bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation
Authors: Brodie Eoin L. , DeSantis Todd Z. , Joyner Dominique C. , Baek Seung M. , Larsen Joern T. , Andersen Gary L. , Hazen Terry C. , Richardson Paul M. , Herman Donald J. , Tokunaga Tetsu K. , Wan Jiamin M. , Firestone Mary K. 
Published: September 2006

ABSTRACT

Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as
Geothrix fermentans
(confirmed by quantitative PCR) and those within the
Geobacteraceae
were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.
Identification of a Diagnostic Marker To Detect Freshwater Cyanophages of Filamentous Cyanobacteria
Authors: Baker Andrea C. , Goddard Victoria J. , Davy Joanne , Schroeder Declan C. , Adams David G. , Wilson William H. 
Published: September 2006

ABSTRACT

Cyanophages are viruses that infect the cyanobacteria, globally important photosynthetic microorganisms. Cyanophages are considered significant components of microbial communities, playing major roles in influencing host community diversity and primary productivity, terminating cyanobacterial water blooms, and influencing biogeochemical cycles. Cyanophages are ubiquitous in both marine and freshwater systems; however, the majority of molecular research has been biased toward the study of marine cyanophages. In this study, a diagnostic probe was developed to detect freshwater cyanophages in natural waters. Oligonucleotide PCR-based primers were designed to specifically amplify the major capsid protein gene from previously characterized freshwater cyanomyoviruses that are infectious to the filamentous, nitrogen-fixing cyanobacterial genera
Anabaena
and
Nostoc
. The primers were also successful in yielding PCR products from mixed virus communities concentrated from water samples collected from freshwater lakes in the United Kingdom. The probes are thought to provide a useful tool for the investigation of cyanophage diversity in freshwater environments.
Fiber-Optic Microarray for Simultaneous Detection of Multiple Harmful Algal Bloom Species
Authors: Ahn Soohyoun , Kulis David M. , Erdner Deana L. , Anderson Donald M. , Walt David R. 
Published: September 2006

ABSTRACT

Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species
Alexandrium fundyense
,
Alexandrium ostenfeldii
, and
Pseudo-nitzschia australis
. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 μm) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.
Tick-Borne Rickettsial Pathogens in Ticks and Small Mammals in Korea
Authors: Kim Chul-Min , Yi Ying-Hua , Yu Do-Hyeon , Lee Mi-Jin , Cho Mae-Rim , Desai Atul R. , Shringi Smriti , Klein Terry A. , Kim Heung-Chul , Song Jin-Won , Baek Luck-Ju , Chong Sung-Tae , O'Guinn Monica L. , Lee John S. , Lee In-Yong , Park Jin-Ho , Foley Janet , Chae Joon-Seok 
Published: September 2006

ABSTRACTIn order to investigate the prevalence of tick-borne infectious agents among ticks, ticks comprising five species from two genera (Hemaphysalisspp. andIxodesspp.) were screened using molecular techniques. Ticks (3,135) were collected from small wild-caught mammals or by dragging/flagging in the Republic of Korea (ROK) and were pooled into a total of 1,638 samples (1 to 27 ticks per pool). From the 1,638 tick samples, species-specific fragments ofAnaplasma phagocytophilum(1 sample),Anaplasma platys(52 samples),Ehrlichia chaffeensis(29 samples),Ehrlichia ewingii(2 samples),Ehrlichia canis(18 samples), andRickettsia rickettsii(28 samples) were amplified by PCR assay. Twenty-one pooled and individual tick samples had mixed infections of two (15 samples) or three (6 samples) pathogens. In addition, 424 spleen samples from small captured mammals (389 rodents, 33 insectivores, and 2 weasels) were screened for selected zoonotic pathogens. Species-specific DNA fragments ofA. phagocytophilum(110 samples),A. platys(68 samples),E. chaffeensis(8 samples),E. ewingii(26 samples),E. canis(51 samples), andRickettsiasp. (22 samples) were amplified by PCR assay. One hundred thirty small mammals had single infections, while 4, 14, and 21 striped field mice (Apodemus agrarius) had mixed infections of four, three, and two pathogens, respectively. Phylogenetic analysis based on nucleotide sequence comparison also revealed that Korean strains ofE. chaffeensisclustered closely with those from China and the United States, while theRickettsia(rOmpA) sequences clustered within a clade together with a Chinese strain. These results suggest that these agents should be considered in differential diagnosis while examining cases of acute febrile illnesses in humans as well as animals in the ROK.
Abundance of
narG
,
nirS
,
nirK
, and
nosZ
Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland
Authors: Kandeler Ellen , Deiglmayr Kathrin , Tscherko Dagmar , Bru David , Philippot Laurent 
Published: September 2006

