Comparison of the growth of filamentous fungi and yeasts in lignocellulose-derived media

Synthetic biology approaches to improve tolerance of inhibitors in lignocellulosic hydrolysates

Increasing attention is being focused on using lignocellulose for valuable products. Microbial decomposition can convert lignocellulose into renewable biofuels and other high-value bioproducts, contributing to sustainable development. However, the presence of inhibitors in lignocellulosic hydrolysates can negatively affect microorganisms during fermentation. Improving microbial tolerance to these hydrolysates is a major focus in metabolic engineering. Traditional detoxification methods increase costs, so there is a need for cheap and efficient cell-based detoxification strategies. Synthetic biology approaches offer several strategies for improving microbial tolerance, including redox balancing, membrane engineering, omics-guided technologies, expression of protectants and transcription factors, irrational engineering, cell flocculation, and other novel technologies. Advances in molecular biology, high-throughput sequencing, and artificial intelligence (AI) allow for precise strain modification and efficient industrial production. Developing AI-based computational models to guide synthetic biology efforts and creating large-scale heterologous libraries with automation and high-throughput technologies will be important for future research.

Metabolic Engineering of Komagataella phaffii for Xylose Utilization from Cellulosic Biomass

Cellulosic biomass hydrolysates are rich in glucose and xylose, but most microorganisms, including Komagataella phaffii, are unable to utilize xylose effectively. To address this limitation, we engineered a K. phaffii strain optimized for xylose metabolism through the xylose oxidoreductase pathway and promoter optimization. A promoter library with varying strengths was used to fine-tune the expression levels of the XYL1, XYL2, and XYL3 genes, resulting in a strain with a strong promoter for XYL2 and weaker promoters for XYL1 and XYL3. This engineered strain exhibited superior growth, achieving 14 g cells/L and a maximal growth rate of 0.4 g cells/L-h in kenaf hydrolysate, outperforming a native strain by 17%. This study is the first to report the introduction of the xylose oxidoreductase pathway into K. phaffii, demonstrating its potential as an industrial platform for producing yeast protein and other products from cellulosic biomass.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

Fungal Lignocellulose Utilisation Strategies from a Bioenergetic Perspective: Quantification of Related Functional Traits Using Biocalorimetry

In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, and zygomycete species, were investigated in a standardised laboratory environment, employing wheat straw as a globally relevant lignocellulosic substrate. Our study demonstrates that biocalorimetry can be employed successfully to determine growth-related fungal activity parameters, such as apparent maximum growth rates (AMGR), cultivation times until the observable onset of fungal growth at AMGR (tAMGR), quotients formed from the AMGR and tAMGR (herein referred to as competitive growth potential, CGP), and heat yield coefficients (YQ/X), the latter indicating the degree of resource investment into fungal biomass versus other functional attributes. These parameters seem suitable to link fungal potentials for biomass production to corresponding ecological strategies employed during resource utilisation, and therefore may be considered as fungal life history traits. A close connection exists between the CGP and YQ/X values, which suggests an interpretation that relates to fungal life history strategies.

Engineering multifunctional enzymes for agro-biomass utilization

Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.

Applicability and information value of biocalorimetry for the monitoring of fungal solid-state fermentation of lignocellulosic agricultural by-products

The applicability of biocalorimetry for monitoring fungal conversion of lignocellulosic agricultural by-products during solid-state fermentation (SSF) was substantiated through linking the non-invasive measurement of metabolic heat fluxes to conventional invasive determination of fungal activity (growth, substrate degradation, enzyme activity) parameters. For this, the fast-growing, cellulose-utilising ascomycete Stachybotrys chlorohalonata and the comparatively slow-growing litter-decay basidiomycete Stropharia rugosoannulata were investigated as model organisms during growth on solid wheat straw. Both biocalorimetric and non-calorimetric data may suggest R (ruderal)- and C (combative)-selected life history strategies in S. chlorohalonata and S. rugosoannulata, respectively. For both species, a strong linear correlation of the released metabolic heat with the corresponding fungal biomass was observed. Species-specific Y_Q/X values (metabolic heat released per fungal biomass unit) were obtained, which potentially enable use of biocalorimetric signals for the quantification of fungal biomass during single-species SSF processes. Moreover, Y_Q/X values may also indicate different fungal life history strategies and therefore be considered as useful parameters aiding fungal ecology research.

Evaluation of Nutritional Composition of Pure Filamentous Fungal Biomass as a Novel Ingredient for Fish Feed

The rapid growth of aquaculture and the lack of fish meal demand new sustainable ingredients. Although fungal biomass is found to be a promising sustainable fish feed supplementation candidate, the characteristics of this protein-rich source are closely influenced by the quality of the applied growth medium. In this work, the nutritional properties of pure filamentous fungal biomass provided from the cultivation of Aspergillus oryzae, Neurospora intermedia and Rhzopus oryzae were evaluated to assess their potential as alternative novel protein sources in fish feed. In this regard, fungal biomass yields of up to 0.19 ± 0.005 (g dry biomass/g substrate glucose) were obtained during submerged cultivation of fungal strains. The pure fungal biomass acquired could contain significant amounts of protein up to 62.2 ± 1.2% (w/w). The obtained protein had a high quality with notable inclusion of essential amino acids such as lysine, arginine, methionine and threonine with comparable concentrations to those of fish meal. Fungal biomass is mainly considered as protein source, however, entitlement of 6.9 ± 0.5, 4.0 ± 0.7 and 17.2 ± 1.1% (w/w) of lipids and ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA) of 1.37:1, 1.74:1 and 1.47:1 in A. oryzae, N. intermedia and R. oryzae, respectively, signal health benefits for the fish. Considering the results, protein-rich pure fungal biomass with amino acid composition is greatly compatible with fish meal, and contains essential nutrients such as fatty acids and minerals. This pure biomass constitutes a promising sustainable alternative supplement to be introduced in fish feed industry.

