bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability
Authors: Morrow Kathleen M. , Moss Anthony G. , Chadwick Nanette E. , Liles Mark R. 
Published: July 2012

ABSTRACTScleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean,Montastraea faveolataandPorites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here thatM. faveolataandP. astreoidesharbor distinct, host-specific bacteria but that specificity varies by species and site.P. astreoidesgenerally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus,Endozoicomonas, within the orderOceanospirillales. The bacterial assemblages associated withM. faveolataare significantly more diverse and exhibit higher specificity at the family level thanP. astreoidesassemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.
Novel Mutations Associated with Resistance to Bacillus sphaericus in a Polymorphic Region of the Culex quinquefasciatus cqm1 Gene
Authors: Chalegre Karlos Diogo de Melo , Romão Tatiany Patrícia , Tavares Daniella Aliny , Santos Eloína Mendonça , Ferreira Lígia Maria , Oliveira Cláudia Maria Fontes , de-Melo-Neto Osvaldo Pompílio , Silva-Filha Maria Helena Neves Lobo 
Published: July 2012

ABSTRACTBin toxin fromBacillus sphaericusacts onCulex quinquefasciatuslarvae by binding to Cqm1 midgut-bound receptors, and disruption of thecqm1gene is the major cause of resistance. The goal of this work was to screen for a laboratory-selected resistancecqm1RECallele in field populations in the city of Recife, Brazil, and to describe other resistance-associated polymorphisms in thecqm1gene. Thecqm1RECallele was detected in the four nontreated populations surveyed at frequencies from 0.001 to 0.017, and sequence analysis from these samples revealed a novel resistant allele (cqm1REC-D16) displaying a 16-nucletotide (nt) deletion which is distinct from the 19-nt deletion associated withcqm1REC. Yet a third resistant allele (cqm1REC-D25), displaying a 25-nt deletion, was identified in samples from a treated area exposed toB. sphaericus. A comparison of the three deletion events revealed that all are located within the same 208-nt region amplified during the screening procedure. They also introduce equivalent frameshifts in the sequence and generate the same premature stop codon, leading to putative transcripts encoding truncated proteins which are unable to locate to the midgut epithelium. The populations analyzed in this study contained a variety of alleles with mutations disrupting the function of the corresponding Bin toxin receptor. Their locations reveal a hot spot that can be exploited to assess the resistance risk through DNA screening.
Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly
Authors: Emerson Joanne B. , Thomas Brian C. , Andrade Karen , Allen Eric E. , Heidelberg Karla B. , Banfield Jillian F. 
Published: July 2012

ABSTRACTViruses of theBacteriaandArchaeaplay important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we createdde novoassemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places “snapshot” viral metagenomes, collected at a single time and location, in context.
Weak Transcription of the
cry1Ac
Gene in Nonsporulating Bacillus thuringiensis Cells
Authors: Yang Hui , Wang Pinshu , Peng Qi , Rong Rong , Liu Chunxia , Lereclus Didier , Zhang Jie , Song Fuping , Huang Dafang 
Published: July 2012

ABSTRACT

The
cry1Ac
gene of
Bacillus thuringiensis
subsp.
kurstaki
HD-73 (
B. thuringiensis
HD-73) is a typical example of a sporulation-dependent crystal gene and is controlled by sigma E and sigma K during sporulation. To monitor the production and accumulation of Cry1Ac at the cellular level, we developed a green fluorescent protein-based reporter system. The production of Cry1Ac was monitored in
spo0A
,
sigE
, and
sigK
mutants, and these mutants were able to express the Cry1Ac-green fluorescent protein fusion protein. In nonsporulating
B. thuringiensis
HD-73 cells, low-level expression of
cry1Ac
was also observed. Reverse transcription-PCR and Western blotting results confirmed that the
cry1Ac
promoter has low activity in nonsporulating
B. thuringiensis
cells. A beta-galactosidase assay demonstrated that the transcription of the
cry1Ac
gene during exponential and transition phases is positively regulated by Spo0A. Additional bioassay results indicated that
spo0A
and
sigE
mutants containing the
cry1Ac-gfp
fusion exhibited insecticidal activity against
Plutella xylostella
larvae.
A Convenient and Robust
In Vivo
Reporter System To Monitor Gene Expression in the Human Pathogen Helicobacter pylori
Authors: Vannini Andrea , Agriesti Francesca , Mosca Flaviana , Roncarati Davide , Scarlato Vincenzo , Danielli Alberto 
Published: July 2012

