Polysaccharides and phenolic compounds as substrate for yeasts isolated from rotten wood and description of Cryptococcus fagi sp.nov.

Pieces of rotten wood collected in the forest were screened for the presence of yeasts. In spring time 3 tree species were sampled, followed by 9 species in summer. Yeast strains were identified by traditional methods. Identifications were confirmed by sequencing of ribosomal DNA in case of doubt. In total 14 yeast species of ascomycetous affiliation and 6 anamorphic basidiomycetous yeasts were isolated and identified. Most species were represented by only one strain, but Candida bertae by two and Trichosporon porosum by six strains, all from different wood samples. Three strains represented novel species, one of which is described as Cryptococcus fagi Middelhoven et Scorzetti. The type strain is CBS 9964 (JCM 13614). All strains were tested for growth on several polysaccharides as sole carbon source. Only some of these polymers supported growth of ascomycetous yeasts. Basidiomycetous yeasts assimilated soluble starch, pullulan, dextran, xylan, polygalacturonate, galactomannan and tannic acid or at least some of these. Cryptococcus podzolicus and T. porosum were the most active in this respect. None of the isolated strains grew on carboxymethyl cellulose, colloidal chitin, arabinogalactan and gum xanthan. Phenolic compounds were assimilated by several strains, belonging to the Trichosporonales and the Microbotryum and Stephanoascus/Blastobotrys clades, but not by members of the Tremellales (Cryptococcus musci excepted) and the Debaryomyces/Lodderomyces clade. Most of the ascomycetes assimilated n-hexadecane.     

Utilization of tartaric acid and related compounds by yeasts: taxonomic implications.

A survey of yeasts capable of growing on L(+)-tartaric acid as the sole source of carbon and energy showed that this organic acid is assimilated by a significant number of species of basidiomycetous affinity and is seldom utilized by ascomycetous yeasts. This conclusion was further supported by the fact that among approximately 100 isolates from various natural substrates, using selective media with L(+)-tartaric acid, only one strain of ascomycetous affinity was obtained. In a more comprehensive survey 442 yeast strains belonging to 138 species, mostly of basidiomycetous affinity, were also screened for the assimilation of different aldaric acids: D(-)-tartaric acid, meso-tartaric acid, L(-)-malic acid, D(+)-glucaric acid (saccharic acid), and galactaric acid (mucic acid). L(+)-Tartrate was the most frequently utilized tartaric acid isomer (55% of the total number of strains of basidiomycetous affinity belonging to either the Tremellales/Filobasidiales or the Ustilaginales) when compared with the D(-) and meso forms, which were assimilated by 12 and 18% of the total number of strains, respectively (mainly of tremellaceous species). Saccharic acid was utilized by about 75% of the total number of species of Tremellales affinity and by less than 20% of the ustilaginaceous species. Assimilation of mucic acid occurred in more than 50% of the tremellaceous species and only in 5% of the species related to the Ustilaginales. These tests, not used in standard yeast identification sets, appear to contribute to distinguishing taxa at or above the species level.     

Utilization of amines by yeasts

461 Strains of the yeast collection of the Centraalbureau voor Schimmelcultures (CBS) were screened for their ability to utilize 9 different amines as a sole carbon and energy source and/or as nitrogen source. A miniaturized technique with microtiter plates was used. None of the primary and methylated amines tested (i.e. methylamine, dimethylamine, trimethylamine, tetramethylammonium chloride, choline, ethylamine, propylamine, butylamine and benzylamine) were utilized as a carbon and energy source, although the majority of yeasts (86%) were able to utilize one or more of these compounds as a nitrogen source. The ability to utilize ethylamine and higher homologues occurred more frequently than the ability to utilize methylated amines. In almost all genera the utilization of primary and methylated amines was found, with utilizing and non-utilizing species occurring within a genus. The occurrence of specific assimilation patterns of amine utilization among yeasts and the inability of these organisms to utilize amines as a carbon and energy source is discussed.     