Antioxidant Production in Dunaliella

Microalgae have become an attractive natural source of a diverse range of biomolecules, including enzymatic and non-enzymatic antioxidants; nevertheless, economically sustainable production of such compounds from microalgae biomass is still challenging. The main hurdles are: (a) increasing microalgae yield; (b) achieving optimal cultivation conditions; (c) energy-efficient and cost-effective downstream processing (extraction and purification); (d) optimal storage of post-processed antioxidant molecules. This review provides a detailed overview of enzymatic and non-enzymatic antioxidants in the cellular metabolism of the commercially important microalgae Dunaliella, industrial applications of antioxidant enzymes, strategies to enhanced antioxidant accumulation in cells, and the opportunities and limitations of current technologies for antioxidant enzymes production from microalgae biomass as an alternative to common microbial sources.

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

Consolidated bioprocesses for efficient bioconversion of palm biomass wastes into biodiesel feedstocks by oleaginous fungi and yeasts

Consolidated bioprocesses for bioconversion of lignocellulosic biomass into biodiesel feedstocks were developed. Palm empty fruit bunch (EFB) was biologically pretreated coupling with fungal lipid production (121.4 ± 2.7 mg/g-EFB) by lignocellulolytic oleaginous fungi prior to lipid production by oleaginous yeasts. In subsequent separate hydrolysis and fermentation (SHF) of fungal pretreated EFB (FPEFB), the oleaginous yeast with the maximum lipid yield of 37.0 ± 0.1 mg/g-FPEFB was screened. While a higher lipid yield of 47.9 ± 1.5 mg/g-FPEFB was achieved in simultaneous saccharification and fermentation (SSF) with less enzyme requirement. Fed-batch SSF of non-sterile FPEFB was proven as a practical and efficient strategy to increase lipid yield up to 53.4 ± 0.5 mg/g-FPEFB. Total lipid yield by both fungi and yeast was 165.0 ± 4.4 mg/g-EFB. Interestingly, the consolidated bioprocesses of enzyme and lipid production also achieved comparable total lipid yield of 149.3 ± 6.6 mg/g-EFB. These strategies may contribute greatly to cost-effective and sustainable bioconversion of lignocellulosic biomass into biodiesel feedstocks.

Genetic Engineering of Filamentous Fungi for Efficient Protein Expression and Secretion

Filamentous fungi are considered as unique cell factories for protein production due to the high efficiency of protein secretion and superior capability of post-translational modifications. In this review, we firstly introduce the secretory pathway in filamentous fungi. We next summarize the current state-of-the-art works regarding how various genetic engineering strategies are applied for enhancing protein expression and secretion in filamentous fungi. Finally, in a future perspective, we discuss the great potential of genome engineering for further improving protein expression and secretion in filamentous fungi.

Production of Aspergillus niger biomass on sugarcane distillery wastewater: physiological aspects and potential for biodiesel production

Background

Sugarcane distillery waste water (SDW) or vinasse is the residual liquid waste generated during sugarcane molasses fermentation and alcohol distillation. Worldwide, this effluent is responsible for serious environmental issues. In Reunion Island, between 100 and 200 thousand tons of SDW are produced each year by the three local distilleries. In this study, the potential of Aspergillus niger to reduce the pollution load of SDW and to produce interesting metabolites has been investigated.

Results

The fungal biomass yield was 35 g L⁻¹ corresponding to a yield of 0.47 g of biomass/g of vinasse without nutrient complementation. Analysis of sugar consumption indicated that mono-carbohydrates were initially released from residual polysaccharides and then gradually consumed until complete exhaustion. The high biomass yield likely arises from polysaccharides that are hydrolysed prior to be assimilated as monosaccharides and from organic acids and other complex compounds that provided additional C-sources for growth. Comparison of the size exclusion chromatography profiles of raw and pre-treated vinasse confirmed the conversion of humic- and/or phenolic-like molecules into protein-like metabolites. As a consequence, chemical oxygen demand of vinasse decreased by 53%. Interestingly, analysis of intracellular lipids of the biomass revealed high content in oleic acid and physical properties relevant for biodiesel application.

Conclusions

The soft-rot fungus A. niger demonstrated a great ability to grow on vinasse and to degrade this complex and hostile medium. The high biomass production is accompanied by a utilization of carbon sources like residual carbohydrates, organic acids and more complex molecules such as melanoidins. We also showed that intracellular lipids from fungal biomass can efficiently be exploited into biodiesel.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0045-6) contains supplementary material, which is available to authorized users.