, and oleic acid supplementation were used, we obtained a cell concentration, a P(3HB-co-3HV) concentration, a P(3HB-co-3HV) content, and a 3HV fraction of 203.1 g/liter, 158.8 g/liter, 78.2 wt%, and 10.6 mol%, respectively; this resulted in a high level of productivity, 2.88 g of P(3HB-co-3HV)/liter-h.
Purification and Characterization of Monovalent Cation-Activated Levodione Reductase from
Corynebacterium aquaticum
M-13
Authors: Wada Masaru , Yoshizumi Ayumi , Nakamori Shigeru , Shimizu Sakayu 
Published: December 2019

ABSTRACT

(6
R
)-2,2,6-Trimethyl-1,4-cyclohexanedione (levodione) reductase was isolated from a cell extract of the soil isolate
Corynebacterium aquaticum
M-13. This enzyme catalyzed regio- and stereoselective reduction of levodione to (4
R
,6
R
)-4-hydroxy-2,2,6-trimethylcyclohexanone (actinol). The relative molecular mass of the enzyme was estimated to be 142,000 Da by high-performance gel permeation chromatography and 36,000 Da by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme required NAD
+
or NADH as a cofactor, and it catalyzed reversible oxidoreduction between actinol and levodione. The enzyme was highly activated by monovalent cations, such as K
+
, Na
+
, and NH
4
+
. The NH
2
-terminal and partial amino acid sequences of the enzyme showed that it belongs to the short-chain alcohol dehydrogenase/reductase family. This is the first report of levodione reductase.
Evaluation of
Cryptosporidium parvum
Genotyping Techniques
Authors: Sulaiman Irshad M. , Xiao Lihua , Lal Altaf A. 
Published: December 2019

ABSTRACT

We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of
Cryptosporidium
parasites. Genomic DNA from three species of
Cryptosporidium
parasites (genotype 1 and genotype 2 of
C. parvum
,
C. muris
, and
C. serpentis
), two
Eimeria
species (
E. neischulzi
and
E. papillata
), and
Giardia duodenalis
were used to evaluate the specificity of primers. Furthermore, the sensitivity of the genotyping primers was tested by using genomic DNA isolated from known numbers of oocysts obtained from a genotype 2
C. parvum
isolate. PCR amplification was repeated at least three times with all of the primer pairs. Of the 11 protocols studied, 10 amplified
C. parvum
genotypes 1 and 2, and the expected fragment sizes were obtained. Our results indicate that two species-differentiating protocols are not
Cryptosporidium
specific, as the primers used in these protocols also amplified the DNA of
Eimeria
species. The sensitivity studies revealed that two nested PCR-restriction fragment length polymorphism (RFLP) protocols based on the small-subunit rRNA and dihydrofolate reductase genes are more sensitive than single-round PCR or PCR-RFLP protocols.
Distribution of Bifidobacterial Species in Human Intestinal Microflora Examined with 16S rRNA-Gene-Targeted Species-Specific Primers
Authors: Matsuki Takahiro , Watanabe Koichi , Tanaka Ryuichiro , Fukuda Masafumi , Oyaizu Hiroshi 
Published: December 2019

ABSTRACT

In order to clarify the distribution of bifidobacterial species in the human intestinal tract, a 16S rRNA-gene-targeted species-specific PCR technique was developed and used with DNAs extracted from fecal samples obtained from 48 healthy adults and 27 breast-fed infants. To cover all of the bifidobacterial species that have been isolated from and identified in the human intestinal tract, species-specific primers for
Bifidobacterium longum
,
B. infantis
,
B. dentium
, and
B. gallicum
were developed and used with primers for
B. adolescentis
,
B. angulatum
,
B. bifidum
,
B. breve
, and the
B. catenulatum
group (
B. catenulatum
and
B. pseudocatenulatum
) that were developed in a previous study (T. Matsuki, K. Watanabe, R. Tanaka, and H. Oyaizu, FEMS Microbiol. Lett. 167:113–121, 1998). The specificity of the nine primers was confirmed by PCR, and the species-specific PCR method was found to be a useful means for identifying
Bifidobacterium
strains isolated from human feces. The results of an examination of bifidobacterial species distribution showed that the
B. catenulatum
group was the most commonly found taxon (detected in 44 of 48 samples [92%]), followed by
B. longum
and
B. adolescentis
, in the adult intestinal bifidobacterial flora and that
B. breve
,
B. infantis
, and
B. longum
were frequently found in the intestinal tracts of infants. The present study demonstrated that qualitative detection of the bifidobacterial species present in human feces can be accomplished rapidly and accurately.
Utilization of Trihalogenated Propanes by
Agrobacterium radiobacter
AD1 through Heterologous Expression of the Haloalkane Dehalogenase from
Rhodococcus
sp. Strain m15-3
Authors: Bosma Tjibbe , Kruizinga Edwin , de Bruin Erik J. , Poelarends Gerrit J. , Janssen Dick B. 
Published: December 2019

