bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Characterization of a
Mycobacterium
Species Capable of Degrading Three- and Four-Ring Aromatic and Aliphatic Hydrocarbons
Authors: Churchill Sharon A. , Harper Jennifer P. , Churchill Perry F. 
Published: December 2019

ABSTRACT

Mycobacterium
sp. strain CH1 was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated freshwater sediments and identified by analysis of 16S rDNA sequences. Strain CH1 was capable of mineralizing three- and four-ring PAHs including phenanthrene, pyrene, and fluoranthene. In addition, strain CH1 could utilize phenanthrene or pyrene as a sole carbon and energy source. A lag phase of at least 3 days was observed during pyrene mineralization. This lag phase decreased to less than 1 day when strain CH1 was grown in the presence of phenanthrene or fluoranthene. Strain CH1 also was capable of using a wide range of alkanes as sole carbon and energy sources. No DNA hybridization was detected with the
nahAc
gene probe, indicating that enzymes involved in PAH metabolism are not related to the well-characterized naphthalene dioxygenase gene. DNA hybridization was not detected when the
alkB
gene from
Pseudomonas oleovorans
was used under high-stringency conditions. However, there was slight but detectable hybridization under low-stringency conditions. This suggests a distant relationship between genes involved in alkane oxidation.
Production and Distribution of Endoglucanase, Cellobiohydrolase, and β-Glucosidase Components of the Cellulolytic System of
Volvariella volvacea
, the Edible Straw Mushroom
Authors: Cai Yi Jin , Chapman Sandra J. , Buswell John A. , Chang Shu-ting 
Published: December 2019

ABSTRACT

The edible straw mushroom,
Volvariella volvacea
, produces a multicomponent enzyme system consisting of endo-1,4-β-glucanase, cellobiohydrolase, and β-glucosidase for the conversion of cellulose to glucose. The highest levels of endoglucanase and cellobiohydrolase were recorded in cultures containing microcrystalline cellulose (Avicel) or filter paper, while lower but detectable levels of activity were also produced on carboxymethyl cellulose, cotton wool, xylitol, or salicin. Biochemical analyses of different culture fractions in cultures exhibiting peak enzyme production revealed that most of the endoglucase was present either in the culture filtrate (45.8% of the total) or associated with the insoluble pellet fraction remaining after centrifugation of homogenized mycelia (32.6%). Cellobiohydrolase exhibited a similar distribution pattern, with 58.9% of the total enzyme present in culture filtrates and 31.0% associated with the pellet fraction. Conversely, most β-glucosidase activity (63.9% of the total) was present in extracts of fungal mycelia whereas only 9.4% was detected in culture filtrates. The endoglucanase and β-glucosidase distribution patterns were confirmed by confocal laser scanning microscopy combined with immunolabelling. Endoglucanase was shown to be largely cell wall associated or located extracellularly, with the highest concentrations being present in a region 1 to 2 μm wide immediately adjacent to the outer surface of (and possibly including) the hyphal wall and extending 60 to 70 μm from the hyphal tip. Immunofluorescence patterns indicated little if any intracellular endoglucanase. Most β-glucosidase was located intracellularly in the apical area extending 60 to 70 μm below the hyphal tip, although enzyme was also evident in the extracellular region extending approximately 15 μm all around the hyphal tip and trailing back along the length of the hypha. The regions of the hypha located some distance from the apical region appeared to be devoid of intracellular β-glucosidase, and the enzyme appears to be associated almost exclusively with, or located on the outside surface of, the hyphal wall.
Leaching of Pyrite by Acidophilic Heterotrophic Iron-Oxidizing Bacteria in Pure and Mixed Cultures
Authors: Bacelar-Nicolau Paula , Johnson D. Barrie 
Published: December 2019

