bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of Three-Way Randomly Amplified Polymorphic DNA Analysis as a Typing Method for Twelve
Salmonella
Serotypes
Authors: Soto S. M. , Guerra B. , González-Hevia M. A. , Mendoza M. C. 
Published: December 2019

ABSTRACT

The potential of a three-way randomly amplified polymorphic DNA (RAPD) procedure (RAPD typing) for typing
Salmonella enterica
strains assigned to 12 serotypes was analyzed. The series of organisms used included 235 strains (326 isolates) collected mainly from clinical samples in the Principality of Asturias and 9 reference strains. RAPD typing was performed directly with broth cultures of bacteria by using three selected primers and optimized PCR conditions. The profiles obtained with the three primers were used to define RAPD types and to evaluate the procedure as a typing method at the species and serotype levels. The typeability was 100%; the reproducibility and in vitro stability could be considered good. The concordance of RAPD typing methods with serotyping methods was 100%, but some profiles obtained with two of the three primers were obtained with strains assigned to different serotypes. The discrimination index (DI) within the series of organisms was 0.94, and the DI within serotypes Typhimurium, Enteritidis, and Virchow were 0.72, 0.52, and 0.66, respectively. Within these serotypes the most common RAPD types were differentiated into phage types and vice versa; combining the types identified by the two procedures (RAPD typing and phage typing) resulted in further discrimination (DI, 0.96, 0.74, and 0.87, respectively). The efficiency, rapidity, and flexibility of the RAPD typing method support the conclusion that it can be used as a tool for identifying
Salmonella
organisms and as a typing method that is complementary to serotyping and phage typing methods.
Culture-Independent Characterization of a Gene Responsible for Nitrogen Fixation in the Symbiotic Microbial Community in the Gut of the Termite
Neotermes koshunensis
Authors: Noda Satoko , Ohkuma Moriya , Usami Ron , Horikoshi Koki , Kudo Toshiaki 
Published: December 2019

ABSTRACT

Expression of the nitrogen fixation gene,
nifH
, in the gut of the termite
Neotermes koshunensis
was characterized without cultivation.
nifH
cDNA was directly amplified from mRNA of the mixed microbial population in the gut by reverse transcription (RT)-PCR. Analyses of the RT-PCR products revealed that, among the diverse
nifH
sequences, only a few corresponding to an alternative nitrogenase (encoded by the
anf
gene) were preferentially transcribed in the termite gut. Expression of the
anf
gene was further investigated quantitatively under several termite feeding conditions by competitive PCR. The levels of expression of the
anf
gene were largely congruent with the nitrogen fixation activity displayed by the termite. The amounts of the genomic
anf
gene in the population showed no significant change, indicating that the level of expression was critical for nitrogen fixation activity. Interestingly, no significant decrease in the expression level was observed when the diet contained molybdenum (Mo), which represses ordinary
anf
genes. A 3.6-kb DNA region downstream of the
anf
gene was isolated and found to contain reading frames homologous to
anfH
,
anfD
, and
anfG
of the
Bacteria
domain which encode subunits of an alternative nitrogenase having no Mo as a cofactor. This DNA region also contained reading frames encoding
glnB
-like proteins, which is a common feature of the nitrogenase genes of the
Archaea
domain. These results indicate that the
anf
group of nitrogenase genes is the most important group of genes responsible for nitrogen fixation in
N. koshunensis
and that the
anf
gene possesses novel features with respect to the regulation of its expression and its gene organization.
Impacts of the Reduction of Nutrient Levels on Bacterial Water Quality in Distribution Systems
Authors: Volk Christian J. , LeChevallier Mark W. 
Published: December 2019

