Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

Lipomyces tetrasporous is an oleaginous yeast that can utilize a variety of plant-based sugars. It accumulates lipids during growth on lignocellulosic biomass hydrolysates. We present the annotated genome sequence of L. tetrasporous NRRL Y-64009 to aid in its development as a platform organism for producing lipids and lipid-based bioproducts.

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33-9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032-0.131 (g/g) and lipid contents were 13.5-53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

SUMMARY

The yeast Rhodotorula toruloides was used to produce oil using sugars extracted from a bioenergy grass.

A survey of yeast from the Yarrowia clade for lipid production in dilute acid pretreated lignocellulosic biomass hydrolysate

Yarrowia lipolytica is an oleaginous yeast species that has attracted attention as a model organism for synthesis of single cell oil. Among over 50 isolates of Y. lipolytica identified, only a few of the strains have been studied extensively. Furthermore, 12 other yeast species were recently assigned to the Yarrowia clade, and most are not well characterized in terms of cell growth and lipid accumulation, especially in industrially relevant conditions. In the present study, we investigated biomass and lipid production by 57 yeast isolates, representing all 13 species in the Yarrowia clade, on a non-detoxified dilute acid-pretreated switchgrass hydrolysate under highly aerobic conditions. The objective was to compare yeast physiology during growth in an abundant, low-cost biomass feedstock and to expand diversity of genetically tractable, oleaginous yeasts available for lipid research. Screening of 45 Y. lipolytica isolates demonstrated considerable variation within the species in terms of lipid accumulation (min = 0.1 g/L; max = 5.1 g/L; mean = 2.3 g/L); three strains (NRRL YB-420, YB-419, and YB-392) were especially promising for cellulosic biomass conversion with average improvements of 43, 57, and 64%, respectively, in final lipid titer as compared to control strain W29. Subsequently, evaluation of strains from 13 distinct species in the Yarrowia clade identified Candida phangngensis PT1-17 as the top lipid producer with a maximum titer of 9.8 g/L lipid, which was over twofold higher than the second-best species in the clade (Candida hollandica NRRL Y-48254). A small set of the most promising strains from the screenings was further characterized to evaluate inhibitor tolerance, lipid production kinetics, and fatty acid distribution. We expect that the results of this study will pave the way for new biotechnological applications involving previously overlooked and under-characterized strains within the Yarrowia clade.

Techniques for the Evolution of Robust Pentose-fermenting Yeast for Bioconversion of Lignocellulose to Ethanol

Lignocellulosic biomass is an abundant, renewable feedstock useful for production of fuel-grade ethanol and other bio-products. Pretreatment and enzyme saccharification processes release sugars that can be fermented by yeast. Traditional industrial yeasts do not ferment xylose (comprising up to 40% of plant sugars) and are not able to function in concentrated hydrolyzates. Concentrated hydrolyzates are needed to support economical ethanol recovery, but they are laden with toxic byproducts generated during pretreatment. While detoxification methods can render hydrolyzates fermentable, they are costly and generate waste disposal liabilities. Here, adaptive evolution and isolation techniques are described and demonstrated to yield derivatives of the native Scheffersomyces stipitis strain NRRL Y-7124 that are able to efficiently convert hydrolyzates to economically recoverable ethanol despite adverse culture conditions. Improved individuals are enriched in an evolving population using multiple selection pressures reliant on natural genetic diversity of the S. stipitis population and mutations induced by exposures to two diverse hydrolyzates, ethanol or UV radiation. Final evolution cultures are dilution plated to harvest predominant isolates, while intermediate populations, frozen in glycerol at various stages of evolution, are enriched on selective media using appropriate stress gradients to recover most promising isolates through dilution plating. Isolates are screened on various hydrolyzate types and ranked using a novel procedure involving dimensionless relative performance index (RPI) transformations of the xylose uptake rate and ethanol yield data. Using the RPI statistical parameter, an overall relative performance average is calculated to rank isolates based on multiple factors, including culture conditions (varying in nutrients and inhibitors) and kinetic characteristics. Through application of these techniques, derivatives of the parent strain had the following improved features in enzyme saccharified hydrolyzates at pH 5-6: reduced initial lag phase preceding growth, reduced diauxic lag during glucose-xylose transition, significantly enhanced fermentation rates, improved ethanol tolerance and accumulation to 40 g/L.

Conversion of SPORL pretreated Douglas fir forest residues into microbial lipids with oleaginous yeasts

Sugars were extracted from Douglas fir residues using SPORL pretreatment and cellulases. The sugars were converted to lipids producing a titer of 13.4 g l⁻¹ in 3 d using a 2-stage culture.

Evolved strains of Scheffersomyces stipitis achieving high ethanol productivity on acid- and base-pretreated biomass hydrolyzate at high solids loading

BACKGROUND

Lignocellulosic biomass is an abundant, renewable feedstock useful for the production of fuel-grade ethanol via the processing steps of pretreatment, enzyme hydrolysis, and microbial fermentation. Traditional industrial yeasts do not ferment xylose and are not able to grow, survive, or ferment in concentrated hydrolyzates that contain enough sugar to support economical ethanol recovery since they are laden with toxic byproducts generated during pretreatment.