ABSTRACT

Thirty years of intensive research have significantly contributed to our understanding of
Helicobacter pylori
biology and pathogenesis. However, the lack of convenient genetic tools, in particular the limited effectiveness of available reporter systems, has notably limited the toolbox for fundamental and applied studies. Here, we report the construction of a bioluminescent
H. pylori
reporter system based on the
Photorhabdus luminescens luxCDABE
cassette. The system is constituted of a promoterless
lux
acceptor strain in which promoters and sequences of interest can be conveniently introduced by double homologous recombination of a suicide transformation vector. We validate the robustness of this new
lux
reporter system in noninvasive
in vivo
monitoring of dynamic transcriptional responses of inducible as well as repressible promoters and demonstrate its suitability for the implementation of genetic screens in
H. pylori
.
Significance of the Bacteriophage Treatment Schedule in Reducing Salmonella Colonization of Poultry
Authors: Bardina Carlota , Spricigo Denis A. , Cortés Pilar , Llagostera Montserrat 
Published: July 2012

ABSTRACT

Salmonella
remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen. Among the many approaches to reducing
Salmonella
colonization of broilers, bacteriophage offers several advantages. In this study, three bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) obtained from our collection that exhibited a broad host range against
Salmonella enterica
serovar Enteritidis and
Salmonella enterica
serovar Typhimurium were characterized with respect to morphology, genome size, and restriction patterns. A cocktail composed of the three bacteriophages was more effective in promoting the lysis of
S.
Enteritidis and
S.
Typhimurium cultures than any of the three bacteriophages alone. In addition, the cocktail was able to lyse the
Salmonella enterica
serovars Virchow, Hadar, and Infantis. The effectiveness of the bacteriophage cocktail in reducing the concentration of
S.
Typhimurium was tested in two animal models using different treatment schedules. In the mouse model, 50% survival was obtained when the cocktail was administered simultaneously with bacterial infection and again at 6, 24, and 30 h postinfection. Likewise, in the White Leghorn chicken specific-pathogen-free (SPF) model, the best results, defined as a reduction of
Salmonella
concentration in the chicken cecum, were obtained when the bacteriophage cocktail was administered 1 day before or just after bacterial infection and then again on different days postinfection. Our results show that frequent treatment of the chickens with bacteriophage, and especially prior to colonization of the intestinal tract by
Salmonella
, is required to achieve effective bacterial reduction over time.
Enumerating Viruses by Using Fluorescence and the Nature of the Nonviral Background Fraction
Authors: Pollard Peter C. 
Published: July 2012

ABSTRACT
Bulk fluorescence measurements could be a faster and cheaper way of enumerating viruses than epifluorescence microscopy, flow cytometry, or transmission electron microscopy (TEM). However, since viruses are not imaged, the background fluorescence compromises the signal, and we know little about its nature. In this paper the size ranges of nucleotides that fluoresce in the presence of SYBR gold were determined for wastewater and a range of freshwater samples using a differential filtration method. Fluorescence excitation-emission matrices (FEEMs) showed that >70% of the SYBR fluorescence was in the <10-nm size fraction (background) and was not associated with intact viruses. This was confirmed using TEM. The use of FEEMs to develop a fluorescence-based method for counting viruses is an approach that is fundamentally different from the epifluorescence microscopy technique used for enumerating viruses. This high fluorescence background is currently overlooked, yet it has had a most pervasive influence on the development of a simple fluorescence-based method for quantifying viral abundance in water.
Fast and Sensitive Detection of Bacillus anthracis Spores by Immunoassay
Authors: Morel Nathalie , Volland Hervé , Dano Julie , Lamourette Patricia , Sylvestre Patricia , Mock Michèle , Créminon Christophe 
Published: July 2012

ABSTRACT

Bacillus anthracis
is one of the most dangerous potential biological weapons, and it is essential to develop a rapid and simple method to detect
B. anthracis
spores in environmental samples. The immunoassay is a rapid and easy-to-use method for the detection of
B. anthracis
by means of antibodies directed against surface spore antigens. With this objective in view, we have produced a panel of monoclonal antibodies against
B. anthracis
and developed colorimetric and electrochemiluminescence (ECL) immunoassays. Using Meso Scale Discovery ECL technology, which is based on electrochemiluminescence (ECL) detection utilizing a sulfo-Tag label that emits light upon electrochemical stimulation (using a dedicated ECL plate reader, an electrical current is placed across the microplate with electrodes integrated into the bottom of the plate, resulting in a series of electrically induced reactions leading to a luminescent signal), a detection limit ranging between 0.3 × 10
3
and 10
3
CFU/ml (i.e., 30 to 100 spores per test), depending on the
B. anthracis
strain assayed, was achieved. In complex matrices (5 mg/ml of soil or simulated powder), the detection level (without any sample purification or concentration) was never altered more than 3-fold compared with the results obtained in phosphate-buffered saline.
Contribution of Surfactin and SwrA to Flagellin Expression, Swimming, and Surface Motility in Bacillus subtilis
Authors: Ghelardi Emilia , Salvetti Sara , Ceragioli Mara , Gueye Sokhna A. , Celandroni Francesco , Senesi Sonia 
Published: July 2012

