Project description:Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured “ruffled” phenotype in the colony periphery and an unstructured “smooth” phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase (dig1 deletion, sfl1 deletion) or decrease (tec1deletion) the degree of colony structure. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns, including patterns that correlate closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8, CIS3, FLO11, MSB2 and SFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.
Project description:An adult P. rus colony was imported from Indonesia following the CITES protocols (Permit number 14846/IV/SATS-LN/2007) and kept in the Animal Facilities of the Justus Liebig University, Giessen. The colony was maintained in a circulating artificial seawater system at approximately 26 °C with 20-40 µmol photons m-2s-1 (T5 light) of photosynthetically active radiation on a 10:14 h light-dark cycle. A fragment of approx. 9 cm2 was separated from the colony and used as a source of tissue for hologenomic DNA/RNA isolation. Tissue was removed by scraping the fragment´s surface with a sterilized razor blade.
Project description:Saprotrophic fungi, such as Aspergillus niger, grow as mycelial colonies that are often considered uniform entities. To test this uniformity, we analyzed pie-slice sections of a colony grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics. The colony tuned its response to the local carbon source composition. Plant biomass degrading CAZymes and intracellular carbon catabolic enzymes were more abundant in parts of the colony containing the corresponding sugars. For example a stronger pectinolytic response was observed in the part of the colony grown on the pectin-rich sugar beet pulp. Our results argue against a situation in which small molecules are transported efficiently through the colony and favour high diversity within the fungal colony in natural biotopes, where the substrate is typically heterogeneous. It also demonstrates the high level of plasticity of A. niger in reponse to the composition of the prevailing lignocellulose.
Project description:Metaproteomes of individual Trichodesmium colonies collected from a single location in the Carribbean sea (65.22W, 17.02N) at 17:00 local time. Some colonies were associated with auto-fluorescent mineral particles. Their proteomes were analyzed individually to investigate the effect of the minerals on colony physiology.