bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting
Authors: Verbruggen Erik , Kuramae Eiko E. , Hillekens Remy , de Hollander Mattias , Kiers E. Toby , Röling Wilfred F. M. , Kowalchuk George A. , van der Heijden Marcel G. A. 
Published: August 2012

ABSTRACTThe cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing theBacillus thuringiensisCry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA- and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA- and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as within-field temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.
Discovery of a Novel (+)-γ-Lactamase from Bradyrhizobium japonicum USDA 6 by Rational Genome Mining
Authors: Zhu Shaozhou , Gong Cuiyu , Song Dawei , Gao Shuaihua , Zheng Guojun 
Published: August 2012

ABSTRACT

A novel (+)-γ-lactamase used for the resolution of racemic γ-lactam from
Bradyrhizobium japonicum
USDA 6 was found as a result of sequence-structure guided genome mining. It consists of 409 amino acids, only 49% of which are identical to the amino acid sequences of the known (+)-γ-lactamase from
Sulfolobus solfataricus
. This is only the third (+)-γ-lactamase gene to be reported.
Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak
Authors: Hernandez Sonia M. , Keel Kevin , Sanchez Susan , Trees Eija , Gerner-Smidt Peter , Adams Jennifer K. , Cheng Ying , Ray Al , Martin Gordon , Presotto Andrea , Ruder Mark G. , Brown Justin , Blehert David S. , Cottrell Walter , Maurer John J. 
Published: August 2012

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. This
Salmonella
serovar is also responsible for die-offs in songbird populations. In 2009, there was an
S
. Typhimurium epizootic reported in pine siskins in the eastern United States. At the time, there was also a human outbreak with this serovar that was associated with contaminated peanuts. As peanuts are also used in wild-bird food, it was hypothesized that the pine siskin epizootic was related to this human outbreak. A comparison of songbird and human
S
. Typhimurium pulsed-field gel electrophoresis (PFGE) patterns revealed that the epizootic was attributed not to the peanut-associated strain but, rather, to a songbird strain first characterized from an American goldfinch in 1998. This same
S
. Typhimurium strain (PFGE type A3) was also identified in the PulseNet USA database, accounting for 137 of 77,941 total
S
. Typhimurium PFGE entries. A second molecular typing method, multiple-locus variable-number tandem-repeat analysis (MLVA), confirmed that the same strain was responsible for the pine siskin epizootic in the eastern United States but was distinct from a genetically related strain isolated from pine siskins in Minnesota. The pine siskin A3 strain was first encountered in May 2008 in an American goldfinch and later in a northern cardinal at the start of the pine siskin epizootic. MLVA also confirmed the clonal nature of
S
. Typhimurium in songbirds and established that the pine siskin epizootic strain was unique to the finch family. For 2009, the distribution of PFGE type A3 in passerines and humans mirrored the highest population density of pine siskins for the East Coast.
Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters
Authors: Staley Christopher , Gordon Katrina V. , Schoen Mary E. , Harwood Valerie J. 
Published: August 2012

ABSTRACT

Before new, rapid quantitative PCR (qPCR) methods for assessment of recreational water quality and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant source has been diluted in environmental waters is needed. This study determined the limits of detection and quantification of the human-associated
Bacteroides
sp. (HF183) and human polyomavirus (HPyV) qPCR methods for sewage diluted in buffer and in five ambient, Florida water types (estuarine, marine, tannic, lake, and river). HF183 was quantifiable in sewage diluted up to 10
−6
in 500-ml ambient-water samples, but HPyVs were not quantifiable in dilutions of >10
−4
. Specificity, which was assessed using fecal composites from dogs, birds, and cattle, was 100% for HPyVs and 81% for HF183. Quantitative microbial risk assessment (QMRA) estimated the possible norovirus levels in sewage and the human health risk at various sewage dilutions. When juxtaposed with the MST marker detection limits, the QMRA analysis revealed that HF183 was detectable when the modeled risk of gastrointestinal (GI) illness was at or below the benchmark of 10 illnesses per 1,000 exposures, but the HPyV method was generally not sensitive enough to detect potential health risks at the 0.01 threshold for frequency of illness. The tradeoff between sensitivity and specificity in the MST methods indicates that HF183 data should be interpreted judiciously, preferably in conjunction with a more host-specific marker, and that better methods of concentrating HPyVs from environmental waters are needed if this method is to be useful in a watershed management or monitoring context.
Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils
Authors: Andrew David R. , Fitak Robert R. , Munguia-Vega Adrian , Racolta Adriana , Martinson Vincent G. , Dontsova Katerina 
Published: August 2012

