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

Investigating the lignocellulolytic gut microbiome of huhu grubs (Prionoplus reticularis) using defined diets and dietary switch

The huhu beetle (Prionoplus reticularis) is the largest endemic beetle found throughout Aotearoa New Zealand, and is characterised by feeding on wood during its larval stage. It has been hypothesised that its gut microbiome plays a fundamental role in the degradation of wood. To explore this idea we examined the fungal and bacterial community composition of huhu grubs' frass, using amplicon sequencing. Grubs were reared on an exclusive diet of either a predominantly cellulose source (cotton) or lignocellulose source (pine) for 4 months; subsequently a diet switch was performed and the grubs were grown for another 4 months. The fungal community of cellulose-reared huhu grubs was abundant in potential cellulose degraders, contrasting with the community of lignocellulose-reared grubs, which showed abundant potential soft rot fungi, yeasts, and hemicellulose and cellulose degraders. Cellulose-reared grubs showed a less diverse fungal community, however, diet switch from cellulose to lignocellulose resulted in a change in community composition that showed grubs were still capable of utilising this substrate. Conversely, diet seemed to have a limited influence on huhu grub gut bacterial communities.

Pilot-scale bioethanol production from the starch of avocado seeds using a combination of dilute acid-based hydrolysis and alcoholic fermentation by Saccharomyces cerevisiae

BACKGROUND

A processing methodology of raw starch extraction from avocado seeds (ASs) and a sequential hydrolysis and fermentation bioprocess in just a few steps was successfully obtained for the bioethanol production by a single yeast Saccharomyces cerevisiae strain and this research was also to investigate the optimum conditions for the pretreatment of biomass and technical procedures for the production of bioethanol. It successfully resulted in high yields and productivity of all the experiments from the laboratory scale and the pilot plant. Ethanol yields from pretreated starch are comparable with those in commercial industries that use molasses and hydrolyzed starch as raw materials.

RESULTS

Before the pilot-scale bioethanol production, studies of starch extraction and dilute sulfuric acid-based pretreatment was carefully conducted. The amount of starch extracted from dry and fresh avocado seed was 16.85 g ± 0.34 g and 29.79 ± 3.18 g of dry starch, representing a yield of ∼17% and 30%, respectively. After a dilute sulfuric acid pretreatment of starch, the released reducing sugars (RRS) were obtained and the hydrolysate slurries containing glucose (109.79 ± 1.14 g/L), xylose (0.99 ± 0.06 g/L), and arabinose (0.38 ± 0.01 g/L). The efficiency of total sugar conversion was 73.40%, with a productivity of 9.26 g/L/h. The ethanol fermentation in a 125 mL flask fermenter showed that Saccharomyces cerevisiae (Fali, active dry yeast) produced the maximum ethanol concentration, p_max at 49.05 g/L (6.22% v/v) with a yield coefficient, Y_p/s of 0.44 g_Ethanol/g_Glucose, a productivity or production rate, r_p at 2.01 g/L/h and an efficiency, Ef of 85.37%. The pilot scale experiments of the ethanol fermentation using the 40-L fermenter were also successfully achieved with essentially good results. The values of p_max,Y_p/s, r_p, and Ef of the 40-L scale were at 50.94 g/L (6.46% v/v), 0.45 g_Ethanol/g_Glucose, 2.11 g/L/h, and 88.74%, respectively. Because of using raw starch, major by-products, i.e., acetic acid in the two scales were very low, in ranges of 0.88-2.45 g/L, and lactic acid was not produced, which are less than those values in the industries.

CONCLUSIONS

The sequential hydrolysis and fermentation process of two scales for ethanol production using the combination of hydrolysis by utilizing dilute sulfuric acid-based pretreatment and fermentation by a single yeast Saccharomyces cerevisiae strain is practicable and feasible for realistic and effective scale-up strategies of bioethanol production from the starch of avocado seeds.