ABSTRACT

Multicellular communities produced by
Bacillus subtilis
can adopt sliding or swarming to translocate over surfaces. While sliding is a flagellum-independent motility produced by the expansive forces in a growing colony, swarming requires flagellar functionality and is characterized by the appearance of hyperflagellated swarm cells that associate in bundles or rafts during movement. Previous work has shown that swarming by undomesticated
B. subtilis
strains requires
swrA
, a gene that upregulates the expression of flagellar genes and increases swimming motility, and surfactin, a lipopeptide biosurfactant that also facilitates sliding. Through an analysis of
swrA
+
and
swrA
mutant laboratory strains with or without a mutation in
sfp
(a gene involved in surfactin production), we show that both
swrA
and surfactin upregulate the transcription of the flagellin gene and increase bacterial swimming. Surfactin also allows the nonswarming
swrA
mutant strain to efficiently colonize moist surfaces by sliding. Finally, we reconfirm the essential role of
swrA
in swarming and show that surfactin, which increases surface wettability, allows
swrA
+
strains to produce swarm cells on media at low humidity.
Impact of Short-Term Acidification on Nitrification and Nitrifying Bacterial Community Dynamics in Soilless Cultivation Media
Authors: Cytryn Eddie , Levkovitch Irit , Negreanu Yael , Dowd Scot , Frenk Sammy , Silber Avner 
Published: July 2012

ABSTRACT

Soilless medium-based horticulture systems are highly prevalent due to their capacity to optimize growth of high-cash crops. However, these systems are highly dynamic and more sensitive to physiochemical and pH perturbations than traditional soil-based systems, especially during nitrification associated with ammonia-based fertilization. The objective of this study was to assess the impact of nitrification-generated acidification on ammonia oxidation rates and nitrifying bacterial community dynamics in soilless growth media. To achieve this goal, perlite soilless growth medium from a commercial bell pepper greenhouse was incubated with ammonium in bench-scale microcosm experiments. Initial quantitative real-time PCR analysis indicated that betaproteobacterial ammonia oxidizers were significantly more abundant than ammonia-oxidizing archaea, and therefore, research focused on this group. Ammonia oxidation rates were highest between 0 and 9 days, when pH values dropped from 7.4 to 4.9. Pyrosequencing of betaproteobacterial ammonia-oxidizing
amoA
gene fragments indicated that r-strategist-like
Nitrosomonas
was the dominant ammonia-oxidizing bacterial genus during this period, seemingly due to the high ammonium concentration and optimal growth conditions in the soilless media. Reduction of pH to levels below 4.8 resulted in a significant decrease in both ammonia oxidation rates and the diversity of ammonia-oxidizing bacteria, with increased relative abundance of the r-strategist-like
Nitrosospira
. Nitrite oxidizers (
Nitrospira
and
Nitrobacter
) were on the whole more abundant and less sensitive to acidification than ammonia oxidizers. This study demonstrates that nitrification and nitrifying bacterial community dynamics in high-N-load intensive soilless growth media may be significantly different from those in
in-terra
agricultural systems.
Substrate and Inhibitor Spectra of Ethylbenzene Dehydrogenase: Perspectives on Application Potential and Catalytic Mechanism
Authors: Knack Daniel , Hagel Corina , Szaleniec Maciej , Dudzik Agnieszka , Salwinski Aleksander , Heider Johann 
Published: July 2012