RESULTS

Repetitive culturing in two types of concentrated hydrolyzates was applied along with ethanol-challenged xylose-fed continuous culture to force targeted evolution of the native pentose fermenting yeast Scheffersomyces (Pichia) stipitis strain NRRL Y-7124 maintained in the ARS Culture Collection, Peoria, IL. Isolates collected from various enriched populations were screened and ranked based on relative xylose uptake rate and ethanol yield. Ranking on hydrolyzates with and without nutritional supplementation was used to identify those isolates with best performance across diverse conditions.

CONCLUSIONS

Robust S. stipitis strains adapted to perform very well in enzyme hydrolyzates of high solids loading ammonia fiber expansion-pretreated corn stover (18% weight per volume solids) and dilute sulfuric acid-pretreated switchgrass (20% w/v solids) were obtained. Improved features include reduced initial lag phase preceding growth, significantly enhanced fermentation rates, improved ethanol tolerance and yield, reduced diauxic lag during glucose-xylose transition, and ability to accumulate >40 g/L ethanol in <167 h when fermenting hydrolyzate at low initial cell density of 0.5 absorbance units and pH 5 to 6.

Microbial lipid production from AFEX™ pretreated corn stover

Comparison of cellulosic ethanol and cellulosic lipid production from corn stover.

Microbial lipid-based lignocellulosic biorefinery: feasibility and challenges

Although single-cell oil (SCO) has been studied for decades, lipid production from lignocellulosic biomass has received substantial attention only in recent years as biofuel research moves toward producing drop-in fuels. This review gives an overview of the feasibility and challenges that exist in realizing microbial lipid production from lignocellulosic biomass in a biorefinery. The aspects covered here include biorefinery technologies, the microbial oil market, oleaginous microbes, lipid accumulation metabolism, strain development, process configurations, lignocellulosic lipid production, technical hurdles, lipid recovery, and technoeconomics. The lignocellulosic SCO-based biorefinery will be feasible only if a combination of low- and high-value lipids are coproduced, while lignin and protein are upgraded to high-value products.

Selection of Biocontrol Agents of Pink Rot Based on Efficacy and Growth Kinetics Index Rankings

The microbiota of 84 different agricultural soils were transferred to separate samples of a γ irradiation-sterilized field soil enriched with potato periderm, and the resulting soils were assayed for biological suppressiveness to Phytophthora erythroseptica and their effect on zoospore production. The 13 most suppressive soil samples, which reduced zoospore production by 14 to 93% and disease severity on tubers by 6 to 21%, were used to isolate 279 organisms. Fourteen strains that reduce pink rot infections in preliminary tests were selected for further study. Six bacterial strains that reduced the severity of disease (P ≤ 0.05, Fischer's protected least significant difference) in subsequent tests were identified as Bacillus simplex (three strains), Pantoea agglomerans, Pseudomonas koreensis, and P. lini. Relative performance indices (RPIs) for biocontrol efficacy and for each of four kinetic parameters, including total colony-forming units (CFU_max), biomass production values (DW_max), cell production after 8 h (OD₈), and time of recovery from oxygen depletion (DT) were calculated for each strain. Overall RPI_Eff,Kin values for each strain then were calculated using strain RPI values for both efficacy (RPI_Eff) and kinetics (RPI_Kin). Strains with the highest RPI_Eff,Kin possess the best biocontrol efficacy of the strains tested and liquid culture growth characteristics that suggest commercial development potential.

Measurement of oxygen solubility in fermentation media: a colorimetric method

Methods of measuring oxygen solubility in culture media are scarce, and those available are tedious to apply. A simple colorimetric assay was developed and applied to the analysis of oxygen solubility during alcoholic fermentation. The method was based on the consumption of oxygen by glucose oxidase activity and the production of the pink quinone of syringaldazine by coupled peroxidase activity. Color formation at 526 nm progressed through an optimum that was a linear function of the oxygen added to the assay. Sensitivity was maximized by operating at pH 7 and limiting the medium sample volume added. Each assay took 10-15 min to prepare and react. Reaction time was minimized by using abundant glucose and enzyme concentrations. Data obtained by the assay developed showed good agreement with published oxygen solubilities in water and selected media at various temperatures. Subsequent analyses of fermentation broths indicated falling sugar concentration to be primarily responsible for increases in oxygen solubility during fermentation. For example, during fermentations started with 230 g/L xylose or glucose, oxygen solubility could increase by 41% due to sugar consumption alone. This procedure can provide the solubility data needed to accurately calibrate in-line electronic probes for monitoring dissolved oxygen concentration during fermentation processes.

Production of 3-hydroxypropionaldehyde from glycerol

3-Hydroxypropionaldehyde is a precursor to acrolein, which can be used as an intermediate for making acrylic acid and a variety of other useful industrial chemicals. Conversion of glycerol, a renewable resource, to 3-hydroxypropionaldehyde was attempted via action of glycerol dehydrase isolated from Lactobacillus sp. strain NRRL B-1720. This method, however, was unsatisfactory because enzyme activity was lost within 60 to 90 min after the reaction initiation. Fermentation of glycerol by whole cells of Klebsiella pneumoniae NRRL B-199 in the presence of optimal semicarbazide hydrochloride proved more effective. Using this technique, glycerol solutions of 30 g/liter yielded 3-hydroxypropionaldehyde solutions of 13.1 g/liter. Thus, a conversion efficiency equal to 55% of the theoretical maximum was realized.

Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae

BACKGROUND

Biofuels offer a viable alternative to petroleum-based fuel. However, current methods are not sufficient and the technology required in order to use lignocellulosic biomass as a fermentation substrate faces several challenges. One challenge is the need for a robust fermentative microorganism that can tolerate the inhibitors present during lignocellulosic fermentation. These inhibitors include the furan aldehyde, furfural, which is released as a byproduct of pentose dehydration during the weak acid pretreatment of lignocellulose. In order to survive in the presence of furfural, yeast cells need not only to reduce furfural to the less toxic furan methanol, but also to protect themselves and repair any damage caused by the furfural. Since furfural tolerance in yeast requires a functional pentose phosphate pathway (PPP), and the PPP is associated with reactive oxygen species (ROS) tolerance, we decided to investigate whether or not furfural induces ROS and its related cellular damage in yeast.

RESULTS

We demonstrated that furfural induces the accumulation of ROS in Saccharomyces cerevisiae. In addition, furfural was shown to cause cellular damage that is consistent with ROS accumulation in cells which includes damage to mitochondria and vacuole membranes, the actin cytoskeleton and nuclear chromatin. The furfural-induced damage is less severe when yeast are grown in a furfural concentration (25 mM) that allows for eventual growth after an extended lag compared to a concentration of furfural (50 mM) that prevents growth.

CONCLUSION

These data suggest that when yeast cells encounter the inhibitor furfural, they not only need to reduce furfural into furan methanol but also to protect themselves from the cellular effects of furfural and repair any damage caused. The reduced cellular damage seen at 25 mM furfural compared to 50 mM furfural may be linked to the observation that at 25 mM furfural yeast were able to exit the furfural-induced lag phase and resume growth. Understanding the cellular effects of furfural will help direct future strain development to engineer strains capable of tolerating or remediating ROS and the effects of ROS.

Growth, death, and oxygen uptake kinetics of Pichia stipitis on xylose

Pichia stipitis NRRL Y-7124 has potential application in the fermentation of xylose-rich waste streams, produced by wood hydrolysis. Kinetic models of cell growth, death, and oxygen uptake were investigated in batch and oxygen-limited continuous cultures fed a rich synthetic medium. Variables included rates of dilution (D) and oxygen transfer (K(1)a) and concentrations of xylose (X), ethanol (E), and dissolved oxygen (C(ox)). Sustained cell growth required the presence of oxygen. Given excess xylose, specific growth rate (micro) was a Monod function of C(ox). Specific oxygen uptake rate was proportional to mu by a yield coefficient relating biomass production to oxygen consumption; but oxygen uptake for maintenance was negligible. Thus steady-state C(OX) depended only on D, while steady-state biomass concentration was controlled by both D and K(1)a. Given excess oxygen, cells grew subject to Monod limitation by xylose, which became inhibitory above 40 g/L. Ethanol inhibition was consistent with Luong's model, and 64. 3 g/L was the maximum ethanol concentration allowing growth. Actively growing cells died at a rate that was 20% of micro. The dying portion increased with E and X.

Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae

Furfural and 5-hydroxymethylfurfural (HMF) are representative inhibitors generated from biomass pretreatment using dilute acid hydrolysis that interfere with yeast growth and subsequent fermentation. Few yeast strains tolerant to inhibitors are available. In this study, we report a tolerant strain, Saccharomyces cerevisiae NRRL Y-50049, which has enhanced biotransformation ability to convert furfural to furan methanol (FM), HMF to furan di-methanol (FDM), and produce a normal yield of ethanol. Our recent identification of HMF and development of protocol to synthesize the HMF metabolic conversion product FDM allowed studies on fermentation metabolic kinetics in the presence of HMF and furfural. Individual gene-encoding enzymes possessing aldehyde reduction activities demonstrated cofactor preference for NADH or NADPH. However, protein extract from whole yeast cells showed equally strong aldehyde reduction activities coupled with either cofactor. Deletion of a single candidate gene did not affect yeast growth in the presence of the inhibitors. Our results suggest that detoxification of furfural and HMF by the ethanologenic yeast S. cerevisiae strain Y-50049 likely involves multiple gene mediated NAD(P)H-dependent aldehyde reduction. Conversion pathways of furfural and HMF relevant to glycolysis and ethanol production were refined based on our findings in this study.

Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR

Gene expression analysis provides significant insight to understand regulatory mechanisms of biology, yet acquisition and reproduction of quality data, as well as data confirmation and verification remain challenging due to a lack of proper quality controls across different assay platforms. We present a set of six universal external RNA quality controls for microbial mRNA expression analysis that can be applied to both DNA oligo microarray and real-time qRT-PCR including using SYBR Green and TaqMan probe-based chemistry. This set of controls was applied for Saccharomyces cerevisiae and Pseudomonas fluorescens Pf-5 microarray assays and qRT-PCR for yeast gene expression analysis. Highly fitted linear relationships between detected signal intensity and mRNA input were described. Valid mRNA detection range, from 10 to 7000 pg and from 100 fg to 1000 pg were defined for microarray and qRT-PCR assay, respectively. Quantitative estimation of mRNA abundance was tested using randomly selected yeast ORF including function unknown genes using the same source of samples by the two assay platforms. Estimates of mRNA abundance by the two methods were similar and highly correlated in an overlapping detection range from 10 to 1000 pg. The universal external RNA controls provide a means to compare microbial gene expression data derived from different experiments and different platforms for verification and confirmation. Such quality controls ensure reliability and reproducibility of gene expression data, and provide unbiased normalization reference for validation, quantification, and estimate of variation of gene expression experiments. Application of these controls also improves efficiency and facilitates high throughput applications of gene expression analysis using the qRT-PCR assay.

