Changes in microbial communities and their predictive functionalities during fermentation of toddy, an alcoholic beverage of India.

Toddy is a traditional mild-alcoholic drink of India, which is produced from fresh palm saps by natural fermentation. We studied the successional changes in bacterial and fungal communities during the natural fermentation (0 h-96 h) of toddy. During fermentation, alcohol content of the fermenting saps increased significantly from 0.6 %±0.15 to 5.6 %±0.02, pH decreased from 6.33 %±0.02-3.93 ± 0.01, volatile and titratable acidity acidity (g/100 mL) increased from 0.17 ± 0.02 (0 h) to 0.48 ± 0.02 (96 h) and 1.30 ± 0.005 (0 h) to 2.47 ± 0.005 (96 h), respectively. Total sugar content and ˚BRIX also decreased during the fermentation. Firmicutes (78.25 %) was the most abundant phylum followed by Proteobacteria (21.57 %). Leuconostoc was the most abundant genus in the early stages of fermentation. However, Lactobacillus and Gluconoacetobacter were found abundant with increase in pH during the later phases of fermentation (72 h-96 h). Ascomycota (99.02 %) was the most abundant fungal phylum. Hanseniaspora was the abundant yeast in the initial stages of fermentation, whereas the population of Saccharomyces increased significantly after 24 h of fermentation. Torulaspora, Lachancea and Starmerella showed their heterogeneous distribution throughout the fermentation. Computational analysis of metagenomes based on KEGG and MetaCyc databases showed different predictive functional profiles such as folate biosynthesis, glutathione metabolism, terpenoids biosynthesis and biosynthesis of amino acids with significant differences between the fresh palm saps and fermenting saps during toddy fermentation.

Bioflavour production from tomato and pepper pomaces by Kluyveromyces marxianus and Debaryomyces hansenii.

Bioflavours are called natural flavour and/or fragrance compounds which are produced using metabolic pathway of the microorganism and/or plant cells or their enzyme systems with bioengineering approaches. The aim of this study was to investigate bioflavour production from tomato and red pepper pomaces by Kluyveromyces marxianus and Debaryomyces hansenii. Obtained specific growth rates of K. marxianus and D. hansenii in tomato pomace were 0.081/h and 0.177/h, respectively. The bioflavour profile differed between the yeasts. Both yeasts can produce esters and alcohols such as phenyl ethyl alcohol, isoamyl alcohol, isoamyl acetate, phenyl ethyl acetate and isovaleric acid. "Tarhana" and "rose" were descriptive flavour terms for tomato and pepper pomaces fermented by K. marxianus, respectively. Tomato pomace fermented by D. hansenii had the most intense "green bean" flavour while "fermented vegetable" and "storage/yeast" were defined as characteristic flavour terms for pepper pomaces fermented by D. hansenii.

Influence of inhibitory compounds and minor sugars on xylitol production by Debaryomyces hansenii.

To obtain in-depth information on the overall metabolic behavior of the new good xylitol producer Debaryomyces hansenii UFV-170, batch bioconversions were carried out using semisynthetic media with compositions simulating those of typical acidic hemicellulose hydrolysates of sugarcane bagasse. For this purpose, we used media containing glucose (4.3-6.5 g/L), xylose (60.1-92.1 g/L), or arabinose (5.9-9.2 g/L), or binary or ternary mixtures of them in either the presence or absence of typical inhibitors of acidic hydrolysates, such as furfural (1.0-5.0 g/L), hydroxymethylfurfural (0.01- 0.30 g/L), acetic acid (0.5-3.0 g/L), and vanillin (0.5-3.0 g/L). D. hansenii exhibited a good tolerance to high sugar concentrations as well as to the presence of inhibiting compounds in the fermentation media. It was able to produce xylitol only from xylose, arabitol from arabinose, and no glucitol from glucose. Arabinose metabolization was incomplete, while ethanol was mainly produced from glucose and, to a lesser less extent, from xylose and arabinose. The results suggest potential application of this strain in xyloseto- xylitol bioconversion from complex xylose media from lignocellulosic materials.