ABSTRACT

This study evaluated the impacts of reducing nutrient levels on bacterial water quality in drinking water. Two American Water System facilities (sites NJ102a and IN610) with histories of coliform problems were involved, and each water utility received two pilot distribution systems (annular reactors). One reactor simulated the conventional treatment conditions (control), while the other reactor was used to assess the effect of biological filtration and subsequent reduced biodegradable organic matter levels on suspended (water column) and biofilm bacterial concentrations in the distribution systems. Biodegradable organic matter levels were reduced approximately by half after biological treatment. For site NJ102a, the geometric mean of the assimilable organic carbon concentrations was 217 μg/liter in the plant effluent and 91 μg/liter after biological filtration. For both sites, plant effluent biodegradable dissolved organic carbon levels averaged 0.45 mg/liter, versus 0.19 to 0.22 mg/liter following biological treatment. Biological treatment improved the stability of free chlorine residuals, while it had little effect on chloramine consumption patterns. High bacterial levels from the biological filters resulted in higher bacterial concentrations entering the test reactors than entering the control reactors. On average, biofilms in the model systems were reduced by 1 log unit (from 1.4 × 10
5
to 1.4 × 10
4
CFU/cm
2
) and 0.5-log unit (from 2.7 × 10
5
to 7.8 × 10
4
CFU/cm
2
) by biological treatment at sites NJ102a and IN610, respectively. Interestingly, it required several months of biological treatment before there was an observable impact on bacterial water quality in the system, suggesting that the effect of the treatment change was influenced by other factors (i.e., pipe conditions or disinfection, etc.).
Lactobacillus salivarius
CTC2197 Prevents
Salmonella enteritidis
Colonization in Chickens
Authors: Pascual Mònica , Hugas Marta , Badiola Jose Ignacio , Monfort Josep Maria , Garriga Margarita 
Published: December 2019

ABSTRACT

A rifampin-resistant
Lactobacillus salivarius
strain, CTC2197, was assessed as a probiotic in poultry, by studying its ability to prevent
Salmonella enteritidis
C-114 colonization in chickens. When the probiotic strain was dosed by oral gavage together with
S. enteritidis
C-114 directly into the proventriculus in 1-day-old Leghorn chickens, the pathogen was completely removed from the birds after 21 days. The same results were obtained when the probiotic strain was also administered through the feed and the drinking water apart from direct inoculation into the proventriculus. The inclusion of
L. salivarius
CTC2197 in the first day chicken feed revealed that a concentration of 10
5
CFU g
−1
was enough to ensure the colonization of the gastrointestinal tract of the birds after 1 week. However, between 21 and 28 days,
L. salivarius
CTC2197 was undetectable in the gastrointestinal tract of some birds, showing that more than one dose would be necessary to ensure its presence till the end of the rearing time. Freeze-drying and freezing with glycerol or skim milk as cryoprotective agents, appeared to be suitable methods to preserve the probiotic strain. The inclusion of the
L. salivarius
CTC2197 in a commercial feed mixture seemed to be a good way to supply it on the farm, although the strain showed sensitivity to the temperatures used during the feed mixture storage and in the chicken incubator rooms. Moreover, survival had been improved after several reinoculations in chicken feed mixture.
Isolation, Oxygen Sensitivity, and Virulence of NADH Oxidase Mutants of the Anaerobic SpirocheteBrachyspira(Serpulina)hyodysenteriae, Etiologic Agent of Swine Dysentery
Authors: Stanton Thad B. , Rosey Everett L. , Kennedy Michael J. , Jensen Neil S. , Bosworth Brad T. 
Published: December 2019

ABSTRACTBrachyspira(Serpulina)hyodysenteriae, the etiologic agent of swine dysentery, uses the enzyme NADH oxidase to consume oxygen. To investigate possible roles for NADH oxidase in the growth and virulence of this anaerobic spirochete, mutant strains deficient in oxidase activity were isolated and characterized. The cloned NADH oxidase gene (nox; GenBank accession no.U19610) on plasmid pER218 was inactivated by replacing 321 bp of coding sequence with either a gene for chloramphenicol resistance (cat) or a gene for kanamycin resistance (kan). The resulting plasmids, respectively, pCmΔNOX and pKmΔNOX, were used to transform wild-typeB. hyodysenteriaeB204 cells and generate the antibiotic-resistant strains Nox-Cm and Nox-Km. PCR and Southern hybridization analyses indicated that the chromosomal wild-typenoxgenes in these strains had been replaced, through allelic exchange, by the inactivatednoxgene containingcatorkan. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western immunoblot analysis revealed that bothnoxmutant cell lysates were missing the 48-kDa Nox protein. Soluble NADH oxidase activity levels in cell lysates of Nox-Cm and Nox-Km were reduced 92 to 96% compared to the activity level in parent strain B204. In an aerotolerance test, cells of bothnoxmutants were at least 100-fold more sensitive to oxygen exposure than were cells of the wild-type parent strain B204. In swine experimental infections, bothnoxmutants were less virulent than strain B204 in that fewer animals were colonized by the mutant cells and infected animals displayed mild, transient signs of disease, with no deaths. These results provide evidence that NADH oxidase serves to protectB. hyodysenteriaecells against oxygen toxicity and that the enzyme, in that role, contributes to the pathogenic ability of the spirochete.
Metabolism of Acrylate to β-Hydroxypropionate and Its Role in Dimethylsulfoniopropionate Lyase Induction by a Salt Marsh Sediment Bacterium,
Alcaligenes faecalis
M3A
Authors: Ansede John H. , Pellechia Perry J. , Yoch Duane C. 
Published: December 2019