Nitrogen source and mineral optimization enhance d-xylose conversion to ethanol by the yeast Pichia stipitis NRRL Y-7124

Nutrition-based strategies to optimize xylose to ethanol conversion by Pichia stipitis were identified in growing and stationary-phase cultures provided with a defined medium varied in nitrogen, vitamin, purine/pyrimidine, and mineral content via full or partial factorial designs. It is surprising to note that stationary-phase cultures were unable to ferment xylose (or glucose) to ethanol without the addition of a nitrogen source, such as amino acids. Ethanol accumulation increased with arginine, alanine, aspartic acid, glutamic acid, glycine, histidine, leucine, and tyrosine, but declined with isoleucine. Ethanol production from 150 g/l xylose was maximized (61+/-9 g/l) by providing C:N in the vicinity of approximately 57-126:1 and optimizing the combination of urea and amino acids to supply 40-80 % nitrogen from urea and 60-20 % from amino acids (casamino acids supplemented with tryptophan and cysteine). When either urea or amino acids were used as sole nitrogen source, ethanol accumulation dropped to 11 or 24 g/l, respectively, from the maximum of 46 g/l for the optimal nitrogen combination. The interaction of minerals with amino acids and/or urea was key to optimizing ethanol production by cells in both growing and stationary-phase cultures. In nongrowing cultures supplied with nitrogen as amino acids, ethanol concentration increased from 24 to 54 g/l with the addition of an optimized mineral supplement of Fe, Mn, Mg, Ca, Zn, and others.

Proline-based modulation of 2,4-diacetylphloroglucinol and viable cell yields in cultures of Pseudomonas fluorescens wild-type and over-producing strains

The antifungal compound 2,4-diacetylphloroglucinol (DAPG) is produced in the rhizosphere of wheat by pseudomonad populations responsible for the natural biological control phenomenon known as "take-all decline." Studies were conducted to elucidate the impact of DAPG and its co-product 2,4,6-trihydroxyacetophenone (THA) on the production of Pseudomonas fluorescens for biological control. Increasing DAPG from 0.1 g/l to 0.5 g/l and THA from 0.05 g/l to 0.5 g/l significantly inhibited the growth and lowered the yield of viable bacteria in liquid cultures. On further examination of these metabolites applied in seed coatings, levels of DAPG and THA exceeding 0.05 mg/g seed significantly reduced wheat germination percentages. The three-way interaction of DAPG, THA, and culture medium ingredients was significant, and greatest seed germination loss (40-50%) was observed when 0.5 mg DAPG and 0.25 mg THA were combined in a coating of 0.5 ml culture medium per gram of seed. Based on the results of Biolog GN microplate, flask, and fermentor screens of C sources, proline was found to optimize the viable cell yields of the P. fluorescens strains tested. The combination of proline with glucose and urea as C and N sources in growth media could be optimized to minimize DAPG production and maximize the vitality of P. fluorescens Q8R1-96 and Q69c-80:miniTn5:phl20 (DAPG over-producer). In production cultures, the proline supply rate offers a potentially useful means to optimize the biological control agent yield and quality.

Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPE1, and TKL1 in Saccharomyces cerevisiae

Engineering yeast to be more tolerant to fermentation inhibitors, furfural and 5-hydroxymethylfurfural (HMF), will lead to more efficient lignocellulose to ethanol bioconversion. To identify target genes involved in furfural tolerance, a Saccharomyces cerevisiae gene disruption library was screened for mutants with growth deficiencies in the presence of furfural. It was hypothesized that overexpression of these genes would provide a growth benefit in the presence of furfural. Sixty two mutants were identified whose corresponding genes function in a wide spectrum of physiological pathways, suggesting that furfural tolerance is a complex process. We focused on four mutants, zwf1, gnd1, rpe1, and tkl1, which represent genes encoding pentose phosphate pathway (PPP) enzymes. At various concentrations of furfural and HMF, a clear association with higher sensitivity to these inhibitors was demonstrated in these mutants. PPP mutants were inefficient at reducing furfural to the less toxic furfuryl alcohol, which we propose is a result of an overall decreased abundance of reducing equivalents or to NADPH's role in stress tolerance. Overexpression of ZWF1 in S. cerevisiae allowed growth at furfural concentrations that are normally toxic. These results demonstrate a strong relationship between PPP genes and furfural tolerance and provide additional putative target genes involved in furfural tolerance.