Conversion of pentoses by yeasts

The utilization and conversion of D-xylose, D-xylulose, L-arabinose, and xylitol by yeast strains have been investigated with the following results: (1) The majority of yeasts tested utilize D-xylose and produce polyols, ethanol, and organic acids. The type and amount of products formed varies with the yeast strains used. The most commonly detected product is xylitol. (2)The majority of yeasts tested utilize D-xylulose aerobically and fermentatively to produce ethanol, xylitol, D-arabitol, and organic acids. The type and amount of products varies depending upon the yeast strains used. (3) Xylitol is a poor carbon and energy source for most yeasts tested. Some yeast strains produce small amounts of ethanol from xylitol. (4) Most yeast strains utilize L-arabinose, and L-arabitol is the common product. Small amounts of ethanol are also produced by some yeast strains. (5) Of the four substrates examined, D-xylulose was the perferred substrate, followed by D-xylose, L-arabinose, and xylitol. (6) Mutant yeast strains that exhibit different metabolic product patterns can be induced and isolated from Candida sp. Saccharomyces cerevisiae, and other yeasts. These mutant strains can be used for ethanol production from D-xylose as well as for the study of metabolic regulation of pentose utilization in yeasts.     

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.     

Regulation of the utilization of glucose and aromatic substrates in four strains of Pseudomonas putida

During the oxidation of various mixtures of glucose and aromatic substrates by four strains of Pseudomonas putida, diauxic growth was not observed. Strain A3.12 grew faster on benzoate than on glucose, whereas three other strains showed faster growth on glucose than on the aromatic test substrates. Growth rates on mixtures of glucose and aromatics were intermediate between those on the single substrates.The presence of glucose in media containing aromatic substrates accelerated in the bacteria the appearance of the ability to oxidize aromatic substrates. During growth of the organisms on binary mixtures of aromatics, simultaneous utilization of these compounds occurred, the utilization ratio depending on the quality of the compounds as carbon and energy sources. Addition of glucose to dual aromatic substrate media greatly increased the utilization ratio in favour of the better aromatic substrate.With decreasing concentration of glucose in relation to that of aromatic substrates, the rate of carbon assimilation from glucose increased. Enzymological and radiochemical studies demonstrated that even in the presence of an excess of aromatic substrates, glucose was exclusively catabolized via the 2-keto-3-deoxy-6-phosphogluconate pathway. In contrast, the rate of carbon assimilation from ¹⁴C-ring-labelled benzoate and anisate was unaffected by the presence of an excess of glucose.Abbreviations KDPG 2-keto-3-deoxy-6-phosphogluconate - PP pentose-phosphate - OD optical density     

A comparison of the nitrogen metabolic networks of Kluyveromyces marxianus and Saccharomyces cerevisiae

In grape must, nitrogen is available as a complex mixture of various compounds (ammonium and amino acids). Wine yeasts assimilate these multiple sources in order to suitably fulfil their anabolic requirements during alcoholic fermentation. Nevertheless, the order of uptake and the intracellular fate of these sources are likely to differ between strains and species. Using a two-pronged strategy of isotopic filiation and RNA sequencing, the metabolic network of nitrogen utilization and its regulation in Kluyveromyces marxianus were described, in comparison with those of Saccharomyces cerevisiae. The data highlighted differences in the assimilation of ammonium and arginine between the two species. The data also revealed that the metabolic fate of certain nitrogen sources differed, thereby resulting in the production of various amounts of key wine aroma compounds. These observations were corroborated by the gene expression analysis.     

Bullera taiwanensis sp nov and Bullera formosensis sp nov,two new ballistoconidium-forming yeast species isolated from plant leaves in Taiwan

Two strains of ballistoconidiogenous yeasts that contain xylose and form Q-10 ubiquinone were isolated from plant leaves collected in Taiwan and were found to represent two new species. The taxonomic properties of both coincide with the genus Bullera so they are described as Bullera taiwanensis sp. nov. and Bullera formosensis sp. nov. In a phylogenetic tree based on the nucleotide sequences of 18S ribosomal DNAs, these two species are distant from the clusters where the remaining members of the genus Bullera are located, i.e., Bullera taiwanensis is located in the Filobasidium lineage (Filobasidiales clade) and Bullera formosensis is located in the Cryptococcus humicola-Trichosporon lineage (Trichosporonales clade).     

