Transcriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing

Background Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using both next generation RNA-sequencing and GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes. Results The transcriptome of dormant conidia was shown to be highly differentiated from that of germinating conidia and major changes in response to environmental shift occurred within the first hour of germination. The breaking of dormancy was associated with increased transcript levels of genes involved in the biosynthesis of proteins, RNA turnover and respiratory metabolism. Increased transcript levels of genes involved in metabolism of nitrate at the onset of germination implies its use as a source of nitrogen. The transcriptome of dormant conidia contained a significant component of antisense transcripts that changed during germination. Conclusion Dormant conidia contained transcripts of genes involved in fermentation, gluconeogenesis and the glyoxylate cycle. The presence of such transcripts in dormant conidia may indicate the generation of energy from non-carbohydrate substrates during starvation-induced conidiation or for maintenance purposes during dormancy. The immediate onset of metabolism of internal storage compounds after the onset of germination, and the presence of transcripts of relevant genes, suggest that conidia are primed for the onset of germination. For some genes, antisense transcription is regulated in the transition from resting conidia to fully active germinants

Estimating taxon-specific population dynamics in diverse microbial communities

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon- specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortal- ity, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes

Metabolic activity in dormant conidia ofAspergillus nigerand developmental changes during conidial outgrowth

The early stages of development of Aspergillus niger conidia during outgrowth were explored by combining genome-wide gene expression analysis (RNAseq), proteomics, Warburg manometry and uptake studies. Resting conidia suspended in water were demonstrated for the first time to be metabolically active as low levels of oxygen uptake and the generation of carbon dioxide were detected, suggesting that low-level respiratory metabolism occurs in conidia for maintenance. Upon triggering of spore germination, generation of CO2 increased dramatically. For a short period, which coincided with mobilisation of the intracellular polyol, trehalose, there was no increase in uptake of O2 indicating that trehalose was metabolised by fermentation. Data from genome-wide mRNA profiling showed the presence of transcripts associated with fermentative and respiratory metabolism in resting conidia. Following triggering of conidial outgrowth, there was a clear switch to respiration after 25 min, confirmed by cyanide inhibition. No effect of SHAM, salicylhydroxamic acid, on respiration suggests electron flow via cytochrome c oxidase. Glucose entry into spores was not detectable before 1 h after triggering germination. The impact of sorbic acid on germination was examined and we showed that it inhibits glucose uptake. O2 uptake was also inhibited, delaying the onset of respiration and extending the period of fermentation. In conclusion, we show that conidia suspended in water are not completely dormant and that conidial outgrowth involves fermentative metabolism that precedes respiration

Phylogenetic organization of bacterial activity.

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism\u27s ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.The ISME Journal advance online publication, 4 March 2016; doi:10.1038/ismej.2016.28

Verpackungsmaterial (Teil 1), Dezember 2013

Dezember 2013: Wichtig ist natürlich auch das entsprechende Verpackungsmaterial, welches zum Teil erst noch bestellt werden musste. Zu sehen ist auch der Karton mit den frühesten Bildern, die Karl Lutz aufgenommen hatte

Los gehts!, Januar 2014

Gestern ging es (endlich) los! Die ersten Fotos und Negative aus den Jahren 1916 und 1919 wurden gescannt und verzeichnet.Davor mussten erst noch ein paar Kleinigkeiten geklärt werden: Welchen Dateinamen bekommen die gescannten Bilder? Wie genau werden diese jetzt verzeichnet? Werden die Negative mit der matten oder der glänzende Seite nach oben auf den Scanner gelegt? Nicht, dass nachher alle Bilder spiegelverkehrt gescannt werden

Über 2000 Fotos gescannt!

Mittlerweile haben unsere Ehrenamtlichen über 2000 Fotos, Dias und Negative des Nachlasses Karl Lutz digitalisiert und verzeichnet. Das Digitalisieren an sich macht wenig Probleme, beim Verzeichnen wird es dafür etwas komplizierter: Karl Lutz hat zwar viele Fotos mit Datumsangaben und Beschriftungen zu den Orten bzw. Motiven versehen (die aber auch erst einmal entziffert werden müssen), was sehr hilfreich ist. Versucht man aber seine Route anhand der Ortsnamen zu verfolgen, stößt man oft an G..

Sortieren von Dubletten, 02.02.2014

Auch diese Woche ging die Bearbeitung des Nachlasses Lutz weiter. Dabei mussten die Negative und Positive erst einmal sortiert werden, da Karl Lutz Motive oft mehrere Male fotografiert und dabei die Beleuchtung, den Ausschnitt etc. veränderte. Damit nicht ein und dasselbe Motive mehrmals gescannt werden, wurden die zusammengehörigen Bilder auf dem Leuchttisch geordnet. Danach wurde jeweils das beste Bild ausgesucht, gescannt und verzeichnet. Die übrig gebliebenen Fotos werden natürlich nicht ..

Archivar - Kamera - Weltkrieg

Das Blog soll in Form eines Online-Tagebuchs über die Bearbeitung des umfangreichen Fotonachlasses des Archivars Dr. Karl Lutz berichten. Lutz hat im 2. Weltkrieg akribisch fotografiert, vor allem an der Ostfront sowie in Italien. Es ist der Blick eines Archivars und Historikers, der aus den Bildern erscheint. Die mehreren Tausend Fotos liegen in unterschiedlichen Formaten vor, sie sind oft restaurierungsbedürftig. Im Stadtarchiv Speyer werden sie ab demnächst von einmer ehrenamtlichen Arbeit..

Verpackungsmaterial (Teil 2), Januar 2014

Auf Nachfrage hier eine kleine Erklärung, wie Fotos, Dias, Positive etc. verschiedener Größen eigentlich archivgerecht verpackt werden: Wichtig ist zuerst immer, dass das Verpackungsmaterial alterungsbeständig und säurefrei ist. Für Fotomaterialien sollten zusätzlich die Anforderungen des Photographic Activity Test (PAT) erfüllt sein, welcher im Rahmen von simulierten Langzeittests prüft, ob das Archivmaterial negative Auswirkungen auf das zu archivierende Fotomaterial hat. Dias werden in lä..