Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose.

BACKGROUND: Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS: We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION: In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.

Understanding the influence of processing conditions on the extraction of rhamnogalacturonan-I "hairy" pectin from sugar beet pulp.

Sugar beet pectin is rich in rhamnogalacturonan-I (RG-I) region, which is a potential source of prebiotics. RG-I pectin cannot be extracted the same way as commercial homogalacturan-rich pectin using hot acid. Therefore, this study has explored several alternative methods, including microwave-assisted extraction (MAE) and conventional-solvent extraction (CSE) at atmospheric pressure using different solvents, and microwave-assisted hydrothermal extraction (MAHE) under pressure using water. No conclusive differences in microwave and conventional heating were found with heating rate controlled. The optimum treatment times of both MAE and CSE at 90 °C atmospheric pressure and regardless of the solvents used were 120 min; however, MAHE at 130 °C under pressure can dramatically reduce the time to 10 min. Alcohol-insoluble solids (AIS) extracted using pH13 solvent by MAE had both the highest RG-I yield at 25.3% and purity at 260.2 mg/g AIS, followed by AIS extracts using water by MAHE with 7.5% and 166.7 mg/g AIS respectively.

Process simulation and life cycle assessment of converting autoclaved municipal solid waste into butanol and ethanol as transport fuels.

In 2015/2016, the total municipal solid waste (MSW) collected by local authority in the U.K. was 26 million tonnes and over 57% is still put into landfill or incinerated. MSW is a promising feedstock for bio-butanol production as it has a high lignocellulosic fibre content such as paper, wood, and food waste, about 50 wt% of a typical MSW stream. The study evaluates acetone, butanol, ethanol and hydrogen production from autoclaved municipal solid waste feedstock. Life cycle assessment is undertaken to evaluate the acetone, butanol, ethanol and hydrogen production process, considering cogeneration of heat and power from residual biogenic waste based on experimental data and process modelling. Acetone, butanol, and ethanol product yield can be achieved at 12.2 kg butanol, 1.5 kg ethanol, 5.7 kg acetone, and 0.9 kg hydrogen per tonne MSW. The product yield is relatively low compared to other lignocellulosic feedstocks primarily because of the lower hydrolysis yield (38% for glucose) achieved in this study; however, hydrolysis yields could be improved in future optimisation work. The conversion shows a net primary energy demand of -1.11 MJ/MJ liquid biofuels (butanol and ethanol) and net greenhouse gas emission of -12.57 g CO2eq/MJ liquid biofuels, achieving a greenhouse gas reduction of 115% compared to gasoline comparator.

Effect of moisture content on thermal and water absorption properties of microfibrillar cellulose with polymeric additives.

The aim of this study was 1) to investigate the influence of polymeric additives such as carboxyl methyl cellulose (CMC) and locust bean gum (LBG) added before and after homogenisation on the moisture uptake of microfibrillar cellulose (MFC) in the dry and semi-wet state; and 2) to further understand the thermally induced structural transitions of low moisture MFC in the presence of the polymeric additives. A higher moisture content in the highly dense MFC network maintains the fibrillated network structure, which is lost during the drying process resulting in MFC aggregates. The addition of polymeric additives results in the regaining of the structure upon redispersion of the dry material with CMC being more effective than LBG). Results also indicated that CMC has a high level of compatibility with MFC, whereas LBG appears to have limited distribution in the MFC dense microfibrillar network and probably exists as a separate phase when added after homogenisation, however co-processing of LBG and cellulose significantly changed this behaviour. The presence of low-temperature transitions in MFC/additives/water mixtures indicates the involvement of these semi-flexible polymeric additives in the formation of liquid crystals when added to MFC in low moisture environments (2% and 20% w/w). An insight is offered into the theory of surface interactions between MFC and polymeric additives, which prevents the agglomeration of microfibrils present in the highly fibrillated suspension upon drying.

Chloroplast-rich material from the physical fractionation of pea vine (Pisum sativum) postharvest field residue (Haulm).

An innovative procedure for plant chloroplasts isolation has been proposed, which consists of juice extraction by physical fractionation from plant material and recovery of its chloroplast-rich fraction (CRF) by centrifugation. This simple method has been applied to pea vine haulm subjected to different post-harvest treatments: blanching, storage at different relative humidity values and fermentation. Additionally, freeze storage of the extracted juice was carried out. The macronutrient (total lipids, proteins, ash and carbohydrates) and micronutrient (fatty acids, chlorophylls, ß-carotene, α-tocopherol and ascorbic acid) content and composition of the CRF have been determined. The CRF isolated from fresh pea vine haulm is a potential source of essential micronutrients (α-linolenic acid, ß-carotene, α-tocopherol) and carbohydrates, whereas the post-harvest treatments trialled have a detrimental effect on the nutritional content. Industrial applications for the recovered nutritionally rich fraction, such as food supplement ingredient or animal feeding, are likely envisaged, while optimising the use of green haulm.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

BACKGROUND: The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. RESULTS: We investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns. CONCLUSIONS: The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.