ABSTRACT

Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 10
5
to 8.9 × 10
5
copies per nanogram of DNA but smaller amounts of
narG
,
nirK
, and
nosZ
target molecules. Thus, numbers of
narG
,
nirK
,
nirS
, and
nosZ
copies per nanogram of DNA ranged from 2.1 × 10
3
to 2.6 × 10
4
, 7.4 × 10
2
to 1.4 × 10
3
, 2.5 × 10
2
to 6.4 × 10
3
, and 1.2 × 10
3
to 5.5 × 10
3
, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of
narG
and
nirS
versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of
nirK
and
nosZ
genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of
nirK
and
nosZ
communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.
An Oxidoreductase Is Involved in Cercosporin Degradation by the Bacterium
Xanthomonas campestris
pv. zinniae
Authors: Taylor Tanya V. , Mitchell Thomas K. , Daub Margaret E. 
Published: September 2006

ABSTRACT

The polyketide toxin cercosporin plays a key role in pathogenesis by fungal species of the genus
Cercospora
. The bacterium
Xanthomonas campestris
pv. zinniae is able to rapidly degrade this toxin. Growth of
X. campestris
pv. zinniae strains in cercosporin-containing medium leads to the breakdown of cercosporin and to the formation of xanosporic acid, a nontoxic breakdown product. Five non-cercosporin-degrading mutants of a strain that rapidly degrades cercosporin (XCZ-3) were generated by ethyl methanesulfonate mutagenesis and were then transformed with a genomic library from the wild-type strain. All five mutants were complemented with the same genomic clone, which encoded a putative transcriptional regulator and an oxidoreductase. Simultaneous expression of these two genes was necessary to complement the mutant phenotype. Sequence analysis of the mutants showed that all five mutants had point mutations in the oxidoreductase gene and no mutations in the regulator. Quantitative reverse transcription-PCR (RT-PCR) showed that the expression of both of these genes in the wild-type strain is upregulated after exposure to cercosporin. Both the oxidoreductase and transcriptional regulator genes were transformed into three non-cercosporin-degrading bacteria to determine if they are sufficient for cercosporin degradation. Quantitative RT-PCR analysis confirmed that the oxidoreductase was expressed in all transconjugants. However, none of the transconjugants were able to degrade cercosporin, suggesting that additional factors are required for cercosporin degradation. Further study of cercosporin degradation in
X. campestris
pv. zinniae may allow for the engineering of
Cercospora
-resistant plants by using a suite of genes.
Elucidation of the
hrp
Clusters of
Xanthomonas oryzae
pv. oryzicola That Control the Hypersensitive Response in Nonhost Tobacco and Pathogenicity in Susceptible Host Rice
Authors: Zou Li-fang , Wang Xing-ping , Xiang Yong , Zhang Bing , Li Yu-Rong , Xiao You-lun , Wang Jin-sheng , Walmsley Adrian R. , Chen Gong-you 
Published: September 2006

ABSTRACT

Xanthomonas oryzae
pv. oryzicola, the cause of bacterial leaf streak in rice, possesses clusters of
hrp
genes that determine its ability to elicit a hypersensitive response (HR) in nonhost tobacco and pathogenicity in host rice. A 27-kb region of the genome of
X. oryzae
pv. oryzicola (RS105) was identified and sequenced, revealing 10
hrp
, 9
hrc
(
hrp
conserved), and 8
hpa
(
hrp
-associated) genes and 7 regulatory plant-inducible promoter boxes. While the region from
hpa2
to
hpaB
and the
hrpF
operon resembled the corresponding genes of other xanthomonads, the
hpaB
-
hrpF
region incorporated an
hrpE3
gene that was not present in
X. oryzae
pv. oryzae. We found that an
hrpF
mutant had lost the ability to elicit the HR in tobacco and pathogenicity in adult rice plants but still caused water-soaking symptoms in rice seedlings and that Hpa1 is an HR elicitor in nonhost tobacco whose expression is controlled by an
hrp
regulator, HrpX. Using an Hrp phenotype complementation test, we identified a small
hrp
cluster containing the
hrpG
and
hrpX
regulatory genes, which is separated from the core
hrp
cluster. In addition, we identified a gene,
prhA
(plant-regulated
hrp
), that played a key role in the Hrp phenotype of
X. oryzae
pv. oryzicola but was neither in the core
hrp
cluster nor in the
hrp
regulatory cluster. A
prhA
mutant failed to reduce the HR in tobacco and pathogenicity in rice but caused water-soaking symptoms in rice. This is the first report that
X. oryzae
pv. oryzicola possesses three separate DNA regions for HR induction in nonhost tobacco and pathogenicity in host rice, which will provide a fundamental base to understand pathogenicity determinants of
X. oryzae
pv. oryzicola compared with those of
X. oryzae
pv. oryzae.
Discrimination of Multiple
Dehalococcoides
Strains in a Trichloroethene Enrichment by Quantification of Their Reductive Dehalogenase Genes
Authors: Holmes Victor F. , He Jianzhong , Lee Patrick K. H. , Alvarez-Cohen Lisa 
Published: September 2006

