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Unterseher M.,University of Greifswald | Siddique A.B.,University of Greifswald | Brachmann A.,Biozentrum der LMU Munich | Persoh D.,Ruhr University Bochum

Comparative investigations of plant-associated fungal communities (mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology. © 2016 Unterseher et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

Geigenberger P.,Ludwig Maximilians University of Munich | Tiessen A.,CINVESTAV | Meurer J.,Biozentrum der LMU Munich
Methods in Molecular Biology

Chloroplasts are the chemical factories of plant cells because they are able to fix inorganic carbon and -convert it to a wide-range of photoassimilates that are exported to the cytosol and other sub-cellular compartments. If the regulation of these processes is to be understood, the in vivo concentrations of a large number of metabolites have to be measured in all of these compartments separately. Sophisticated analytical approaches and continued advances in the technology of mass spectrometry coupled to a variety of fractionation and separation techniques allow the reliable analysis of a comprehensive complement of metabolites in photosynthetic tissues. Metabolomic approaches allow the multi-parallel analysis of a wide-range of metabolic intermediates and have been used for rapid phenotyping of different genotypes and environmental effects in plants. In addition to this, methods have been developed to analyse metabolite levels in different sub-cellular compartments of plant cells. Here, we describe methods for sub-cellular fractionation of Arabidopsis leaves using a non-aqueous density gradient technique, sample preparation suitable for metabolite profiling using gas-chromatography-mass spectrometry, and calculation of sub-cellular metabolite concentrations. © 2011 Springer Science+Business Media, LLC. Source

Koeck D.E.,TU Munich | Ludwig W.,TU Munich | Wanner G.,Biozentrum der LMU Munich | Zverlov V.V.,TU Munich | And 3 more authors.
International Journal of Systematic and Evolutionary Microbiology

Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9 % 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1 %) were 16:0 dimethyl acetal, 16:0 fatty acid methyl ester and 16:0 aldehyde. The DNA G + C content was 36.6 mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov, sp. nov, is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T (=DSM 29228T =CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov, sp. nov. © 2015 IUMS. Source

Manavski N.,Biozentrum der LMU Munich | Torabi S.,Biozentrum der LMU Munich | Lezhneva L.,Biozentrum der LMU Munich | Lezhneva L.,Umea University | And 3 more authors.
Plant Cell

The seedling-lethal Arabidopsis thaliana high chlorophyll fluorescence145 (hcf145) mutation leads to reduced stability of the plastid tricistronic psaA-psaB-rps14 mRNA and photosystem I (PSI) deficiency. Here, we genetically mapped the HCF145 gene, which encodes a plant-specific, chloroplast-localized, modular protein containing two homologous domains related to the polyketide cyclase family comprising 37 annotated Arabidopsis proteins of unknown function. Two further highly conserved and previously uncharacterized tandem repeat motifs at the C terminus, herein designated the transcript binding motif repeat (TMR) domains, confer sequence-specific RNA binding capability to HCF145. Homologous TMR motifs are often found as multiple repeats in quite diverse proteins of green and red algae and in the cyanobacterium Microcoleus sp PCC 7113 with unknown function. HCF145 represents the only TMR protein found in vascular plants. Detailed analysis of hcf145 mutants in Arabidopsis and Physcomitrella patens as well as in vivo and in vitro RNA binding assays indicate that HCF145 has been recruited in embryophyta for the stabilization of the psaA-psaB-rps14 mRNA via specific binding to its 59 untranslated region. The polyketide cyclase-related motifs support association of the TMRs to the psaA RNA, presumably pointing to a regulatory role in adjusting PSI levels according to the requirements of the plant cell. © 2015 American Society of Plant Biologists. Source

Glasser C.,Helmholtz Center for Environmental Research | Haberer G.,Helmholtz Center for Environmental Research | Finkemeier I.,Biozentrum der LMU Munich | Pfannschmidt T.,Friedrich - Schiller University of Jena | And 7 more authors.
Molecular Plant

Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pathways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and protein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network. © The Author 2014. Source

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