Bioenergy production in Pakistan: Potential, progress, and prospect

Pakistan is a developing country with a rapidly growing population. It is currently facing serious economic and energy challenges. Pakistan's energy demand is increasing by the day, and it now stands at 84 MTOE. Currently, the use of fossil fuels dominates Pakistan's energy sector. Conversely, indigenous fossil fuel resources are rapidly depleting and will be unable to meet rising energy demands in the future. Therefore, to withstand its energy needs, the country will need to explore alternative energy production methods. Biomass is one of the alternatives that has enormous potential to help Pakistan combat its growing energy crisis. In this review, we first present an overview of bioenergy, biomass resources, and biomass conversion technologies. We then discuss in detail the current state of the energy mix of Pakistan. Subsequently, we show that annual production of about 121 MT of agricultural residues, 427 MT of animal manure, and 7.5 MT of MSW in Pakistan offer a variety of bioenergy options ranging from biofuels to bio-electricity production. Overall, these biomass resources in Pakistan have the potential to generate 20,709 MW of bio-electricity and 12,615 million m³ of biogas annually in Pakistan. Though these resources hold promising potential for bioenergy production in the country, however, there are some critical challenges that need to be considered, and some of which are extremely difficult to overcome for a developing country like Pakistan. This work is expected to provide a useful basis for biomass management and utilization in Pakistan to harvest eco-friendly and sustainable green energy locally.

Development of high temperature simultaneous saccharification and fermentation by thermosensitive Saccharomyces cerevisiae and Bacillus amyloliquefaciens

Scarcity of energy and pollution are two major challenges that have become a threat to all living things worldwide. Bioethanol is a renewable, ecological-friendly clean energy that may be utilized to address these issues. This study aimed to develop simultaneous saccharification and fermentation (SSF) process through high temperature-substrate adaptation and co-cultivation of S. cerevisiae with other potential amylolytic strains. In this study, we adapted our previously screened thermosensitive Saccharomyces cerevisiae Dj-3 strain up-to 42 °C and also screened three potential thermotolerant amylolytic strains based on their starch utilization capability. We performed SSF fermentation at high temperature by adapted Dj-3 and amylolytic strains using 10.0% starch feedstock. Interestingly, we observed significant ethanol concentration [3.86% (v/v)] from high temperature simultaneous saccharification and fermentation (HSSF) of adapted Bacillus amyloliquefaciens (C-7) and Dj-3. We attribute the significant ethanol concentration from starch of this HSSF process to C-7’s high levels of glucoamylase activity (4.01 U/ml/min) after adaptation in starch (up-to 42 °C) as well as Dj-3's strong glucose fermentation capacity and also their ethanol stress tolerance capability. This study suggests the significant feasibility of our HSSF process.

Consolidated bioprocessing for bioethanol production by metabolically engineered Bacillus subtilis strains

Bioethanol produced by fermentative microorganisms is regarded as an alternative to fossil fuel. Bioethanol to be used as a viable energy source must be produced cost-effectively by removing expense-intensive steps such as the enzymatic hydrolysis of substrate. Consolidated bioprocessing (CBP) is believed to be a practical solution combining saccharification and fermentation in a single step catalyzed by a microorganism. Bacillus subtills with innate ability to grow on a diversity of carbohydrates seems promising for affordable CBP bioethanol production using renewable plant biomass and wastes. In this study, the genes encoding alcohol dehydrogenase from Z. mobilis (adh_Z) and S. cerevisiae (adh_S) were each used with Z. mobilis pyruvate decarboxylase gene (pdc_Z) to create ethanologenic operons in a lactate-deficient (Δldh) B. subtilis resulting in NZ and NZS strains, respectively. The S. cerevisiae adh_S caused significantly more ethanol production by NZS and therefore was used to make two other operons including one with double copies of both pdc_Z and adh_S and the other with a single pdc_Z but double adh_S genes expressed in N(ZS)2 and NZS2 strains, respectively. In addition, two fusion genes were constructed with pdc_Z and adh_S in alternate orientations and used for ethanol production by the harboring strains namely NZ:S and NS:Z, respectively. While the increase of gene dosage was not associated with elevated carbon flow for ethanol production, the fusion gene adh_S:pdc_Z resulted in a more than two times increase of productivity by strain NS:Z as compared with NZS during 48 h fermentation. The CBP ethanol production by NZS and NS:Z using potatoes resulted in 16.3 g/L and 21.5 g/L ethanol during 96 h fermentation, respectively. For the first time in this study, B. subtilis was successfully used for CBP ethanol production with S. cerevisiae alcohol dehydrogenase. The results of the study provide insights on the potentials of B. subtilis for affordable bioethanol production from inexpensive plant biomass and wastes. However, the potentials need to be improved by metabolic and process engineering for higher yields of ethanol production and plant biomass utilization.