ABSTRACT

Dimethylsulfoniopropionate (DMSP) is degraded to dimethylsulfide (DMS) and acrylate by the enzyme DMSP lyase. DMS or acrylate can serve as a carbon source for both free-living and endophytic bacteria in the marine environment. In this study, we report on the mechanism of DMSP-acrylate metabolism by
Alcaligenes faecalis
M3A. Suspensions of citrate-grown cells expressed a low level of DMSP lyase activity that could be induced to much higher levels in the presence of DMSP, acrylate, and its metabolic product, β-hydroxypropionate. DMSP was degraded outside the cell, resulting in an extracellular accumulation of acrylate, which in suspensions of citrate-grown cells was then metabolized at a low endogenous rate. The inducible nature of acrylate metabolism was evidenced by both an increase in the rate of its degradation over time and the ability of acrylate-grown cells to metabolize this molecule at about an eight times higher rate than citrate-grown cells. Therefore, acrylate induces both its production (from DMSP) and its degradation by an acrylase enzyme.
1
H and
13
C nuclear magnetic resonance analyses were used to identify the products resulting from [1-
13
C]acrylate metabolism. The results indicated that
A. faecalis
first metabolized acrylate to β-hydroxypropionate outside the cell, which was followed by its intracellular accumulation and subsequent induction of DMSP lyase activity. In summary, the mechanism of DMSP degradation to acrylate and the subsequent degradation of acrylate to β-hydroxypropionate in the aerobic β-Proteobacterium
A. faecalis
has been described.
Acetogenic and Sulfate-Reducing Bacteria Inhabiting the Rhizoplane and Deep Cortex Cells of the Sea Grass
Halodule wrightii
Authors: Küsel Kirsten , Pinkart Holly C. , Drake Harold L. , Devereux Richard 
Published: December 2019

ABSTRACT

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizospheres that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacteria and clostridia were enriched in sediments colonized by the sea grasses
Halodule wrightii
and
Thalassia testudinum
compared to an adjacent unvegetated sediment. Most-probable-number analyses found that in contrast to butyrate-producing clostridia, acetogens and acetate-utilizing sulfate reducers were enriched by an order of magnitude in rhizosphere sediments. Although sea grass roots are oxygenated in the daytime, colorimetric root incubation studies demonstrated that acetogenic O-demethylation and sulfidogenic iron precipitation activities were tightly associated with washed, sediment-free
H. wrightii
roots. This suggests that the associated anaerobes are able to tolerate exposure to oxygen. To localize and quantify the anaerobic microbial colonization, root thin sections were hybridized with newly developed
33
P-labeled probes that targeted (i) low-G+C-content gram-positive bacteria, (ii) cluster I species of clostridia, (iii) species of
Acetobacterium
, and (iv) species of
Desulfovibrio
. Microautoradiography revealed intercellular colonization of the roots by
Acetobacterium
and
Desulfovibrio
species. Acetogenic bacteria occurred mostly in the rhizoplane and outermost cortex cell layers, and high numbers of sulfate reducers were detected on all epidermal cells and inward, colonizing some 60% of the deepest cortex cells. Approximately 30% of epidermal cells were colonized by bacteria that hybridized with an archaeal probe, strongly suggesting the presence of methanogens. Obligate anaerobes within the roots might contribute to the vitality of sea grasses and other aquatic plants and to the biogeochemistry of the surrounding sediment.
A New Selective Medium for
Bifidobacterium
spp
Authors: Nebra Y. , Blanch A. R. 
Published: December 2019

