From straw to salmon: a technical design and energy balance for production of yeast oil for fish feed from wheat straw

BACKGROUND

Aquaculture is a major user of plant-derived feed ingredients, such as vegetable oil. Production of vegetable oil and protein is generally more energy-intensive than production of the marine ingredients they replace, so increasing inclusion of vegetable ingredients increases the energy demand of the feed. Microbial oils, such as yeast oil made by fermentation of lignocellulosic hydrolysate, have been proposed as a complement to plant oils, but energy assessments of microbial oil production are needed. This study presents a mass and energy balance for a biorefinery producing yeast oil through conversion of wheat straw hydrolysate, with co-production of biomethane and power.

RESULTS

The results showed that 1 tonne of yeast oil (37 GJ) would require 9.2 tonnes of straw, 14.7 GJ in fossil primary energy demand, 14.6 GJ of process electricity and 13.3 GJ of process heat, while 21.5 GJ of biomethane (430 kg) and 6 GJ of excess power would be generated simultaneously. By applying economic allocation, the fossil primary energy demand was estimated to 11.9 GJ per tonne oil.

CONCLUSIONS

Fossil primary energy demand for yeast oil in the four scenarios studied was estimated to be 10-38% lower than for the commonly used rapeseed oil and process energy demand could be met by parallel combustion of lignin residues. Therefore, feed oil can be produced from existing non-food biomass without causing agricultural expansion.

Oleaginous yeasts for biochemicals, biofuels and food from lignocellulose-hydrolysate and crude glycerol

Microbial lipids produced from lignocellulose and crude glycerol (CG) can serve as sustainable alternatives to vegetable oils, whose production is, in many cases, accompanied by monocultures, land use changes or rain forest clearings. Our projects aim to understand the physiology of microbial lipid production by oleaginous yeasts, optimise the production and establish novel applications of microbial lipid compounds. We have established methods for fermentation and intracellular lipid quantification. Following the kinetics of lipid accumulation in different strains, we found high variability in lipid formation even between very closely related oleaginous yeast strains on both, wheat straw hydrolysate and CG. For example, on complete wheat straw hydrolysate, we saw that one Rhodotorula glutinis strain, when starting assimilating D-xylosealso assimilated the accumulated lipids, while a Rhodotorula babjevae strain could accumulate lipids on D-xylose. Two strains (Rhodotorula toruloides CBS 14 and R. glutinis CBS 3044) were found to be the best out of 27 tested to accumulate lipids on CG. Interestingly, the presence of hemicellulose hydrolysate stimulated glycerol assimilation in both strains. Apart from microbial oil, R. toruloides also produces carotenoids. The first attempts of extraction using the classical acetone-based method showed that β-carotene is the major carotenoid. However, there are indications that there are also substantial amounts of torulene and torularhodin, which have a very high potential as antioxidants.

Production of short-chain fatty acids (SCFAs) as chemicals or substrates for microbes to obtain biochemicals

Carboxylic acids have become interesting platform molecules in the last years due to their versatility to act as carbon sources for different microorganisms or as precursors for the chemical industry. Among carboxylic acids, short-chain fatty acids (SCFAs) such as acetic, propionic, butyric, valeric, and caproic acids can be biotechnologically produced in an anaerobic fermentation process from lignocellulose or other organic wastes of agricultural, industrial, or municipal origin. The biosynthesis of SCFAs is advantageous compared to chemical synthesis, since the latter relies on fossil-derived raw materials, expensive and toxic catalysts and harsh process conditions. This review article gives an overview on biosynthesis of SCFAs from complex waste products. Different applications of SCFAs are explored and how these acids can be considered as a source of bioproducts, aiming at the development of a circular economy. The use of SCFAs as platform molecules requires adequate concentration and separation processes that are also addressed in this review. Various microorganisms such as bacteria or oleaginous yeasts can efficiently use SCFA mixtures derived from anaerobic fermentation, an attribute that can be exploited in microbial electrolytic cells or to produce biopolymers such as microbial oils or polyhydroxyalkanoates. Promising technologies for the microbial conversion of SCFAs into bioproducts are outlined with recent examples, highlighting SCFAs as interesting platform molecules for the development of future bioeconomy.

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes

BACKGROUND

Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different timepoints of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation.

RESULTS

We observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in β-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2-glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD⁺-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed.

CONCLUSIONS

We suspect that the physiological reason for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy.

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.

Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production

Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.

Oleaginous yeasts respond differently to carbon sources present in lignocellulose hydrolysate

BACKGROUND

Microbial oils, generated from lignocellulosic material, have great potential as renewable and sustainable alternatives to fossil-based fuels and chemicals. By unravelling the diversity of lipid accumulation physiology in different oleaginous yeasts grown on the various carbon sources present in lignocellulose hydrolysate (LH), new targets for optimisation of lipid accumulation can be identified. Monitoring lipid formation over time is essential for understanding lipid accumulation physiology. This study investigated lipid accumulation in a variety of oleaginous ascomycetous and basidiomycetous strains grown in glucose and xylose and followed lipid formation kinetics of selected strains in wheat straw hydrolysate (WSH).

RESULTS

Twenty-nine oleaginous yeast strains were tested for their ability to utilise glucose and xylose, the main sugars present in WSH. Evaluation of sugar consumption and lipid accumulation revealed marked differences in xylose utilisation capacity between the yeast strains, even between those belonging to the same species. Five different promising strains, belonging to the species Lipomyces starkeyi, Rhodotorula glutinis, Rhodotorula babjevae and Rhodotorula toruloides, were grown on undiluted wheat straw hydrolysate and lipid accumulation was followed over time, using Fourier transform-infrared (FTIR) spectroscopy. All five strains were able to grow on undiluted WSH and to accumulate lipids, but to different extents and with different productivities. R. babjevae DVBPG 8058 was the best-performing strain, accumulating 64.8% of cell dry weight (CDW) as lipids. It reached a culture density of 28 g/L CDW in batch cultivation, resulting in a lipid content of 18.1 g/L and yield of 0.24 g lipids per g carbon source. This strain formed lipids from the major carbon sources in hydrolysate, glucose, acetate and xylose. R. glutinis CBS 2367 also consumed these carbon sources, but when assimilating xylose it consumed intracellular lipids simultaneously. Rhodotorula strains contained a higher proportion of polyunsaturated fatty acids than the two tested Lipomyces starkeyi strains.

