bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Artificial Defoliation of Pines on the Structure and Physiology of the Soil Fungal Community of a Mixed Pine-Spruce Forest
Authors: Cullings Ken , Raleigh Christopher , New Michael H. , Henson Joan 
Published: April 2005

ABSTRACT

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (
P
< 0.001); the frequency of members of the ectomycorrhizal fungus genus
Cenococcum
decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of
Cenococcum
organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (
P
< 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.
Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer
Authors: Erwin Daniel P. , Erickson Issac K. , Delwiche Mark E. , Colwell Frederick S. , Strap Janice L. , Crawford Ronald L. 
Published: April 2005

ABSTRACTPCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both thepmoAgene of the MMO particulate form and theamoAgene of ammonia monooxygenase; A189-mb661, which specifically targets thepmoAgene; and mmoXA-mmoXB, which amplifies themmoXgene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genusMethylocystis. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest toMethylobacterandMethylomonasspp. Sequences similar to that of theamoAgene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotrophMethylocystissp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.
Genetic Diversity of Benzoyl Coenzyme A Reductase Genes Detected in Denitrifying Isolates and Estuarine Sediment Communities
Authors: Song Bongkeun , Ward Bess B. 
Published: April 2005

ABSTRACT

Benzoyl coenzyme A (benzoyl-CoA) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-CoA) in the metabolism of many aromatic compounds. The diversity of benzoyl-CoA reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the Arthur Kill in New Jersey and the Chesapeake Bay in Maryland was investigated. Degenerate primers were developed from the known benzoyl-CoA reductase genes from
Thauera aromatica
,
Rhodopseudomonas palustris
, and
Azoarcus evansii
. PCR amplification detected benzoyl-CoA reductase genes in the denitrifying isolates belonging to α-, β-, or γ-
Proteobacteria
as well as in the sediment samples. Phylogenetic analysis, sequence similarity comparison, and conserved indel determination grouped the new sequences into either the
bcr
type (found in
T. aromatica
and
R. palustris)
or the
bzd
type (found in
A. evansii
). All the
Thauera
strains and the isolates from the genera
Acidovorax
,
Bradyrhizobium
,
Paracoccus
,
Ensifer
, and
Pseudomonas
had
bcr
-type benzoyl-CoA reductases with amino acid sequence similarities of more than 97%. The genes detected from
Azarocus
strains were assigned to the
bzd
type. A total of 50 environmental clones were detected from denitrifying consortium and sediment samples, and 28 clones were assigned to either the
bcr
or the
bzd
type of benzoyl-CoA reductase genes. Thus, we could determine the genetic capabilities for anaerobic degradation of aromatic compounds in sediment communities of the Chesapeake Bay and the Arthur Kill on the basis of the detection of two types of benzoyl-CoA reductase genes. The detected genes have future applications as genetic markers to monitor aromatic compound degradation in natural and engineered ecosystems.
Vertical Distribution of the Free-Living Amoeba Population in Soil under Desert Shrubs in the Negev Desert, Israel
Authors: Rodriguez-Zaragoza Salvador , Mayzlish Einav , Steinberger Yosef 
Published: April 2005

ABSTRACT

A field study was designed to examine the effect of desert shrubs on the dynamics of free-living amoebae in arid soil. Soil samples from 0- to 50-cm depths were collected at 10-cm intervals in each of the four seasons. The vertical distributions of the four main morphological types of amoebae, grouped according to their mobility, and of small flagellate populations were measured under the canopies of
Hammada scoparia
and
Atriplex halimus
, shrubs belonging to the chloride-absorbing xerohalophytes. The result obtained from the field study demonstrated that the total number of protozoa was significantly higher during the wet seasons (winter and spring) than during the dry seasons. The protozoan population was more diverse under the canopy of
H. scoparia
during the wet seasons, reaching 8,000 individuals per 1 g of dry soil, whereas during the dry seasons, the populations were higher under the canopy of
A. halimus
, with a mean of 250 individuals. The protozoan population in the deeper layers (40 to 50 cm) was found to be as active as that in the upper layers, demonstrating that, in the desert, soil columns below 20 cm are fertile and worth studying. The type 1 amoebae (e.g.,
Acanthamoeba
and
Filamoeba
spp.) were the most abundant throughout the study period, and their numbers were significantly higher than those of the other amoeba types.
Molecular Assays for Targeting Human and Bovine Enteric Viruses in Coastal Waters and Their Application for Library-Independent Source Tracking
Authors: Fong Theng-Theng , Griffin Dale W. , Lipp Erin K. 
Published: April 2005

