A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall–degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

Graphical abstractHighlights► Thermal analysis provides real-time data on hydrothermal reactions under realistic conditions. ► From DSC, hemicellulose hydrolysis has low enthalpy change but xylose degradation is exothermic. ► Hydrothermal exothermic degradation reactions may be similar to early stage biomass pyrolysis. ► DMTA shows that the polymeric structure of lignin in biomass is degraded at high temperatures. ► Hydrothermal reactions are effective at greater than 50% solids content.

Inhibitors released by the breakdown of plant cell walls prevent efficient conversion of sugar into ethanol. The aim of this study was to develop a fast and reliable inhibitor sensitivity assay for ethanologenic yeast strains. The assay comprised bespoke 96-well plates containing inhibitors in isolation or combination in a format that was compatible with the Phenotypic Microarray Omnilog reader (Biolog, hayward, CA, USA). A redox reporter within the assay permits analysis of inhibitor sensitivity in aerobic and/or anaerobic conditions. Results from the assay were verified using growth on spot plates and tolerance assays in which maintenance of viability was assessed. The assay allows for individual and synergistic effects of inhibitors to be determined. It was observed that the presence of both acetic and formic acid significantly inhibited the yeast strains assessed, although this impact could be partially mitigated by buffering to neutral pH. Scheffersomyces stipitis, Candida spp., and Pichia guilliermondii demonstrated increased sensitivity to short chain weak acids at concentrations typically present in lignocellulosic hydrolysates. S. cerevisiae exhibited robustness to short chain weak acids at these concentrations. However, S. stipitis, Candida spp., and P. guilliermondii displayed increased tolerance to HMF when compared to that observed for S. cerevisiae. The results demonstrate that the phenotypic microarray assay developed in the current study is a valuable tool that can be used to identify yeast strains with desirable resistance to inhibitory compounds found in lignocellulosic hydrolysates.

BackgroundSaprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers.ResultsIn this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study.ConclusionsBy comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.

Samples of ball milled cellulose were prepared by ball milling pulps from eucalyptus and softwood (spruce/pine). Water sorption isotherms were obtained by both dynamic vapor sorption and equilibration over saturated salt solutions, in the water content range of 5-42% db (db = dry basis; water as a % age of total solids). Dynamic mechanical analysis using a pocket technique showed a water content dependent thermal transition occurring at the same temperature for the two pulp samples, which was interpreted as a glass transition. Fitting the data to a Couchman-Karasz relationship predicted a value for T g of the dry cellulose of approximately 478 K, which was similar to values previously reported for other dry polysaccharides. No clear glass transition could be observed calorimetrically, although an endotherm at approximately 333 K was measured, which in polymers is normally attributed to enthalpic relaxation, however the lack of dependence of this endotherm on water content suggests that the melting of some weak associations, such as residual hydrogen bonds, could be a more credible explanation. An exotherm was also observed on heating, which was dependent on water content and which was attributed to partial crystallization of the cellulose. This was confirmed by Wide angle X-ray diffraction and cross polarization magic angle spinning 13C NMR (CPMAS NMR). The recrystallisation was predominantly to form I of cellulose. This was thought to be caused by a small amount of residual form I (probably less than 5%) acting as a template for the crystallizing material. Differential scanning calorimetry reheat curves showed the appearance of freezable water for water contents higher than 20%, as a result of a transfer of water to the amorphous phase following crystallization. The increase in cellulose rigidity following crystallization was also confirmed by CPMAS NMR relaxation. Low resolution proton NMR T 2 relaxation suggested the presence of proton water/cellulose exchange, which was active at water contents of 20% and above