ABSTRACT

While many anaerobic microbial communities are capable of reductively dechlorinating tetrachloroethene (PCE) and trichloroethene (TCE) to dichloroethene (DCE), vinyl chloride (VC), and finally ethene, the accumulation of the highly toxic intermediates,
cis
-DCE (cDCE) and VC, presents a challenge for bioremediation processes. Members of the genus
Dehalococcoides
are apparently solely responsible for dechlorination beyond DCE, but isolates of
Dehalococcoides
each metabolize only a subset of PCE dechlorination intermediates and the interactions among distinct
Dehalococcoides
strains that result in complete dechlorination are not well understood. Here we apply quantitative PCR to 16S rRNA and reductase gene sequences to discriminate and track
Dehalococcoides
strains in a TCE enrichment derived from soil taken from the Alameda Naval Air Station (ANAS) using a four-gene plasmid standard. This standard increased experimental accuracy such that 16S rRNA and summed reductase gene copy numbers matched to within 10%. The ANAS culture was found to contain only a single
Dehalococcoides
16S rRNA gene sequence, matching that of
D. ethenogenes
195, but both the
vcrA
and
tceA
reductive dehalogenase genes. Quantities of these two genes in the enrichment summed to the quantity of the
Dehalococcoides
16S rRNA gene. Further, between ANAS subcultures enriched on TCE, cDCE, or VC, the relative copy number of the two dehalogenases shifted 14-fold, indicating that the genes are present in two different
Dehalococcoides
strains. Comparison of cell yields in VC-, cDCE-, and TCE-enriched subcultures suggests that the
tceA
-containing strain is responsible for nearly all of the TCE and cDCE metabolism in ANAS, whereas the
vcrA
-containing strain is responsible for all of the VC metabolism.
Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related toRoseburiaspp. orEubacterium rectale
Authors: Aminov Rustam I. , Walker Alan W. , Duncan Sylvia H. , Harmsen Hermie J. M. , Welling Gjalt W. , Flint Harry J. 
Published: September 2006

ABSTRACTPhylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains ofRoseburiaandEubacterium rectalewith 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.
Composition and Metabolic Activities of Bacterial Biofilms Colonizing Food Residues in the Human Gut
Authors: Macfarlane Sandra , Macfarlane George T. 
Published: September 2006

ABSTRACTBacteria growing in the human large intestine live in intimate association with the host and play an important role in host digestive processes, gut physiology, and metabolism. Fecal bacteria have been investigated extensively, but few studies have been done on biofilms that form on digestive wastes in the large bowel. The aims of this investigation were to investigate the composition and metabolic activities of bacterial communities that colonize the surfaces of food residues in fecal material, with respect to their role in the fermentation of complex carbohydrates. Fresh stools were obtained from 15 healthy donors, and food residues were separated by filtration. Adherent bacteria were removed by surfactant treatment for microbiological analysis and fermentation studies. Scanning electron microscopy and fluorescent in situ hybridization in conjunction with confocal laser scanning microscopy (CLSM) were used to visualize intact biofilms. Results showed that bacterial populations strongly adhering to particulate matter were phenotypically similar in composition to unattached communities, with bacteroides and bifidobacteria predominating. Biofilms comprised a mixture of living and dead bacteria, and CLSM showed that bifidobacteria in the biofilms occurred as isolated dispersed cells and in microcolonies near the interface with the substratum. Fermentation experiments with a variety of complex carbohydrates demonstrated that biofilm populations were more efficient in digesting polysaccharides, while nonadhering communities fermented oligosaccharides most rapidly. Acetate was the principal fermentation product formed by biofilm bacteria, whereas higher levels of butyrate were produced by nonadherent populations, showing that the two communities were metabolically distinct.
Quantification of the Effects of Salt Stress and Physiological State on Thermotolerance of
Bacillus cereus
ATCC 10987 and ATCC 14579
Authors: den Besten Heidy M. W. , Mataragas Marios , Moezelaar Roy , Abee Tjakko , Zwietering Marcel H. 
Published: September 2006

