bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Method of Cloning the Obligate Intracellular Bacterium
Coxiella burnetii
Authors: Beare Paul A. , Howe Dale , Cockrell Diane C. , Heinzen Robert A. 
Published: April 2007

ABSTRACT

Coxiella burnetii
is an obligate intracellular bacterium that replicates in a large lysosome-like parasitophorous vacuole (PV). Current methods of cloning
C. burnetii
are laborious and technically demanding. We have developed an alternative cloning method that involves excision of individual
C. burnetii
-laden PVs from infected cell monolayers by micromanipulation. To demonstrate the cloning utility and efficiency of this procedure, we coinfected Vero cells with isogenic variants of the Nine Mile strain of
C. burnetii
. Coinhabited PVs harboring Nine Mile phase II (NMII) and Nine Mile phase I (NMI) or Nine Mile crazy (NMC) were demonstrated by immunofluorescence. PVs were then randomly excised from cells coinfected with NMI and NMC by micromanipulation, and PVs harboring both strains were identified by PCR. Fresh Vero cells were subsequently infected with organisms from coinhabited PVs, and the PV excision and PCR screening process was repeated. Without exception, PVs obtained from second-round excisions contained clonal populations of either NMII or NMC, demonstrating that micromanipulation is an efficient and reproducible procedure for obtaining
C. burnetii
clones.
Relationship between Sublethal Injury and Inactivation of Yeast Cells by the Combination of Sorbic Acid and Pulsed Electric Fields
Authors: Somolinos M. , García D. , Condón S. , Mañas P. , Pagán R. 
Published: April 2007

ABSTRACTThe objective of this study was to investigate the occurrence of sublethal injury after the pulsed-electric-field (PEF) treatment of two yeasts,Dekkera bruxellensisandSaccharomyces cerevisiae, as well as the relation of sublethal injury to the inactivating effect of the combination of PEF and sorbic acid. PEF caused sublethal injury in both yeasts: more than 90% of survivingD. bruxellensiscells and 99% of survivingS. cerevisiaecells were sublethally injured after 50 pulses at 12 kV/cm in buffer at pHs of both 7.0 and 4.0. The proportion of sublethally injured cells reached a maximum after 50 pulses at 12.0 kV/cm (S. cerevisiae) or 16.5 kV/cm (D. bruxellensis), and it kept constant or progressively decreased at greater electric field strengths and with longer PEF treatments. Sublethally PEF-injured cells showed sensitivity to the presence of sorbic acid at a concentration of 2,000 ppm. A synergistic inactivating effect of the combination of PEF and sorbic acid was observed. Survivors of the PEF treatment were progressively inactivated in the presence of 2,000 ppm of sorbic acid at pH 3.8, with the combined treatments achieving more than log105 cycles of dead cells under the conditions investigated. This study has demonstrated the occurrence of sublethal injury after exposure to PEF, so yeast inactivation by PEF is not an all-or-nothing event. The combination of PEF and sorbic acid has proven to be an effective method to achieve a higher level of yeast inactivation. This work contributes to the knowledge of the mechanism of microbial inactivation by PEF, and it may be useful for improving food preservation by PEF technology.
Aerobic Anoxygenic Phototrophic Bacteria Attached to Particles in Turbid Waters of the Delaware and Chesapeake Estuaries
Authors: Waidner Lisa A. , Kirchman David L. 
Published: April 2007