Utilization of ethylamine by yeasts

Summary Thirty-two yeast species (162 strains) have been examined for their ability to utilize ethylamine hydrochloride as sole source of nitrogen. The possible taxonomic use of this property is discussed. The utilization of ethylamine was, with one exception, found to coincide with an ability to utilize L(+)-lysine. In view of the fact that non-industrial yeasts readily utilize ethylamine, its use as a cheap, selective nitrogen source in media employed for the determination of purity of pitching yeast should be considered.     

Relation between phylogeny and physiology in some ascomycetous yeasts

The question of whether yeasts with similar physiological properties are closely related has been examined using recently published phylogenetic analyses of 26S domain D1/D2 rDNA nucleotide sequences from all currently recognized ascomycetous yeasts. When apparently unique metabolic pathways are examined, some relationships between physiology and rDNA phylogeny are evident. Most Candida and Pichia species that are able to assimilate methanol as the sole carbon source are in a clade delimited by C. nanospora and C. boidinii. Exceptions are P. capsulata and P. pastoris which are phylogenetically separated from the other methanol-assimilating yeasts. Yeasts subject to the petite mutation, resulting in respiratory deficiency, belong to three different clades, viz. a Saccharomyces clade delimited by S. cerevisiae and S. rosinii,the Dekkera/Brettanomyces clade, and some Schizosaccharomyces species (‘Archiascomycete’ clade). However, petite mutants were also found in Zygosaccharomyces fermentati and some other more distantly related species. Yeasts able to assimilate n-hexadecane, uric acid or amines as sole carbon source are broadly distributed over the ascomycetous phylogenetic tree. However, species that assimilate adenine as sole carbon source are closely related. Most of these species also assimilated glycine, uric acid, n-hexadecane, putrescine and branched-chain aliphatic compounds such as isobutanol, leucine and isoleucine. Among the Saccharomycetales, species utilizing all or the great majority of these eight compounds are in the Stephanoascus/Arxula/Blastobotrys clade. Candida blankii, which is distantly related to this clade, proved to be an exception and assimilated six of eight of these compounds. This revised version was published online in June 2006 with corrections to the Cover Date.     

Studies on the Utilization of Hydrocarbons by Microorganisms

Many strains of the hydrocabon-utilizing yeasts were isolated from various kinds of natural sources by accumulation culture.

Among those yeasts, two strains, S315YI and S131YI, which were identified with Candida tropilcais, assimilated hydrocarbons abundantly. As for type cultures, it was found that many strains of them could utilize hydrocarbons too, especially the strains which belonged to Genus Candida. However, as regards to the ability in utilizing hydrocarbons, no yeast from type culture collections utilized hydrocarbons better than the yeasts newly isolated from nature. Addition of the natural nutrients such as corn steep liquor to the cultural broth of Strain S315Y1 showed no effect on the production of yeast cells.

The yeast Strain S315Y1 assimilated the higher boiling points fraction of n-paraffins in comparison with the hydrocarbon-utilizing bacterium, Pseudomonas aeruginosa S7B1, which had been reported by the authors. Ribonucleic acid contents of dried cells of the yeast Strain S315Y1 and S131Y1 were 5.3 and 4.4% respectively by Schmidt-Thannhauser-Schneider method.     

