Consolidated bioprocessing strategy for ethanol production from Jerusalem artichoke tubers by Kluyveromyces marxianus under high gravity conditions

Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation

Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.

Biotechnology and Bioprocesses: Their Contribution to Sustainability

Significant advancements in biotechnology have resulted in the development of numerous fundamental bioprocesses, which have consolidated research and development and industrial progress in the field. These bioprocesses are used in medical therapies, diagnostic and immunization procedures, agriculture, food production, biofuel production, and environmental solutions (to address water-, soil-, and air-related problems), among other areas. The present study is a first approach toward the identification of scientific and technological bioprocess trajectories within the framework of sustainability. The method included a literature search (Scopus), a patent search (Patentscope), and a network analysis for the period from 2010 to 2019. Our results highlight the main technological sectors, countries, institutions, and academic publications that carry out work or publish literature related to sustainability and bioprocesses. The network analysis allowed for the identification of thematic clusters associated with sustainability and bioprocesses, revealing different related scientific topics. Our conclusions confirm that biotechnology is firmly positioned as an emerging knowledge area. Its dynamics, development, and outcomes during the study period reflect a substantial number of studies and technologies focused on the creation of knowledge aimed at improving economic development, environmental protection, and social welfare.

Lignocellulosic biomass for bioethanol: an overview on pretreatment, hydrolysis and fermentation processes

Bioethanol is currently the only alternative to gasoline that can be used immediately without having to make any significant changes in the way fuel is distributed. In addition, the carbon dioxide (CO2) released during the combustion of bioethanol is the same as that used by the plant in the atmosphere for its growth, so it does not participate in the increase of the greenhouse effect. Bioethanol can be obtained by fermentation of plants containing sucrose (beet, sugar cane…) or starch (wheat, corn…). However, large-scale use of bioethanol implies the use of very large agricultural surfaces for maize or sugarcane production. Lignocellulosic biomass (LCB) such as agricultural residues for the production of bioethanol seems to be a solution to this problem due to its high availability and low cost even if its growth still faces technological difficulties. In this review, we present an overview of lignocellulosic biomass, the different methods of pre-treatment of LCB and the various fermentation processes that can be used to produce bioethanol from LCB.

Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation

The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.

Identification of hexose kinase genes in Kluyveromyces marxianus and thermo-tolerant one step producing glucose-free fructose strain construction

In yeast, the hexose assimilation is started at hexose phosphorylation. However, in Kluyveromyces marxianus, the hexokinase (HXK) and glucokinase (GLK) genes were not identified by experiments. Meanwhile, the glucose-free fructose product requires more cost-efficient method. In this study, the KmHXK1 and KmGLK1 genes were functionally identified through gene disruption, over-expression and recombinant enzymes characterization. Both glucose and fructose assimilation ability decreased significantly in KmHXK1 disrupted strain YLM001, however, this ability was not changed obviously in KmGLK1 disrupted strain YLM002. When over-expressing KmGLK1 in YLM001, only the glucose assimilation ability was recovered in obtained strain (YLM005). The kinetic constant analysis of recombinant enzymes also proved that KmHXK1 could phosphorylate glucose (Vmax 553.01 U/mg, Km 0.83 mM) and fructose (Vmax 609.82 U/mg, Km 0.52 mM), and KmGLK1 only phosphorylate glucose with a Vmax of 0.73 U/mg and a Km 4.09 mM. A thermo-tolerant strain YGR003 which produced glucose-free fructose from Jerusalem artichoke tuber in one step was constructed based on the obtained information. The highest production and fastest productivity were 234.44 g/L and 10.26 g/L/h, respectively, which were several folds of the results in previous reports.

Utilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals

Inulins are polysaccharides that belong to an important class of carbohydrates known as fructans and are used by many plants as a means of storing energy. Inulins contain 20 to several thousand fructose units joined by β-2,1 glycosidic bonds, typically with a terminal glucose unit. Plants with high concentrations of inulin include: agave, asparagus, coffee, chicory, dahlia, dandelion, garlic, globe artichoke, Jerusalem artichoke, jicama, onion, wild yam, and yacón. To utilize inulin as its carbon and energy source directly, a microorganism requires an extracellular inulinase to hydrolyze the glycosidic bonds to release fermentable monosaccharides. Inulinase is produced by many microorganisms, including species of Aspergillus, Kluyveromyces, Penicillium, and Pseudomonas. We review various inulinase-producing microorganisms and inulin feedstocks with potential for industrial application as well as biotechnological efforts underway to develop sustainable practices for the disposal of residues from processing inulin-containing crops. A multi-stage biorefinery concept is proposed to convert cellulosic and inulin-containing waste produced at crop processing operations to valuable biofuels and bioproducts using Kluyveromyces marxianus, Yarrowia lipolytica, Rhodotorula glutinis, and Saccharomyces cerevisiae as well as thermochemical treatments.