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations

Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32.

Clavispora santaluciae f.a., sp. nov., a novel ascomycetous yeast species isolated from grapes

During a study of yeast diversity in Azorean vineyards, four strains were isolated which were found to represent a novel yeast species based on the sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and of the D1/D2 domain of the large subunit (LSU) rRNA gene, together with their physiological characteristics. An additional strain isolated from Drosophila suzukii in Italy had identical D1/D2 sequences and very similar ITS regions (five nucleotide substitutions) to the Azorean strains. Phylogenetic analysis using sequences of the ITS region and D1/D2 domain showed that the five strains are closely related to Clavispora lusitaniae, although with 56 nucleotide differences in the D2 domain. Intraspecies variation revealed between two and five nucleotide differences, considering the five strains of Clavispora santaluciae. Some phenotypic discrepancies support the separation of the new species from their closely related ones, such as the inability to grow at temperatures above 35 °C, to produce acetic acid and the capacity to assimilate starch. Neither conjugations nor ascospore formation were observed in any of the strains. The name Clavispora santaluciae f.a., sp. nov., is proposed to accommodate the above noted five strains (holotype, CBS 16465^T; MycoBank no., MB 835794).

Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts

Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.

Production of ethanol from Jerusalem artichoke by mycelial pellets

Mycelial pellets formed by Aspergillus niger A-15 were used to immobilize the ethanol producing yeast Saccharomyces cerevisiae C-15. The operation parameters, such as agitation speed, temperature and mixed proportion of strains were studied. The optimal adsorption 66.9% was obtained when speed was 80r/min, temperature was 40 °C and mixed proportion(mycelial pellets: yeasts) was 1:10. With Jerusalem artichoke flour as substrate, 12.8% (V/V) of ethanol was obtained after 48 h by simultaneous saccharification and fermentation using mycelial pellets. And mycelial pellets could tolerate 19% (volume fraction) ethanol. The above results proved that this new technology was feasible, and it had the advantages of higher ethanol yield, long service life, repeated use, easy operation and lower cost in producing ethanol.

Consolidated Bioprocess for Bioethanol Production from Raw Flour of Brosimum alicastrum Seeds Using the Native Strain of Trametes hirsuta Bm-2

Consolidated bioprocessing (CBP), which integrates biological pretreatment, enzyme production, saccharification, and fermentation, is a promising operational strategy for cost-effective ethanol production from biomass. In this study, the use of a native strain of Trametes hirsuta (Bm-2) was evaluated for bioethanol production from Brosimum alicastrum in a CBP. The raw seed flour obtained from the ramon tree contained 61% of starch, indicating its potential as a raw material for bioethanol production. Quantitative assays revealed that the Bm-2 strain produced the amylase enzyme with activity of 193.85 U/mL. The Bm-2 strain showed high tolerance to ethanol stress and was capable of directly producing ethanol from raw flour at a concentration of 13 g/L, with a production yield of 123.4 mL/kg flour. This study demonstrates the potential of T. hirsuta Bm-2 for starch-based ethanol production in a consolidated bioprocess to be implemented in the biofuel industry. The residual biomass after fermentation showed an average protein content of 22.5%, suggesting that it could also be considered as a valuable biorefinery co-product for animal feeding.

Ethanol Decreases Pseudomonas aeruginosa Flagellar Motility through the Regulation of Flagellar Stators