Carbon-to-Nitrogen Ratio and Carbon Loading of Production Media Influence Freeze-Drying Survival and Biocontrol Efficacy of Cryptococcus nodaensis OH 182.9

ABSTRACT Fusarium head blight (FHB), caused by Gibberella zeae, is a devastating disease of wheat worldwide. Cryptococcus nodaensis OH 182.9 is an effective biocontrol agent for this disease. Development of a dried product of OH 182.9 would have potential advantages of ease of handling, favorable economics, and acceptance by end users. Isolate OH 182.9 was grown for 48 and 72 h in semi-defined complete liquid (SDCL) medium with carbon-to-nitrogen (C/N) ratios of 6.5:1, 9:1, 11:1, 15:1, and 30:1, and in SDCL C/N 30:1 media with varied carbon loadings of 7, 14, 21, and 28 g/liter. Total biomass production and cell survival at 15 days after freeze-drying were evaluated. Biomass production of OH 182.9 (CFU per milliliter) was not different for all cultivation time by medium C/N or carbon loading combinations. In general, cells harvested at 48 h survived freeze-drying better than those harvested at 72 h. Survival of freeze-dried cells was greatest for cells grown for 48 h in C/N30:1 medium. Cells produced in C/N 6.5:1 medium generally exhibited the poorest survival. For the C/N 30:1 media, cells from 7 g/liter carbon loading medium harvested after 48 h had the best survival after freeze-drying. The difference in freeze-dried cell populations between superior and inferior treatments was typically 1 to 2 log units at 15 days after freeze-drying. The biomass of OH 182.9 produced in SDCL with varied C/N ratios and in SDCL C/N 30:1 media with differing carbon loadings was tested for biocontrol efficacy against FHB in greenhouse studies. The biomass harvested from SDCL C/N 9:1, 11:1, and 15:1 media after 48 h significantly reduced symptoms of FHB. None of the treatments with cells harvested at 72 h consistently reduced FHB severity (P </= 0.05). Cells grown in SDCL C/N 30:1 media with 7 and 14 g/liter carbon loading significantly reduced FHB disease severity. Cells harvested from SDCL C/N 9:1, 11:1, and 30:1 with 14 g/liter carbon increased the 100-kernel weight compared with the disease control. The potential of improving OH 182.9 product quality via management of the nutritional environment of the production medium is demonstrated in this study.

Enhanced biotransformation of furfural and hydroxymethylfurfural by newly developed ethanologenic yeast strains

Furfural and hydroxymethylfurfural (HMF) are representative inhibitors among many inhibitive compounds derived from biomass degradation and saccharification for bioethanol fermentation. Most yeasts, including industrial strains, are susceptible to these inhibitory compounds, especially when multiple inhibitors are present. Additional detoxification steps add cost and complexity to the process and generate additional waste products. To promote efficient bioethanol production, we studied the mechanisms of stress tolerance, particularly to fermentation inhibitors such as furfural and HMF. We recently reported a metabolite of 2,5-bis-hydroxymethylfuran as a conversion product of HMF and characterized a dose-dependent response of ethanologenic yeasts to inhibitors. In this study, we present newly adapted strains that demonstrated higher levels of tolerance to furfural and HMF. Saccharomyces cerevisiae 307-12H60 and 307-12H120 and Pichia stipitis 307 10H60 showed enhanced biotransformation ability to reduce HMF to 2,5-bis-hydroxymethylfuran at 30 and 60 mM, and S. cerevisiae 307-12-F40 converted furfural into furfuryl alcohol at significantly higher rates compared to the parental strains. Strains of S. cerevisiae converted 100% of HMF at 60 mM and S. cerevisiae 307-12-F40 converted 100% of furfural into furfuryl alcohol at 30 mM. The results of this study suggest a possible in situ detoxification of the inhibitors by using more inhibitor-tolerant yeast strains for bioethanol fermentation. The development of such tolerant strains provided a basis and useful materials for further studies on the mechanisms of stress tolerance.

Antifungal and sprout regulatory bioactivities of phenylacetic acid, indole-3-acetic acid, and tyrosol isolated from the potato dry rot suppressive bacterium Enterobacter cloacae S11:T:07

Enterobacter cloacae S11: T:07 (NRRL B-21050) is a promising biological control agent that has significantly reduced both fungal dry rot disease and sprouting in laboratory and pilot potato storages. The metabolites phenylacetic acid (PAA), indole-3-acetic acid (IAA), and tyrosol (TSL) were isolated from S11:T:07 liquid cultures provided with three different growth media. The bioactivities of these metabolites were investigated via thin-layer chromatography bioautography of antifungal activity, wounded potato assays of dry rot suppressiveness, and cored potato eye assays of sprout inhibition. Relative accumulations of PAA, IAA, and TSL in cultures were nutrient dependent. For the first time, IAA, TSL, and PAA were shown to have antifungal activity against the dry rot causative pathogen Gibberella pulicaris, and to suppress dry rot infection of wounded potatoes. Disease suppression was optimal when all three metabolites were applied in combination. Dosages of IAA that resulted in disease suppression also resulted in sprout inhibition. These results suggest the potential for designing culture production and formulation conditions to achieve a dual purpose biological control agent able to suppress both dry rot and sprouting of stored potatoes.