ABSTRACT

Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-
a
concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary.
Explorative Multifactor Approach for Investigating Global Survival Mechanisms of
Campylobacter jejuni
under Environmental Conditions
Authors: Moen Birgitte , Oust Astrid , Langsrud Øyvind , Dorrell Nick , Marsden Gemma L. , Hinds Jason , Kohler Achim , Wren Brendan W. , Rudi Knut 
Published: April 2005

ABSTRACT

Explorative approaches such as DNA microarray experiments are becoming increasingly important in microbial research. Despite these major technical advancements, approaches to study multifactor experiments are still lacking. We have addressed this problem by using rotation testing and a novel multivariate analysis of variance (MANOVA) approach (50-50 MANOVA) to investigate interacting experimental factors in a complex experimental design. Furthermore, a new rotation testing based method was introduced to calculate false-discovery rates for each response. This novel analytical concept was used to investigate global survival mechanisms in the environment of the major food-borne pathogen
C. jejuni.
We simulated nongrowth environmental conditions by investigating combinations of the factors temperature (5 and 25°C) and oxygen tension (anaerobic, microaerobic, and aerobic). Data were generated with DNA microarrays for information about gene expression patterns and Fourier transform infrared (FT-IR) spectroscopy to study global macromolecular changes in the cell. Microarray analyses showed that most genes were either unchanged or down regulated compared to the reference (day 0) for the conditions tested and that the 25°C anaerobic condition gave the most distinct expression pattern with the fewest genes expressed. The few up-regulated genes were generally stress related and/or related to the cell envelope. We found, using FT-IR spectroscopy, that the amount of polysaccharides and oligosaccharides increased under the nongrowth survival conditions. Potential mechanisms for survival could be to down regulate most functions to save energy and to produce polysaccharides and oligosaccharides for protection against harsh environments. Basic knowledge about the survival mechanisms is of fundamental importance in preventing transmission of this bacterium through the food chain.
Analysis of Fluorescent Protein Expression in Transformants ofRickettsia monacensis, an Obligate Intracellular Tick Symbiont
Authors: Baldridge Gerald D. , Burkhardt Nicole , Herron Michael J. , Kurtti Timothy J. , Munderloh Ulrike G. 
Published: April 2005

ABSTRACTWe developed and applied transposon-based transformation vectors for molecular manipulation and analysis of spotted fever group rickettsiae, which are obligate intracellular bacteria that infect ticks and, in some cases, mammals. Using the Epicentre EZ::TN transposon system, we designed transposons for simultaneous expression of a reporter gene and a chloramphenicol acetyltransferase (CAT) resistance marker. Transposomes (transposon-transposase complexes) were electroporated intoRickettsia monacensis, a rickettsial symbiont isolated from the tickIxodes ricinus. Each transposon contained an expression cassette consisting of the rickettsialompApromoter and a green fluorescent protein (GFP) reporter gene (GFPuv) or theompBpromoter and a red fluorescent protein reporter gene (DsRed2), followed by theompAtranscription terminator and a secondompApromoter CAT gene cassette. Selection with chloramphenicol gave rise to rickettsial populations with chromosomally integrated single-copy transposons as determined by PCR, Southern blotting, and sequence analysis. Reverse transcription-PCR and Northern blots demonstrated transcription of all three genes. GFPuv transformant rickettsiae exhibited strong fluorescence in individual cells, but DsRed2 transformants did not. Western blots confirmed expression of GFPuv inR. monacensisand inEscherichia coli, but DsRed2 was expressed only inE. coli. The DsRed2 gene, but not the GFPuv gene, contains many GC-rich amino acid codons that are rare in the preferred codon suite of rickettsiae, possibly explaining the failure to express DsRed2 protein inR. monacensis. We demonstrated that our vectors provide a means to study rickettsia-host cell interactions by visualizing GFPuv-fluorescentR. monacensisassociated with actin tails in tick host cells.
Lipid Biomarkers and Carbon Isotope Signatures of a Microbial (
Beggiatoa
) Mat Associated with Gas Hydrates in the Gulf of Mexico
Authors: Zhang Chuanlun L. , Huang Zhiyong , Cantu James , Pancost Richard D. , Brigmon Robin L. , Lyons Timothy W. , Sassen Roger 
Published: April 2005