ABSTRACT

A new selective antibiotic-free medium for
Bifidobacterium
spp. is defined. This medium has lactulose as the main carbon source and includes methylene blue, propionic acid, and lithium chloride as inhibitors of some related bacterial species. The low pH of the medium contributes to the inhibition of the growth of
Enterobacteriaceae
. This new selective medium has a simple composition, and the level of recovery it yields is similar to those yielded by nonselective media for
Bifidobacterium
strains. It could thus be used for routine analysis in environmental or food microbiology.
Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading
Methylomonas
sp. Strains and Detection of Methanotrophs during In Situ Bioremediation
Authors: Shigematsu Toru , Hanada Satoshi , Eguchi Masahiro , Kamagata Yoichi , Kanagawa Takahiro , Kurane Ryuichiro 
Published: December 2019

ABSTRACT

The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb
Kpn
I fragment from
Methylomonas
sp. strain KSWIII and a 7.5-kb
Sal
I fragment from
Methylomonas
sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from
M. capsulatus
Bath in the group X methanotrophs than to those from
Methylosinus trichosporium
OB3b and
Methylocystis
sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the
mmoX
gene. The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.
Swimming MarineSynechococcusStrains with Widely Different Photosynthetic Pigment Ratios Form a Monophyletic Group
Authors: Toledo Gerardo , Palenik B. , Brahamsha B. 
Published: December 2019

ABSTRACTUnicellular marine cyanobacteria are ubiquitous in both coastal and oligotrophic regimes. The contribution of these organisms to primary production and nutrient cycling is substantial on a global scale. Natural populations of marineSynechococcusstrains include multiple genetic lineages, but the link, if any, between unique phenotypic traits and specific genetic groups is still not understood. We studied the genetic diversity (as determined by the DNA-dependent RNA polymeraserpoC1gene sequence) of a set of marineSynechococcusisolates that are able to swim. Our results show that these isolates form a monophyletic group. This finding represents the first example of correspondence between a physiological trait and a phylogenetic group in marineSynechococcus. In contrast, the phycourobilin (PUB)/phycoerythrobilin (PEB) pigment ratios of members of the motile clade varied considerably. An isolate obtained from the California Current (strain CC9703) displayed a pigment signature identical to that of nonmotile strain WH7803, which is considered a model for low-PUB/PEB-ratio strains, whereas several motile strains had higher PUB/PEB ratios than strain WH8103, which is considered a model for high-PUB/PEB-ratio strains. These findings indicate that the PUB/PEB pigment ratio is not a useful characteristic for defining phylogenetic groups of marineSynechococcusstrains.
Attributes of Atmospheric Carbon Monoxide Oxidation by Maine Forest Soils
Authors: King G. M. 
Published: December 2019

ABSTRACT

CO, one of the most important trace gases, regulates tropospheric methane, hydroxyl radical, and ozone contents. Ten to 25% of the estimated global CO flux may be consumed by soils annually. Depth profiles for
14
CO oxidation and CO concentration indicated that CO oxidation occurred primarily in surface soils and that photooxidation of soil organic matter did not necessarily contribute significantly to CO fluxes. Kinetic analyses revealed that the apparent

K
m

was about 18 nM (17 ppm) and the
V
max
was 6.9 μmol g (fresh weight)
−1
h
−1
; the apparent