ABSTRACT

Ethylbenzene dehydrogenase (EbDH) catalyzes the initial step in anaerobic degradation of ethylbenzene in denitrifying bacteria, namely, the oxygen-independent hydroxylation of ethylbenzene to (
S
)-1-phenylethanol. In our study we investigate the kinetic properties of 46 substrate analogs acting as substrates or inhibitors of the enzyme. The apparent kinetic parameters of these compounds give important insights into the function of the enzyme and are consistent with the predicted catalytic mechanism based on a quantum chemical calculation model. In particular, the existence of the proposed substrate-derived radical and carbocation intermediates is substantiated by the formation of alternative dehydrogenated and hydroxylated products from some substrates, which can be regarded as mechanistic models. In addition, these results also show the surprisingly high diversity of EbDH in hydroxylating different kinds of alkylaromatic and heterocyclic compounds to the respective alcohols. This may lead to attractive industrial applications of ethylbenzene dehydrogenase for a new process of producing alcohols via hydroxylation of the corresponding aromatic hydrocarbons rather than the customary procedure of reducing the corresponding ketones.
Genetic Diversity and Mating Type Distribution of Tuber melanosporum and Their Significance to Truffle Cultivation in Artificially Planted Truffiéres in Australia
Authors: Linde C. C. , Selmes H. 
Published: July 2012

ABSTRACT

Tuber melanosporum
is a truffle native to Europe and is cultivated in countries such as Australia for the gastronomic market, where production yields are often lower than expected. We assessed the genetic diversity of
T. melanosporum
with six microsatellite loci to assess the effect of genetic drift on truffle yield in Australia. Genetic diversity as assessed on 210 ascocarps revealed a higher allelic diversity compared to previous studies from Europe, suggesting a possible genetic expansion and/or multiple and diverse source populations for inoculum. The results also suggest that the single sequence repeat diversity of locus ME2 is adaptive and that, for example, the probability of replication errors is increased for this locus. Loss of genetic diversity in Australian populations is therefore not a likely factor in limiting ascocarp production. A survey of nursery seedlings and trees inoculated with
T. melanosporum
revealed that <70% of seedlings and host trees were colonized with
T. melanosporum
and that some trees had been contaminated by
Tuber brumale
, presumably during the inoculation process. Mating type (MAT1-1-1 and MAT1-2-1) analyses on seedling and four- to ten-year-old host trees found that 100% of seedlings but only approximately half of host trees had both mating types present. Furthermore, MAT1-1-1 was detected significantly more commonly than MAT1-2-1 in established trees, suggesting a competitive advantage for MAT1-1-1 strains. This study clearly shows that there are more factors involved in ascocarp production than just the presence of both mating types on host trees.
Exploring the Natural Fungal Biodiversity of Tropical and Temperate Forests toward Improvement of Biomass Conversion
Authors: Berrin Jean-Guy , Navarro David , Couturier Marie , Olivé Caroline , Grisel Sacha , Haon Mireille , Taussac Sabine , Lechat Christian , Courtecuisse Régis , Favel Anne , Coutinho Pedro M. , Lesage-Meessen Laurence 
Published: July 2012

ABSTRACT

In this study, natural fungal diversity in wood-decaying species was explored for biomass deconstruction. In 2007 and 2008, fungal isolates were collected in temperate forests mainly from metropolitan France and in tropical forests mainly from French Guiana. We recovered and identified 74 monomorph cultures using morphological and molecular identification tools. Following production of fungal secretomes under inductive conditions, we evaluated the capacity of these fungal strains to potentiate a commercial
Trichoderma reesei
cellulase cocktail for the release of soluble sugars from biomass. The secretome of 19 isolates led to an improvement in biomass conversion of at least 23%. Of the isolates, the
Trametes gibbosa
BRFM 952 (Banque de Ressources Fongiques de Marseille) secretome performed best, with 60% improved conversion, a feature that was not universal to the
Trametes
and related genera. Enzymatic characterization of the
T. gibbosa
BRFM 952 secretome revealed an unexpected high activity on crystalline cellulose, higher than that of the
T. reesei
cellulase cocktail. This report highlights the interest in a systematic high-throughput assessment of collected fungal biodiversity to improve the enzymatic conversion of lignocellulosic biomass. It enabled the unbiased identification of new fungal strains issued from biodiversity with high biotechnological potential.
Lack of Cry1Fa Binding to the Midgut Brush Border Membrane in a Resistant Colony of Plutella xylostella Moths with a Mutation in the
ABCC2
Locus
Authors: Hernández-Martínez Patricia , Hernández-Rodríguez Carmen Sara , Krishnan Vidisha , Crickmore Neil , Escriche Baltasar , Ferré Juan 
Published: July 2012

ABSTRACT

Previous studies reported “mode 1”
Bacillus thuringiensis
resistance in a colony of diamondback moths (NO-QA), and recently, this resistance has been mapped to an ABC transporter (
ABCC2
) locus. We report the lack of binding of Cry1Fa to insects derived from this colony and compare our data with those from other insects with
ABCC2
-associated resistance.