The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp

Abstract

Understanding the interaction between filamentous fungi and their natural and biotechnological environments has been of great interest for the scientific community. Submerged cultures are preferred over solid cultures at a laboratory scale to study the natural response of fungi to different stimuli found in nature (e.g., carbon/nitrogen sources, pH).

Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger

“…The response to the presence of cellulose is most likely triggered when the pectin and hemicellulose content is depleting. The slow utilization of cellulose by A. niger was already described ( Garrigues et al., 2021 ; Kun et al., 2021 ), and is further supported by our growth profile results, showing growth only after long incubation times.…”

“…However, the contribution of the major TFs to the overall degradation of sugar beet pulp by A. niger has not been reported in detail. Transcriptome data of the A. niger reference (CBS 138852) strain showed the preferential use of sugar beet pulp components of this fungus, which correlates with previously reported observations ( Garrigues et al., 2021 ). Our data confirmed that after 2 h, sucrose was the primary carbohydrate of sugar beet pulp utilized by A. niger .…”

“…Sugar beet pulp mainly consists of pectin, cellulose, and xyloglucan ( Thibault and Rouau, 1990 ), as confirmed by the sugar composition analysis ( Table S1 ). The process of sugar beet pulp degradation by A. niger in both solid and liquid cultures has already been reported ( Benoit et al., 2015 ; Garrigues et al., 2021 ). Moreover, the contribution of three major TFs to the degradation of sugar beet pectin was previously assessed (Kowalczyk et al., 2017).…”

“…In contrast, in liquid cultures, the deletion of araR had the strongest effect on the exoproteome after both 8 and 24 h, as evidenced by SDS-PAGE analysis. The phenotypic difference between these mutants is most likely related to the different experimental time courses and culturing conditions, which cannot be directly compared ( Garrigues et al., 2021 ).…”

Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina

“…In fact, previous studies revealed that a variety of culture conditions, e.g., solid vs. liquid, shaken vs. still, and high-density vs. low-density, have an extensive influence on microbial physiology [ 62 , 63 , 64 , 65 ]. In Aspergillus niger , the fungal transcriptomic response to sugar beet pulp was significantly different between solid culture and submerged culture, the latter inducing wider transcriptome variability [ 66 ]. Additionally, the fungal proteome and secretome complexity were affected by the cultivation modes in Aspergillus and Trichoderma species [ 67 , 68 , 69 ].…”