ABSTRACT

Seven strains of heterotrophic iron-oxidizing acidophilic bacteria were examined to determine their abilities to promote oxidative dissolution of pyrite (FeS
2
) when they were grown in pure cultures and in mixed cultures with sulfur-oxidizing
Thiobacillus
spp. Only one of the isolates (strain T-24) oxidized pyrite when it was grown in pyrite-basal salts medium. However, when pyrite-containing cultures were supplemented with 0.02% (wt/vol) yeast extract, most of the isolates oxidized pyrite, and one (strain T-24) promoted rates of mineral dissolution similar to the rates observed with the iron-oxidizing autotroph
Thiobacillus ferrooxidans
. Pyrite oxidation by another isolate (strain T-21) occurred in cultures containing between 0.005 and 0.05% (wt/vol) yeast extract but was completely inhibited in cultures containing 0.5% yeast extract. Ferrous iron was also needed for mineral dissolution by the iron-oxidizing heterotrophs, indicating that these organisms oxidize pyrite via the “indirect” mechanism. Mixed cultures of three isolates (strains T-21, T-23, and T-24) and the sulfur-oxidizing autotroph
Thiobacillus thiooxidans
promoted pyrite dissolution; since neither strains T-21 and T-23 nor
T. thiooxidans
could oxidize this mineral in yeast extract-free media, this was a novel example of bacterial synergism. Mixed cultures of strains T-21 and T-23 and the sulfur-oxidizing mixotroph
Thiobacillus acidophilus
also oxidized pyrite but to a lesser extent than did mixed cultures containing
T. thiooxidans
. Pyrite leaching by strain T-23 grown in an organic compound-rich medium and incubated either shaken or unshaken was also assessed. The potential environmental significance of iron-oxidizing heterotrophs in accelerating pyrite oxidation is discussed.
Characteristics of Garden Dormice That Contribute to Their Capacity as Reservoirs for Lyme Disease Spirochetes
Authors: Matuschka Franz-Rainer , Allgöwer Rainer , Spielman Andrew , Richter Dania 
Published: December 2019

ABSTRACT
To describe the contribution of garden dormice to the epizootiology of Lyme disease, we compared their reservoir capacity for these pathogens to that of other sympatric hosts. Garden dormice are trapped most abundantly during early spring and again during midsummer, when their offspring forage. They are closely associated with moist forests. Garden dormice serve as hosts to nymphal ticks far more frequently than do other small mammals. Spirochetal infection is most prevalent in dormice, and many more larval ticks acquire infection in the course of feeding on these than on other rodents in the study site. Mature dormice appear to contribute more infections to the vector population than juveniles do. Replete larval ticks generally detach while their dormouse hosts remain within their nests. The population of garden dormice contributes five- to sevenfold more infections to the vector population than the mouse population does. Their competence, nymphal feeding density, and preference for a tick-permissive habitat combine to favor garden dormice over other putative reservoir hosts of Lyme disease spirochetes.
Characterization of Two Novel Propachlor Degradation Pathways in Two Species of Soil Bacteria
Authors: Martin Margarita , Mengs Gerardo , Allende Jose Luis , Fernandez Javier , Alonso Ramon , Ferrer Estrella 
Published: December 2019

ABSTRACT

Propachlor (2-chloro-
N
-isopropylacetanilide) is an acetamide herbicide used in preemergence. In this study, we isolated and characterized a soil bacterium,
Acinetobacter
strain BEM2, that was able to utilize this herbicide as the sole and limiting carbon source. Identification of the intermediates of propachlor degradation by this strain and characterization of new metabolites in the degradation of propachlor by a previously reported strain of
Pseudomonas
(PEM1) support two different propachlor degradation pathways. Washed-cell suspensions of strain PEM1 with propachlor accumulated
N
-isopropylacetanilide, acetanilide, acetamide, and catechol.
Pseudomonas
strain PEM1 grew on propachlor with a generation time of 3.4 h and a

K
s

of 0.17 ± 0.04 mM.
Acinetobacter
strain BEM2 grew on propachlor with a generation time of 3.1 h and a