The kinetics of inhibitor production resulting from hydrothermal deconstruction of wheat straw studied using a pressurised microwave reactor.

BACKGROUND: The use of a microwave synthesis reactor has allowed kinetic data for the hydrothermal reactions of straw biomass to be established from short times, avoiding corrections required for slow heating in conventional reactors, or two-step heating. Access to realistic kinetic data is important for predictions of optimal reaction conditions for the pretreatment of biomass for bioethanol processes, which is required to minimise production of inhibitory compounds and to maximise sugar and ethanol yields. RESULTS: The gravimetric loss through solubilisation of straw provided a global measure of the extent of hydrothermal deconstruction. The kinetic profiles of furan and lignin-derived inhibitors were determined in the hydrothermal hydrolysates by UV analysis, with concentrations of formic and acetic acid determined by HPLC. Kinetic analyses were either carried out by direct fitting to simple first order equations or by numerical integration of sequential reactions. CONCLUSIONS: A classical Arrhenius activation energy of 148 kJmol-1 has been determined for primary solubilisation, which is higher than the activation energy associated with historical measures of reaction severity. The gravimetric loss is primarily due to depolymerisation of the hemicellulose component of straw, but a minor proportion of lignin is solubilised at the same rate and hence may be associated with the more hydrophilic lignin-hemicellulose interface. Acetic acid is liberated primarily from hydrolysis of pendant acetate groups on hemicellulose, although this occurs at a rate that is too slow to provide catalytic enhancement to the primary solubilisation reactions. However, the increase in protons may enhance secondary reactions leading to the production of furans and formic acid. The work has suggested that formic acid may be formed under these hydrothermal conditions via direct reaction of sugar end groups rather than furan breakdown. However, furan degradation is found to be significant, which may limit ultimate quantities generated in hydrolysate liquors.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.

BACKGROUND: Saprobic 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. RESULTS: In 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. CONCLUSIONS: By 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.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.

BACKGROUND: Saprobic 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. RESULTS: In 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. CONCLUSIONS: By 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.

Structural reorganisation of cellulose fibrils in hydrothermally deconstructed lignocellulosic biomass and relationships with enzyme digestibility.

BACKGROUND: The investigation of structural organisation in lignocellulose materials is important to understand changes in cellulase accessibility and reactivity resulting from hydrothermal deconstruction, to allow development of strategies to maximise bioethanol process efficiencies. To achieve progress, wheat straw lignocellulose and comparative model wood cellulose were characterised following increasing severity of hydrothermal treatment. Powder and fibre wide-angle X-ray diffraction techniques were employed (WAXD), complemented by enzyme kinetic measurements up to high conversion. RESULTS: Evidence from WAXD indicated that cellulose fibrils are not perfectly crystalline. A reduction in fibril crystallinity occurred due to hydrothermal treatment, although dimensional and orientational data showed that fibril coherency and alignment were largely retained. The hypothetical inter-fibril spacing created by hydrothermal deconstruction of straw was calculated to be insufficient for complete access by cellulases, although total digestion of cellulose in both treated straw and model pulp was observed. Both treated straw and model pulps were subjected to wet mechanical attrition, which caused separation of smaller fibril aggregates and fragments, significantly increasing enzyme hydrolysis rate. No evidence from WAXD measurements was found for preferential hydrolysis of non-crystalline cellulose at intermediate extent of digestion, for both wood pulp and hydrothermally treated straw. CONCLUSIONS: The increased efficiency of enzyme digestion of cellulose in the lignocellulosic cell wall following hydrothermal treatment is a consequence of the improved fibril accessibility due to the loss of hemicellulose and disruption of lignin. However, incomplete accessibility of cellulase at the internal surfaces of fibrillar aggregates implies that etching type mechanisms will be important in achieving complete hydrolysis. The reduction in crystalline perfection following hydrothermal treatment may lead to an increase in fibril reactivity, which could amplify the overall improvement in rate of digestion due to accessibility gains. The lack of preferential digestion of non-crystalline cellulose is consistent with the existence of localised conformational disorder, at surfaces and defects, according to proposed semicrystalline fibril models. Cellulases may not interact in a fully selective manner with such disordered environments, so fibril reactivity may be considered as a function of average conformational states.

Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.

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.

The mechanisms of hydrothermal deconstruction of lignocellulose: new insights from thermal-analytical and complementary studies.