CONCLUSIONS

There is considerable metabolic diversity among oleaginous yeasts, even between closely related species and strains, especially when converting xylose to biomass and lipids. Monitoring the kinetics of lipid accumulation and identifying the molecular basis of this diversity are keys to selecting suitable strains for high lipid production from lignocellulose.

Microbial lipid production from crude glycerol and hemicellulosic hydrolysate with oleaginous yeasts

BACKGROUND

Crude glycerol (CG) and hemicellulose hydrolysate (HH) are low-value side-products of biodiesel transesterification and pulp-and paper industry or lignocellulosic ethanol production, respectively, which can be converted to microbial lipids by oleaginous yeasts. This study aimed to test the ability of oleaginous yeasts to utilise CG and HH and mixtures of them as carbon source.

RESULTS

Eleven out of 27 tested strains of oleaginous yeast species were able to grow in plate tests on CG as sole carbon source. Among them, only one ascomycetous strain, belonging to Lipomyces starkeyi, was identified, the other 10 strains were Rhodotorula spec. When yeasts were cultivated in mixed CG/ HH medium, we observed an activation of glycerol conversion in the Rhodotorula strains, but not in L. starkeyi. Two strains-Rhodotorula toruloides CBS 14 and Rhodotorula glutinis CBS 3044 were further tested in controlled fermentations in bioreactors in different mixtures of CG and HH. The highest measured average biomass and lipid concentration were achieved with R. toruloides in 10% HH medium mixed with 55 g/L CG-19.4 g/L and 10.6 g/L, respectively, with a lipid yield of 0.25 g lipids per consumed g of carbon source. Fatty acid composition was similar to other R. toruloides strains and comparable to that of vegetable oils.

CONCLUSIONS

There were big strain differences in the ability to convert CG to lipids, as only few of the tested strains were able to grow. Lipid production rates and yields showed that mixing GC and HH have a stimulating effect on lipid accumulation in R. toruloides and R. glutinis resulting in shortened fermentation time to reach maximum lipid concentration, which provides a new perspective on converting these low-value compounds to microbial lipids.

Production and characterization of yeasts grown on media composed of spruce-derived sugars and protein hydrolysates from chicken by-products

Background

A possible future shortage of feed protein will force mankind to explore alternative protein sources that can replace conventional soymeal or fishmeal. Several large industrial organic side-streams could potentially be upgraded to feed protein using a fermentation process to generate single cell protein. Yeast is the most widely accepted microorganism for production of single cell protein, because of its superior nutritional quality and acceptability among consumers. Here, we have assessed the growth of four different yeasts, Cyberlindnera jadinii, Wickerhamomyces anomalus, Blastobotrys adeninivorans and Thermosacc^® Dry (Saccharomyces cerevisiae), on media composed of enzymatically saccharified sulfite-pulped spruce wood and hydrolysates of by-products from chicken, and we have characterized the resulting yeast biomass.

Results

Generally, the yeast grew very well on the spruce- and chicken-based medium, with typical yields amounting to 0.4–0.5 g of cell dry weight and 0.2–0.3 g of protein per g of sugar. B. adeninivorans stood out as the most versatile yeast in terms of nutrient consumption and in this case yields were as high as 0.9 g cells and 0.5 g protein per g of sugar. The next best performing yeast in terms of yield was W. anomalus with up to 0.6 g cells and 0.3 g protein per g sugar. Comparative compositional analyses of the yeasts revealed favorable amino acid profiles that were similar to the profiles of soymeal, and even more so, fish meal, especially for essential amino acids.

Conclusions

The efficient conversion of industrial biomass streams to yeast biomass demonstrated in this study opens new avenues towards better valorization of these streams and development of sustainable feed ingredients. Furthermore, we conclude that production of W. anomalus or B. adeninivorans on this promising renewable medium may be potentially more efficient than production of the well-known feed ingredient C. jadinii. Further research should focus on medium optimization, development of semi-continuous and continues fermentation protocols and exploration of downstream processing methods that are beneficial for the nutritional values of the yeast for animal feed.

Insertional tagging of the Scheffersomyces stipitis gene HEM25 involved in regulation of glucose and xylose alcoholic fermentation

Amid known microbial bioethanol producers, the yeast Scheffersomyces (Pichia) stipitis is particularly promising in terms of alcoholic fermentation of both glucose and xylose, the main constituents of lignocellulosic biomass hydrolysates. However, the ethanol yield and productivity, especially from xylose, are still insufficient to meet the requirements of a feasible industrial technology; therefore, the construction of more efficient S. stipitis ethanol producers is of great significance. The aim of this study was to isolate the insertional mutants of S. stipitis with altered ethanol production from glucose and xylose and to identify the disrupted gene(s). Mutants obtained by random insertional mutagenesis were screened for their growth abilities on solid media with different sugars and for resistance to 3-bromopyruvate. Of more than 1,300 screened mutants, 17 were identified to have significantly changed ethanol yields during the fermentation. In one of the best fermenting strains (strain 4.6), insertion was found to occur within the ORF of a homolog to the Saccharomyces cerevisiae gene HEM25 (YDL119C), encoding a mitochondrial glycine transporter required for heme synthesis. The role of HEM25 in heme accumulation, respiration, and alcoholic fermentation in the yeast S. stipitis was studied using strain 4.6, the complementation strain Comp-a derivative from the 4.6 strain with expression of the WT HEM25 allele and the deletion strain hem25Δ. As hem25Δ produced lower amounts of ethanol than strain 4.6, we assume that the phenotype of strain 4.6 may be caused not only by HEM25 disruption but additionally by some point mutation.