ABSTRACT

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that, if abundant, may be biogeochemically important in the oceans. We used epifluorescence microscopy and quantitative PCR (qPCR) to examine the abundance of these bacteria by enumerating cells with bacteriochlorophyll
a
(bChl
a
) and the light-reaction center gene
pufM
, respectively. In the surface waters of the Delaware estuary, AAP bacteria were abundant, comprising up to 34% of prokaryotes, although the percentage varied greatly with location and season. On average, AAP bacteria made up 12% of the community as measured by microscopy and 17% by qPCR. In the surface waters of the Chesapeake, AAP bacteria were less abundant, averaging 6% of prokaryotes. AAP bacterial abundance was significantly correlated with light attenuation (
r
= 0.50) and ammonium (
r
= 0.42) and nitrate (
r
= 0.71) concentrations. Often, bChl
a
-containing bacteria were mostly attached to particles (31 to 94% of total AAP bacteria), while usually 20% or less of total prokaryotes were associated with particles. Of the cells containing
pufM
, up to 87% were associated with particles, but the overall average of particle-attached cells was 15%. These data suggest that AAP bacteria are particularly competitive in these two estuaries, in part due to attachment to particles.
Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica
Authors: Mikucki Jill A. , Priscu John C. 
Published: April 2007

ABSTRACT

Blood Falls is the surface manifestation of brine released from below the Taylor Glacier, McMurdo Dry Valleys, Antarctica. Geochemical analyses of Blood Falls show that this brine is of a marine origin. The discovery that 74% of clones and isolates from Blood Falls share high 16S rRNA gene sequence homology with phylotypes from marine systems supports this contention. The bacterial 16S rRNA gene clone library was dominated by a phylotype that had 99% sequence identity with
Thiomicrospira arctica
(46% of the library), a psychrophilic marine autotrophic sulfur oxidizer. The remainder of the library contained phylotypes related to the classes
Betaproteobacteria
,
Deltaproteobacteria
, and
Gammaproteobacteria
and the division
Bacteroidetes
and included clones whose closest cultured relatives metabolize iron and sulfur compounds. These findings are consistent with the high iron and sulfate concentrations detected in Blood Falls, which are likely due to the interactions of the subglacial brine with the underlying iron-rich bedrock. Our results, together with previous reports, suggest that the brine below the Taylor Glacier hosts a viable ecosystem with microorganisms capable of growth, supported by chemical energy present in reduced iron and sulfur compounds. The metabolic and phylogenetic structure of this subglacial microbial assemblage appears to be controlled by glacier hydrology, bedrock lithology, and the preglacial ecosystem.
Multilocus Sequence Typing Confirms the Close Genetic Interrelatedness of Three Distinct Flavescence Dorée Phytoplasma Strain Clusters and Group 16SrV Phytoplasmas Infecting Grapevine and Alder in Europe
Authors: Arnaud Guillaume , Malembic-Maher Sylvie , Salar Pascal , Bonnet Patrick , Maixner Michael , Marcone Carmine , Boudon-Padieu Elisabeth , Foissac Xavier 
Published: April 2007

ABSTRACT

Vineyards of southern France and northern Italy are affected by the flavescence dorée (FD) phytoplasma, a quarantine pathogen transmitted by the leafhopper of Nearctic origin
Scaphoideus titanus
. To better trace propagation of FD strains and identify possible passage between the vineyard and wild plant compartments, molecular typing of phytoplasma strains was applied. The sequences of the two genetic loci
map
and
uvrB
-
degV
, along with the sequence of the
secY
gene, were determined among a collection of FD and FD-related phytoplasmas infecting grapevine, alder, elm, blackberry, and Spanish broom in Europe. Sequence comparisons and phylogenetic analyses consistently indicated the existence of three FD phytoplasma strain clusters. Strain cluster FD1 (comprising isolate FD70) displayed low variability and represented 17% of the disease cases in the French vineyard, with a higher incidence of the cases in southwestern France. Strain cluster FD2 (comprising isolates FD92 and FD-D) displayed no variability and was detected both in France (83% of the cases) and in Italy, whereas the more-variable strain cluster FD3 (comprising isolate FD-C) was detected only in Italy. The clonal property of FD2 and its wide distribution are consistent with diffusion through propagation of infected-plant material. German Palatinate grapevine yellows phytoplasmas (PGY) appeared variable and were often related to some of the alder phytoplasmas (AldY) detected in Italy and France. Finally, phylogenetic analyses concluded that FD, PGY, and AldY were members of the same phylogenetic subclade, which may have originated in Europe.
Competitive Fitness of Isolates Enriched on Phenanthrene Sorbed to Model Phases
Authors: Colores Gregory M. , Ward David M. , Inskeep William P. 
Published: April 2007