ABSTRACT

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (
Carnegiea gigantea
) and cardón (
Pachycereus pringlei
) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant
Crenarchaeota
class
Thermoprotei
, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla
Proteobacteria
,
Actinobacteria
,
Planctomycetes
,
Firmicutes
,
Bacteroidetes
,
Chloroflexi
, and
Acidobacteria
. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.
Counterselection System for Geobacillus kaustophilus HTA426 through Disruption of
pyrF
and
pyrR
Authors: Suzuki Hirokazu , Murakami Ayano , Yoshida Ken-ichi 
Published: August 2012

ABSTRACT

Counterselection systems facilitate marker-free genetic modifications in microbes by enabling positive selections for both the introduction of a marker gene into the microbe and elimination of the marker from the microbe. Here we report a counterselection system for
Geobacillus kaustophilus
HTA426, established through simultaneous disruption of the
pyrF
and
pyrR
genes. The
pyrF
gene, essential for pyrimidine biosynthesis and metabolization of 5-fluoroorotic acid (5-FOA) to toxic metabolites, was disrupted by homologous recombination. The resultant MK54 strain (Δ
pyrF
) was auxotrophic for uracil and resistant to 5-FOA. MK54 complemented with
pyrF
was prototrophic for uracil but insensitive to 5-FOA in the presence of uracil. To confer 5-FOA sensitivity, the
pyrR
gene encoding an attenuator to repress pyrimidine biosynthesis by sensing uracil derivatives was disrupted. The resultant MK72 strain (Δ
pyrF
Δ
pyrR
) was auxotrophic for uracil and resistant to 5-FOA. MK72 complemented with
pyrF
was prototrophic for uracil and 5-FOA sensitive even in the presence of uracil. The results suggested that
pyrF
could serve as a counterselection marker in MK72, which was demonstrated by efficient marker-free integrations of heterologous β-galactosidase and α-amylase genes. The integrated genes were functionally expressed in
G. kaustophilus
and conferred new functions on the thermophile. This report describes the first establishment of a
pyrF
-based counterselection system in a
Bacillus
-related bacterium, along with the first demonstration of homologous recombination and heterologous gene expression in
G. kaustophilus
. Our results also suggest a new strategy for establishment of counterselection systems.
Detection of Salmonella enterica Isolates Producing CTX-M Cephalosporinase in U.S. Livestock Populations
Authors: Wittum Thomas E. , Mollenkopf Dixie F. , Erdman Matthew M. 
Published: August 2012

ABSTRACT

We report the detection of
Salmonella
carrying
bla
CTX-M
in U.S. livestock populations. We identified 12 of 2,034 (0.6%)
Salmonella
isolates originating from turkeys, horses, and pigs from at least 6 U.S. states, all carrying
bla
CTX-M-1
, many on a pandemic sequence type 1 IncN plasmid.
Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes
Authors: Yue Min , Schmieder Robert , Edwards Robert A. , Rankin Shelley C. , Schifferli Dieter M. 
Published: August 2012

ABSTRACT

A novel targeted massive parallel sequencing approach identified genetic variation in eight known or predicted fimbrial adhesins for 46
Salmonella
strains. The results highlight associations between specific adhesin alleles, host species, and antimicrobial resistance. The differentiation of allelic variants has potential applications for diagnostic microbiology and epidemiological investigations.
Human Infections Attributable to thed-Tartrate-Fermenting Variant of Salmonella enterica Serovar Paratyphi B in Germany Originate in Reptiles and, on Rare Occasions, Poultry
Authors: Toboldt Anne , Tietze Erhard , Helmuth Reiner , Fruth Angelika , Junker Ernst , Malorny Burkhard 
Published: August 2012