Pseudomonas aeruginosa frequently encounters microbes that produce ethanol. Low concentrations of ethanol reduced P. aeruginosa swim zone area by up to 45% in soft agar. The reduction of swimming by ethanol required the flagellar motor proteins MotAB and two PilZ domain proteins (FlgZ and PilZ). PilY1 and the type 4 pilus alignment complex (comprising PilMNOP) were previously implicated in MotAB regulation in surface-associated cells and were required for ethanol-dependent motility repression. As FlgZ requires the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) to represses motility, we screened mutants lacking genes involved in c-di-GMP metabolism and found that mutants lacking diguanylate cyclases SadC and GcbA were less responsive to ethanol. The double mutant was resistant to its effects. As published previously, ethanol also represses swarming motility, and the same genes required for ethanol effects on swimming motility were required for its regulation of swarming. Microscopic analysis of single cells in soft agar revealed that ethanol effects on swim zone area correlated with ethanol effects on the portion of cells that paused or stopped during the time interval analyzed. Ethanol increased c-di-GMP in planktonic wild-type cells but not in ΔmotAB or ΔsadC ΔgcbA mutants, suggesting c-di-GMP plays a role in the response to ethanol in planktonic cells. We propose that ethanol produced by other microbes induces a regulated decrease in P. aeruginosa motility, thereby promoting P. aeruginosa colocalization with ethanol-producing microbes. Furthermore, some of the same factors involved in the response to surface contact are involved in the response to ethanol.IMPORTANCE Ethanol is an important biologically active molecule produced by many bacteria and fungi. It has also been identified as a potential marker for disease state in cystic fibrosis. In line with previous data showing that ethanol promotes biofilm formation by Pseudomonas aeruginosa, here we report that ethanol reduces swimming motility using some of the same proteins involved in surface sensing. We propose that these data may provide insight into how microbes, via their metabolic byproducts, can influence P. aeruginosa colocalization in the context of infection and in other polymicrobial settings.

Single pot bioprocessing for ethanol production from biogenic municipal solid waste

Burgeoning global energy demand and rapid diminution of fossil fuel reserves urged to seek for a sustainable energy source like bioethanol. Single pot bioprocessing (SPB) strategy employing in-house laccase, cellulase plus xylanase and amylase along with hexose and pentose sugar fermenting yeasts (Saccharomyces cerevisiae and Pichia stipitis) is designed in this study for ethanol production from biogenic municipal solid waste (BMSW). BMSW when subjected to simultaneous pretreatment and saccharification (SPS) resulted in 79.69% enzymatic digestibility and fared better compared to alkali pretreated counterparts (14.03%-51.10%). The maximum total sugar release in case of SPS was 146.9 g/L in 24 h. The maximum ethanol concentration of 5.24% (v/v) in 30 h was obtained from SPB of BMSW at 25% (w/v) solid loading. SPB for ethanol production from BMSW is an interesting and effective alternative to MSW going to landfill or incineration with an added perk of waste to wealth conversion.

Enhanced Bioethanol Production from Potato Peel Waste Via Consolidated Bioprocessing with Statistically Optimized Medium

In this study, an extensive screening was undertaken to isolate some amylolytic microorganisms capable of producing bioethanol from starchy biomass through Consolidated Bioprocessing (CBP). A total of 28 amylolytic microorganisms were isolated, from which 5 isolates were selected based on high α-amylase and glucoamylase activities and identified as Candida wangnamkhiaoensis, Hyphopichia pseudoburtonii (2 isolates), Wickerhamia sp., and Streptomyces drozdowiczii based on 26S rDNA and 16S rDNA sequencing. Wickerhamia sp. showed the highest ethanol production (30.4 g/L) with fermentation yield of 0.3 g ethanol/g starch. Then, a low cost starchy waste, potato peel waste (PPW) was used as a carbon source to produce ethanol by Wickerhamia sp. Finally, in order to obtain maximum ethanol production from PPW, a fermentation medium was statistically designed. The effect of various medium ingredients was evaluated initially by Plackett-Burman design (PBD), where malt extracts, tryptone, and KH₂PO₄ showed significantly positive effect (p value < 0.05). Using Response Surface Modeling (RSM), 40 g/L (dry basis) PPW and 25 g/L malt extract were found optimum and yielded 21.7 g/L ethanol. This study strongly suggests Wickerhamia sp. as a promising candidate for bioethanol production from starchy biomass, in particular, PPW through CBP.

Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts

In this study, the potential of selected psychrotolerant yeast strains for phenol biodegradation was studied. From 39 strains isolated from soil and water samples from Rucianka peat bog, three psychrotolerant yeast strains, A011, B021, and L012, showed the ability to degrade phenol. The result shows that all three yeast strains could degrade phenol at 500 and 750 mg l-1 concentration, whereas strains A011 and L012 could degrade phenol at 1000 mg l-1 concentration. The time needed for degradation of each phenol concentration was no longer than 2 days. Strains A011, B021, and L012 were identified based on 26S rDNA and ITS sequence analysis as belonging to species Candida subhashii, Candida oregonensis, and Schizoblastosporion starkeyi-henricii, respectively.