ABSTRACT

The food-borne pathogen
Bacillus cereus
can acquire enhanced thermal resistance through multiple mechanisms. Two
Bacillus cereus
strains, ATCC 10987 and ATCC 14579, were used to quantify the effects of salt stress and physiological state on thermotolerance. Cultures were exposed to increasing concentrations of sodium chloride for 30 min, after which their thermotolerance was assessed at 50°C. Linear and nonlinear microbial survival models, which cover a wide range of known inactivation curvatures for vegetative cells, were fitted to the inactivation data and evaluated. Based on statistical indices and model characteristics, biphasic models with a shoulder were selected and used for quantification. Each model parameter reflected a survival characteristic, and both models were flexible, allowing a reduction of parameters when certain phenomena were not present. Both strains showed enhanced thermotolerance after preexposure to (non)lethal salt stress conditions in the exponential phase. The maximum adaptive stress response due to salt preexposure demonstrated for exponential-phase cells was comparable to the effect of physiological state on thermotolerance in both strains. However, the adaptive salt stress response was less pronounced for transition- and stationary-phase cells. The distinct tailing of strain ATCC 10987 was attributed to the presence of a subpopulation of spores. The existence of a stable heat-resistant subpopulation of vegetative cells could not be demonstrated for either of the strains. Quantification of the adaptive stress response might be instrumental in understanding adaptation mechanisms and will allow the food industry to develop more accurate and reliable stress-integrated predictive modeling to optimize minimal processing conditions.
Novel Intermediates of Acenaphthylene Degradation by
Rhizobium
sp. Strain CU-A1: Evidence for Naphthalene-1,8-Dicarboxylic Acid Metabolism
Authors: Poonthrigpun Siriwat , Pattaragulwanit Kobchai , Paengthai Sarunya , Kriangkripipat Thanyanuch , Juntongjin Kanchana , Thaniyavarn Suthep , Petsom Amorn , Pinphanichakarn Pairoh 
Published: September 2006

ABSTRACT

The acenaphthylene-degrading bacterium
Rhizobium
sp. strain CU-A1 was isolated from petroleum-contaminated soil in Thailand. This strain was able to degrade 600 mg/liter acenaphthylene completely within three days. To elucidate the pathway for degradation of acenaphthylene, strain CU-A1 was mutagenized by transposon Tn
5
in order to obtain mutant strains deficient in acenaphthylene degradation. Metabolites produced from Tn
5
-induced mutant strains B1, B5, and A53 were purified by thin-layer chromatography and silica gel column chromatography and characterized by mass spectrometry. The results suggested that this strain cleaved the fused five-membered ring of acenaphthylene to form naphthalene-1,8-dicarboxylic acid via acenaphthenequinone. One carboxyl group of naphthalene-1,8-dicarboxylic acid was removed to form 1-naphthoic acid which was transformed into salicylic acid before metabolization to gentisic acid. This work is the first report of complete acenaphthylene degradation by a bacterial strain.
Relevance of the Endosymbiosis of
Blochmannia floridanus
and Carpenter Ants at Different Stages of the Life Cycle of the Host
Authors: Zientz Evelyn , Beyaert Ivo , Gross Roy , Feldhaar Heike 
Published: September 2006

ABSTRACT

Expression of several genes possibly involved in the symbiotic relationship between the obligate intracellular endosymbiont
Blochmannia floridanus
and its ant host
Camponotus floridanus
was investigated at different developmental stages of the host by real-time quantitative PCR. These included a set of genes related to nitrogen metabolism (
ureC
,
ureF
,
glnA
, and
speB
) as well as genes involved in the synthesis of the aromatic amino acid tyrosine (
tyrA
,
aspC
, and
hisC
). The overall transcriptional activity of
Blochmannia
was found to be quite low during early developmental stages and to increase steadily with host age. However, a concerted peak of gene expression related to nitrogen recycling could be detected around the entire process of pupation, while expression of biosynthesis pathways for aromatic amino acids was elevated only during a short phase in pupation. These data suggest an important role of certain metabolic functions for the symbiotic interactions of the bacteria and an individual host organism in early phases of development. General relevance of
Blochmannia
for its ant host was tested in fostering experiments with worker groups of
Camponotus floridanus
, and their success in raising pupae from first-instar larvae was used as a fitness measure. Groups treated with antibiotics had a significantly reduced success in raising the brood in comparison to untreated control groups, indicating that the symbiosis is relevant for the development of the entire colony.
Cloning of the Novel Gene Encoding β-Agarase C from a Marine Bacterium,
Vibrio
sp. Strain PO-303, and Characterization of the Gene Product
Authors: Dong Jinhua , Hashikawa Shinnosuke , Konishi Takafumi , Tamaru Yutaka , Araki Toshiyoshi 
Published: September 2006

ABSTRACT

The β-agarase C gene (
agaC
) of a marine bacterium,
Vibrio
sp. strain PO-303, consisted of 1,437 bp encoding 478 amino acid residues. β-Agarase C was identified as the first β-agarase that cannot hydrolyze neoagarooctaose and smaller neoagarooligosaccharides and was assigned to a novel glycoside hydrolase family.