Why do some yeast species require niacin for growth? Different modes of NAD synthesis.

NAD holds a key position in metabolism and cellular regulatory events as a major redox carrier and a signalling molecule. NAD biosynthesis pathways have been reconstructed and compared in seven yeast species with completely sequenced genomes, including Saccharomyces cerevisiae, Kluyveromyces lactis, Candida glabrata, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and Schizosaccharomyces pombe. Both amino acid and nucleotide sequence similarity analysis in silico indicated that de novo NAD biosynthesis might not exist in K. lactis, C. glabrata and Schiz. pombe, while other species have the kynurenine pathway. It also showed that the NAD salvage pathway via nicotinic acid and nicotinic acid mononucleotide is conserved in all of these yeasts. Deletion of KlNPT1 (the gene for nicotinate phosphoribosyl-transferase) is lethal, which demonstrates that this salvage pathway, utilizing exogenous nicotinic acid, is the unique route to synthesize NAD in K. lactis. The results suggested that the basis of the variation of niacin requirements in yeasts lies in their different combinations of NAD biosynthesis pathways. The de novo pathway is absent but the salvage pathway is conserved in niacin-negative yeasts, while both pathways coexist in niacin-positive yeasts.

Debaryomyces singareniensis sp. nov., a novel yeast species isolated from a coal mine soil in India.

Three strains (AP19, AP19-4 and AP19-6) of a novel yeast species were isolated from soil from the Singareni coal mines, Andhra Pradesh, India. They were morphologically, physiologically and phylogenetically identical and produced one to four spherical ascospores per ascus. Phylogenetic analysis using the D1/D2 variable domain of the large-subunit rRNA gene indicated that the closest relative of these strains is Debaryomyces etchellsii (2.6% divergence). Other species related to these strains are D. mycophilus (5.1% divergence) and species of the D. hansenii cluster (4.9-5.6% divergence). The novel species differs by 20 and 15 physiological tests from D. etchellsii and D. mycophilus, respectively. Phylogenetic analysis of the internal transcribed spacer (ITS) region also indicated that strains of the new species are related to D. etchellsii (7.7% divergence), followed by species of the D. hansenii cluster (9-10% divergence). In the small-subunit rRNA gene sequences, they differed from D. etchellsii by seven substitutions and one insertion or deletion of a base in a sequence (indel) and from D. mycophilus by 17 substitutions and 1 indel. The physiological, biochemical and molecular data suggest that these strains belong to a novel species, for which we propose the name Debaryomyces singareniensis sp. nov. The type strain of AP19(T) (=MTCC 7061(T)=CBS 10405(T)). The Mycobank number of the new species is MB510046.

Cell wall involvement in the glycerol response to high osmolarity in the halotolerant yeast Debaryomyces hansenii.

Osmotic stress was studied through the induction of the gene coding for glycerol 3-phosphate dehydrogenase (DhGPD1) in the halotolerant yeast Debaryomyces hansenii. This yeast responded to modifications in turgor pressure by stimulating the transcription of DhGPD1 when exposed to solutes that cause turgor stress (NaCl or sorbitol), but did not respond to water stress mediated by ethanol. In contrast to what has been documented to occur in Saccharomyces cerevisiae, D. hansenii protoplasts did not show induction in the transcription of DhGPD1 showing a limitation in their response to solute stress. The results presented indicate that the presence of the cell wall is of significance for the induction of DhGPD1 and hence for osmotic regulation in halotolerant D. hansenii. It appears that the main osmosensor that links high osmolarity with glycerol accumulation may be of a different nature in this yeast.

Mechanisms underlying the halotolerant way of Debaryomyces hansenii.