Consolidated ethanol production from Jerusalem artichoke tubers at elevated temperature by Saccharomyces cerevisiae engineered with inulinase expression through cell surface display

Ethanol fermentation from Jerusalem artichoke tubers was performed at elevated temperatures by the consolidated bioprocessing strategy using Saccharomyces cerevisiae MK01 expressing inulinase through cell surface display. No significant difference was observed in yeast growth when temperature was controlled at 38 and 40 °C, respectively, but inulinase activity with yeast cells was substantially enhanced at 40 °C. As a result, enzymatic hydrolysis of inulin was facilitated and ethanol production was improved with 89.3 g/L ethanol produced within 72 h from 198.2 g/L total inulin sugars consumed. Similar results were also observed in ethanol production from Jerusalem artichoke tubers with 85.2 g/L ethanol produced within 72 h from 185.7 g/L total sugars consumed. On the other hand, capital investment on cooling facilities and energy consumption for running the facilities would be saved, since regular cooling water instead of chill water could be used to cool down the fermentation system.

Growth, ethanol production, and inulinase activity on various inulin substrates by mutant Kluyveromyces marxianus strains NRRL Y-50798 and NRRL Y-50799

Economically important plants contain large amounts of inulin. Disposal of waste resulting from their processing presents environmental issues. Finding microorganisms capable of converting inulin waste to biofuel and valuable co-products at the processing site would have significant economic and environmental impact. We evaluated the ability of two mutant strains of Kluyveromyces marxianus (Km7 and Km8) to utilize inulin for ethanol production. In glucose medium, both strains consumed all glucose and produced 0.40 g ethanol/g glucose at 24 h. In inulin medium, Km7 exhibited maximum colony forming units (CFU)/mL and produced 0.35 g ethanol/g inulin at 24 h, while Km8 showed maximum CFU/mL and produced 0.02 g ethanol/g inulin at 96 h. At 24 h in inulin + glucose medium, Km7 produced 0.40 g ethanol/g (inulin + glucose) and Km8 produced 0.20 g ethanol/g (inulin + glucose) with maximum CFU/mL for Km8 at 72 h, 40 % of that for Km7 at 36 h. Extracellular inulinase activity at 6 h for both Km7 and Km8 was 3.7 International Units (IU)/mL.

Engineering a natural Saccharomyces cerevisiae strain for ethanol production from inulin by consolidated bioprocessing

BACKGROUND

The yeast Saccharomyces cerevisiae is an important eukaryotic workhorse in traditional and modern biotechnology. At present, only a few S. cerevisiae strains have been extensively used as engineering hosts. Recently, an astonishing genotypic and phenotypic diversity of S. cerevisiae was disclosed in natural populations. We suppose that some natural strains can be recruited as superior host candidates in bioengineering. This study engineered a natural S. cerevisiae strain with advantages in inulin utilization to produce ethanol from inulin resources by consolidated bioprocess. Rational engineering strategies were employed, including secretive co-expression of heterologous exo- and endo-inulinases, repression of a protease, and switch between haploid and diploid strains.

RESULTS

Results from co-expressing endo- and exo-inulinase genes showed that the extracellular inulinase activity increased 20 to 30-fold in engineered S. cerevisiae strains. Repression of the protease PEP4 influenced cell physiology in late stationary phase. Comparison between haploid and diploid engineered strains indicated that diploid strains were superior to haploid strains in ethanol production albeit not in production and secretion of inulinases. Ethanol fermentation from both inulin and Jerusalem artichoke tuber powder was dramatically improved in most engineered strains. Ethanol yield achieved in the ultimate diploid strain JZD-InuMKCP was close to the theoretical maximum. Productivity achieved in the strain JZD-InuMKCP reached to 2.44 and 3.13 g/L/h in fermentation from 200 g/L inulin and 250 g/L raw Jerusalem artichoke tuber powder, respectively. To our knowledge, these are the highest productivities reported up to now in ethanol fermentation from inulin resources.

CONCLUSIONS

Although model S. cerevisiae strains are preferentially used as hosts in bioengineering, some natural strains do have specific excellent properties. This study successfully engineered a natural S. cerevisiae strain for efficient ethanol production from inulin resources by consolidated bioprocess, which indicated the feasibility of natural strains used as bioengineering hosts. This study also presented different properties in enzyme secretion and ethanol fermentation between haploid and diploid engineering strains. These findings provided guidelines for host selection in bioengineering.

Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system

BACKGROUND

The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum.

RESULTS

Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins.

CONCLUSIONS

Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification in parallel with the synergistic system of various polysaccharide-degrading enzymes. Furthermore, the complex enzyme system of S. commune holds significant potential for application in biomass saccharification. These discoveries will help unveil the diversity of natural lignocellulose-degrading mechanisms, and advance the design of more efficient enzyme mixtures for the deconstruction of lignocellulosic feedstocks.

Direct ethanol production from starch using a natural isolate, Scheffersomyces shehatae: Toward consolidated bioprocessing

Consolidated bioprocessing (CBP), which integrates enzyme production, saccharification and fermentation into a one-step process, is a promising strategy for cost-effective ethanol production from starchy biomass. To gain insights into starch-based ethanol production using CBP, an extensive screening was undertaken to identify naturally occurring yeasts that produce ethanol without the addition of any amylases. Three yeast strains were capable of producing a significant amount of ethanol. Quantitative assays revealed that Scheffersomyces shehatae JCM 18690 was the strain showing the highest ethanol production ability. This strain was able to utilize starch directly, and the ethanol concentration reached 9.21 g/L. We attribute the ethanol-producing ability of this strain to the high levels of glucoamylase activity, fermentation potential and ethanol stress tolerance. This study strongly suggests the possibility of starch-based ethanol production by consolidated bioprocessing using natural yeasts such as S. shehatae JCM 18690.

The prospects of Jerusalem artichoke in functional food ingredients and bioenergy production

Jerusalem artichoke, a native plant to North America has recently been recognized as a promising biomass for bioeconomy development, with a number of advantages over conventional crops such as low input cultivation, high crop yield, wide adaptation to climatic and soil conditions and strong resistance to pests and plant diseases. A variety of bioproducts can be derived from Jerusalem artichoke, including inulin, fructose, natural fungicides, antioxidant and bioethanol. This paper provides an overview of the cultivation of Jerusalem artichoke, derivation of bioproducts and applicable production technologies, with an expectation to draw more attention on this valuable crop for its applications as biofuel, functional food and bioactive ingredient sources.

Transcriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology

BACKGROUND

Ethanol production from non-crop materials, such as Jerusalem artichokes, would make a great contribution to the energy industry. The non-conventional yeast, Kluyveromyces marxianus, is able to carry out ethanol fermentation of sugar molecules obtained from inulin-containing materials by consolidated bioprocessing. Lower inulin concentrations and micro-aeration can lead to a relatively fast and ideal fermentation process; however, it is unclear what causes the inhibition of higher concentrations of inulin and the promotion effect of aeration.

RESULTS

Next-generation sequencing technology was used to study the global transcriptional response of K. marxianus Y179 under three fermentation conditions, including 120 g/L inulin without aeration (120-N), 230 g/L inulin without aeration (230-N), 230 g/L inulin with aeration by ORP controlling at -130 mV (230-130mV). A total of 35.55 million clean reads were generated from three samples, of which 4,820 predicted that open reading frames were annotated. For differential expression analysis, 950 and 1,452 differentially expressed genes were discovered under the conditions of 230-130mV and 120-N, respectively, and the sample 230-N was used as the control. These genes are mainly associated with the pathways of central carbon metabolism and ethanol formation. Increased expression of inulinase and the low activity of the autophagy-related gene, ATG8, ensured fast and ideal fermentation processes.

CONCLUSIONS

Despite being reported as the "crabtree-negative" species, K. marxianus Y179 could achieve favorable ethanol fermentation profiles under micro-aeration and high inulin concentrations. K. marxianus Y179 cells responded to inulin concentrations and micro-aeration that is involved in the whole ethanol metabolism network. These results will serve as an important foundation for further exploration of the regulatory mechanisms involved in ethanol fermentation from inulin by consolidated bioprocessing and also provide a valuable reference for future studies on optimization and reconstruction of the metabolism network in K. marxianus.

Synergy of crude enzyme cocktail from cold-adapted Cladosporium cladosporioides Ch2-2 with commercial xylanase achieving high sugars yield at low cost

BACKGROUND

The efficiency and cost of current lignocellulosic enzymes still limit the large-scale production of cellulosic ethanol in industry. Residual lignin after pretreatment severely depresses the activity of polysaccharide hydrolases and the h ydrolysis of holocellulose. If we include in hydrolase mixture construction the ligninase involved in lignin degradation, which mainly includes laccase, manganese peroxidases (MnP) and lignin peroxidase (LiP), it is feasible that this could greatly improve the fermentable sugars yield.