K
m

was similar to the apparent

K
m

for atmospheric methane consumption, but the
V
max
was more than 100 times higher. Atmospheric CO oxidation responded sensitively to soil water regimes; decreases in water content in initially saturated soils resulted in increased uptake, and optimum uptake occurred at water contents of 30 to 60%. However, extended drying led to decreased uptake and net CO production. Rewetting could restore CO uptake, albeit with a pronounced hysteresis. The responses to changing temperatures indicated that the optimum temperature for net uptake was between 20 and 25°C and that there was a transition to net production at temperatures above 30°C. The responses to methyl fluoride and acetylene indicated that populations other than ammonia oxidizers and methanotrophs must be involved in forest soils. The response to acetylene was notable, since the strong initial inhibition was reversed after 12 h of incubation; in contrast, methyl fluoride did not have an inhibitory effect. Ammonium did not inhibit CO uptake; the level of nitrite inhibition was initially substantial, but nitrite inhibition was reversible over time. Nitrite inhibition appeared to occur through indirect effects based on abiological formation of NO.
A Study of Deep-Sea Natural Microbial Populations and Barophilic Pure Cultures Using a High-Pressure Chemostat
Authors: Wirsen Carl O. , Molyneaux Stephen J. 
Published: December 2019

ABSTRACT
Continuous cultures in which a high-pressure chemostat was used were employed to study the growth responses of (i) deep-sea microbial populations with the naturally occurring carbon available in seawater and with limiting concentrations of supplemental organic substrates and (ii) pure cultures of copiotrophic barophilic and barotolerant deep-sea isolates in the presence of limiting carbon concentrations at various pressures, dilution rates, and temperatures. We found that the growth rates of natural populations could not be measured or were extremely low (e.g., a doubling time of 629 h), as determined from the difference between the dilution rate and the washout rate. A low concentration of supplemental carbon (0.33 mg/liter) resulted in positive growth responses in the natural population, which resulted in an increase in the number of cells and eventually a steady population of cells. We found that the growth responses to imposed growth pressure by barophilic and barotolerant pure-culture isolates that were previously isolated and characterized under high-nutrient-concentration conditions were maintained under the low-nutrient-concentration limiting conditions (0.33 to 3.33 mg of C per liter) characteristic of the deep-sea environment. Our results indicate that deep-sea microbes can respond to small changes in substrate availability. Also, barophilic microbes that are copiotrophic as determined by their isolation in the presence of high carbon concentrations and their preference for high carbon concentrations are versatile and are able to compete and grow as barophiles in the low-carbon-concentration oligotrophic deep-sea environment in which they normally exist.
Molecular Analysis of the 18S rRNA Gene of
Cryptosporidium serpentis
in a Wild-Caught Corn Snake (
Elaphe guttata guttata
) and a Five-Species Restriction Fragment Length Polymorphism- Based Assay That Can Additionally Discern
C. parvum
from
C. wrairi
Authors: Kimbell L. M. , Miller D. L. , Chavez W. , Altman N. 
Published: December 2019

ABSTRACT

An adult wild-caught corn snake (
Elaphe guttata guttata
) was presented for humane euthanasia and necropsy because of severe cryptosporidiosis. The animal was lethargic and >5% dehydrated but in good flesh. Gastric lavage was performed prior to euthanasia. Histopathologic findings included gastric mucosal hypertrophy and a hemorrhagic erosive gastritis. Numerous 5- to 7-μm-diameter round extracellular organisms were associated with the mucosal hypertrophy. A PCR, acid-fast stains, Giemsa stains, and an enzyme immunoassay were all positive for
Cryptosporidium
spp. PCR and restriction fragment length polymorphism (RFLP) analysis on gastric lavage and gastric mucosal specimens, and subsequent sequencing of the 18S rRNA gene, enabled a distinct molecular characterization of the infecting organism as
Cryptosporidium serpentis
. Until recently, studies on snake
Cryptosporidium
have relied on host specificity and gross and histopathologic observations to identify the infecting species. A multiple alignment of our sequence against recently published sequences of the 18S rRNA gene of
C. serpentis
(GenBank accession no.
AF093499
,
AF093500
, and
AF093501
[L. Xiao et al., unpublished data, 1998]) revealed 100% homology with the
C. serpentis
(
Snake
) sequence (
AF093499
) previously described by Xiao et al. An RFLP method to differentiate the five presently sequenced strains of
Cryptosporidium
at this locus was developed. This assay, which uses
Spe
I and
Ssp
I, complements a previously reported assay by additionally distinguishing the bovine strain of
Cryptosporidium
from
Cryptosporidium wrairi
.