The yeast Debaryomyces hansenii is usually found in salty environments such as the sea and salted food. It is capable of accumulating sodium without being intoxicated even when potassium is present at low concentration in the environment. In addition, sodium improves growth and protects D. hansenii in the presence of additional stress factors such as high temperature and extreme pH. An array of advantageous factors, as compared with Saccharomyces cerevisiae, is putatively involved in the increased halotolerance of D. hansenii: glycerol, the main compatible solute, is kept inside the cell by an active glycerol-Na+ symporter; potassium uptake is not inhibited by sodium; sodium protein targets in D. hansenii seem to be more resistant. The whole genome of D. hansenii has been sequenced and is now available at http://cbi.labri.fr/Genolevures/ and, so far, no genes specifically responsible for the halotolerant behaviour of D. hansenii have been found.

Effects of aliphatic acids, furfural, and phenolic compounds on Debaryomyces hansenii CCMI 941.

Debaryomyces hansenii is a polyol overproducing yeast that can have a potential use for upgrading lignocellulosic hydrolysates. Therefore, the establishment of its tolerance to metabolic inhibitors found in hydrolysates is of major interest. We studied the effects of selected aliphatic acids, phenolic compounds, and furfural. Acetic acid favored biomass production for concentrations <6.0 g/L. Formic acid was more toxic than acetic acid and induced xylitol accumulation (maximum yield of 0.21 g/g of xylose). All tested phenolics strongly decreased the specific growth rate. Increased toxicity was found for hydroquinone, syringaldehyde, and 4-methylcatechol and was correlated to the compound's hydrophobicity. Increasing the amount of furfural led to longer lag phases and had a detrimental effect on specific growth rate and biomass productivity.

Comparative analysis of trehalose production by Debaryomyces hansenii and Saccharomyces cerevisiae under saline stress.

The comparative analysis of growth, intracellular content of Na+ and K+, and the production of trehalose in the halophilic Debaryomyces hansenii and Saccharomyces cerevisiae were determined under saline stress. The yeast species were studied based on their ability to grow in the absence or presence of 0.6 or 1.0 M NaCl and KCl. D. hansenii strains grew better and accumulated more Na+ than S. cerevisiae under saline stress (0.6 and 1.0 M of NaCl), compared to S. cerevisiae strains under similar conditions. By two methods, we found that D. hansenii showed a higher production of trehalose, compared to S. cerevisiae; S. cerevisiae active dry yeast contained more trehalose than a regular commercial strain (S. cerevisiae La Azteca) under all conditions, except when the cells were grown in the presence of 1.0 M NaCl. In our experiments, it was found that D. hansenii accumulates more glycerol than trehalose under saline stress (2.0 and 3.0 M salts). However, under moderate NaCl stress, the cells accumulated more trehalose than glycerol. We suggest that the elevated production of trehalose in D. hansenii plays a role as reserve carbohydrate, as reported for other microorganisms.

Optimization of Brewery's spent grain dilute-acid hydrolysis for the production of pentose-rich culture media.

Dilute-acid hydrolysis of brewery's spent grain to obtain a pentose-rich fermentable hydrolysate was investigated. The influence of operational conditions on polysaccharide hydrolysis was assessed by the combined severity parameter (CS) in the range of 1.39-3.06. When the CS increased, the pentose sugars concentration increased to a maximum at a CS of 1.94, whereas the maximum glucose concentration was obtained for a CS of 2.65. The concentrations of furfural, hydroxymethylfurfural (HMF), as well as formic and levulinic acids and total phenolic compounds increased with severity. Optimum hydrolysis conditions were found at a CS of 1.94 with >95% of feedstock pentose sugars recovered in the monomeric form, together with a low content of furfural, HMF, acetic and formic acids, and total phenolic compounds. This hydrolysate containing glucose, xylose, and arabinose (ratio 10:67:32) was further supplemented with inorganic salts and vitamins and readily fermented by the yeast Debaryomyces hansenii CCMI 941 without any previous detoxification stage. The yeast was able to consume all sugars, furfural, HMF, and acetic acid with high biomass yield, 0.68 C-mol/C-mol, and productivity, 0.92 g/(L.h). Detoxification with activated charcoal resulted in a similar biomass yield and a slight increase in the volumetric productivity (11%).

Oenological properties of Hanseniaspora osmophila and Kloeckera corticis from wines produced by spontaneous fermentations of normal and dried grapes.

