Genomotyping of Pseudomonas putida strains using P-putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas strains was investigated. To this end, microarray hybridizations were performed with genomic DNAs of subcultures of P. putida KT2440 (DSM6125), the type strain (DSM291(T)), plasmid pWW0-containing KT2440-derivative strain mt-2 (DSM3931), the solvent-tolerant P. putida S12, and several other Pseudomonas strains. Depending on the strain tested, 22 to 99% of all genetic elements were identified in the genomic DNAs. The efficacy of these microarrays to study cellular function was determined for all strains included in the study. The vast majority of DSM6125 genes encoding proteins of primary metabolism and genes involved in the catabolism of aromatic compounds were identified in the genomic DNA of strain S12: a prerequisite for reliable transcriptomics analyses. The genomotypic comparisons between Pseudomonas strains were used to construct highly discriminative phylogenetic relationships. DSM6125 and DSM3931 were indistinguishable and clustered together with strain S12 in a separate group, distinct from DSM291(T). Pseudomonas monteilii (DSM14164) clustered well with P. putida strains.

Phenotypic diversity amongst strains of Pleurotus sajor-caju: implications for cultivation in and environments

In arid regions, biodiversity and biomass are limited by water availability, and this problem has been compounded by desertification associated with global climate change. The saprotrophic macrofungi that are indigenous to hot subtropical and tropical regions, such as Pleurotus spp., can play key roles in water sequestration, nutrient cycling, human nutrition, and bioremediation of waste materials. We studied 15 strains of Pleurotus sajor-caju, a widespread and phenotypically-diverse species, to establish variability in growth response and primordium development over a range of stress parameters: osmotic potential (-0.5 to -5 MPa), temperature (5-40 degrees C) and pH (2-12). The initiation of primordia precedes basidiome production and therefore represents a key stage in bioremediation strategies and fungi-driven nutrient cycles. Primordia were produced at low pH (4-6), at suboptimal growth temperatures (<or =25 degrees C), and under moderate water stress (-0.5 to -3.5 MPa). Although the growth windows for different strains were similar, their maximum growth rates and the optimum conditions for growth varied. We discuss the phenotypic diversity of Pleurotus strains and discuss their potential for cultivation, bioremediation and ecological regeneration.

Isolation and characterisation of bacterial strains containing enantioselective DMSO reductase activity: application to the kinetic resolution of racemic sulfoxides

The kinetic resolution of racemic sulfoxides by dimethyl sulfoxide (DMSO) reductases was investigated with a range of microorganisms. Three bacterial isolates (provisionally identified as Citrobacter braakii, Klebsiella sp. and Serratia sp.) expressing DMSO reductase activity were isolated from environmental samples by anaerobic enrichment with DMSO as terminal electron acceptor. The organisms reduced a diverse range of racemic sulfoxides to yield either residual enantiomer depending upon the strain used. C. braakii DMSO-11 exhibited wide substrate specificity that included dialkyl, diaryl and alkylaryl sulfoxides, and was unique in its ability to reduce the thiosulfinate 1,4-dihydrobenzo-2, 3-dithian-2-oxide. DMSO reductase was purified from the periplasmic fraction of C. braakii DMSO-11 and was used to demonstrate unequivocally that the DMSO reductase was responsible for enantiospecific reductive resolution of racemic sulfoxides.