ABSTRACTIn this study, the population structure, incidence, and potential sources of human infection caused by thed-tartrate-fermenting variant ofSalmonella entericaserovar Paratyphi B [S. Paratyphi B (dT+)] was investigated. In Germany, the serovar is frequently isolated from broilers. Therefore, a selection of 108 epidemiologically unrelatedS. entericaserovar Paratyphi B (dT+) strains isolated in Germany between 2002 and 2010 especially from humans, poultry/poultry meat, and reptiles was investigated by phenotypic and genotypic methods. Strains isolated from poultry and products thereof were strongly associated with multilocus sequence type ST28 and showed antimicrobial multiresistance profiles. Pulsed-field gel electrophoresis XbaI profiles were highly homogeneous, with only a few minor XbaI profile variants. All strains isolated from reptiles, except one, were strongly associated with ST88, another distantly related type. Most of the strains were susceptible to antimicrobial agents, and XbaI profiles were heterogeneous. Strains isolated from humans yielded seven sequence types (STs) clustering in three distantly related lineages. The first lineage, comprising five STs, represented mainly strains belonging to ST43 and ST149. The other two lineages were represented only by one ST each, ST28 and ST88. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was mostly in agreement with the multilocus sequence type. Because ST28 was frequently isolated from poultry but rarely in humans over the 9-year period investigated, overall, this study indicates that in GermanyS. entericaserovar Paratyphi B (dT+) poses a health risk preferentially by contact with reptiles and, to a less extent, by exposure to poultry or poultry meat.
Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts
Authors: Chandler James Angus , Eisen Jonathan A. , Kopp Artyom 
Published: August 2012

ABSTRACT

The combination of ecological diversity with genetic and experimental tractability makes
Drosophila
a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in
Drosophila
physiology, behavior, and fitness, most recent work has focused on
Drosophila
-bacterial interactions. In order to get a more complete understanding of the
Drosophila
microbiome, we characterized the yeast communities associated with different
Drosophila
species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the
Drosophila
-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in
Drosophila
bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach.
Influence of Light on Carbon Utilization in Aerobic Anoxygenic Phototrophs
Authors: Hauruseu Dzmitry , Koblížek Michal 
Published: August 2012

ABSTRACT

Aerobic anoxygenic phototrophs contain photosynthetic reaction centers composed of bacteriochlorophyll. These organisms are photoheterotrophs, as they require organic carbon substrates for their growth whereas light-derived energy has only an auxiliary function. To establish the contribution of light energy to their metabolism, we grew the phototrophic strain
Erythrobacter
sp. NAP1 in a carbon-limited chemostat regimen on defined carbon sources (glutamate, pyruvate, acetate, and glucose) under conditions of different light intensities. When grown in a light-dark cycle, these bacteria accumulated 25% to 110% more biomass in terms of carbon than cultures grown in the dark. Cultures grown on glutamate accumulated the most biomass at moderate light intensities of 50 to 150 μmol m
−2
s
−1
but were inhibited at higher light intensities. In the case of pyruvate, we did not find any inhibition of growth by high irradiance. The extent of anaplerotic carbon fixation was detemined by radioactive bicarbonate incorporation assays. While the carboxylation activity provided 4% to 11% of the cellular carbon in the pyruvate-grown culture, in the glutamate-grown cells it provided only approximately 1% of the carbon. Additionally, we tested the effect of light on respiration and photosynthetic electron flow. With increasing light intensity, respiration decreased to approximately 25% of its dark value and was replaced by photophosphorylation. The additional energy from light allows the aerobic anoxygenic phototrophs to accumulate the supplied organic carbon which would otherwise be respired. The higher efficiency of organic carbon utilization may provide an important competitive advantage during growth under carbon-limited conditions.
Detailed Assessment of the Kinetics of Hg-Cell Association, Hg Methylation, and Methylmercury Degradation in Several Desulfovibrio Species
Authors: Graham Andrew M. , Bullock Allyson L. , Maizel Andrew C. , Elias Dwayne A. , Gilmour Cynthia C. 
Published: August 2012

