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. Overall design: Aspergillus niger colony growing on a pie-slice culture with separated substrates in each section. Each of the three substrate sections on each plate were in turned divided into 3 compartments, each representing a unique configuration of neighboring compartments. Corresponding compartments on each plate were designated replicates of the same condition, e.g. samples P7-1, P11-1, and P14-1 are replicates for compartment 1.