Spruce sugars and poultry hydrolysate as growth medium in repeated fed-batch fermentation processes for production of yeast biomass

The production of microbial protein in the form of yeast grown on lignocellulosic sugars and nitrogen-rich industrial residues is an attractive approach for reducing dependency on animal and plant protein. Growth media composed of enzymatically saccharified sulfite-pulped spruce wood, enzymatic hydrolysates of poultry by-products and urea were used for the production of single-cell protein. Strains of three different yeast species, Cyberlindnera jadinii, Wickerhamomyces anomalus and Blastobotrys adeninivorans, were cultivated aerobically using repeated fed-batch fermentation up to 25 L scale. Wickerhamomyces anomalus was the most efficient yeast with yields of 0.6 g of cell dry weight and 0.3 g of protein per gram of glucose, with cell and protein productivities of 3.92 g/L/h and 1.87 g/L/h, respectively. Using the conditions developed here for producing W. anomalus, it would take 25 industrial (200 m³) continuously operated fermenters to replace 10% of the fish feed protein used in Norway.

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

FT-NIR: a tool for rapid intracellular lipid quantification in oleaginous yeasts

BACKGROUND

Lipid extraction for quantification of fat content in oleaginous yeasts often requires strong acids and harmful organic solvents; it is laborious and time-consuming. Therefore, in most cases just endpoint measurements of lipid accumulation are performed and kinetics of intracellular lipid accumulation is difficult to follow. To address this, we created a prediction model using Fourier-transform near-infrared (FT-NIR) spectroscopy. This method allows to measure lipid content in yeast.

METHODS

The FT-NIR calibration sets were constructed from spectra of freeze-dried cells of the oleaginous yeasts Rhodotorula toruloides CBS 14, Lipomyces starkeyi CBS 1807 and Yarrowia lipolytica CBS 6114. The yeast cells were obtained from different cultivation conditions. Freeze-dried cell pellets were scanned using FT-NIR in the Multi Purpose Analyser (MPA) from Bruker. The obtained spectra were assigned corresponding to total fat content, obtained from lipid extraction using a modified Folch method. Quantification models using partial least squares (PLS) regression were built, and the calibration sets were validated on independently cultivated samples. The R. toruloides model was additionally tested on Rhodotorula babjevae DBVPG 8058 and Rhodotorula glutinis CBS 2387.

RESULTS

The R ² of the FT-NIR model for R. toruloides was 98%, and the root mean square error of cross-validation (RMSECV) was 1.53. The model was validated using a separate set of R. toruloides samples with a root mean square error of prediction (RMSEP) of 3.21. The R ² of the Lipomyces model was 96%, with RMSECV 2.4 and RMSEP 3.8. The R ² of the mixed model, including all tested yeast strains, was 90.5%, with RMSECV 2.76 and RMSEP 3.22, respectively. The models were verified by predicting the total fat content in newly cultivated and freeze-dried samples. Additionally, the kinetics of lipid accumulation of a culture were followed and compared with standard lipid extraction methods.

CONCLUSIONS

Using FT-NIR spectroscopy, we have developed a faster, less laborious and non-destructive quantification of yeast intracellular lipid content compared to methods using lipid extraction.

Biochemical profiling, prediction of total lipid content and fatty acid profile in oleaginous yeasts by FTIR spectroscopy

BACKGROUND

Oleaginous yeasts are considered as a potential lipid source for food, feed and biofuel production. In order to make the yeast-based lipid production environmentally and economically sustainable, there is a need for screening studies in order to find the best yeast lipid producers on different substrates, and to optimize cultivation conditions. Since the target parameter of such screening studies are lipid amounts and profiles, an analytical technique that is able to perform lipid analyses rapidly, reproducible and with high precision is highly desirable. The main objective of this study was to establish the non-invasive high-throughput Fourier transform infrared (FTIR) spectroscopy analysis for the prediction of lipid content and profile in oleaginous yeasts.

RESULTS

High-throughput FTIR spectroscopy allowed characterizing the total biochemical profile of oleaginous yeasts and enabled us to identify strains and substrate(s) providing the highest total lipid content. Some of the yeast strains grown under nitrogen-limiting conditions with glucose/xylose/mixture of glucose and xylose as carbon sources were accumulating lipids with a high proportion of free fatty acids. FTIR spectra were used to predict gravimetric and gas chromatography data by establishing multivariate calibration models. Coefficients of determination (R ²) for calibration models were obtained in a range between 0.62 and 0.92 for predicting lipid content. When using an independent test set, R ² values between 0.53 and 0.79 were achieved for predicting fatty acid profile. The best spectral region(s) for the prediction of total lipid content was 3100-2800 cm^-1 combined with 1800-700 cm^-1, and for prediction of summed saturated (SAT), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids: 3100-2800 cm^-1, 3100-2800 cm^-1 combined with 1700-1715 cm^-1 and 3100-2800 cm^-1 combined with 1800-1715 cm^-1, respectively. The highest lipid accumulation was observed for strains Rhodotorula babjevae DBVPG 8058 on glucose and mixture of glucose and xylose and Lipomyces starkeyi CBS 2512 on xylose.

CONCLUSIONS

Applying FTIR spectroscopy combined with multivariate data analysis allows performing rapid, non-invasive, reproducible and precise quantitative predictions of total lipid content and lipid profile. It allows also detecting different lipid fractions as triacylglycerols (TAGs) and free fatty acids and evaluating the total biochemical profile of cells. Several yeast strains with high lipid accumulation were identified.

Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis

Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

Oleaginous yeast as a component in fish feed

This study investigates the replacement of vegetable oil (VO) in aquaculture feed for Arctic char (Salvelinus alpinus) with oil produced by the oleaginous yeast Lipomyces starkeyi grown in lignocellulose (wheat straw) hydrolysate. VO is extensively used to partially replace fish oil in aquaculture feed, which can be seen as non-sustainable. VO itself is becoming a limited resource. Plant oils are used in many different applications, including food, feed and biodiesel. Its replacement in non-food applications is desirable. For this purpose, yeast cells containing 43% lipids per g dry weight were mechanically disrupted and incorporated into the fish feed. There were no significant differences in this pilot study, regarding weight and length gain, feed conversion ratio, specific growth rate, condition factor and hepatosomatic index between the control and the yeast oil fed group. Fatty and amino acid composition of diet from both groups was comparable. Our results in fish demonstrate that it is possible to replace VO by yeast oil produced from lignocellulose, which may broaden the range of raw materials for food production and add value to residual products of agriculture and forestry.

Yeasts and bacteria associated with kocho, an Ethiopian fermented food produced from enset (Ensete ventricosum)

Enset (Ensete ventricosum) is the basis of the staple food consumed by about 20% of the Ethiopian population. Kocho is one of the food products generated from enset by spontaneous fermentation of decorticated and pulverized pseudostem and corm sections. We isolated culturable microbes associated with kocho from different stages of fermentation. Twelve yeast species, six lactic acid bacteria (LABs) species and eleven species of aerobic bacteria were identified by sequencing ITS/D1D2 regions of 26S rDNA of yeasts and 16S rDNA of bacteria, respectively. More yeast species were identified in fresh (fermented for 2–5 days) kocho, compared to long-term (7–12 months) fermented kocho, while we observed an opposite trend for LABs. In fresh kocho, the most frequently isolated yeast species were Pichia exigua, Galactomyces geotrichum, and Pichia fermentans. From mid-term (3–4 months) kocho most frequently Candida cabralensis, G. geotrichum, and Candida ethanolica were isolated. In the long-term fermentations, the most frequently isolated yeast was Saturnispora silva. Lactobacillus plantarum was the most frequently isolated LAB in both fresh and mid-term kocho. In long-term fermented kocho, Acetobacter pasteurianus and L. plantarum were most frequently isolated. L. plantarum was consistently isolated from all the three stages of fermentation. Aerobic bacteria in fresh kocho were mostly gram-negative, with Raoultella planticola and Pantoea agglomerans being the most frequently isolated species. In long-term fermented kocho, mainly gram-positive, spore-forming bacteria of the genus Bacillus were found, among them also species of the Bacillus cereus group, Bacillus anthracis and Bacillus thurigiensis.

Bioethanol and lipid production from the enzymatic hydrolysate of wheat straw after furfural extraction

This study investigates biofuel production from wheat straw hydrolysate, from which furfural was extracted using a patented method developed at the Latvian State Institute of Wood Chemistry. The solid remainder after furfural extraction, corresponding to 67.6% of the wheat straw dry matter, contained 69.9% cellulose of which 4% was decomposed during the furfural extraction and 26.3% lignin. Enzymatic hydrolysis released 44% of the glucose monomers in the cellulose. The resulting hydrolysate contained mainly glucose and very little amount of acetic acid. Xylose was not detectable. Consequently, the undiluted hydrolysate did not inhibit growth of yeast strains belonging to Saccharomyces cerevisiae, Lipomyces starkeyi, and Rhodotorula babjevae. In the fermentations, average final ethanol concentrations of 23.85 g/l were obtained, corresponding to a yield of 0.53 g ethanol per g released glucose. L. starkeyi generated lipids with a rate of 0.08 g/h and a yield of 0.09 g per g consumed glucose. R. babjevae produced lipids with a rate of 0.18 g/h and a yield of 0.17 per g consumed glucose. In both yeasts, desaturation increased during cultivation. Remarkably, the R. babjevae strain used in this study produced considerable amounts of heptadecenoic, α,- and γ-linolenic acid.

Greenhouse gas performance of biochemical biodiesel production from straw: soil organic carbon changes and time-dependent climate impact

BACKGROUND

Use of bio-based diesel is increasing in Europe. It is currently produced from oilseed crops, but can also be generated from lignocellulosic biomass such as straw. However, removing straw affects soil organic carbon (SOC), with potential consequences for the climate impact of the biofuel. This study assessed the climate impacts and energy balance of biodiesel production from straw using oleaginous yeast, with subsequent biogas production from the residues, with particular emphasis on SOC changes over time. It also explored the impact of four different scenarios for returning the lignin fraction of the biomass to soil to mitigate SOC changes. Climate impact was assessed using two methods, global warming potential (GWP) and a time-dependent temperature model (∆T _s ) that describes changes in mean global surface temperature as a function of time or absolute temperature change potential (AGTP).

RESULTS

Straw-derived biodiesel reduced GWP by 33-80% compared with fossil fuels and primary fossil energy use for biodiesel production was 0.33-0.80 MJ_prim/MJ, depending on the scenario studied. Simulations using the time-dependent temperature model showed that a scenario where all straw fractions were converted to energy carriers and no lignin was returned to soil resulted in the highest avoided climate impact. The SOC changes due to straw removal had a large impact on the results, both when using GWP and the time-dependent temperature model.

CONCLUSIONS

In a climate perspective, it is preferable to combust straw lignin to produce electricity rather than returning it to the soil if the excess electricity replaces natural gas electricity, according to results from both GWP and time-dependent temperature modelling. Using different methods to assess climate impact did not change the ranking between the scenarios, but the time-dependent temperature model provided information about system behaviour over time that can be important for evaluation of biofuel systems, particularly in relation to climate target deadlines.