ABSTRACT
We evaluated the competitive fitness of three phenanthrene-mineralizing isolates that were provided with nonsorbed or sorbed phenanthrene in competition experiments. One isolate had a clear advantage when presented with Amberlite IRC-50-sorbed phenanthrene, yet none were favored when presented with nonsorbed or Amberlite XAD-7-sorbed phenanthrene. Our results indicate that contaminant availability alone does not determine the isolates’ competitive fitness.
Alteration of Soil Rhizosphere Communities following Genetic Transformation of White Spruce
Authors: LeBlanc Philippe M. , Hamelin Richard C. , Filion Martin 
Published: April 2007

ABSTRACT

The application of plant genetic manipulations to agriculture and forestry with the aim of alleviating insect damage through
Bacillus thuringiensis
transformation could lead to a significant reduction in the release of pesticides into the environment. However, many groups have come forward with very valid and important questions related to potentially adverse effects, and it is crucial to assess and better understand the impact that this technology might have on ecosystems. In this study, we analyzed rhizosphere soil samples collected from the first
B. thuringiensis
-transformed trees [with insertion of the CryIA(b) toxin-encoding gene] grown in Canada (Val-Cartier, QC, Canada) as part of an ecological impact assessment project. Using a robust amplified rRNA gene restriction analysis approach coupled with 16S rRNA gene sequencing, the rhizosphere-inhabiting microbial communities of white spruce (
Picea glauca
) genetically modified by biolistic insertion of the
cryIA
(
b
),
uidA
(beta-glucuronidase), and
nptII
genes were compared with the microbial communities associated with non-genetically modified counterparts and with trees in which only the genetic marker genes
uidA
and
nptII
have been inserted. Analysis of 1,728 rhizosphere bacterial clones (576 clones per treatment) using a Cramér-von Mises statistic analysis combined with a Monte Carlo comparison clearly indicated that there was a statistically significant difference (
P
< 0.05) between the microbial communities inhabiting the rhizospheres of trees carrying the
cryIA
(
b
),
uidA
, and
nptII
transgenes, trees carrying only the
uidA
and
nptII
transgenes, and control trees. Clear rhizosphere microbial community alterations due to
B. thuringiensis
tree genetic modification have to our knowledge never been described previously and open the door to interesting questions related to
B. thuringiensis
genetic transformation and also to the impact of commonly used
uidA
and
nptII
genetic marker genes.
Alpha-Amylase Starch Binding Domains: Cooperative Effects of Binding to Starch Granules of Multiple Tandemly Arranged Domains
Authors: Guillén D. , Santiago M. , Linares L. , Pérez R. , Morlon J. , Ruiz B. , Sánchez S. , Rodríguez-Sanoja R. 
Published: April 2007

ABSTRACT

The
Lactobacillus amylovorus
alpha-amylase starch binding domain (SBD) is a functional domain responsible for binding to insoluble starch. Structurally, this domain is dissimilar from other reported SBDs because it is composed of five identical tandem modules of 91 amino acids each. To understand adsorption phenomena specific to this SBD, the importance of their modular arrangement in relationship to binding ability was investigated. Peptides corresponding to one, two, three, four, or five modules were expressed as His-tagged proteins. Protein binding assays showed an increased capacity of adsorption as a function of the number of modules, suggesting that each unit of the SBD may act in an additive or synergic way to optimize binding to raw starch.
Presence and Sources of Fecal Coliform Bacteria in Epilithic Periphyton Communities of Lake Superior
Authors: Ksoll Winfried B. , Ishii Satoshi , Sadowsky Michael J. , Hicks Randall E. 
Published: April 2007

