Abstract
Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes and nitrate utilization were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate that A. niger employs different enzymatic tools to adapt its metabolism as it colonizes complex environments.
Highlights
In their natural biotope, fungal colonies are not exposed to carbon depletion, but instead different parts of the mycelium are exposed to heterogeneous carbon sources with variable composition
A. niger was inoculated at a central point and the mycelium extended by radial growth so that the colony centre represents the oldest hyphae and the periphery is made up of the newly formed hyphae
Extracellular proteins can cross the membrane the gene expression is limited to the colony on top of the membrane
Summary
In their natural biotope, fungal colonies are not exposed to carbon depletion, but instead different parts of the mycelium are exposed to heterogeneous carbon sources with variable composition. To study differentiation of gene expression in a more “natural” situation, we grew A. niger on a crude plant biomass substrate, sugar beet pulp (SBP). A. niger is one of the most important industrial fungi worldwide and is a model organism for plant biomass utilization, enzyme secretion and carbon metabolism in fungi. Sugar beet (Beta vulgaris) is the main crop for sugar production in Europe (http://epp.eurostat.ec.europa.eu). In United States, sugar beet has provided about 55 percent of the total sugar produced domestically since the mid-1990 s (http:// www.ers.usda.gov). Sugar beet pulp waste from the sugar industry is a potential source of carbon for biofuel production, provided that these complex carbon molecules can be efficiently degraded[8]. In this study we investigated how A. niger uses its enzymatic toolbox throughout the vegetative mycelial colony to degrade sugar beet pulp
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