Utilization of phenol by hydrocarbon assimilating yeasts

Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan

Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.

Isolation and characterization of biarylic structure-degrading yeasts: hydroxylation potential of dibenzofuran

Yeast communities from heavily polluted sediments that received the discharge from oil refineries and other industries were studied. Yeast species were isolated from these sediments and their ability to degrade dibenzofuran were determined. Twenty-four different yeast strains were isolated and cultured on aromatic medium; two Candida krusei strains. Candida tenuis, Candida tropicalis, two Pichia anomala strains, Pichia haplophila, two Rhodotorula glutinis strains, Rhodotorula mucilaginosa, two Trichosporon pullulans strains and Yarrowia lipolytica were able to hydroxylate dibenzofuran. Three metabolites were identified by HPLC analysis: 3-hydroxydibenzofuran was in all the cases the most abundant isomer, and while 4-hydroxydibenzofuran was also common, 2-hydroxydibenzofuran was detected in very small quantities and with few species. In the R. glutinis and Y. lipolytica cultures a ring cleavage product was also found. While in the R. gluttinis assays the hydroxydibenzofuran was detected earlier, at 2 days' incubation time, in the other yeast experiments they were observed at the 4-5th incubation days with the maximum amounts at the 7th day. Our results confirmed the ability of autochthonous yeast species to hydroxylate dibenzofuran and to cleave the rings, and it is the first report for C. krusei, C. tenuis, P. anomala, P. haplophila and R. mucilaginosa. The ecological relevance of this study is based on the fact that dibenzofuran is a xenobiotic not easily transformed, so the catabolic activities observed in authochonous yeasts contribute to broadening the biodegradable substrate spectrum.

Phenol degradation by yeasts isolated from industrial effluents

Yeast strains of the genera Aureobasidium, Rhodotorula and Trichosporon were isolated from stainless steel effluents and tested for their ability to utilize phenol as the sole carbon source. Fourteen strains grew in the presence of up to 10 mm phenol. Only the strain Trichosporon sp. LE3 was able to grow in the presence of up to 20 mm phenol. An inhibitory effect was observed at concentrations higher than 11 mm, resulting in reduction of specific growth rates. Phenol degradation was a function of strain, time of incubation and initial phenol concentration. All strains exhibited activity of catechol 1,2-dioxygenase and phenol hydroxylase in free cell extracts from cells grown on phenol, suggesting that catechol was oxidized by the ortho type of ring fission. Addition of glucose and benzoate reduced the phenol consumption rate, and both substrates were used simultaneously. Glucose concentrations higher than 0.25% inhibited the induction of phenol oxidation by non-proliferating cells and inhibited phenol oxidation by pre-induced cells.

[Taxonomy and ecology of the genus Candida]

Candida is a heterogeneous genus which contains about a quarter of all yeast species. It includes not only species of uncertain affiliation but also unrelated strains whose phylogenetic relationships have not been resolved. A great variety of CoQ types are present in the genus, the mol % G + C ranges from 30-63%, and species that were found to sporulate have teleomorphic counterparts in 11 different genera. Candida species are mainly associated with plants, rotting vegetation, with insects which feed on plants or with food. In line with this, 71% of Candida species utilize xylose (wood degradation), 57% of species use cellobiose (cellulose degradation), 29% oxidize aliphatic hydrocarbons (components of plant cuticula), 27% of species degrade starch as a plant storage material, and 7% utilize methanol as a possible metabolite from pectin catabolism. 85% of species require individual vitamins produced mainly in plant materials. 65% of Candida species are not able to grow at temperatures of 37 degrees C. In comparison only relatively few species occur normally in humans and other warm blooded animals. About 16% of type strains and selected strains for comparative purposes (CBS) were isolated from human specimens. Perhaps up to 10% of Candida species may be of medical importance, though this has so far only been clearly demonstrated for less than 5% of currently known species.

Multiple p450alk (cytochrome P450 alkane hydroxylase) genes from the halotolerant yeast Debaryomyces hansenii

The halotolerant alkane-assimilating yeast Debaryomyces hansenii was examined for P450 alkane hydroxylase genes known to be required for alkane assimilation in Candida. Four distinct P450alk gene segments and an allelic segment were isolated using PCR based on degenerate primers derived from the CYP52 family of alkane-inducible P450 genes. A screen of a genomic library (15-20kb inserts) constructed for this study, using a probe based on the PCR-isolated segments, yielded seven clones. This has led to the isolation and sequence of two full-length genes DH-ALK1 and DH-ALK2. These genes, each with an ORF of 1557 bp (519 aa), contained no apparent introns and showed 64% nucleotide sequence homology (61% based on the deduced amino acid sequences). The deduced proteins had predicted molecular weights of 59,254Da (DH-ALK1) and 59,614Da (DH-ALK2) and have been designated CYP52A12 and CYP52A13 by the P450 Nomenclature Committee. Phylogenetic analysis based on Neighbor Joining Tree showed that DH-ALK1 and DH-ALK2 constitute new genes located on two distinct branches and are most related to the gene CYP52A3 (60% deduced aa homology) and are least related to the gene CYP52C2 (41% deduced aa homology), both of C. maltosa. The isolated genes will provide tools to better understand the diversity of the P450alk family in eukaryotic microorganisms adapted to varied environmental conditions.