ABSTRACT

The kinetics of inorganic Hg [Hg(II)
i
] association, methylation, and methylmercury (MeHg) demethylation were examined for a group of
Desulfovibrio
species with and without MeHg production capability. We employed a detailed method for assessing MeHg production in cultures, including careful control of medium chemistry, cell density, and growth phase, plus mass balance of Hg(II)
i
and MeHg during the assays. We tested the hypothesis that differences in Hg(II)
i
sorption and/or uptake rates drive observed differences in methylation rates among
Desulfovibrio
species. Hg(II)
i
associated rapidly and with high affinity to both methylating and nonmethylating species. MeHg production by Hg-methylating strains was rapid, plateauing after ∼3 h. All MeHg produced was rapidly exported. We also tested the idea that all
Desulfovibrio
species are capable of Hg(II)
i
methylation but that rapid demethylation masks its production, but we found this was not the case. Therefore, the underlying reason why MeHg production capability is not universal in the
Desulfovibrio
is not differences in Hg affinity for cells nor differences in the ability of strains to degrade MeHg. However, Hg methylation rates varied substantially between Hg-methylating
Desulfovibrio
species even in these controlled experiments and after normalization to cell density. Thus, biological differences may drive cross-species differences in Hg methylation rates. As part of this study, we identified four new Hg methylators (
Desulfovibrio aespoeensis
,
D. alkalitolerans
,
D. psychrotolerans
, and
D. sulfodismutans
) and four nonmethylating species (
Desulfovibrio alcoholivorans
,
D. tunisiensis
,
D. carbinoliphilus
, and
D. piger
) in our ongoing effort to generate a library of strains for Hg methylation genomics.
Correlation of Intracellular Trehalose Concentration with Desiccation Resistance of Soil Escherichia coli Populations
Authors: Zhang Qian , Yan Tao 
Published: August 2012

ABSTRACTNaturalized soilEscherichia colipopulations need to resist common soil desiccation stress in order to inhabit soil environments. In this study, four representative soilE. colistrains and one lab strain, MG1655, were tested for desiccation resistance via die-off experiments in sterile quartz sand under a potassium acetate-induced desiccation condition. The desiccation stress caused significantly lower die-off rates of the four soil strains (0.17 to 0.40 day−1) than that of MG1655 (0.85 day−1). Cellular responses, including extracellular polymeric substance (EPS) production, exogenous glycine betaine (GB) uptake, and intracellular compatible organic solute synthesis, were quantified and compared under the desiccation and hydrated control conditions. GB uptake appeared not to be a specific desiccation response, while EPS production showed considerable variability among theE. colistrains. AllE. colistrains produced more intracellular trehalose, proline, and glutamine under the desiccation condition than the hydrated control, and only the trehalose concentration exhibited a significant correlation with the desiccation-contributed die-off coefficients (Spearman's ρ = −1.0;P= 0.02).De novotrehalose synthesis was further determined for 15E. colistrains from both soil and nonsoil sources to determine its prevalence as a specific desiccation response. MostE. colistrains (14/15) synthesized significantly more trehalose under the desiccation condition, and the soilE. colistrains produced more trehalose (106.5 ± 44.9 μmol/mg of protein [mean ± standard deviation]) than the nonsoil reference strains (32.5 ± 10.5 μmol/mg of protein).
Stability of Sponge-Associated Bacteria over Large Seasonal Shifts in Temperature and Irradiance
Authors: Erwin Patrick M. , Pita Lucía , López-Legentil Susanna , Turon Xavier 
Published: August 2012

ABSTRACTComplex microbiomes reside in marine sponges and consist of diverse microbial taxa, including functional guilds that may contribute to host metabolism and coastal marine nutrient cycles. Our understanding of these symbiotic systems is based primarily on static accounts of sponge microbiota, while their temporal dynamics across seasonal cycles remain largely unknown. Here, we investigated temporal variation in bacterial symbionts of three sympatric sponges (Irciniaspp.) over 1.5 years in the northwestern (NW) Mediterranean Sea, using replicated terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of bacterial 16S rRNA gene sequences. Bacterial symbionts inIrciniaspp. exhibited host species-specific structure and remarkable stability throughout the monitoring period, despite large fluctuations in temperature and irradiance. In contrast, seawater bacteria exhibited clear seasonal shifts in community structure, indicating that different ecological constraints act on free-living and on symbiotic marine bacteria. Symbiont profiles were dominated by persistent, sponge-specific bacterial taxa, notably affiliated with phylogenetic lineages capable of photosynthesis, nitrite oxidation, and sulfate reduction. Variability in the sponge microbiota was restricted to rare symbionts and occurred most prominently in warmer seasons, coincident with elevated thermal regimes. Seasonal stability of the sponge microbiota supports the hypothesis of host-specific, stable associations between bacteria and sponges. Further, the core symbiont profiles revealed in this study provide an empirical baseline for diagnosing abnormal shifts in symbiont communities. Considering that these sponges have suffered recent, episodic mass mortalities related to thermal stresses, this study contributes to the development of model sponge-microbe symbioses for assessing the link between symbiont fluctuations and host health.