K
s

of 0.3 ± 0.07 mM. Incubations with strain BEM2 resulted in accumulation of
N
-isopropylacetanilide,
N
-isopropylaniline, isopropylamine, and catechol. Both degradative pathways were inducible, and the principal product of the carbon atoms in the propachlor ring was carbon dioxide. These results and biodegradation experiments with the identified metabolites indicate that metabolism of propachlor by
Pseudomonas
sp. strain PEM1 proceeds through a different pathway from metabolism by
Acinetobacter
sp. strain BEM2.
A Novel Chromogenic Ester Agar Medium for Detection of Salmonellae
Authors: Cooke Venitia M. , Miles R. J. , Price R. G. , Richardson A. C. 
Published: December 2019

ABSTRACT

A novel agar medium, chromogenic
Salmonella
esterase (CSE) agar, for the differentiation of salmonellae is described. The agar contains peptones and nutrient extracts together with the following (grams per liter unless otherwise specified): 4-[2-(4-octanoyloxy-3,5-dimethoxyphenyl)-vinyl]-quinolinium-1-(propan-3-yl carboxylic acid) bromide (SLPA-octanoate; bromide form), 0.3223; lactose, 14.65; trisodium citrate dihydrate, 0.5; Tween 20, 3.0; ethyl 4-dimethylaminobenzoate, 0.035% (wt/vol), novobiocin, 70 mg liter
−1
. The key component of the medium is SLPA-octanoate, a newly synthesized ester formed from a C
8
fatty acid and a phenolic chromophore. In CSE agar, the ester is hydrolyzed by
Salmonella
spp. to yield a brightly colored phenol which remains tightly bound within colonies. After 24 h of incubation at 37 or 42°C, colonies of typical
Salmonella
spp. were burgundy colored on a transparent yellow background, whereas non-
Salmonella
spp. were white, cream, yellow or transparent. CSE agar was evaluated by using a panel of strains including a high proportion of
Salmonella
and non-
Salmonella
strains giving atypical reactions on other differential agars. The sensitivity (93.1%) of CSE agar for non-
typhi
salmonellae compared favorably with those of Rambach (82.8%), xylose-lysine-deoxycholate (XLD; 91.4%), Hektoen-enteric (89.7%), and SM ID (91.4%) agars. The specificity (93.9%) was also comparable to those of other
Salmonella
media (SM ID agar, 95.9%; Rambach agar, 91.8%; XLD agar, 91.8%; Hektoen-enteric agar, 87.8%). Strains of
Citrobacter freundii
and
Proteus
spp. giving false-positive reactions with other media gave a negative color reaction on CSE agar. CSE agar enabled the detection of >30
Salmonella
serotypes, including
agona
,
anatum
,
enteritidis
,
hadar
,
heidelberg
,
infantis
,
montevideo
,
thompson
,
typhimurium
, and
virchow
, which accounted for 91.8% of the salmonella isolates recorded by the Public Health Laboratory Service (Colindale, London, England) for 1997.
Isolation of
Deinococcus
Species from Commercial Oyster Extract
Authors: Chan W. F. , O’Toole D. K. 
Published: December 2019

ABSTRACT

Deinococci with radiation resistance greater than that of
Deinococcus radiophilus
(ATCC 27603) were isolated from three commercial oyster extracts stored at 4, 20, and 30°C. During storage the number of other bacteria declined and deinococci became the predominant group in the microflora, particularly at 20°C, although at 30°C the number of deinococci as well rapidly declined. The results suggest that the natural habitat of deinococci is an aerobic environment containing a slightly elevated saline content, soluble protein, and low sugar levels.
Detection of Shiga-Like Toxin (

stx
1

and

stx
2

), Intimin (
eaeA
), and Enterohemorrhagic
Escherichia coli
(EHEC) Hemolysin (EHEC
hlyA
) Genes in Animal Feces by Multiplex PCR
Authors: Fagan Peter K. , Hornitzky Michael A. , Bettelheim Karl A. , Djordjevic Steven P. 
Published: December 2019

