Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the reportings of 371 articles and comprises 1190 biochemically unique reactions and 871 ORFs. Inclusion of isoenzymes increases the total number of reactions to 2240. A graphical map of the metabolic network is presented. All levels of the reconstruction process were based on manual curation. From the reconstructed metabolic network, a mathematical model was constructed and validated with data on yields, fluxes and transcription. The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform

Antarctic subglacial lake exploration: a new frontier in microbial ecology

To date, wherever life has been sought on Earth, it has almost always been found—from high in the stratosphere (Imshenetskii et al., 1975, 1978, 1986; Wainwright et al., 2003) to deep in the ocean trenches (Takamia et al., 1997; D'Hondt et al., 2004) and even within the Earth's crust itself (Pedersen, 2000). Microorganisms have also been found in some of the most extreme environments. They have been found to exist in ice, boiling water, acid, salt crystals, toxic waste and even in the water cores of nuclear reactors (Rothschild and Mancinelli, 2001). Antarctic subglacial lake ecosystems have the potential to be one of the most extreme environments on Earth, with combined stresses of high pressure, low temperature, permanent darkness, low-nutrient availability and oxygen concentrations derived from the ice that provided the original meltwater (Siegert et al., 2003), where the predominant mode of nutrition is likely to be chemoautotrophic. Yet, to date, the identification of significant subglacial bacterial activity in the Arctic, beneath glaciers (Skidmore et al., 2000, 2005) and in subglacial lakes (Gaidos et al., 2004), as well as extensive work on permafrost communities and work in the deep sea, suggests that life can survive and potentially thrive in these types of environment. Microbial life has been shown to function at gigapascal pressures (Sharma et al., 2002) and bacteria recovered from the deep ocean at around 4000 m have been shown to retain both structural integrity and metabolic activity. They have shown activity in the Antarctic at −17 °C (Carpenter et al., 2000) and to exist in the pore spaces between ice crystals (Thomas and Dieckmann, 2002)