Formulation of Bacillus spp. for Biological Control of Plant Diseases

ABSTRACT Maximizing the potential for successfully developing and deploying a biocontrol product begins with a carefully crafted microbial screening procedure, proceeds with developing mass production protocols that optimize product quantity and quality, and ends with devising a product formulation that preserves shelf-life, aids product delivery, and enhances bioactivity. Microbial selection procedures that require prospective bio-control agents to possess both efficacy and amenability to production in liquid culture increase the likelihood of selecting agents with enhanced commercial development potential. Scale-up of biomass production procedures must optimize product quantity without compromise of product efficacy or amenability to stabilization and formulation. Formulation of Bacillus spp. for use against plant pathogens is an enormous topic in general terms but limited in published specifics regarding formulations used in commercially available products. Types of formulations include dry products such as wettable powders, dusts, and granules, and liquid products including cell suspensions in water, oils, and emulsions. Cells can also be microencapsulated. Considerations critical to designing successful formulations of microbial biomass are many fold and include preserving biomass viability during stabilization, drying, and rehydration; aiding biomass delivery, target coverage, and target adhesion; and enhancing biomass survival and efficacy after delivery to the target. Solutions to these formulation considerations will not necessarily be compatible. Data from several biocontrol systems including the use of B. subtilis OH 131.1 (NRRL B-30212) to reduce Fusarium head blight of wheat are used to illustrate many of these issues. Using our recently described assay for efficiently evaluating biomass production and formulation protocols, we demonstrate the effectiveness, in vitro, of UV protectant compounds lignin (PC 1307) and Blankophor BBH in reducing OH 131.1 morbidity when cells were exposed to UV light from artificial sunlight.

Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran

Renewable lignocellulosic materials are attractive low-cost feedstocks for bioethanol production. Furfural and 5-hydroxymethylfurfural (HMF) are among the most potent inhibitory compounds generated from acid hydrolysis of lignocelluloses to simple sugars for fermentation. In Saccharomyces cerevisiae ATCC 211239 and NRRL Y-12632 and Pichia stipitis NRRL Y-7124, furfural and HMF inhibition were determined to be dose-dependent at concentrations from 10 to 120 mM. The yeast strains were more sensitive to inhibition by furfural than HMF at the same concentration, while combined treatment of furfural and HMF synergistically suppressed cell growth. A metabolite transformed from HMF by strain NRRL Y-12632 was isolated from the culture supernatant, and conclusively identified as 2,5-bis-hydroxymethylfuran, a previously postulated HMF alcohol, with a composition of C6H8O3 and a molecular weight of 128. It is proposed that, in the presence of HMF, the yeast reduces the aldehyde group on the furan ring of HMF into an alcohol, in a similar manner as for furfural. The accumulation of this biotransformed metabolite may be less toxic to yeast cultures than HMF, as evidenced by the rapid yeast fermentation and growth rates associated with HMF conversion. The ability of yeasts to adapt to and transform furfural and HMF offers the potential for in situ detoxification of these inhibitors and suggests a genetic basis for further development of highly tolerant strains for biofuel production.

Greenhouse and Field Evaluation of Biological Control of Fusarium Head Blight on Durum Wheat

Fusarium head blight (FHB) is a devastating disease that causes extensive yield and quality losses to wheat and barley. In durum wheat, the pathogen-produced toxin deoxynivalenol (DON) is retained in semolina at ˜50%, and the causal agent of FHB, Gibberella zeae, has a strong adverse effect on pasta color. Two bacteria and two yeast strains with known efficacy against G. zeae on hexaploid wheats were produced in liquid culture and assayed on two cultivars of durum wheat in greenhouse bioassays. All antagonists reduced FHB severity on cultivar Renville, and three of the four reduced severity on cultivar Ben, with Bacillus subtilis strain AS 43.3 decreasing FHB severity by as much as 90%. In separate greenhouse bioassays, the car-bon:nitrogen ratio of the medium used to produce antagonists did not consistently influence antagonist efficacy. All antagonist/production medium combinations but one were effective in reducing disease on both durum cultivars. Of six antagonists tested at field sites, Cryptococcus sp. OH 71.4 and C. nodaensis OH 182.9 reduced disease severity by as much as 57% in Peoria, IL, while Cryptococcus sp. OH 181.1 reduced disease severity by as much as 59% in a trial at Langdon, ND. Antagonists did not influence the DON content of grain in the Peoria trial. Relative performance indices for four antagonists calculated from greenhouse and field results on the two durum cultivars demonstrated that the bioassay location, but not the cultivar of durum, influenced the relative performance of antagonists. Yeast antagonists OH 71.4, OH 181.1, and OH 182.9 appear to have the highest potential for contributing to the reduction of FHB on du-rum wheat in the field.