ABSTRACT

A multiplex PCR was developed for the rapid detection of genes encoding Shiga toxins 1 and 2 (

stx
1

and

stx
2

), intimin (
eaeA
), and enterohemolysin A (
hlyA
) in 444 fecal samples derived from healthy and clinically affected cattle, sheep, pigs, and goats. The method involved non-solvent-based extraction of nucleic acid from an aliquot of an overnight culture of feces in EC (modified) broth. The detection limit of the assay for both fecal samples and pure cultures was between 18 and 37 genome equivalents.

stx
1

and
hlyA
were the most commonly encountered virulence factors.
A Comparative Study of Methods To Validate Formaldehyde Decontamination of Biological Safety Cabinets
Authors: Munro Kerry , Lanser Janice , Flower Robert 
Published: December 2019

ABSTRACT

Methods of validation of formaldehyde decontamination of biological safety cabinets were compared. Decontamination of metal strips inoculated with
Mycobacterium bovis
, poliovirus, or
Bacillus
spp. spores was compared with the results obtained with three biological indicators. Conditions for successful decontamination, particularly relative humidity, were defined. The Attest 1291 biological indicator was the only biological indicator which was an aid in the detection of gross decontamination failure.
High-Affinity Methane Oxidation by a Soil Enrichment Culture Containing a Type II Methanotroph
Authors: Dunfield Peter F. , Liesack Werner , Henckel Thilo , Knowles Roger , Conrad Ralf 
Published: December 2019

ABSTRACT

Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH
4
). After 4 years of growth and periodic dilution (>10
20
times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [

K
m(app)

] for CH
4
of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the

K
m(app)

increased when the culture was transferred to higher mixing ratios of CH
4
(1,000 ppmv, or 1%). Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH
4
revealed a single gene product of
pmoA
, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH
4
and phylogenetically positioned based on its 16S rRNA,
pmoA
, and
mxaF
gene sequences as a type II strain of the
Methylocystis/Methylosinus
group. A coculture of this strain with a
Variovorax
sp., when grown on <275 ppmv of CH
4
, had a

K
m(app)

(129 to 188 nM) similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH
4
varies with growth conditions and that the oxidation of atmospheric CH
4
observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species.
Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints
Authors: Heuer Holger , Hartung Kathrin , Wieland Gabriele , Kramer Ina , Smalla Kornelia 
Published: December 2019

ABSTRACT

Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (
Escherichia coli
16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5′ exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.
Sensitivity, Specificity, and Predictive Values of Three
Salmonella
Rapid Detection Kits Using Fresh and Frozen Poultry Environmental Samples versus Those of Standard Plating
Authors: Peplow Melissa O. , Correa-Prisant Maria , Stebbins Martha E. , Jones Frank , Davies Peter 
Published: December 2019

ABSTRACT

To reduce human exposure to
Salmonella
spp. in poultry products, broiler chicken flocks have been tested by culture methods. Since the standard techniques may take 3 to 5 days, rapid detection methods have been developed. In this study we tested the performance of three rapid tests originally developed for food samples by using environmental samples obtained from poultry houses. These rapid tests were Reveal, an enzyme-linked immunosorbent assay from Neogen Corp.; BIND, a bacterial ice nucleation detection method from Idetek Corp.; and a filter monitor method from Future Medical Technologies, Inc. For the standard culture, brilliant green with novabiocin and xylose–lysine–tergitol-4 agar were used for presumptive identification, and identities were confirmed by using poly-O antisera. Environmental samples were collected from farms belonging to an integrated poultry company prior to chick placement and 1 week before slaughter. Sensitivities, specificities, and predictive values with 95% confidence intervals were calculated. Statistical differences were determined by using McNemar’s chi square test. The sensitivities of the different tests were not stable, varying widely between sample times, and were affected by freezing of the samples. All of the rapid tests had low sensitivities, which led to many false-negative results. All tests were able to detect
Salmonella
spp. at a concentration of 10 CFU/ml in at least one of four trials. The BIND and Reveal tests were simple to use with multiple samples and reduced laboratory time by up to 1 day. Based on our results, we do not recommend that any of these rapid tests, in their present state of development, be utilized with environmental samples collected with drag swabs.
Isolation from Estuarine Sediments of a
Desulfovibrio
Strain Which Can Grow on Lactate Coupled to the Reductive Dehalogenation of 2,4,6-Tribromophenol
Authors: Boyle Alfred W. , Phelps Craig D. , Young L. Y. 
Published: December 2019

