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To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of 10 closely related Shewanella strains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and to rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms, when the organisms were grown under identical conditions, were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera. comparative genomics | evolution | proteomics | speciation | phenotype

Stable isotope probing with [[super 13]C]biphenyl is used for studying the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A DNA-stable isotope probing-based cosmid library has enabled the retrieval of functional genes from an uncultivated organism that is capable of polychlorinated biphenyl (PCB) metabolism and has shown dispersed dioxygenase gene organization in nature.

The phylogenetic position of Spirobacillus cienkowskii is established through the analysis of genes encoding the 16S rRNA and [beta]-subunit of topoisomerase and has confirmed the presence of the pathogen in multiple species of Daphnia. The geographic distribution, host range and virulence of Spirobacillus cienkowskii have shown that it plays a vital role in the ecology and evolution of daphniids.

Burkholderia xenovarans strain LB400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic ortho dehalogenation operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. Inoculation at different cell densities did not affect the extent of polychlorinated biphenyl biodegradation.

Research indicates that phylogenetically meanigful specific primer sets for the 16s rRNA genes can be employed as single or multiplex polymerase chain reaction for the dection and analysis of the diversity in Xylella fastidiosa. Data indicate that the method detects X. fastidiosa in field samples, in disease vectror insects, and in nonsymptomatic infected plants.

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea , indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests. [ABSTRACT FROM AUTHOR]

The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and on screening of 28 800 clones, four fosmids were identified as containing verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analyzed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved to be suitable for the recovery of verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterized, bacterial phylum. [ABSTRACT FROM AUTHOR]