Selection and Evaluation of Microorganisms for Biocontrol of Fusarium Head Blight of Wheat Incited by Gibberella zeae

Gibberella zeae incites Fusarium head blight (FHB), a devastating disease that causes extensive yield and quality losses to wheat and barley. Of over 700 microbial strains obtained from wheat anthers, 54 were able to utilize tartaric acid as a carbon source when the compound was supplied as choline bitartrate in liquid culture. Four tartaric acid-utilizing and three nonutilizing strains reduced FHB in initial tests and were selected for further assays. Antagonists were effective against three different isolates of G. zeae when single wheat florets were inoculated with pathogen and antagonist inoculum. All seven antagonists increased 100-kernel weight when applied simultaneously with G. zeae isolate Z3639 (P ≤ 0.05). Bacillus strains AS 43.3 and AS 43.4 and Cryptococcus strain OH 182.9 reduced disease severity by >77, 93, and 56%, respectively. Five antagonists increased 100-kernel weight of plants inoculated with G. zeae isolate DAOM 180378. All antagonists except one increased 100-kernel weight, and four of seven antagonists reduced disease severity (P ≤ 0.05) when tested against G. zeae isolate Fg-9-96. In spray-inoculation experiments, Bacillus strains AS 43.3 and AS 43.4 and Cryptococcus strains OH 71.4 and OH 182.9 reduced disease severity, regardless of the sequence, timing, and concentration of inoculum application (P ≤ 0.05), though 100-kernel weight did not always increase when antagonists were applied 4 h after inoculum of G. zeae. Overall, 4 of 54 isolates that utilized tartaric acid in vitro were effective against G. zeae versus only 3 of 170 isolates tested that did not utilize tartaric acid (P ≤ 0.05, χ-square test of goodness of fit), demonstrating the potential benefit of prescreening candidate antagonists of FHB for their ability to utilize tartaric acid. Biological control shows promise as part of an integrated pest management program for managing FHB.

Isolation, identification, and accumulation of 2-acetamidophenol in liquid cultures of the wheat take-all biocontrol agent Pseudomonas fluorescens 2-79

Pseudomonas fluorescens strain 2-79 (NRRL B-15132) is a classic biological control agent known to produce phenazine-l-carboxylic acid (PCA) as its primary means of suppressing take-all disease of wheat. In addition to PCA, an unknown metabolite was discovered in a liquid culture used to produce the biocontrol agent. The objective of the current study was to isolate, identify, and evaluate the accumulation of this compound in production cultures. Upon centrifugal fractionation of a production culture, thin-layer chromatography (TLC) analyses of extracts of the cells and cell-free supernatant indicated the compound to be primarily in the supernatant. Purified compound was obtained by extraction of culture supernatant, followed by flash chromatography of the extract and preparative TLC. The 'H and 13C nuclear magnetic resonance and electron impact mass spectra indicated the compound to be 2-acetamidophenol (AAP). Measured by reversed-phase HPLC, the accumulations of AAP and PCA in cultures of strain 2-79 reached 0.05 g/l and 1 g/l, respectively. The accumulations of AAP and PCA in liquid cultures were linearly correlated (P < 0.001), as shown by studies of cultures stimulated to yield varying levels of PCA by controlling levels of oxygen transfer, pH, and growth medium composition. In this study, oxygen limitation, a defined amino-acid-free medium, and neutral pH stimulated maximal production of both AAP and PCA. Furthermore, a transposon mutant of 2-79 [2A40 2-79 (phz-)] unable to produce PCA did not accumulate AAP. These findings indicate that AAP and PCA are likely to share a common segment of biosynthetic pathway. This is the first report of AAP production by a strain of P. fluorescens. Possible routes of AAP production are discussed relative to current knowledge of the phenazine biosynthetic pathway of strain 2-79. The pertinence of AAP to the design of commercial seed inoculants of phenazine-producing bacteria for controlling wheat take-all is also considered.

Effects of antagonist cell concentration and two-strain mixtures on biological control of fusarium dry rot of potatoes

ABSTRACT Eighteen bacterial strains were individually assayed against Gibberella pulicaris (5 x 10(5) conidia per ml) by coinoculating antagonist and pathogen in wounds in cv. Russet Burbank potatoes. All antagonist concentrations (10(6), 10(7), and 10(8) CFU/ml) decreased disease (38 to 76% versus control, P < 0.05). When four strains were assayed at 11 concentrations (range 10(5) to 10(8) CFU/ml) against G. pulicaris, linear regression of the log-dose, log-response data was significant for all four strains (P < 0.001 to 0.01, R(2) = 0.50 to 0.74). Challenging G. pulicaris with all possible antagonist pairings within 2 sets of 10 antagonist strains (5 x 10(5) CFU of each strain per ml) resulted in 16 of 90 pairs controlling disease better than predicted based on averaging the performance of the individual strains making up the pair (P < 0.10). Successful pairs reduced disease by ~70% versus controls, a level of control comparable to that obtained with 100 times the inoculum dose of a single antagonist strain. Neither strain genus nor soil of origin were useful in predicting successful antagonist pairs. Factors potentially influencing dose-response relationships and the effectiveness of antagonist pairs in controlling disease are discussed.

Liquid-culture pH, temperature, and carbon (not nitrogen) source regulate phenazine productivity of the take-all biocontrol agent Pseudomonas fluorescens 2-79