ABSTRACT

Strain TBP-1, an anaerobic bacterium capable of reductively dehalogenating 2,4,6-tribromophenol to phenol, was isolated from estuarine sediments of the Arthur Kill in the New York/New Jersey harbor. It is a gram-negative, motile, vibrio-shaped, obligate anaerobe which grows on lactate, pyruvate, hydrogen, and fumarate when provided sulfate as an electron acceptor. The organism accumulates acetate when grown on lactate and sulfate, contains desulfoviridin, and will not grow in the absence of NaCl. It will not utilize acetate, succinate, propionate, or butyrate for growth via sulfate reduction. When supplied with lactate as an electron donor, strain TBP-1 will utilize sulfate, sulfite, sulfur, and thiosulfate for growth but not nitrate, fumarate, or acrylate. This organism debrominates 2-, 4-, 2,4-, 2,6-, and 2,4,6-bromophenol but not 3- or 2,3-bromophenol or monobrominated benzoates. It will not dehalogenate monochlorinated, fluorinated, or iodinated phenols or chlorinated benzoates. Together with its physiological characteristics, its 16S rRNA gene sequence places it in the genus
Desulfovibrio
. The average growth yield of strain TBP-1 grown on a defined medium supplemented with lactate and 2,4,6-bromophenol is 3.71 mg of protein/mmol of phenol produced, and the yield was 1.42 mg of protein/mmol of phenol produced when 4-bromophenol was the electron acceptor. Average growth yields (milligrams of protein per millimole of electrons utilized) for
Desulfovibrio
sp. strain TBP-1 grown with 2,4,6-bromophenol, 4-bromophenol, or sulfate are 0.62, 0.71, and 1.07, respectively. Growth did not occur when either lactate or 2,4,6-bromophenol was omitted from the growth medium. These results indicate that
Desulfovibrio
sp. strain TBP-1 is capable of growth via halorespiration.
Fusarium subglutinans
f. sp.
pini
Represents a Distinct Mating Population in the
Gibberella fujikuroi
Species Complex
Authors: Britz H. , Coutinho T. A. , Wingfield M. J. , Marasas W. F. O. , Gordon T. R. , Leslie J. F. 
Published: December 2019

ABSTRACT

Fusarium
strains in the
Gibberella fujikuroi
species complex cause diseases on a variety of economically important plants. One of these diseases, pitch canker of
Pinus
spp., is caused by strains identified as
Fusarium subglutinans
f. sp.
pini
. Fertile crosses were detected between
F. subglutinans
f. sp.
pini
strains from South Africa, California, and Florida.
F. subglutinans
f. sp.
pini
strains were not cross-fertile with the standard tester strains of six of the seven other mating populations of
G. fujikuroi
. Sporadic perithecia with ascospores were obtained in two crosses with the mating population B tester strains. These perithecia were homothallic, and the ascospores derived from these perithecia were vegetatively compatible with the mating population B tester strain parent. We concluded that fertile
F. subglutinans
f. sp.
pini
isolates represent a new mating population (mating population H) of
G. fujikuroi
and that they belong to a unique biological species in a distinct taxon.