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Spring S.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | Riedel T.,Helmholtz Center for Infection Research | Riedel T.,French National Center for Scientific Research
BMC Microbiology

Background: Populations of aerobic anoxygenic photoheterotrophic bacteria in marine environments are dominated by members of the Roseobacter lineage within the Alphaproteobacteria and the OM60/NOR5 clade of gammaproteobacteria. A wealth of information exists about the regulation of pigment production and mixotrophic growth in various members of the Roseobacter clade, but a detailed knowledge about aerobic bacteriochlorophyll a-containing gammaproteobacteria is still limited to one strain of the species Congregibacter litoralis. Results: The production of photosynthetic pigments and light-dependent mixotrophic growth was analysed in Luminiphilus syltensis DSM 22749T, Chromatocurvus halotolerans DSM 23344T and Pseudohaliea rubra DSM 19751T, representing three taxonomically diverse strains of bacteriochlorophyll a-containing gammaproteobacteria affiliated to the OM60/NOR5 clade. In these strains the expression of a photosynthetic apparatus depended mainly on the type of carbon source and availability of oxygen. The effect of illumination on pigment expression varied significantly between strains. In contrast to Chromatocurvus halotolerans, pigment production in Luminiphilus syltensis and Pseudohaliea rubra was repressed by light of moderate intensities, probably indicating a higher sensitivity to light-induced oxidative stress. The efficiency of using light for mixotrophic growth did not correlate with the cellular level of photosynthetic pigments, but depended mainly on the type of metabolized substrate with malate being the optimal carbon source in most cases. Conclusions: Oligotrophic growth conditions or carbon limitation were not required for light-dependent mixotrophic growth in members of the OM60/NOR5 clade. The ability of using light as energy source and the fine tuning of photosynthesis gene expression depended mainly on the type of carbon source and oxygen availability, which indicates that the regulation of pigment production is controlled by the cellular redox state. While light has the main impact on the regulation of photosynthetic pigments in photoheterotrophic representatives of the Roseobacter lineage this was not the case in strains of the OM60/NOR5 clade. © 2013 Spring and Riedel; licensee BioMed Central Ltd. Source

Yurkov A.M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | Golubev W.I.,Russian Academy of Sciences
Mycological Progress

Previous studies reported Cryptococcus laurentii strains to secrete mycocins of different inhibition range. These mycocinogenic strains were studied by molecular methods to verify their phylogenetic relationships. Based on the combined analysis of LSU and ITS sequence data, these strains were confirmed to belong to the species C. laurentii. Therefore, different strains of the same basidiomycetous yeast C. laurentii secrete a distinct mycocin. This trait has not been demonstrated for basidiomycetous yeasts before. Additionally, this study provides several DNA-barcodes (LSU, ITS and RPB1) and reports their variability for this species. © 2012 German Mycological Society and Springer-Verlag Berlin Heidelberg. Source

Schumann P.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | Maier T.,Bruker
Methods in Microbiology

Since the introduction of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for classification and identification of prokaryotes approximately 20 years ago, this technique has found increasing application in medical diagnostics, pharmaceutical quality control and environmental research as well as in veterinary medicine and the food industry. MALDI-TOF MS has become a promising alternative to conventional identification techniques and is even beginning to outcompete phenotypic and sequencing technologies with respect to reliability, speed and cost. MALDI-TOF MS applications in microbiology have had a high impact on the scientific literature and various procedures for specific applications have been proposed. However, there is still a need for proven and tested protocols for how to prepare samples for problematic organisms and for suggestions on how to optimise measurement conditions in order to record high-quality spectra for unambiguous identification and typing. The discriminatory power of protein mass spectra is compared with the taxonomic resolution of established tools for classification, identification and typing of bacteria in order to define the optimal fields of application of MALDI-TOF MS. © 2014 Elsevier Ltd. Source

Vaas L.A.I.,Fungal Biodiversity Center | Sikorski J.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | Hofner B.,Friedrich - Alexander - University, Erlangen - Nuremberg | Fiebig A.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | And 3 more authors.

opm is an R package designed to analyse multidimensional OmniLog® phenotype microarray (PM) data. opm provides management, visualization and statistical analysis of PM data, including curve-parameter estimation and discretization, dedicated and customizable plots, metadata management, automated generation of textual and tabular reports, mapping of substrates to databases, batch conversion of files and export to phylogenetic software in the YAML markup language. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved. Source

Spring S.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
ISME Journal

The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.The ISME Journal advance online publication, 14 June 2016; doi:10.1038/ismej.2016.84. © 2016 International Society for Microbial Ecology Source

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