Lipid production from hemicellulose with Lipomyces starkeyi in a pH regulated fed-batch cultivation

This study investigated lipid production from the hemicellulosic fraction of birch wood by the oleaginous yeast Lipomyces starkeyi. Birch wood chips were thermochemically pretreated by hot water extraction, and the liquid phase, containing 45.1 g/l xylose as the major sugar, 13.1 g/l acetic acid and 4.7 g/l furfural, was used for cultivations of L. starkeyi CBS1807. The hydrolysate strongly inhibited yeast growth; the strain could only grow in medium containing 30% hydrolysate at pH 6. At pH 5, growth stopped already upon the addition of about 10% hydrolysate. In fed-batch cultures fed with hydrolysate or a model xylose-acetic acid mixture, co-consumption of xylose and acetic acid was observed, which resulted in a pH increase. This phenomenon was utilized to establish a pH-stat fed-batch cultivation in which, after an initial feeding, hydrolysate or model mixture was connected to the pH-regulation system of the bioreactor. Under these conditions we obtained growth and lipid production in cultures grown on either xylose or glucose during the batch phase. In cultivations fed with model mixture, a maximum lipid content of 60.5% of the cell dry weight (CDW) was obtained; however, not all xylose was consumed. When feeding hydrolysate, growth was promoted and carbon sources were completely consumed, resulting in higher CDW with maximum lipid content of 51.3%. In both cultures the lipid concentration was 8 g/l and a lipid yield of 0.1 g/g carbon source was obtained. Lipid composition was similar in all cultivations, with C18:1 and C16:0 being the most abundant fatty acids. Copyright © 2016 John Wiley & Sons, Ltd.

A systems analysis of biodiesel production from wheat straw using oleaginous yeast: process design, mass and energy balances

BACKGROUND

Biodiesel is the main liquid biofuel in the EU and is currently mainly produced from vegetable oils. Alternative feedstocks are lignocellulosic materials, which provide several benefits compared with many existing feedstocks. This study examined a technical process and its mass and energy balances to gain a systems perspective of combined biodiesel (FAME) and biogas production from straw using oleaginous yeasts. Important process parameters with a determining impact on overall mass and energy balances were identified and evaluated.

RESULTS

In the base case, 41% of energy in the biomass was converted to energy products, primary fossil fuel use was 0.37 MJ_prim/MJ produced and 5.74 MJ fossil fuels could be replaced per kg straw dry matter. The electricity and heat produced from burning the lignin were sufficient for process demands except in scenarios where the yeast was dried for lipid extraction. Using the residual yeast cell mass for biogas production greatly increased the energy yield, with biogas contributing 38% of total energy products.

CONCLUSIONS

In extraction methods without drying the yeast, increasing lipid yield and decreasing the residence time for lipid accumulation are important for the energy and mass balance. Changing the lipid extraction method from wet to dry makes the greatest change to the mass and energy balance. Bioreactor agitation and aeration for lipid accumulation and yeast propagation is energy demanding. Changes in sugar concentration in the hydrolysate and residence times for lipid accumulation greatly affect electricity demand, but have relatively small impacts on fossil energy use (NER) and energy yield (EE). The impact would probably be greater if externally produced electricity were used.

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping

BACKGROUND

It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome.

METHODS

In this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work.

RESULTS

We obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.

The effect of a combined biological and thermo-mechanical pretreatment of wheat straw on energy yields in coupled ethanol and methane generation

Ethanol and biogas are energy carriers that could contribute to a future energy system independent of fossil fuels. Straw is a favorable bioenergy substrate as it does not compete with food or feed production. As straw is very resistant to microbial degradation, it requires a pretreatment to insure efficient conversion to ethanol and/or methane. This study investigates the effect of combining biological pretreatment and steam explosion on ethanol and methane yields in order to improve the coupled generation process. Results show that the temperature of the steam explosion pretreatment has a particularly strong effect on possible ethanol yields, whereas combination with the biological pretreatment showed no difference in overall energy yield. The highest overall energy output was found to be 10.86 MJ kg VS(-1) using a combined biological and steam explosion pretreatment at a temperature of 200°C.

Dekkera bruxellensis--spoilage yeast with biotechnological potential, and a model for yeast evolution, physiology and competitiveness

Dekkera bruxellensis is a non-conventional yeast normally considered a spoilage organism in wine (off-flavours) and in the bioethanol industry. But it also has potential as production yeast. The species diverged from Saccharomyces cerevisiae 200 mya, before the whole genome duplication. However, it displays similar characteristics such as being Crabtree- and petite positive, and the ability to grow anaerobically. Partial increases in ploidy and promoter rewiring may have enabled evolution of the fermentative lifestyle in D. bruxellensis. On the other hand, it has genes typical for respiratory yeasts, such as for complex I or the alternative oxidase AOX1. Dekkera bruxellensis grows more slowly than S. cerevisiae, but produces similar or greater amounts of ethanol, and very low amounts of glycerol. Glycerol production represents a loss of energy but also functions as a redox sink for NADH formed during synthesis of amino acids and other compounds. Accordingly, anaerobic growth required addition of certain amino acids. In spite of its slow growth, D. bruxellensis outcompeted S. cerevisiae in glucose-limited cultures, indicating a more efficient energy metabolism and/or higher affinity for glucose. This review tries to summarize the latest discoveries about evolution, physiology and metabolism, and biotechnological potential of D. bruxellensis.