ABSTRACT

White and orange mats are ubiquitous on surface sediments associated with gas hydrates and cold seeps in the Gulf of Mexico. The goal of this study was to determine the predominant pathways for carbon cycling within an orange mat in Green Canyon (GC) block GC 234 in the Gulf of Mexico. Our approach incorporated laser-scanning confocal microscopy, lipid biomarkers, stable carbon isotopes, and 16S rRNA gene sequencing. Confocal microscopy showed the predominance of filamentous microorganisms (4 to 5 μm in diameter) in the mat sample, which are characteristic of
Beggiatoa
. The phospholipid fatty acids extracted from the mat sample were dominated by 16:1ω7c/t (67%), 18:1ω7c (17%), and 16:0 (8%), which are consistent with lipid profiles of known sulfur-oxidizing bacteria, including
Beggiatoa
. These results are supported by the 16S rRNA gene analysis of the mat material, which yielded sequences that are all related to the vacuolated sulfur-oxidizing bacteria, including
Beggiatoa
,
Thioploca
, and
Thiomargarita
. The δ
13
C value of total biomass was −28.6‰; those of individual fatty acids were −29.4 to −33.7‰. These values suggested heterotrophic growth of
Beggiatoa
on organic substrates that may have δ
13
C values characteristic of crude oil or on their by-products from microbial degradation. This study demonstrated that integrating lipid biomarkers, stable isotopes, and molecular DNA could enhance our understanding of the metabolic functions of
Beggiatoa
mats in sulfide-rich marine sediments associated with gas hydrates in the Gulf of Mexico and other locations.
Mycobacterium aviumsubsp.paratuberculosisin the Catchment Area and Water of the River Taff in South Wales, United Kingdom, and Its Potential Relationship to Clustering of Crohn's Disease Cases in the City of Cardiff
Authors: Pickup R. W. , Rhodes G. , Arnott S. , Sidi-Boumedine K. , Bull T. J. , Weightman A. , Hurley M. , Hermon-Taylor J. 
Published: April 2005

ABSTRACTIn South Wales, United Kingdom, a populated coastal region lies beneath hill pastures grazed by livestock in whichMycobacterium aviumsubsp.paratuberculosisis endemic. The Taff is a spate river running off the hills and through the principal city of Cardiff. We sampled Taff water above Cardiff twice weekly from November 2001 to November 2002.M. aviumsubsp.paratuberculosiswas detected by IS900PCR and culture. Thirty-one of 96 daily samples (32.3%) were IS900PCR positive, and 12 grewM. aviumsubsp.paratuberculosisbovine strains. Amplicon sequences from colonies were identical to the sequence with GenBank accession no.X16293, whereas 16 of 19 sequences from river water DNA extracts had a single-nucleotide polymorphism at position 214. This is consistent with a different strain ofM. aviumsubsp.paratuberculosisin the river, which is unculturable by the methods we used. Parallel studies showed thatM. aviumsubsp.paratuberculosisremained culturable in lake water microcosms for 632 days and persisted to 841 days. Of four reservoirs controlling the catchment area of the Taff,M. aviumsubsp.paratuberculosiswas present in surface sediments from three and in sediment cores from two, consistent with deposition over at least 50 years. Previous epidemiological research in Cardiff demonstrated a highly significant increase of Crohn's disease in 11 districts. These bordered the river except for a gap on the windward side. A topographical relief map shows that this gap is directly opposite a valley open to the prevailing southwesterly winds. This would influence the distribution of aerosols carryingM. aviumsubsp.paratuberculosisfrom the river.
New Tool for Metabolic Pathway Engineering in
Escherichia coli
: One-Step Method To Modulate Expression of Chromosomal Genes
Authors: Meynial-Salles Isabelle , Cervin Marguerite A. , Soucaille Philippe 
Published: April 2005

ABSTRACT

A simple and highly efficient method was developed to produce a library of
Escherichia coli
clones that express a particular chromosomal gene at a wide range of expression levels. The basic strategy was to replace all or part of the upstream region of a coding sequence containing the elements involved in its expression (promoter, operator, gene coding for a regulator, ribosome binding site, and start codon) with a PCR-generated library of expression cassettes.
Novel Major Bacterial Candidate Division within a Municipal Anaerobic Sludge Digester
Authors: Chouari Rakia , Le Paslier Denis , Dauga Catherine , Daegelen Patrick , Weissenbach Jean , Sghir Abdelghani 
Published: April 2005