Strains of Hanseniaspora osmophila and Kloeckera corticis, isolated from wines produced by spontaneous fermentations of normal and dried grapes, were characterized for their fermentation behavior with and without SO(2) at 25 degrees C. All isolates behaved as glucophilic yeasts and yielded ethanol at concentrations of about 9% (v/v); acetic acid, acetaldehyde, ethyl acetate and acetoin were always produced to high concentrations. SO(2) addition had no significant effect on growth yield and fermentation rate. These metabolic features were maintained in the presence of 400 g l(-1) of sugars and at 15 degrees C, and were quite similar to those shown by Saccharomycodes ludwigii. Therefore, H. osmophila and K. corticis should be considered detrimental yeast species, particularly in fermentations of musts from dried grapes.

Isolation of PDX2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria.

In this paper we describe the isolation of a second gene in the newly identified pyridoxine biosynthesis pathway of archaebacteria, some eubacteria, fungi, and plants. Although pyridoxine biosynthesis has been thoroughly examined in Escherichia coli, recent characterization of the Cercospora nicotianae biosynthesis gene PDX1 led to the discovery that most organisms contain a pyridoxine synthesis gene not found in E. coli. PDX2 was isolated by a degenerate primer strategy based on conserved sequences of a gene specific to PDX1-containing organisms. The role of PDX2 in pyridoxine biosynthesis was confirmed by complementation of two C. nicotianae pyridoxine auxotrophs not mutant in PDX1. Also, targeted gene replacement of PDX2 in C. nicotianae results in pyridoxine auxotrophy. Comparable to PDX1, PDX2 homologues are not found in any of the organisms with homologues to the E. coli pyridoxine genes, but are found in the same archaebacteria, eubacteria, fungi, and plants that contain PDX1 homologues. PDX2 proteins are less well conserved than their PDX1 counterparts but contain several protein motifs that are conserved throughout all PDX2 proteins.

Induction of the sexual stage of Pestalotiopsis microspora, a taxol-producing fungus.

Pestalotiopsis microspora, isolate NE-32, is an endophyte of the Himalayan yew (Taxus wallichiana) that produces taxol, an important chemotherapeutic drug used in the treatment of breast and ovarian cancers. Conditions were determined to induce the perfect stage (teleomorph) of this organism in the laboratory as a critical first step to study inheritance of taxol biosynthetic genes. The perfect stage of Pestalotiopsis microspora NE-32 forms in a period of 3-6 weeks on water agarose with dried yew needles at 16-20 degrees C with 12 h of light per day. Morphological analysis of the teleomorph and sequencing of the 18S rDNA indicates that Pestalosphaeria hansenii is the perfect stage of Pestalotiopsis microspora. Only certain plants (e.g. yews, some pines, pecan, oat and some barley cultivars) allow the production of perithecia. Exhaustive methylene chloride extraction of yew (Taxus cuspidata) needles removes their capacity to induce production of perithecia. The methylene chloride extract is able to induce formation of perithecia by strain NE-32 in a bioassay system utilizing the sterilized sheaths of the Cholla cactus (Opuntia bigelovii) spine, indicating that a chemical compound(s) in yew stimulates the formation of the perfect stage. This hydrophobic plant compound(s) has been designated the perithecial-stimulating factor (PSF). The data suggest that plant products may play a role in regulating the biology of endophytic microbes.

Isolation of Hanseniaspora uvarum (Kloeckera apiculata) in humans.

Isolation of Hanseniaspora uvarum, a yeast of the ascomycetes group, whose anamorph corresponds to Kloeckera apiculata, obtained from stool and two ungual specimens from three patients, is reported. This yeast has been found in soil, water, various fruits, bivalve molluscs, crabs, prawns and fruit flies; in Spain, it has been described in the fermentation processes of some wines. In our region, it has also been found in the intestine of mackerel (Scomber scombrus). Its finding in humans constitutes a clinical rarity.

Identity and biodegradative abilities of yeasts isolated from plants growing in an arid climate.

