Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
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 | Year: 2013
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.
Schumann P.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Methods in Microbiology | Year: 2014
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.
Yurkov A.M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Golubev W.I.,Russian Academy of Sciences
Mycological Progress | Year: 2013
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.
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.
Bioinformatics | Year: 2013
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.
Anderson I.,U.S. Department of Energy |
Abt B.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Lykidis A.,U.S. Department of Energy |
Klenk H.-P.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
And 2 more authors.
PLoS ONE | Year: 2012
Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms. © 2012 Anderson et al.
Spring S.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
ISME Journal | Year: 2016
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
Nagel S.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Meyer C.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Kaufmann M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Drexler H.G.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Macleod R.A.F.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
Genes Chromosomes and Cancer | Year: 2014
FOX genes encode transcription factors which regulate basic developmental processes during embryogenesis and in the adult. Several FOX genes show deregulated expression in particular malignancies, representing oncogenes or tumor suppressors. Here, we screened six Hodgkin lymphoma (HL) cell lines for FOX gene activity by comparative microarray profiling, revealing overexpression of FOXC1 and FOXD1, and reduced transcription of FOXN3, FOXO1, and FOXP1. In silico expression analyses of these FOX gene candidates in HL patient samples supported the cell line data. Chromosomal analyses demonstrated an amplification of the FOXC1 locus at 6p25 and a gain of the FOXR2 locus at Xp11, indicting genomic aberrations for their upregulation. Comparative expression profiling and ensuing stimulation experiments revealed implementation of the TGFβ- and WNT-signaling pathways in deregulation of FOXD1 and FOXN3. Functional analysis of FOXP1 implicated miR9 and miR34a as upstream regulators and PAX5, TCF3, and RAG2 as downstream targets. A similar exercise for FOXC1 revealed repression of MSX1 and activation of IPO7, both mediating inhibition of the B-cell specific homeobox gene ZHX2. Taken together, our data show that aberrantly expressed FOX genes and their downstream targets are involved in the pathogenesis of HL via deregulation of B-cell differentiation and may represent useful diagnostic markers and/or therapeutic targets. © 2014 Wiley Periodicals, Inc.
Kollenberg M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Winter S.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Gotz M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
PLoS ONE | Year: 2014
Bemisia tabaci (Gennadius) is one of the economically most damaging insects to crops in tropical and subtropical regions. Severe damage is caused by feeding and more seriously by transmitting viruses. Those of the genus begomovirus (Geminiviridae) cause the most significant crop diseases and are transmitted by B. tabaci in a persistent circulative mode, a process which is largely unknown. To analyze the translocation and to identify critical determinants for transmission, two populations of B. tabaci MEAM1 were compared for transmitting Watermelon chlorotic stunt virus (WmCSV) and Tomato yellow leaf curl virus (TYLCV). Insect populations were chosen because of their high and respectively low virus transmission efficiency to compare uptake and translocation of virus through insects. Both populations harbored Rickettsia, Hamiltonella and Wolbachia in comparable ratios indicating that endosymbionts might not contribute to the different transmission rates. Quantification by qPCR revealed that WmCSV uptake and virus concentrations in midguts and primary salivary glands were generally higher than TYLCV due to higher virus contents of the source plants. Both viruses accumulated higher in insects from the efficiently compared to the poorly transmitting population. In the latter, virus translocation into the hemolymph was delayed and virus passage was impeded with limited numbers of viruses translocated. FISH analysis confirmed these results with similar virus distribution found in excised organs of both populations. No virus accumulation was found in the midgut lumen of the poor transmitter because of a restrained virus translocation. Results suggest that the poorly transmitting population comprised insects that lacked transmission competence. Those were selected to develop a population that lacks virus transmission. Investigations with insects lacking transmission showed that virus concentrations in midguts were reduced and only negligible virus amounts were found at the primary salivary glands indicating for a missing or modified receptor responsible for virus attachment or translocation. © 2014 Kollenberg et al.
Sohngen C.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Bunk B.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Podstawka A.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Gleim D.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Overmann J.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
Nucleic Acids Research | Year: 2014
BacDive - the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. Currently (release 9/2013), BacDive contains entries for 23 458 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. Where available, links to access the respective biological resources are given. The majority of the BacDive data is manually annotated and curated. The BacDive portal offers an easy-to-use simple search and in addition powerful advanced search functionalities allowing to combine more than 30 search fields for text and numerical data. The user can compile individual sets of strains to a download selection that can easily be imported into nearly all spreadsheet applications. © 2013 The Author(s). Published by Oxford University Press.
Goker M.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures |
Klenk H.-P.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures
Standards in Genomic Sciences | Year: 2013
Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre-and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification.