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Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the 'classical' antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepa1516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudo-tuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in proteincoding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

The bacterium Caulobacter crescentus and related stalk bacterial species are known for their distinctive ability to live in low-nutrient environments, a characteristic of most heavy metal-contaminated sites. Caulobacter crescentus is a model organism for studying cell cycle regulation with well-developed genetics. We have identified the pathways responding to heavy-metal toxicity in C. crescentus to provide insights for the possible application of Caulobacter to environmental restoration. We exposed C. crescentus cells to four heavy metals (chromium, cadmium, selenium, and uranium) and analyzed genome-wide transcriptional activities postexposure using an Affymetrix GeneChip microarray. C. crescentus showed surprisingly high tolerance to uranium, a possible mechanism for which may be the formation of extracellular calcium-uranium-phosphate precipitates. The principal response to these metals was protection against oxidative stress (up-regulation of manganese-dependent superoxide dismutase sodA). Glutathione S-transferase, thioredoxin, glutaredoxins, and DNA repair enzymes responded most strongly to cadmium and chromate. The cadmium and chromium stress response also focused on reducing the intracellular metal concentration, with multiple efflux pumps employed to remove cadmium, while a sulfate transporter was down-regulated to reduce nonspecific uptake of chromium. Membrane proteins were also up-regulated in response to most of the metals tested. A two-component signal transduction system involved in the uranium response was identified. Several differentially regulated transcripts from regions previously not known to encode proteins were identified, demonstrating the advantage of evaluating the transcriptome by using whole-genome microarrays.

Researchers report their experience using the GeneChip from Affymetrix Corp. to screen small-subunit ribosomal RNA genes. GeneChip is a photolithography chip that contains 31,179 20-mer oligonucleotides complementary to sequences in the Ribosomal Database Project.

Researchers identified a PCR primer that can detect Salmonella enterica serovar Enteritidis. This bacterium commonly colonizes chickens and is a major cause of food poisoning. The test is able to distinguish serovar Enteritidis from other serovars.

Researchers used suppression subtractive hybridization to detect a 41.7-kb region of the Yersinia pestis genome. A PCR primer for this region was able to distinguish Yersinia pestis from similar species such as Yersinia pseudotuberculosis. Yersinia pestis is the bacterium that causes bubonic plague.

The pathway for methionine biosynthesis in Pseudomonas syringae is similar to the methionine biosynthetic pathway for the fungus Neurospora crassa. This was gleaned from a sequence and mutational analysis of the metXW locus in P syringae, which was isolated, sequenced and evaluated along with the gene metX for its role in methionine biosynthesis and bacterial fitness on leaf surfaces. Results showed that both metX and metW were required for methionine biosynthesis. A number of classes of methionine auxotrophs, including metX and metW mutants, showed reduced fitness on leaf surfaces.

PCR analysis of 198 Bacillus anthracis isolates indicated a variable region of DNA sequence differing in length among the isolates. Five polymorphisms were characterized by the presence of two to six copies of the 12-bp tandem repeat 5'-CAATATCAACAA-3'. This variable-number tandem repeat region is found within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not alter the reading frame of the encoded protein and only modified the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6.

Immigration of bacteria from plants with larger epiphytic bacterial populations accounts for the increase in bacterial populations on navel orange leaves during winter. However, the presence of plant species, such as citrus and olive, in adjacent orchards adversely affects such immigration. Bacterial population increase is 6- to 30-fold greater on navel orange leaves adjacent to plant species other than citrus. Navel orange leaves also show an increasing ability to supercool with increasing distance from the upwind edge of orchards adjacent to plant species other than citrus.

The use of Phylotrac as an integrated desktop application for analysis of PhyloChip microarray data is demonstrated. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archael communities in complex environmental samples.

A study was conducted to assess the application of 454 pyrosequencing to characterize bacterial biofilm communities from two water meters of a drinking water distribution system. The differences observed in the bacterial diversity and composition would provide better insight into the bacterial ecology of drinking water biofilms to enable effective management of water quality in distribution systems.

The full-length sequencing survey of 11,171 16S rRNA genes of the intestinal microbiota of beef cattle which are important for animal health, food safety and methane emissions is reported. The results revealed that animal-to-animal variation in communities that could no be attributed to breed, gender, diet, age or weather and beef communities differ from those of dairy.

Conventional 16S rRNA gene clone library and high-density phylogenetic 16-rRNA gene microarray (PhyloChip) technologies were employed to examine the anaerobic bacteria cultured on several media, and DNA extracted from suitable anaerobic enrichments. The results indicated that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and would pose a challenge to planetary protection implementation activities.

PCR-denaturing gradient gel analysis was used to evaluate the effects of environmental exposures typically associated with asthma protection or risk on the microbial community structure of household dust. The findings indicated that specific bacterial populations within the bacterial community structure are associated with either risk or protection from asthma.

The development of a whole-genome photolithographic microarray which contains probes designed to hybridize to >99% of the predicted protein-coding sequences in genome 'Dehalococcoides ethenogenes' 195 is described. The data information on diversity of Dehalococcoides genomes provides insight into the physiology and evolution of these bacteria.

DNA microarrays are used for monitoring dynamics changes in the transcriptome as 'Dehalococcoides ethenogenes' strain 195 transitioned from exponential growth into stationary phase. Genes encoding the dominant hydrogenase-reductive dehalogenase (RDase) respiratory chain of this strain are expressed at stable levels throughout the experiment, providing molecular evidence that strain 195 can uncouple dechlorination from net growth.

The creation of a reporter that uses the urcA (uranium response in Caulobacter crescentus) promoter to produce a UV-excitable green fluorescent protein in the presence of the uranyl cation is described. The reporter is specific for uranium and has less cross specificity for other metals.

A high-density polygenitic DNA microarray (16S microarray) containing 500,000 probes is employed to monitor changes in bacterial populations during redemption process to determine the relation between microbial community composition and less-soluble uranium U (IV) reoxidation. Observations suggest that reoxidation of uranium under reducing conditions occur despite elevated microbial activity and consistent presence of metal-reducing bacteria.

Genes important for the association of Salmonella enterica Serovar enteritidis with chicken eggs were identified through transposon-mediated mutagenesis in a study. Results indicate that genes involved in cell wall structural and functional integrity, and nuclei acid and amino acid metabolism are important and Serovar Enteritidis is the only bacterium transmitted to humans through intact chicken eggs and its survival in eggs is necessary for transmission to the human population.

Research has been conducted on genetically related group of Bacillus anthracis, B. cereus and B. thuringiensis. The authors discuss the phylogenetic relationships between these non-anthrax-causing Bacillus species.

Reports on the identification of a region of sequence variability among individuals isolates of Bacillus anthracis as well as two closely related species, Bacillus cereus and Bacillus mycoides. Sequence-based approach for rapid differentiation among members of the group; Identification of the region of sequence divergence; Origin of sequence variation.

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population = 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shins in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobac-teria, Methylobacteriaceae, Sphingomonadaceae, and Xanthotnottadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (< 0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine. [ABSTRACT FROM AUTHOR]

Isolates DNA restriction fragments present in Salmonella enterica serovar Enteritidis. Application of suppression subtractive hybridization; Use of the primer pair Sdf I in detecting the isolates; Location of the primer in the chromosome.