Catabolism of benzene compounds by ascomycetous and basidiomycetous yeasts and yeastlike fungi

A literature review is given on growth of yeasts on benzene compounds and on the catabolic pathways involved. Additionally, a yeast collection was screened for assimilation of phenol and 3-hydroxybenzoic acid. Fifteen ascomycetous and thirteen basidiomycetous yeast species were selected and were tested for growth on 84 benzene compounds. It appeared that 63 of these compounds supported growth of one or more yeast species. The black yeastExophiala jeanselmei assimilated 54 of these compounds.The catechol branch of the 3-oxoadipate pathway and its hydroxyhydroquinone variant were involved in phenol and resorcinol catabolism of ascomycetes as well as of basidiomycetes. However, these two groups of yeasts showed characteristic differences in hydroxybenzoate catabolism. In the yeastlike fungusE. jeanselmei and in basidiomycetes of the generaCryptococcus, Leucosporidium andRhodotorula, the protocatechuate branch of the 3-oxoadipate pathway was induced by growth on 3- and 4-hydroxybenzoic acids. In threeTrichosporon species and in all ascomycetous yeasts tested, 4-hydroxybenzoic acid was catabolyzed via protocatechuate and hydroxyhydroquinone. These yeasts were unable to cleave protocatechuate. 3-Hydroxybenzoic and 3-hydroxycinnamic acids were catabolized in ascomycetous yeasts via the gentisate pathway, but in basidiomycetes via protocatechuate.Incomplete oxidation of phenol, some chlorophenols, cresols and xylenols was observed in cultures ofCandida parapsilosis growing on hydroquinone. Most compounds transformed by the growing culture were also converted by the phenol monooxygenase present in cell-free extracts of this yeast. They did not support growth.The relationship between the ability of ascomycetous yeasts to assimilate n-alkanes, amines and benzene compounds, and the presence of Coenzyme Q₉ is discussed.     

Yeasts associated with Drosophila in tropical forests of Rio de Janeiro, Brazil.

The distribution and diversity of yeast species vectored by and from the crop of eight species groups of Drosophila is described for two rain forest sites and an urban wooded area in Rio de Janeiro, Brazil. The typical forest Drosophila groups guarani, tripunctata, and willistoni showed a higher diversity of yeasts than the cosmopolitan melanogaster species group, suggesting different strategies of utilization of substrates. Apiculate yeasts, including Kloeckera apis, Kloeckera javanica, and Kloeckera japonica, were the prevalent species. Geotrichum spp. and Candida citea were also frequent isolates in the forest sites. Similarities between the yeasts from the external surfaces and crops of Drosophila suggested that the feeding substrates were the main source of the yeasts vectored by these flies. Most of the yeasts were strong fermenters and assimilated few compounds, usually sucrose, cellobiose, and glycerol. This indicated a preference of the flies for food sources such as fruits. Some yeasts were primarily isolated from one group of Drosophila; for example, Kloeckera javanica from the melanogaster group, Debaryomyces vanrijiae var. yarrowii from the tripunctata group, and Kluyveromyces delphensis from the willistoni group. These associations and differences in the yeast communities among the fly groups suggested a differentiation of diets and specialization of the yeast-Drosophila association in the tropical forests.     

Diversity of bacterial capabilities in utilizing alkylated benzenes and other aromatic compounds

E. LANG. 1996. Seventeen aerobic bacterial strains known to degrade one or more aromatic compounds were tested for their ability to utilize benzene, seven different methylated benzenes or other aromatic compounds as their sole source of carbon. The results are discussed with respect to the possibility of finding strains which degrade one or more of these compounds by the applied method of screening, and to their taxonomic status.     

Yeasts utilizing methyl alcohol]

The ability to utilize methanol was found in the yeast strains isolated from forest substrates (Zygowillia pini IBFM y-655, Torulopsis molicshiana IBFM y-657) and in the collection yeast cultures (Candida boidinii IBFM y-588 and IBFM )-587). These yeasts assimilated not only methanol but other alcohols (ethanol, glycerol, erythrol, mannitol, and sorbitol), nitrates or nitrites. Their fermentation ability was low.     