Combined moist airtight storage and feed fermentation of barley by the yeast Wickerhamomyces anomalus and a lactic acid bacteria consortium

This study combined moist airtight storage of moist grain with pig feed fermentation. Starter cultures with the potential to facilitate both technologies were added to airtight stored moist crimped cereal grain, and the impact on storage microflora and the quality of feed fermentations generated from the grain was investigated. Four treatments were compared: three based on moist barley, either un-inoculated (M), inoculated with Wickerhamomyces anomalus (W), or inoculated with W. anomalus and LAB starter culture, containing Pediococcus acidilactici DSM 16243, Pediococcus pentosaceus DSM 12834 and Lactobacillus plantarum DSM 12837 (WLAB); and one treatment based on dried barley (D). After 6 weeks of storage, four feed fermentations FM, FW, FWLAB, and FD, were initiated from M, W, WLAB, and D, respectively, by mixing the grain with water to a dry matter content of 30%. Each treatment was fermented in batch initially for 7 days and then kept in a continuous mode by adding new feed daily with 50% back-slop. During the 6 week storage period, the average water activity decreased in M, W and WLAB from 0.96 to 0.85, and cereal pH decreased from approximately 6.0 at harvest to 4.5. Feed fermentation conferred a further pH decrease to 3.8-4.1. In M, W and WLAB, molds and Enterobacteriaceae were mostly below detection limit, whereas both organism groups were detected in D. In fermented feed, Enterobacteriaceae were below detection limit in almost all conditions. Molds were detected in FD, for most of the fermentation time in FM and at some sampling points in FW and FWLAB. Starter organisms, especially W. anomalus and L. plantarum comprised a considerable proportion of the yeast and LAB populations, respectively, in both stored grain and fermented feed. However, autochthonous Pichia kudriavzevii and Kazachstania exigua partially dominated the yeast populations in stored grain and fermented feed, respectively.

Interaction of Lactobacillus vini with the ethanol-producing yeasts Dekkera bruxellensis and Saccharomyces cerevisiae

Lactobacillus vini was recently described as a contaminant in industrial ethanol fermentations and its co-occurrence with Dekkera bruxellensis was noted. We investigated the growth characteristics of L. vini in cocultivation together with either Saccharomyces cerevisiae or D. bruxellensis. Lower cell numbers of both the yeasts and L. vini as well as a decrease in ethanol and lactate formation in mixed batch cultures compared with pure cultures were noted. L. vini formed cell aggregates (flocs) in all cultivation media with different shapes in Man–Rogosa–Sharpe and yeast extract–peptone–dextrose media. Flocs’ size and proportion of cells bound to flocs increased with increasing ethanol concentration. In coculture, formation of lactic acid bacteria–yeast cell aggregates consisting of a bacterial core with an outer layer of yeast cells was observed. L. vini–D. bruxellensis flocs had a bigger surface, due to cells protruding from the pseudomycelium. The involvement of mannose residues in the flocculation between L. vini and yeasts was tested. The presence of mannose induced deflocculation in a concentration-dependent manner. Less mannose was required for the deflocculation of D. bruxellensis as compared with S. cerevisiae.

Adaptation of Dekkera bruxellensis to lignocellulose-based substrate

Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192 H in batch and continuous culture, respectively (adapted cells). Cultivations in semisynthetic medium were run as controls (nonadapted cells). To test the adaptation, cells from these cultures were reinoculated in the lignocellulose medium, and growth and ethanol production characteristics were monitored. Cells adapted to lignocellulose hydrolysate had a shorter lag phase, grew faster, and produced a higher ethanol concentration as compared with nonadapted cells. A stability test showed that after cultivation in rich medium, cells partially lost the adapted phenotype but still showed faster growth and higher ethanol production as compared with nonadapted cells. Because alcohol dehydrogenase genes have been described to be involved in the adaptation to furfural in Saccharomyces cerevisiae, an analogous mechanism of adaptation to lignocelluloses hydrolysate of D. bruxellensis was hypothesized. However, gene expression analysis showed that genes homologous to S. cerevisiae ADH1 were not involved in the adaptation to lignocelluloses hydrolysate in D. bruxellensis.

Temperature-dependent changes in the microbial storage flora of birch and spruce sawdust

Sawdust can be used to make pellets (biofuel) and particle boards and as a potential lignocellulose feedstock in bioethanol production. Microbial activity can affect sawdust quality; hence, we monitored the microbial population in birch- and spruce sawdust after 3 months' storage at various temperatures. Species composition was similar on both materials but was strongly influenced by temperature. Bacteria were present on all materials at all conditions: on birch, 2.8 × 10(8) , 1.1 × 10(8) , and 8.8 × 10(6) , and on spruce, 4.1 × 10(8) , 5.6 × 10(7) , and 1.5 × 10(8)  CFU/g DM, at 2, 20, and 37 °C, respectively. Dominant bacteria at 2, 20, and 37 °C were Pseudomonas spp. (some Enterobacteriaceae spp. present), Luteibacter rhizovicinus, and Fulvimonas sp., respectively. Pseudomonas spp. were absent at ≥20 °C. Among microfungi, yeasts dominated at 2 °C but were absent at 37 °C, whereas molds dominated at 20 and 37 °C. Common yeasts included Cystofilobasidium capitatum, Cystofilobasidium infirmominiatum, Candida saitoana, Candida oregonensis, and Candida railenensis. Ophiostoma quercus was a common mold at 2 and 20 °C, whereas the human pathogens Aspergillus fumigatus and Paecilomyces variotii dominated at 37 °C. Attempts to influence the microflora by addition of the biocontrol yeasts, Wickerhamomyces anomalus and Scheffersomyces stipitis, were unsuccessful, as their growth in sawdust was poor to absent.

Strain- and temperature-dependent changes of fatty acid composition in Wickerhamomyces anomalus and Blastobotrys adeninivorans

The fatty acid (FA) profiles of two strains of the yeasts Wickerhamomyces anomalus and Blastobotrys (Arxula) adeninivorans at cultivation temperatures from 15 to 30 °C were characterized. Besides the common even-numbered C16 and C18 FAs, substantial proportions of the uneven-numbered C17:1 were found in both species. C18:3(n-3) (alpha linolenic acid) made up to 3% of the total FAs in all strains. Considerable strain differences occurred, with regard to both the presence of single FAs and parameters like the double binding index (DBI) and C16:C18 ratio. W. anomalus J121 formed C18:1(n-5) (up to 10.9% of the total FAs) but no C18:1(n-7), whereas in W. anomalus VKM160, no C18:1(n-5) was found but up to 14.6% C18:1(n-7). Similarly, B. adeninivorans CBS 8244 formed exclusively C18:1(n-7) (maximum 9%) and CBS 7377 C18:1(n-5) (maximum 12.6%). W. anomalus J121 had the lowest DBI (0.72) at 15 °C and the highest (0.92) at 20 °C, at which point the values decreased with increasing temperatures. In W. anomalus VKM160 and both B. adeninivorans strains, DBI was highest at 15 °C and decreased with increasing temperature. In J121, the C16:C18 ratio was highest at 15 °C, decreasing at higher temperatures, whereas in the other strains, the opposite trend was observed.

Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation

Dekkera bruxellensis can outcompete Saccharomyces cerevisiae in environments with low sugar concentrations. It is usually regarded as a spoilage yeast but has lately been identified as an alternative ethanol production organism. In this study, global gene expression in the industrial isolate D. bruxellensis CBS 11270 under oxygen and glucose limitation was investigated by whole transcriptome sequencing using the AB SOLiD technology. Among other observations, we noted expression of respiratory complex I NADH-ubiquinone reductase although D. bruxellensis is a Crabtree positive yeast. The observed higher expression of NADH-generating enzymes compared to NAD⁺-generating enzymes might be the reason for the previously observed NADH imbalance and resulting Custer effect in D. bruxellensis. Low expression of genes involved in glycerol production is probably the molecular basis for high efficiency of D. bruxellensis metabolism under nutrient limitation. No D. bruxellensis homologs to the genes involved in the final reactions of glycerol biosynthesis were detected. A high number of expressed sugar transporter genes is consistent with the hypothesis that the competitiveness of D. bruxellensis is due to a higher affinity for the limiting substrate.

The influence of nitrate on the physiology of the yeast Dekkera bruxellensis grown under oxygen limitation

A previous study showed that the use of nitrate by Dekkera bruxellensis might be an advantageous trait when ammonium is limited in sugarcane substrate for ethanol fermentation. The aim of the present work was to evaluate the influence of nitrate on the yeast physiology during cell growth in different carbon sources under oxygen limitation. If nitrate was the sole source of nitrogen, D. bruxellensis cells presented slower growth, diminished sugar consumption and growth-associated ethanol production, when compared to ammonium. These results were corroborated by the increased expression of genes involved in the pentose phosphate (PP) pathway, the tricarboxylic acid (TCA) cycle and ATP synthesis. The presence of ammonium in the mixed medium restored most parameters to the standard conditions. This work may open up a line of investigation to establish the connection between nitrate assimilation and energetic metabolism in D. bruxellensis and their influence on its fermentative capacity in oxygen-limited or oxygen-depleted conditions.

Physiological requirements for growth and competitiveness of Dekkera bruxellensis under oxygen-limited or anaerobic conditions

The effect of glucose and oxygen limitation on the growth and fermentation performances of Dekkera bruxellensis was investigated in order to understand which factors favour its propagation in ethanol or wine plants. Although D. bruxellensis has been described as a facultative anaerobe, no growth was observed in mineral medium under complete anaerobiosis while growth was retarded under severe oxygen limitation. In a continuous culture with no gas inflow, glucose was not completely consumed, most probably due to oxygen limitation. When an air/nitrogen mixture (O(2)-content ca. 5%) was sparged to the culture, growth became glucose-limited. In co-cultivations with Saccharomyces cerevisiae, ethanol yields/g consumed sugar were not affected by the co-cultures as compared to the pure cultures. However, different population responses were observed in both systems. In oxygen-limited cultivation, glucose was depleted within 24 h after challenging with S. cerevisiae and both yeast populations were maintained at a stable level. In contrast, the S. cerevisiae population constantly decreased to about 1% of its initial cell number in the sparged glucose-limited fermentation, whereas the D. bruxellensis population remained constant. To identify the requirements of D. bruxellensis for anaerobic growth, the yeast was cultivated in several nitrogen sources and with the addition of amino acids. Yeast extract and most of the supplied amino acids supported anaerobic growth, which points towards a higher nutrient demand for D. bruxellensis compared to S. cerevisiae in anaerobic conditions.

Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities

The ascomycetous yeast Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) exhibits antimicrobial activities and flavoring features that are responsible for its frequent association with food, beverage and feed products. However, limited information on the genetic background of this yeast and its multiple capabilities are currently available. Here, we present the draft genome sequence of the neotype strain W. anomalus DSM 6766. On the basis of pyrosequencing, a de novo assembly of this strain resulted in a draft genome sequence with a total size of 25.47 Mbp. An automatic annotation using RAPYD generated 11 512 protein-coding sequences. This annotation provided the basis to analyse metabolic capabilities, phylogenetic relationships, as well as biotechnologically important features and yielded novel candidate genes of W. anomalus DSM 6766 coding for proteins participating in antimicrobial activities.

Fermentation of lignocellulosic hydrolysate by the alternative industrial ethanol yeast Dekkera bruxellensis

AIM

Testing the ability of the alternative ethanol production yeast Dekkera bruxellensis to produce ethanol from lignocellulose hydrolysate and comparing it to Saccharomyces cerevisiae.

METHODS AND RESULTS

Industrial isolates of D. bruxellensis and S. cerevisiae were cultivated in small-scale batch fermentations of enzymatically hydrolysed steam exploded aspen sawdust. Different dilutions of hydrolysate were tested. None of the yeasts grew in undiluted or 1:2 diluted hydrolysate [final glucose concentration always adjusted to 40 g l⁻¹ (0.22 mol l⁻¹)]. This was most likely due to the presence of inhibitors such as acetate or furfural. In 1:5 hydrolysate, S. cerevisiae grew, but not D. bruxellensis, and in 1:10 hydrolysate, both yeasts grew. An external vitamin source (e.g. yeast extract) was essential for growth of D. bruxellensis in this lignocellulosic hydrolysate and strongly stimulated S. cerevisiae growth and ethanol production. Ethanol yields of 0.42 ± 0.01 g ethanol (g glucose)⁻¹ were observed for both yeasts in 1:10 hydrolysate. In small-scale continuous cultures with cell recirculation, with a gradual increase in the hydrolysate concentration, D. bruxellensis was able to grow in 1:5 hydrolysate. In bioreactor experiments with cell recirculation, hydrolysate contents were increased up to 1:2 hydrolysate, without significant losses in ethanol yields for both yeasts and only slight differences in viable cell counts, indicating an ability of both yeasts to adapt to toxic compounds in the hydrolysate.