RESULTS

The psychrophilic lignocellulosic enzymes system of Cladosporium cladosporioides Ch2-2 including ligninase and polysaccharide hydrolases was suitable for selective delignification and efficient saccharification of biomass with wide thermal adaptability. The purified laccase was optimally active at 15°C and pH 3.5, exhibiting high thermostability over a broad range of temperatures (between 4 and 40°C). In addition, manganese-independent peroxidase (MIP), a special type of ligninase with the capacity to oxidize dimethyl phthalate (DMP) in the absence of H2O2 and Mn(2+), was optimally active at 20°C and pH 2.5, exhibiting high thermostability over a broad range of temperatures (4 and 28°C), while depressed completely by Fe(2+) and essentially unaffected by EDTA. Synergy between Ch2-2 crude enzymes and commercial xylanase obviously enhanced biomass hydrolysis, which could take the place of expensive commercial cellulase mixture. The maximum value of synergistic degree reached 4.7 at 28°C, resulting in 10.1 mg/mL reducing sugars.

CONCLUSIONS

The psychrophilic enzymes system of C. cladosporioides Ch2-2 with a different synergistic mechanism has huge potential for the enhancement of biomass hydrolysis at mesophilic and low temperatures. The application scope of the lignocellulosic enzyme cocktail could be greatly enlarged by optimizing the operation conditions specific to the characteristics of ligninase.

Consolidated bioprocessing of highly concentrated Jerusalem artichoke tubers for simultaneous saccharification and ethanol fermentation

Consolidated bioprocessing (CBP) of Jerusalem artichoke tuber (Jat) for ethanol production is one of the most promising options for an alternate biofuel technology development. The technical barriers include the weak saccharolytic enzyme (inulinase) activity of the fermentation strain, and the well mixing of the high viscous fermentation slurry at the highly concentrated Jat loading. In this study, Saccharomyces cerevisiae DQ1 was found to produce relatively large amount of inulinase for hydrolysis of inulin in Jat, and the helical ribbon stirring bioreactor used provided well mixing performance under the high Jat loading. Even a highly concentrated Jat loading up to 35% (w/w) in the helical ribbon bioreactor for CBP was allowed. The results obtained from this study have demonstrated a feasibility of developing a CBP process technology in the helical ribbon bioreactor for ethanol production at a high yield 128.7 g/L and the theoretical yield 73.5%, respectively. This level of ethanol yield from Jat is relatively higher than others reported so far. The results of this study could provide a practical CBP process technology in the helical ribbon bioreactor for economically sustainable alternate biofuel production using highly concentrated inulin containing biomass feedstock such as Jat, at least 35%.

Invertase SUC2 Is the key hydrolase for inulin degradation in Saccharomyces cerevisiae

Specific Saccharomyces cerevisiae strains were recently found to be capable of efficiently utilizing inulin, but genetic mechanisms of inulin hydrolysis in yeast remain unknown. Here we report functional characteristics of invertase SUC2 from strain JZ1C and demonstrate that SUC2 is the key enzyme responsible for inulin metabolism in S. cerevisiae.

Thermotolerant Kluyveromyces marxianus and Saccharomyces cerevisiae strains representing potentials for bioethanol production from Jerusalem artichoke by consolidated bioprocessing

Thermotolerant inulin-utilizing yeast strains are desirable for ethanol production from Jerusalem artichoke tubers by consolidated bioprocessing (CBP). To obtain such strains, 21 naturally occurring yeast strains isolated by using an enrichment method and 65 previously isolated Saccharomyces cerevisiae strains were investigated in inulin utilization, extracellular inulinase activity, and ethanol fermentation from inulin and Jerusalem artichoke tuber flour at 40 °C. The strains Kluyveromyces marxianus PT-1 (CGMCC AS2.4515) and S. cerevisiae JZ1C (CGMCC AS2.3878) presented the highest extracellular inulinase activity and ethanol yield in this study. The highest ethanol concentration in Jerusalem artichoke tuber flour fermentation (200 g L(-1)) at 40 °C achieved by K. marxianus PT-1 and S. cerevisiae JZ1C was 73.6 and 65.2 g L(-1), which corresponded to the theoretical ethanol yield of 90.0 and 79.7 %, respectively. In the range of 30 to 40 °C, temperature did not have a significant effect on ethanol production for both strains. This study displayed the distinctive superiority of K. marxianus PT-1 and S. cerevisiae JZ1C in the thermotolerance and utilization of inulin-type oligosaccharides reserved in Jerusalem artichoke tubers. It is proposed that both K. marxianus and S. cerevisiae have considerable potential in ethanol production from Jerusalem artichoke tubers by a high temperature CBP.