Draft Genome Sequences of the Xylose-Fermenting Yeast Scheffersomyces shehatae NBRC 1983T and a Thermotolerant Isolate of S. shehatae ATY839 (JCM 18690)

Draft genome sequences of the type strain (NBRC 1983) and a thermotolerant isolate (ATY839) of the xylose-fermenting yeast Scheffersomyces shehatae were determined. The genome sizes and presumed open reading frames were highly similar between strains NBRC 1983^T and ATY839.

Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid

BACKGROUND

Genomic studies on fungal species with hydrolytic activity have gained increased attention due to their great biotechnological potential for biomass-based biofuel production. The amylolytic yeast Saccharomycopsis fibuligera has served as a good source of enzymes and genes involved in saccharification. Despite its long history of use in food fermentation and bioethanol production, very little is known about the basic physiology and genomic features of S. fibuligera.

RESULTS

We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. The seven chromosome pairs of KJJ81 subgenomes exhibit highly conserved synteny, indicating a very recent hybridization event. The phylogeny inferred from WG comparisons showed an early divergence of S. fibuligera before the separation of the CTG and Saccharomycetaceae clades in the subphylum Saccharomycotina. Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. Notably, the lack of sulfate assimilation genes in the S. fibuligera genome reflects a unique phenotype for Saccharomycopsis clades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome.

CONCLUSIONS

The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. The gene inventory facilitates the discovery of new genes applicable to the production of novel valuable enzymes and chemicals. Moreover, as the first gapless genome assembly in the genus Saccharomycopsis including members with desirable traits for bioconversion, the unique genomic features of S. fibuligera and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.

Enhanced xylose fermentation and hydrolysate inhibitor tolerance of Scheffersomyces shehatae for efficient ethanol production from non-detoxified lignocellulosic hydrolysate

Effective conversion of xylose into ethanol is important for lignocellulosic ethanol production. In the present study, UV-C mutagenesis was used to improve the efficiency of xylose fermentation. The mutated Scheffersomyces shehatae strain TTC79 fermented glucose as efficiently and xylose more efficiently, producing a higher ethanol concentration than the wild-type. A maximum ethanol concentration of 29.04 g/L was produced from 71.31 g/L xylose, which was 58.95 % higher than that of the wild-type. This mutant also displayed significantly improved hydrolysate inhibitors tolerance and increased ethanol production from non-detoxified lignocellulosic hydrolysates. The ethanol yield, productivity and theoretical yield by TTC79 from sugarcane bagasse hydrolysate were 0.46 g/g, 0.20 g/L/h and 90.61 %, respectively, while the corresponding values for the wild-type were 0.20 g/g, 0.04 g/L/h and 39.20 %, respectively. These results demonstrate that S. shehatae TTC79 is a useful non-recombinant strain, combining efficient xylose consumption and high inhibitor tolerance, with potential for application in ethanol production from lignocellulose hydrolysates.

Lignocellulosic ethanol production by starch-base industrial yeast under PEG detoxification

Cellulosic ethanol production from lignocellulosic biomass offers a sustainable solution for transition from fossil based fuels to renewable alternatives. However, a few long-standing technical challenges remain to be addressed in the development of an economically viable fermentation process from lignocellulose. Such challenges include the needs to improve yeast tolerance to toxic inhibitory compounds and to achieve high fermentation efficiency with minimum detoxification steps after a simple biomass pretreatment. Here we report an in-situ detoxification strategy by PEG exo-protection of an industrial dry yeast (starch-base). The exo-protected yeast cells displayed remarkably boosted vitality with high tolerance to toxic inhibitory compounds, and with largely improved ethanol productivity from crude hydrolysate derived from a pretreated lignocellulose. The PEG chemical exo-protection makes the industrial S. cerevisiae yeast directly applicable for the production of cellulosic ethanol with substantially improved productivity and yield, without of the need to use genetically modified microorganisms.