ABSTRACT

Epilithic periphyton communities were sampled at three sites on the Minnesota shoreline of Lake Superior from June 2004 to August 2005 to determine if fecal coliforms and
Escherichia coli
were present throughout the ice-free season. Fecal coliform densities increased up to 4 orders of magnitude in early summer, reached peaks of up to 1.4 × 10
5
CFU cm
−2
by late July, and decreased during autumn. Horizontal, fluorophore-enhanced repetitive-PCR DNA fingerprint analyses indicated that the source for 2% to 44% of the
E. coli
bacteria isolated from these periphyton communities could be identified when compared with a library of
E. coli
fingerprints from animal hosts and sewage. Waterfowl were the major source (68 to 99%) of periphyton
E. coli
strains that could be identified. Several periphyton
E. coli
isolates were genotypically identical (≥92% similarity), repeatedly isolated over time, and unidentified when compared to the source library, suggesting that these strains were naturalized members of periphyton communities. If the unidentified
E. coli
strains from periphyton were added to the known source library, then 57% to 81% of
E. coli
strains from overlying waters could be identified, with waterfowl (15 to 67%), periphyton (6 to 28%), and sewage effluent (8 to 28%) being the major potential sources. Inoculated
E. coli
rapidly colonized natural periphyton in laboratory microcosms and persisted for several weeks, and some cells were released to the overlying water. Our results indicate that
E. coli
from periphyton released into waterways confounds the use of this bacterium as a reliable indicator of recent fecal pollution.
A Novel
Acidimicrobium
Species in Continuous Cultures of Moderately Thermophilic, Mineral-Sulfide-Oxidizing Acidophiles
Authors: Cleaver Adam A. , Burton Nicolas P. , Norris Paul R. 
Published: April 2007

ABSTRACT

A novel species of
Acidimicrobium
appeared to be the predominant ferrous iron oxidizer in a mixed culture that effected the continuous, efficient extraction of nickel from a mineral concentrate at 49°C, but it was not isolated in pure culture. It outcompeted
Acidimicrobium ferrooxidans
, which was expected to have a major role in iron oxidation in reactors gassed with air, and was outnumbered at 49°C only by the sulfur-oxidizing
Acidithiobacillus caldus. Sulfobacillus
species were expected to compete with
Acidimicrobium
species when culture aeration was enriched with carbon dioxide, but they were a minor component of the populations with and without this enrichment.
Sulfobacillus thermosulfidooxidans
replaced the
Acidimicrobium
species and
Acidithiobacillus caldus
when the temperature was increased to 55°C.
Thermoregulation of
N
-Acyl Homoserine Lactone-Based Quorum Sensing in the Soft Rot Bacterium
Pectobacterium atrosepticum
Authors: Latour Xavier , Diallo Stéphanie , Chevalier Sylvie , Morin Danièle , Smadja Bruno , Burini Jean-François , Haras Dominique , Orange Nicole 
Published: April 2007

ABSTRACT

The psychrotolerant bacterium
Pectobacterium atrosepticum
produces four
N
-acyl homoserine lactones under a wide range of temperatures. Their thermoregulation differs from that of the exoenzyme production, described as being under quorum-sensing control. A mechanism involved in this thermoregulation consists of controlling
N
-acyl homoserine lactones synthase production at a transcriptional level.
Multivariate Logistic Regression for Predicting Total Culturable Virus Presence at the Intake of a Potable-Water Treatment Plant: Novel Application of the Atypical Coliform/Total Coliform Ratio
Authors: Black L. E. , Brion G. M. , Freitas S. J. 
Published: April 2007

