Detection of Eubacterial 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductases from Natural Populations of Actinomycetes

Three natural populations of actinomycetes were investigated by PCR for the presence of type I 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG CoA), a gene associated with isoprenoid biosynthesis. The populations were obtained from an agricultural site (69 isolates), a coastal salt marsh (220 isolates), and a desert soil (96 isolates). A set (34) of standard actinomycete reference strains were also investigated. The target gene was only detected in 5 of the 419 actinomycetes screened, which represented 4 from the coastal salt marsh and one reference strain. The isolates that contained the gene were taxonomically diverse (4 Streptomyces spp. and 1 Nocardia sp.). These results suggest that type I HMG CoA containing pathways are rare in actinomycetes and their distribution within actinomycetes populations is not random.     

Molecular studies resolve Nyholmiella (Orthotrichaceae) as separated genus

Two Orthotrichum species of the subgenus Orthophyllum were compared with other representatives of this genus using the internally transcribed spacer regions 1 and 2, the chloroplast trnH-psbA region and ISSR and ISJ DNA markers. The applied DNA markers revealed many bands and mutations specific only to O. gymnostomum and O. obtusifolium. A phylogenetic analysis clearly supported the previous concepts postulating that species of the subgenus Orthophyllum should be recognized as separate genus Nyholmiella.     

Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria

A bacterial isolate, with an optimum growth temperature of about 50 degrees C, was recovered from the hot spring at Egerszalók in Hungary. Phylogenetic analyses using the 16S rRNA gene sequence of strain H-8T indicated that the new organism represented a new genus and species of alpha-1 subclass of the Proteobacteria. The major fatty acids of strain H-8T are 16:0, 18:1 omega7c; the rare fatty acid 19:0 20H cyclo 11,12 is also present. Ubiquinone 9 is the major respiratory quinone, the polar lipids are phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The new isolate forms red-colored colonies, flocculates in liquid media, is heterotrophic and strictly aerobic. Thiosulfate is oxidized to sulfate, but an increase in biomass could not be measured because of the flocculating behavior. Bacteriochloropyll a was detected by direct spectrophotometric analysis when the organism was grown at 30 degrees C, but could not be detected after growth at 50 degrees C. pufL and pufM genes were present. Heterotrophic growth of strain H-8T occurs on a few carbohydrates, amino acids and organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strain H-8T represents a new genus and a new species most closely related to Roseococcus thiosulfatophilus for which we propose the name Rubritepida flocculans.     

Anthrax toxin receptor 2 determinants that dictate the pH threshold of toxin pore formation

The anthrax toxin receptors, ANTXR1 and ANTXR2, act as molecular clamps to prevent the protective antigen (PA) toxin subunit from forming pores until exposure to low pH. PA forms pores at pH approximately 6.0 or below when it is bound to ANTXR1, but only at pH approximately 5.0 or below when it is bound to ANTXR2. Here, structure-based mutagenesis was used to identify non-conserved ANTXR2 residues responsible for this striking 1.0 pH unit difference in pH threshold. Residues conserved between ANTXR2 and ANTXR1 that influence the ANTXR2-associated pH threshold of pore formation were also identified. All of these residues contact either PA domain 2 or the neighboring edge of PA domain 4. These results provide genetic evidence for receptor release of these regions of PA as being necessary for the protein rearrangements that accompany anthrax toxin pore formation.     

Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter

Dimethylsulfone is a major product of the chemical oxidation in the atmosphere of the principal biogenic sulfur gas, dimethylsulfide, but no studies have been reported on the mechanisms for its microbiological degradation. Three novel strains of bacteria have been isolated from enrichment cultures provided with dimethylsulfone as the only carbon and energy substrate. These are novel facultatively methylotrophic species of Hyphonmicrobium and Arthobacter, capable of growth on a range of one-carbon substrates. Cell-free extracts contained activities of enzymes necessary for a reductive/oxidative pathway for dimethylsulfone degradation: membrane-bound-dimethylsulfone and dimethylsulfoxide reductases, dimethylsulfide monooxygenase, and methanethiol oxidase. Enzymatic evidence is also presented for the subsequent oxidation of formaldehyde by formaldehyde and formate dehydrogenases in the Hyphomicrobium strain and by a dissimilatory ribulose monophosphate cycle in the Arthrobacter strains. The strains also grew on dimethylsulfoxide and dimethylsulfide, and dimethylsulfide-grown bacteria oxidized dimethylsulfide and dimethylsulfoxide but not dimethylsulfone. Formaldehyde assimilation was effected in the Hyphomicrobium strain by the serine pathway, but enzymes of the ribulose monophosphate cycle for formaldehyde assimilation were present in the Arthrobacter strains grown on dimethylsulfone. In contrast, one of the Arthrobacter strains was shown to switch to the serine pathway during growth on methanol. Growth yields on dimethylsulfone and formaldehyde were consistent with the occurrence of the serine pathway in Hyphomicrobium strain S1 and the ribulose monophosphate cycle in Arthrobacter strain TGA, and with the proposed reductive pathway for dimethylsulfone degradation in both.     

Population trends of European common birds are predicted by characteristics of their climatic niche

Temperate species are projected to experience the greatest temperature increases across a range of modelled climate change scenarios, and climate warming has been linked to geographical range and population changes of individual species at such latitudes. However, beyond the multiple modelling approaches, we lack empirical evidence of contemporary climate change impacts on populations in broad taxonomic groups and at continental scales. Identifying reliable predictors of species resilience or susceptibility to climate warming is of critical importance in assessing potential risks to species, ecosystems and ecosystem services. Here we analysed long‐term trends of 110 common breeding birds across Europe (20 countries), to identify climate niche characteristics, adjusted to other environmental and life history traits, that predict large‐scale population changes accounting for phylogenetic relatedness among species. Beyond the now well‐documented decline of farmland specialists, we found that species with the lowest thermal maxima (as the mean spring and summer temperature of the hottest part of the breeding distribution in Europe) showed the sharpest declines between 1980 and 2005. Thermal maximum predicted the recent trends independently of other potential predictors. This study emphasizes the need to account for both land‐use and climate changes to assess the fate of species. Moreover, we highlight that thermal maximum appears as a reliable and simple predictor of the long‐term trends of such endothermic species facing climate change.