Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes

Hoeflea alexandrii sp. nov., isolated from the toxic dinoflagellate Alexandrium minutum AL1V

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Molecular characterization of protease producing Idiomarina species isolated from Peruvian saline environments

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, tRNAIle (GAT) and tRNAAla (TGC), which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the tRNAAla gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies. © 2019, The Korean Society for Microbiology and Biotechnolog

Trans-National Acess to BRCs with EMbaRC : A user -oriented Approach to Foster Research and Innovation

The European Consortium of Microbial Resource Centres (EMbaRC) is a ResearchInfrastructure project gathering 8 major microbial Biological Resource Centres(BRCs) in Europe. It aims at improving, coordinating and validating microbialresource delivery to European and international researchers from public andprivate sectors. A major action in EMbaRC is to set up a Training and OutreachProgramme, providing European research teams with a physical access not only tomicrobial BRCs holding bacteria, yeasts, filamentous fungi and plasmids, butalso to associated installations and expertise. Through EU-funded stays for 1to 6 weeks, European scientists performed experiments in various fields ofmicrobiology. Researchers used advanced techniques for identification andtyping of micro-organisms: molecular biology (16S rDNA sequencing, DNA-DNAhybridization, AFLP, PFGE, RAPD, FISH) and chemotaxonomy (MALDI-TOF, FTIR,FAME, enzyme activity high throughput screening). Phenotypic characterisationof isolates (bacteriocin or enzyme production) was also carried out, in somecases to develop polyphasic approaches for identification. Access tomicroscopic facilities (confocal and epifluorescence microscopes) was alsoprovided, notably to biofilm-related projects. In most of the cases, accessprovision was also an opportunity to disseminate good practices in collectionand database management, including preservation techniques and appropriate useof public sequence databases, fostering the operation of European microbialcollections according to appropriate standards and methods. This action alsoimpacts students thanks to the access given to academic users

Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau

Previous investigations of the salinity effects on the microbial community composition have largely been limited to dynamic estuaries and coastal solar salterns. In this study, the effects of salinity and mineralogy on microbial community composition was studied by using a 900-cm sediment core collected from a stable, inland hypersaline lake, Lake Chaka, on the Tibetan Plateau, north-western China. This core, spanning a time of 17 000 years, was unique in that it possessed an entire range of salinity from freshwater clays and silty sands at the bottom to gypsum and glauberite in the middle, to halite at the top. Bacterial and archaeal communities were studied along the length of this core using an integrated approach combining mineralogy and geochemistry, molecular microbiology (16S rRNA gene analysis and quantitative polymerase chain reaction), cultivation and lipid biomarker analyses. Systematic changes in microbial community composition were correlated with the salinity gradient, but not with mineralogy. Bacterial community was dominated by the Firmicutes-related environmental sequences and known species (including sulfate-reducing bacteria) in the freshwater sediments at the bottom, but by halophilic and halotolerant Betaproteobacteria and Bacteroidetes in the hypersaline sediments at the top. Succession of proteobacterial groups along the salinity gradient, typically observed in free-living bacterial communities, was not observed in the sediment-associated community. Among Archaea, the Crenarchaeota were predominant in the bottom freshwater sediments, but the halophilic Halobacteriales of the Euryarchaeota was the most important group in the hypersaline sediments. Multiple isolates were obtained along the whole length of the core, and their salinity tolerance was consistent with the geochemical conditions. Iron-reducing bacteria were isolated in the freshwater sediments, which were capable of reducing structural Fe(III) in the Fe(III)-rich clay minerals predominant in the source sediment. These data have important implications for understanding how microorganisms respond to increased salinity in stable, inland water bodies. © 2007 The Authors.link_to_subscribed_fulltex