ABSTRACT

Trihalogenated propanes are toxic and recalcitrant organic compounds. Attempts to obtain pure bacterial cultures able to use these compounds as sole carbon and energy sources were unsuccessful. Both the haloalkane dehalogenase from
Xanthobacter autotrophicus
GJ10 (DhlA) and that from
Rhodococcus
sp. strain m15-3 (DhaA) were found to dehalogenate trihalopropanes to 2,3-dihalogenated propanols, but the kinetic properties of the latter enzyme are much better. Broad-host-range dehalogenase expression plasmids, based on RSF1010 derivatives, were constructed with the haloalkane dehalogenase from
Rhodococcus
sp. strain m15-3 under the control of the heterologous promoters

P
lac

,

P
dhlA

, and

P
trc

. The resulting plasmids yielded functional expression in several gram-negative bacteria. A catabolic pathway for trihalopropanes was designed by introducing these broad-host-range dehalogenase expression plasmids into
Agrobacterium radiobacter
AD1, which has the ability to utilize dihalogenated propanols for growth. The recombinant strain AD1(pTB3), expressing the haloalkane dehalogenase gene under the control of the
dhlA
promoter, was able to utilize both 1,2,3-tribromopropane and 1,2-dibromo-3-chloropropane as sole carbon sources. Moreover, increased expression of the haloalkane dehalogenase resulted in elevated resistance to trihalopropanes.
Effect of Organic Complex Compounds on
Bacillus thermoamylovorans
Growth and Glucose Fermentation
Authors: Combet-Blanc Y. , Dieng M. C. , Kergoat P. Y. 
Published: December 2019

ABSTRACT

The effect of the concentration of a mixture (1/1 [wt/wt]) of yeast extract and bioTrypcase (YE+bT) on the growth and physiology of a new species,
Bacillus thermoamylovorans
, a moderately thermophilic, non-spore-forming, lactic acid-producing bacterium isolated from palm wine, was studied. At an initial glucose concentration of 100 mM,
B. thermoamylovorans
growth was limited when the concentration of YE+bT was lower than 5.0 g liter
−1
; under these conditions, cellular yield reached a maximum value of 0.4 g of cells per g of YE+bT. Growth limitation due to deficiency in growth factors led to a significant shift in glucose metabolism towards lactate production. Lactate constituted 27.5 and 76% of the end products of glucose fermentation in media containing YE+bT at 20.0 and 1.0 g liter
−1
, respectively. This result markedly differed from published data for lactic bacteria, which indicated that fermentative metabolism remained homolactic regardless of the concentration of YE. Our results showed that the ratio between cellular synthesis and energy production increased with the concentration of YE+bT in the culture medium. They indicate that the industrial production of lactic acid through glucose fermentation by
B. thermoamylovorans
can be optimized by using a medium where glucose is present in excess and the organic additives are limiting.
Helicobacter
Species Colonizing Pig Stomach: Molecular Characterization and Determination of Prevalence
Authors: Cantet Franck , Magras Catherine , Marais Armelle , Federighi Michel , Mégraud Francis 
Published: December 2019

ABSTRACT

The infection rate of 60 pigs (10 pigs from each of six farms) by
Helicobacter
species was studied by two techniques. Histological examination of the cardiac area of the stomach yielded a 58% positive result versus an 80% positive result by PCR with genus-specific primers. Eighty percent of the 16S rRNA gene was amplified, classified in four groups by PCR-restriction fragment length polymorphism, and sequenced. Isolates from all farms except one (farm C) were identified as
Helicobacter heilmannii
type 1, while those from farm C were identified as
H. heilmannii
type 2. Attempts to culture this organism in vitro failed.
Helicobacter pylori
was not found in these animals.
Viability and DNA Maintenance in Nonculturable Spiral
Campylobacter jejuni
Cells after Long-Term Exposure to Low Temperatures
Authors: Lázaro Beatriz , Cárcamo Jose , Audícana Ana , Perales Ildefonso , Fernández-Astorga Aurora 
Published: December 2019

ABSTRACT

Survival of
Campylobacter jejuni
at 4 and 20°C was investigated by using cellular integrity, respiratory activity, two-dimensional (2D) protein profile, and intact DNA content as indicators of potential viability of nonculturable cells. Intact DNA content after 116 days, along with cellular integrity and respiring cells, was detected for up to 7 months at 4°C by pulsed-field gel electrophoresis. Most changes in 2D protein profiles involved up- or down-regulation.