Improvement of Nitrogen Assimilation and Fermentation Kinetics under Enological Conditions by Derepression of Alternative Nitrogen-Assimilatory Pathways in an Industrial Saccharomyces cerevisiae Strain

Metabolism of nitrogen compounds by yeasts affects the efficiency of wine fermentation. Ammonium ions, normally present in grape musts, reduce catabolic enzyme levels and transport activities for nonpreferred nitrogen sources. This nitrogen catabolite repression severely impairs the utilization of proline and arginine, both common nitrogen sources in grape juice that require the proline utilization pathway for their assimilation. We attempted to improve fermentation performance by genetic alteration of the regulation of nitrogen-assimilatory pathways in Saccharomyces cerevisiae. One mutant carrying a recessive allele of ure2 was isolated from an industrial S. cerevisiae strain. This mutation strongly deregulated the proline utilization pathway. Fermentation kinetics of this mutant were studied under enological conditions on simulated standard grape juices with various nitrogen levels. Mutant strains produced more biomass and exhibited a higher maximum CO₂ production rate than the wild type. These differences were primarily due to the derepression of amino acid utilization pathways. When low amounts of dissolved oxygen were added, the mutants could assimilate proline. Biomass yield and fermentation rate were consequently increased, and the duration of the fermentation was substantially shortened. S. cerevisiae strains lacking URE2 function could improve alcoholic fermentation of natural media where proline and other poorly assimilated amino acids are the major potential nitrogen source, as is the case for most fruit juices and grape musts.     

Mycosporines in carotenogenic yeasts

The ability to produce mycosporines (MYCs) in 157 pigmented yeast strains (eight genera, 25 species) isolated from natural environments of Patagonia (Argentina) was assessed. The strains belong to four taxonomic groups: the Sporidiobolales and Erythrobasidium clade of the class Urediniomycetes, and Cystofilobasidiales and Tremellales of the class Hymenomycetes. Induction of MYCs did not occur in all yeast strains tested and appeared to be an exclusive trait of members of the Erythrobasidium clade and Tremellales. This is the first report on the production of MYCs by pigmented species from the latter group, as well as the first extensive screening of mycosporinogenic yeasts. The consistent occurrence of MYCs in some specific phylogenetic groups suggests this trait bears evolutionary significance and that the presence/absence of MYCs may have potential applications in yeast systematics.     

Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181

The 1.3 Mbp genome of HTCC2181, a member of the abundant OM43 clade of coastal bacterioplankton, suggested it is an obligate methylotroph. Preliminary experiments demonstrated that methanol and formaldehyde, but not other common C1 compounds such as methylamine, could support growth. Methanol concentrations in seawater are reportedly < 100 nM, suggesting either that the flux of methanol through plankton pools is very rapid, or that methanol may not be the primary growth substrate for HTCC2181. Therefore, we investigated the apparent extreme substrate range restriction of HTCC2181 in greater detail. Growth rate and maximum cell density of HTCC2181 increased with methanol concentration, yielding a K(s) value of 19 μM. In contrast, no growth was observed in the presence of the methylated (C1) compounds, methyl chloride, trimethylamine-oxide (TMAO) or dimethylsulfoniopropionate (DMSP) when they were the sole substrates. However, growth rate, maximum cell density and cellular ATP content were significantly enhanced when any of these methylated compounds were provided in the presence of a limiting concentration of methanol. These observations fit a model in which the metabolic intermediate formaldehyde is required for net carbon assimilation, allowing C1 substrates that do not produce a formaldehyde intermediate to be oxidized for energy, but not assimilated into biomass. Rates of methanol and TMAO oxidation and assimilation were measured with (14)C-radiolabelled compounds in cultures of HTCC2181 and seawater microbial communities collected off the Oregon coast. The results indicated that in nature as well as in culture, C1 substrates are partitioned between those that are mainly oxidized to produce energy and those that are assimilated. These findings indicate that the combined fluxes of C1 compounds in coastal systems are sufficient to support significant populations of obligate methyltrophs by a metabolic strategy that involves the synergistic metabolism of multiple C1 compounds.