CONCLUSIONS

Dekkera bruxellensis and S. cerevisiae have a similar potential to ferment lignocellulose hydrolysate to ethanol and to adapt to fermentation inhibitors in the hydrolysate.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study investigating the potential of D. bruxellensis to ferment lignocellulosic hydrolysate. Its high competitiveness in industrial fermentations makes D. bruxellensis an interesting alternative for ethanol production from those substrates.

Improved bio-energy yields via sequential ethanol fermentation and biogas digestion of steam exploded oat straw

Using standard laboratory equipment, thermochemically pretreated oat straw was enzymatically saccharified and fermented to ethanol, and after removal of ethanol the remaining material was subjected to biogas digestion. A detailed mass balance calculation shows that, for steam explosion pretreatment, this combined ethanol fermentation and biogas digestion converts 85-87% of the higher heating value (HHV) of holocellulose (cellulose and hemicellulose) in the oat straw into biofuel energy. The energy (HHV) yield of the produced ethanol and methane was 9.5-9.8 MJ/(kg dry oat straw), which is 28-34% higher than direct biogas digestion that yielded 7.3-7.4 MJ/(kg dry oat straw). The rate of biogas formation from the fermentation residues was also higher than from the corresponding pretreated but unfermented oat straw, indicating that the biogas digestion could be terminated after only 24 days. This suggests that the ethanol process acts as an additional pretreatment for the biogas process.

Description of Holtermanniella gen. nov., including Holtermanniella takashimae sp. nov. and four new combinations, and proposal of the order Holtermanniales to accommodate tremellomycetous yeasts of the Holtermannia clade

The novel genus Holtermanniella is proposed here to accommodate four Cryptococcus species closely related to Holtermannia corniformis that are included in the Holtermannia clade (Basidiomycota, Agaricomycotina). Thus, four novel combinations are proposed: Holtermanniella nyarrowii comb. nov., Holtermanniella festucosa comb. nov., Holtermanniella mycelialis comb. nov. and Holtermanniella wattica comb. nov. In addition, a novel anamorphic yeast species was studied with 15 isolates obtained from different habitats around the world. Analysis of the sequences of the D1/D2 region of their large subunit rDNA showed that the novel species is placed phylogenetically within the Holtermannia clade of the Tremellomycetes (Agaricomycotina, Basidiomycota). PCR fingerprinting and sequencing of ITS1–5.8S–ITS2 showed genetic intraspecific variability among the strains: three groups were formed, which did not correlate with geographical origin or substrate. This novel species, designated the type species of Holtermanniella gen. nov., is described as Holtermanniella takashimae sp. nov.; the type strain is CBS 11174T (=HB 982T =DBVPG 8012T). The order Holtermanniales ord. nov. is proposed here to include Holtermannia (the type genus) and Holtermanniella.

A mutation in the COX5 gene of the yeast Scheffersomyces stipitis alters utilization of amino acids as carbon source, ethanol formation and activity of cyanide insensitive respiration

Scheffersomyces stipitis PJH was mutagenized by random integrative mutagenesis and the integrants were screened for lacking the ability to grow with glutamate as sole carbon source. One of the two isolated mutants was damaged in the COX5 gene, which encodes a subunit of the cytochrome c oxidase. BLAST searches in the genome of Sc. stipitis revealed that only one singular COX5 gene exists in Sc. stipitis, in contrast to Saccharomyces cerevisiae, where two homologous genes are present. Mutant cells had lost the ability to grow with the amino acids glutamate, proline or aspartate and other non-fermentable carbon sources, such as acetic acid and ethanol, as sole carbon sources. Biomass formation of the mutant cells in medium containing glucose or xylose as carbon source was lower compared with the wild-type cells. However, yields and specific ethanol formation of the mutant were much higher, especially under conditions of higher aeration. The mutant cells lacked both cytochrome c oxidase activity and cyanide-sensitive respiration, whereas ADH and PDC activities were distinctly enhanced. SHAM-sensitive respiration was obviously essential for the fermentative metabolism, because SHAM completely abolished growth of the mutant cells with both glucose or xylose as carbon source.

Pichia anomala in grain biopreservation

Cereal grain is a major component of food and feed in large parts of the world. The microbial flora on cereal grains may interfere with hygiene and storage stability, palatability and bioavailability of minerals and proteins may depend on the composition of the microbial population. Therefore, it is of primary interest to control the microbial species present on cereal grain. Inoculation of the biocontrol yeast Pichia anomala to cereal feed grain improved feed hygiene by reduction of moulds and Enterobacteriaceae, and enhanced the nutritional value by increasing the protein content and reducing the concentration of the antinutritional compound phytate. P. anomala strains showed a high phytase activity, for some strains also considerable extracellular phytase activity was observed. A certain maximum in biomass concentration was never exceeded indicating cell density induced growth inhibition of P. anomala.

Cryptococcus cerealis sp. nov. a psychrophilic yeast species isolated from fermented cereals

Two yeast strains isolated in 2007 from fermented pig feed were studied, including the analysis of sequences of the D1/D2 and ITS-regions of the rDNA-repeats, their morphology and nutritional physiology. Sequence comparison of the D1/D2 and ITS regions demonstrated that the strains do not belong to any known species. Therefore, a new species, Cryptococcus cerealis with the type strain CBS 10505, is proposed. The species belongs to Filobasidiales (Agaricomycetes, Basidiomycota), and has Cryptococcus saitoi as the closest related species. The new species is psychrophilic, showing significant growth at 4 and 10 degrees C.