Plants harvested in the Canary Islands Lanzarote and Fuerteventura were analyzed for the yeasts inhabiting their surface. Half of the isolates (22 out of 44) were identified as Debaryomyces hansenii. Black ascomycetes, viz. Hortaea werneckii and two Hormonema species were represented by 7 strains. Basidiomycetous yeasts, viz. Cryptococcus sp. (8 strains), Rhodotorula sp. (5 strains), Cerinosterus cyanescens (1 strain) and Pseudozyma sp. (1 strain) constituted a minority of 33%. Thirty strains were screened for their ability to assimilate various plant constituents including lipids of the cuticle and the cell membrane, hemicelluloses, nitrogenous compounds (protein, nucleic acids, amino acids) and benzene compounds. All strains were able to assimilate or to hydrolyze lipids, lecithin included. Many strains of D. hansenii, H. dematioides, H. werneckii, C. cyanescens, Cr. laurentii, Pseudozyma sp. and Rh. glutinis were proteolytic. Hemicelluloses like xylan and pectin were assimilated by black ascomycetous yeasts, Cryptococcus sp., Pseudozyma sp. and Rh. glutinis. Ferulic and hydroxycinnamic acids, gallic and tannic acids were assimilated by some strains of H. dematioides, C. cyanescens, Pseudozyma sp. and Rhodotorula sp.

Effect of NaCl on kinetics of D-glucosamine uptake in yeasts differing in halotolerance.

The initial rate of D-glucosamine uptake by the non-halotolerant yeast Saccharomyces cerevisiae was approximately halved as the apparent half saturation constant (Km) and the apparent maximum velocity (Vmax) changed from 6.6 mM to 16.4 mM and from 22 mumol.g-1.min-1 to 16 mumol.g-1.min-1, respectively, when the salinity in the medium was increased from zero M to 0.68 M NaCl. Corresponding changes in a high affinity transport system in the halotolerant yeast Debaryomyces hansenii were from 1.1 mM to 4.6 mM and from 3.1 mumol.g-1.min-1 to 4.5 mumol.g-1.min-1, implying a practically unchanged transport capacity. In 2.7 M NaCl, Km and Vmax in this system were 24.5 mM and 1.1 mumol.g-1.min-1, respectively, representing a marked decrease in transport capability. Nevertheless, the degree of affinity in this extreme salinity must still be regarded as noteworthy. In addition to the high affinity transport system in D. hansenii, a low affinity system, presumably without relevance in D-glucosamine transport, was observed.

On the mechanism of salt tolerance. Production of glycerol and heat during growth of Debaryomyces hansenii.

As glycerol was suggested as an osmotic agent in the salt tolerant Debaryomyces hansenii the concentrations of total, intracellular, and extracellular glycerol produced by this yeast was followed during growth in 4 mM, 0.68 M, and 2.7 M NaCl media. The total amount of glycerol was not directly proportional to biomass production but to the cultural salinity with maximum concentrations just prior to or at the beginning of the stationary phase. In all cultures the cells lost some glycerol to the media, at 2.7 M NaCl the extracellular glycerol even amounted maximally to 80% of the total. A distinct maximum of intracellular glycerol, related to dry weight or cell number, appeared during the log phase at all NaCl concentrations. As the intracellular calculated glycerol concentrations amounted to 0.2 M, 0.8 M, and 2.6 M in late log phase cells at 4mM, 0.68 M, and 2.7 M NaCl, respectively, whereas the corresponding analysed values for the glycerol concentrations of the media were 0.7 mM, 2.5 mM, and 3.0 mM, glycerol contributes to the osmotic balance of the cells. During the course of growth all cultures showed a decreasing heat production related to cell substance produced, most pronounced at 2.7 M NaCl. At 2.7 M NaCl the total heat production amounted to--1690 kJ per mole glucose consumed in contrast to--1200 and--1130 kJ at 4 mM and 0.68 M NaCl, respectively. The Ym-values were of an inverse order, being 129, 120, and 93 at 4 mM, 0.68 M, and 2.7 M NaCl respectively.