ABSTRACTIn a previous study, we analyzed the molecular diversity ofPlanctomycetalesby PCR amplification and sequencing of 16S rRNA clone libraries generated from a municipal wastewater plant, using planctomycete-specific and universal primer sets (R. Chouari, D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir, Appl. Environ. Microbiol.69:7354-7363, 2003). Only a small fraction (4%) of the 16S rRNA gene sequences of the digester clone library corresponded to thePlanctomycetalesdivision. Importantly, 85.9% of the digester clone sequences are grouped into two different clusters named WWE1 (81.4% of the sequences) and WWE2 (4.5%) and are distantly affiliated with unidentified bacterial sequences retrieved from a methanogenic reactor community and from a termite gut, respectively. In phylogenetic analysis using 16S rRNA gene sequence representatives of the main phylogenetic bacterial divisions, the two clusters are monophyletic, branch apart from each other, and are distantly related toPlanctomycetalesand other bacterial divisions. A novel candidate division is proposed for WWE1, while the WWE2 cluster strongly affiliates with the recently proposedLentisphearaephylum. We designed and validated a 16S rRNA probe targeting WWE1 16S rRNA sequences by both fluorescent in situ hybridization (FISH) and dot blot hybridization (DBH). Results of FISH analysis show that WWE1 representative microorganisms are rods or filamentous shaped, while DBH shows that WWE1 accounts for 12% of the total bacterial rRNA within the anaerobic digester. The remaining 16S rRNA gene sequences are affiliated withVerrucomicrobiaor recently described candidate divisions with no known pure culture representatives, such as OD1, BRC1, or NBL-UPA2, making up less than 3.5% of the clone library, respectively. This inventory expands the known diversity of the latter bacterial division-level lineages.
Detection ofSalmonellaStrains andEscherichia coliO157:H7 in Feces of Small Ruminants and Their Isolation with Various Media
Authors: Pao Steven , Patel Dhartika , Kalantari Aref , Tritschler Joseph P. , Wildeus Stephan , Sayre Brian L. 
Published: April 2005

ABSTRACTSalmonellastrains andEscherichia coliO157:H7 were detected in 17 and 5 small ruminants in Virginia, respectively, of 287 tested. Background microflora interfered with the fecal analysis. The combination ofSalmonellaenzyme immunoassay (EIA) detection and xylose-lysine-deoxycholate agar isolation was satisfactory. Modifying enrichment to a 1:100 dilution enabled effectiveE. coliO157:H7 detection by EIA and isolation by sorbitol-MacConkey agar with cefixime-tellurite.
Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques
Authors: Tamaki Hideyuki , Sekiguchi Yuji , Hanada Satoshi , Nakamura Kazunori , Nomura Nakao , Matsumura Masatoshi , Kamagata Yoichi 
Published: April 2005

ABSTRACT
Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.
Viscoelasticity of
Staphylococcus aureus
Biofilms in Response to Fluid Shear Allows Resistance to Detachment and Facilitates Rolling Migration
Authors: Rupp Cory J. , Fux Christoph A. , Stoodley Paul 
Published: April 2005

ABSTRACT

Staphylococcus aureus
is a leading cause of catheter-related bloodstream infections and endocarditis. Both involve (i) biofilm formation, (ii) exposure to fluid shear, and (iii) high rates of dissemination. We found that viscoelasticity allowed
S. aureus
biofilms to resist detachment due to increased fluid shear by deformation, while remaining attached to a surface. Further, we report that
S. aureus
microcolonies moved downstream by rolling along the lumen walls of a glass flow cell, driven by the flow of the overlying fluid. The rolling appeared to be controlled by viscoelastic tethers. This tethered rolling may be important for the surface colonization of medical devices by nonmotile bacteria.
Characterization of the Export of Bulk Poly(A)
+
mRNA in
Saccharomyces cerevisiae
during the Wine-Making Process
Authors: Izawa Shingo , Takemura Reiko , Miki Takeo , Inoue Yoshiharu 
Published: April 2005

ABSTRACT

Ethanol stress affects the nuclear export of mRNA similarly to heat shock in
Saccharomyces cerevisiae
. However, we have little information about mRNA transport in actual alcoholic fermentation. Here we characterized the transport of mRNA during wine making and found that bulk poly(A)
+
mRNA accumulated in the nucleus as fermentation progressed.
Degradation of β-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from
Sphingomonas paucimobilis
UT26
Authors: Nagata Yuji , Prokop Zbyněk , Sato Yukari , Jerabek Petr , Kumar Ashwani , Ohtsubo Yoshiyuki , Tsuda Masataka , Damborský Jiří 
Published: April 2005

ABSTRACT

β-Hexachlorocyclohexane (β-HCH) is the most recalcitrant among the α-, β-, γ-, and δ-isomers of HCH and causes serious environmental pollution problems. We demonstrate here that the haloalkane dehalogenase LinB, reported earlier to mediate the second step in the degradation of γ-HCH in
Sphingomonas paucimobilis
UT26, metabolizes β-HCH to produce 2,3,4,5,6-pentachlorocyclohexanol.