Strain 2-79 is a biocontrol agent against take-all, an important disease of wheat caused by Gaeumannomyces graminis var. tritici. In the rhizosphere, it produces the antibiotic phenazine 1-carboxylic acid (PCA) as the primary means of disease suppression. One barrier to commercial use of phenazine-producing pseudomonads, like strain 2-79, is the lack of liquid-culture technology for mass production. For instance, there is little published research concerning the impact of liquid-culture secondary metabolism on the biocontrol qualities of the cell harvest, i.e., efficacy, phytotoxicity, and storage survival. Yet it is important to know whether the fermentation process should be designed to enhance or eliminate secondary metabolite accumulation. To enable future exploration of this issue, we identified liquid-culture parameters that could be manipulated to control the phenazine productivity of strain 2-79. Our results indicated that PCA accumulation was very sensitive to the culture pH and temperature. It was possible to produce large cell populations with either high or low phenazine productivity by choosing to control culture pH at 7 and 8 respectively. Although high cell accumulations were achieved over the broad 25-34 degrees C range studied, high, moderate, or low PCA productivities were observed at 25-27 degrees C, 29-32.5 degrees C, or 34 degrees C respectively. When pH was controlled at 7, specific PCA productions at 25 degrees C could be modulated by the choice of carbon source supplied. PCA accumulation per unit biomass reached 0.31 g/g on glucose, 0.16 g/g on glycerol and xylose, and only 0.09 g/g on fructose.(ABSTRACT TRUNCATED AT 250 WORDS)

Pyrrolnitrin Production by Biological Control Agent Pseudomonas cepacia B37w in Culture and in Colonized Wounds of Potatoes

Bacterial strain B37w (= NRRL B-14858), an isolate noteworthy because it inhibits the growth of the bioherbicide fungus Colletotrichum truncatum , was selected for further studies of bacterial antifungal properties. This isolate was identified as a Pseudomonas cepacia strain by performing carbohydrate utilization and fatty acid profile analyses, as well as other biochemical and physiological tests. Petri plate assays revealed that strain B37w exhibited antifungal activity against the potato dry rot fungus Fusarium sambucinum. Using bioautography, we correlated antifungal activity with production of a specific compound. Isolation from strain B37w and identification of the antifungal antibiotic pyrrolnitrin are described. A whole-potato assay revealed B37w's ability to colonize potato wounds. Wounded potatoes were inoculated with B37w, and pyrrolnitrin was detected in these potatoes by thin-layer chromatography-bioautography at a concentration on the order of nanograms per wound. We performed an assay in which we examined efficacy against F. sambucinum -incited potato dry rot and found that B37w inhibited disease development. This is the first report of P. cepacia or pyrrolnitrin activity against the economically important potato pathogen F. sambucinum.

Effects of zinc, iron, cobalt, and manganese on Fusarium moniliforme NRRL 13616 growth and fusarin C biosynthesis in submerged cultures

The influence of zinc, iron, cobalt, and manganese on submerged cultures of Fusarium moniliforme NRRL 13616 was assessed by measuring dry weight accumulation, fusarin C biosynthesis, and ammonia assimilation. Shake flask cultures were grown in a nitrogen-limited defined medium supplemented with various combinations of metal ions according to partial-factorial experimental designs. Zinc (26 to 3,200 ppb [26 to 3,200 ng/ml]) inhibited fusarin C biosynthesis, increased dry weight accumulation, and increased ammonia assimilation. Carbohydrate was found to be the principal component of the increased dry weight in zinc-supplemented cultures. Zinc-deficient cultures synthesized more lipid and lipidlike compounds, such as fusarin C, than did zinc-supplemented cultures. Microscopic examination showed that zinc-deficient hyphae contained numerous lipid globules which were not present in zinc-supplemented cultures. Addition of zinc (3,200 ppb) to 2- and 4-day-old cultures inhibited further fusarin C biosynthesis but did not stimulate additional dry weight accumulation. Iron (10.0 ppm) and cobalt (9.0 ppm) did not affect fusarin C biosynthesis or dry weight accumulation. Manganese (5.1 ppm) did not affect dry weight accumulation but did increase fusarin C biosynthesis in the absence of zinc. Maximum fusarin C levels, 32.3 micrograms/mg (dry weight), were produced when cultures were supplied manganese, whereas minimum fusarin C levels, 0.07 micrograms/mg (dry weight), were produced when zinc, iron, cobalt, and manganese were supplied. These results suggest a multifunctional role for zinc in affecting F. moniliforme metabolism.

Optimizing aerobic conversion of glycerol to 3-hydroxypropionaldehyde

When cells of Klebsiella pneumoniae NRRL B-199 (ATCC 8724) were grown aerobically on a rich glycerol medium and then suspended in buffer supplemented with semicarbazide and glycerol, aerobic conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA) ensued. Depending on conditions, 0.38 to 0.67 g of 3-HPA were formed per gram of glycerol consumed. This means that up to 83.8% of the carbon invested as glycerol could potentially be recovered as the target product, 3-HPA. Production of 3-HPA was sensitive to the age of cells harvested for resuspension and was nonexistent if cells were cultivated on glucose instead of glycerol as the sole carbon source. Compared with 24- and 72-h cells, 48-h cells produced 3-HPA at the highest rate and with the greatest yield. The cell biomass concentration present during the fermentation was never particularly critical to the 3-HPA yield, but initial fermentation rates and 3-HPA accumulation displayed a linear dependence on biomass concentration that faded when biomass exceeded 3 g/liter. Fermentation performance was a function of temperature, and an optimum initial specific 3-HPA productivity occurred at 32 degrees C, although the overall 3-HPA yield increased continuously within the 25 to 37 degrees C range studied. The pH optimum based on fermentation rate was different from that based on overall yield; 8 versus 7, respectively. Initial glycerol concentrations in the 20 to 50 g/liter range optimized initial 3-HPA productivity and yield.