ABSTRACT

Predicting the presence of enteric viruses in surface waters is a complex modeling problem. Multiple water quality parameters that indicate the presence of human fecal material, the load of fecal material, and the amount of time fecal material has been in the environment are needed. This paper presents the results of a multiyear study of raw-water quality at the inlet of a potable-water plant that related 17 physical, chemical, and biological indices to the presence of enteric viruses as indicated by cytopathic changes in cell cultures. It was found that several simple, multivariate logistic regression models that could reliably identify observations of the presence or absence of total culturable virus could be fitted. The best models developed combined a fecal age indicator (the atypical coliform [AC]/total coliform [TC] ratio), the detectable presence of a human-associated sterol (epicoprostanol) to indicate the fecal source, and one of several fecal load indicators (the levels of
Giardia
species cysts, coliform bacteria, and coprostanol). The best fit to the data was found when the AC/TC ratio, the presence of epicoprostanol, and the density of fecal coliform bacteria were input into a simple, multivariate logistic regression equation, resulting in 84.5% and 78.6% accuracies for the identification of the presence and absence of total culturable virus, respectively. The AC/TC ratio was the most influential input variable in all of the models generated, but producing the best prediction required additional input related to the fecal source and the fecal load. The potential for replacing microbial indicators of fecal load with levels of coprostanol was proposed and evaluated by multivariate logistic regression modeling for the presence and absence of virus.
Salinity Constraints on Subsurface Archaeal Diversity and Methanogenesis in Sedimentary Rock Rich in Organic Matter
Authors: Waldron Patricia J. , Petsch Steven T. , Martini Anna M. , Nüsslein Klaus 
Published: April 2007

ABSTRACT

The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl
−
in a subsurface shale rich in CH
4
derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH
4
-producing zone lacked electron acceptors such as O
2
, NO
3
−
, Fe
3+
, or SO
4
2−
. Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl
−
concentrations above ∼1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H
2
/CO
2
) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic
Methanohalophilus
species and a hydrogenotrophic
Methanoplanus
species at high salinity and a single phylotype closely related to
Methanocorpusculum bavaricum
at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH
4
-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters.
Stable Isotope Ratios and Forensic Analysis of Microorganisms
Authors: Kreuzer-Martin Helen W. , Jarman Kristin H. 
Published: April 2007

ABSTRACTIn the aftermath of the anthrax letters of 2001, researchers have been exploring various analytical signatures for the purpose of characterizing the production environment of microorganisms. One such signature is stable isotope ratios, which in heterotrophs, are a function of nutrient and water sources. Here we discuss the use of stable isotope ratios in microbial forensics, using as a database the carbon, nitrogen, oxygen, and hydrogen stable isotope ratios of 247 separate cultures ofBacillus subtilis6051 spores produced on a total of 32 different culture media. In the context of using stable isotope ratios as a signature for sample matching, we present an analysis of variations between individual samples, between cultures produced in tandem, and between cultures produced in the same medium but at different times. Additionally, we correlate the stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen for growth medium nutrients or water with those of spores and show examples of how these relationships can be used to exclude nutrient or water samples as possible growth substrates for specific cultures.
Biodegradation Processes in a Laboratory-Scale Groundwater Contaminant Plume Assessed by Fluorescence Imaging and Microbial Analysis
Authors: Rees Helen C. , Oswald Sascha E. , Banwart Steven A. , Pickup Roger W. , Lerner David N. 
Published: April 2007

ABSTRACT

Flow reactors containing quartz sand colonized with biofilm were set up as physical model aquifers to allow degrading plumes of acetate or phenol to be formed from a point source. A noninvasive fluorescent tracer technique was combined with chemical and biological sampling in order to quantify transport and biodegradation processes. Chemical analysis of samples showed a substantial decrease in carbon concentration between the injection and outflow resulting primarily from dilution but also from biodegradation. Two-dimensional imaging of the aqueous oxygen [O
2
(aq)] concentration field quantified the depletion of O
2
(aq) within the contaminant plume and provided evidence for microbial respiration associated with biodegradation of the carbon source. Combined microbiological, chemical, and O
2
(aq) imaging data indicated that biodegradation was greatest at the plume fringe. DNA profiles of bacterial communities were assessed by temperature gradient gel electrophoresis, which revealed that diversity was limited and that community changes observed depended on the carbon source used. Spatial variation in activity within the plume could be quantitatively accounted for by the changes observed in active cell numbers rather than differences in community structure, the total biomass present, or the increased enzyme activity of individual cells. Numerical simulations and comparisons with the experimental data were used to test conceptual models of plume processes. Results demonstrated that plume behavior was best described by growth and decay of active biomass as a single functional group of organisms represented by active cell counts.