Differential Scanning Calorimetry, Dynamic Mechanical Thermal Analysis, gravimetric and chemical techniques have been used to study hydrothermal reactions of straw biomass. Exothermic degradation initiates above 195 °C, due to breakdown of the xylose ring from hemicellulose, which may be similar to reactions occurring during the early stage pyrolysis of dry biomass, though activated at lower temperature through water mediation. The temperature and magnitude of the exotherm reduce with increasing acid concentration, suggesting a reduction in activation energy and a change in the balance of reaction pathways. The presence of xylan oligomers in auto-catalytic hydrolysates is believed to be due to a low rate constant rather than a specific reaction mechanism. The loss of the lignin glass transition indicates that the lignin phase is reorganised under high temperature auto-catalytic conditions, but remains partially intact under lower temperature acid-catalytic conditions. This shows that lignin degradation reactions are activated thermally but are not effectively catalysed by aqueous acid.

Solvent effects on starch dissolution and gelatinization.

The disruption of starch granular structure during dissolution in varying concentrations of N-methyl morpholine N-oxide (NMMO) has been studied using three maize starches with varying ratios of amylose and amylopectin. Behavior in NMMO has been characterized by differential scanning calorimetry (DSC), microscopy, rapid viscosity analysis (RVA), and rheometry. Exothermic transitions were observed for the three starches in both 78 and 70% NMMO; the transition changed to an endotherm at 60 and 50% NMMO. Consistent with DSC, hot stage microscopy showed that starch granules dissolved at NMMO concentrations of 78 and 70%, whereas in 60 and 50% NMMO, gelatinization behavior similar to that found for starch in water was observed. Mechanical spectroscopy revealed the dominant viscous behavior (G″ > G') of starch at NMMO concentrations of 70 and 78% and more elastic behavior (G' > G″) at lower concentrations. Starch solutions in 78% NMMO obey the Cox-Merz rule, suggesting that the solutions are homogeneous on a molecular level.

Molecular and crystal deformation of cellulose: uniform strain or uniform stress?

The molecular and crystal deformations of a range of lyocell cellulose fibres, produced using different drawing conditions, are reported. The fibres are spun using increasing draw ratios to both increase the molecular and crystal orientation and, consequently, mechanical stiffness. Raman spectroscopy and X-ray diffraction are used to follow molecular and crystal deformation, respectively. It is shown that these techniques are complementary, and that both must be used for semicrystalline cellulose fibres if a full picture of their micromechanics is to be obtained. By following the shift in the 1095 cm(-1) Raman band with respect to external tensile deformation of the fibres we show that we can build up a picture of the microstructure. Using theoretical predictions of the relationship between the Raman band shift rates with respect to strain and stress and the modulus of the fibres we show that the fibres have properties that suggest a hybrid series-series aggregate structure. By using X-ray diffraction we show that the crystal modulus of the fibres appears to change with increasing draw ratio. Furthermore the crystal modulus of the fibres appears to vary systematically with the crystallinity of the sample. Other relationships between the predicted fibre modulus and the experimental values and between the Raman band shift rates and modulus suggest that the assumption of a uniform stress microstructure prior to the measurement of crystal modulus may be an incorrect one. A more realistic structure is proposed for semicrystalline regenerated cellulose fibres, wherein crystals and amorphous regions are both in series and in parallel with each other.

Influence of domain orientation on the mechanical properties of regenerated cellulose fibers.

The determination of the crystal orientation of regenerated cellulose fibers produced under different drawing regimes is presented. Orientation is determined by using wide-angle X-ray diffraction from a synchrotron source and by measuring the azimuthal width of equatorial reflections. The orientation parameter theta is then determined to compare fiber samples. By using a 500 nm beam size, clear differences between the crystal orientations of the skin and the core of the fibers are reported for a range of differently processed fibers for the first time. These results are shown to have implications for the mechanical properties of regenerated cellulose fibers. By applying tensile deformation to fiber bundles it is shown that the most misoriented samples undergo rapid decreases in the orientation parameter, which is an indication of crystal reorientation. However, the more highly oriented fibers undergo little reorientation. An average shear modulus for these fibers is determined by placing the data on a master curve and fitting with a model equation. By using another model for the fibers of low orientation and the shear modulus from the master curve analysis, it is shown that the deformation of less oriented fibers is dominated by shear between crystals, whereas the more oriented filaments are likely to undergo more significant chain deformation. By using a new model for fibers of low orientation, a parameter ksigma is introduced that gives the proportion of the fiber stress that is due to crystal shear. Systematic differences between this parameter for fibers of increasing initial orientation are reported. Moreover it is shown that the fibers of initially lower average orientation are governed by uniform strain, in agreement with the new model, whereas more highly oriented fibers deform under uniform stress. Furthermore, the model that we propose for misoriented domains and the use of a new factor dictating the proportion of shear stress may have general applications in materials engineering.