Isolation and characterization of a dibenzofuran-degrading yeast: identification of oxidation and ring cleavage products

We characterized the ability of a yeast to cleave the aromatic structure of the dioxin-like compound dibenzofuran. The yeast strain was isolated from a dioxin-contaminated soil sample and identified as Trichosporon mucoides. During incubation of glucose-pregrown cells with dibenzofuran, six major metabolites were detected by high-performance liquid chromatography. The formation of four different monohydroxylated dibenzofurans was proven by comparison of analytical data (gas chromatography-mass spectrometry) with that for authentic standards. Further oxidation produced 2, 3-dihydroxydibenzofuran and its ring cleavage product 2-(1-carboxy methylidene)-2,3-dihydrobenzo[b]furanylidene glycolic acid, which were characterized by mass spectrometry and 1H nuclear magnetic resonance spectroscopy. These two metabolites are derived from 2-hydroxydibenzofuran and 3-hydroxydibenzofuran, as shown by incubation experiments using these monohydroxylated dibenzofurans as substrates.

Transformation and mineralization of halophenols by Penicillium simplicissimum SK9117

The metabolism of monohalophenols by Penicillium simplicissimum SK9117, isolated from a sewage plant was investigated. In submerged cultures, 3-, 4-chlorophenol, and 4-bromophenol were metabolized in the presence of phenol. 3-Chlorophenol was transformed to chlorohydroquinone, 4-chlorocatechol, 4-chloro-1,2,3-trihydroxybenzene, and 5-chloro-1,2,3-trihydroxybenzene. With 4-chlorophenol only 4-chlorocatechol was observed as transient product. A release of chloride ions was not observed. Whereas monobromo-, and monochlorophenols could not support growth as sole carbon and energy source, growth and release of fluoride ions were observed with monofluorophenols as substrates. In presence of phenol, the degradation of all monofluorophenols was enhanced. Substrate and cosubstrate disappeared simultaneously. 3-Fluorophenol and 4-fluorophenol were completely mineralized as shown by the equimolar release of fluoride ions.

Enhanced excretion of intermediates of aromatic amino acid catabolism during chlorophenol degradation due to nutrient limitation in the yeast Candida maltosa

Incubation of phenol-induced cells of the yeast Candida maltosa SBUG 700 with mono- and dichlorophenols resulted in the formation of metabolites of the substrates and of further metabolites not related to the degradation pathway of the substrates. These additional compounds, identified as 4-hydroxyphenylacetic acid (4-HPA), phenylacetic acid (PA), indolylacetic acid (IA) and indolylethanol (i.e.) by means of HPLC and GC/MS, were not excreted in incubation experiments with glucose. The excretion of these metabolites of aromatic amino acid metabolism is not caused by toxic effects of the phenol derivatives, but seems to be a result of carbon and nitrogen starvation of yeast cells.

Biotransformation of diphenyl ether by the yeast Trichosporon beigelii SBUG 752

Trichosporon beigelii SBUG 752 was able to transform diphenyl ether. By TLC, HPLC, GC, GC-MS, NMR- and UV-spectroscopy, several oxidation products were identified. The primary attack was initiated by a monooxygenation step, resulting in the formation of 4-hydroxydiphenyl ether, 2-hydroxydiphenyl ether and 3-hydroxydiphenyl ether (48:47:5). Further oxidation led to 3,4-dihydroxydiphenyl ether. As a characteristic product resulting from the cleavage of an aromatic ring, the lactone of 2-hydroxy-4-phenoxymuconic acid was identified. The possible mechanism of ring cleavage to yield this metabolite is discussed.

Biodegradation of nonionic surfactants. I. Biotransformation of 4-(1-nonyl)phenol by a Candida maltosa isolate

Results are reported concerning biodegradation of 4-(1-nonyl)phenol by cultures of a Candida maltosa strain isolated from aerobic sludge samples collected at a depuration plant treating wastewaters from a textile industry. The yeast was able to utilize 4-(1-nonyl)phenol as a sole carbon and energy source. Preliminary attempts to draw the actual metabolic pathway evidenced microbial attack on the alkyl chain with the production of 4-acetylphenol. To the best of our knowledge this is the first report describing a microorganism capable of attacking nonylphenol in axenic culture and at the same time allowing for the identification of its degradation products.

Catabolism of benzene compounds by ascomycetous and basidiomycetous yeasts and yeastlike fungi. A literature review and an experimental approach

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 yeast Exophiala 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 fungus E. jeanselmei and in basidiomycetes of the genera Cryptococcus, Leucosporidium and Rhodotorula, the protocatechuate branch of the 3-oxoadipate pathway was induced by growth on 3- and 4-hydroxybenzoic acids. In three Trichosporon 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 of Candida 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.

Degradation of some phenols and hydroxybenzoates by the imperfect ascomycetous yeasts Candida parapsilosis and Arxula adeninivorans: evidence for an operative gentisate pathway

The imperfect ascomycetous yeasts Candida parapsilosis and Arxula adeninivorans degraded 3-hydroxybenzoic acid via gentisate which was the cleavage substrate. 4-Hydroxybenzoic acid was metabolized via protocatechuate. No cleavage enzyme for the latter was detected. In stead of this NADH- and NADPH-dependent monooxygenases were present. In cells grown at the expense of hydroquinone and 4-hydroxybenzoic acid, enzymes of the hydroxyhydroquinone variant of the 3-oxoadipate pathway were demonstrated, which also took part in the degradation of 2,4-dihydroxybenzoic acid by C. parapsilosis.

Degradation and dehalogenation of monochlorophenols by the phenol-assimilating yeast Candida maltosa

The phenol-assimilating yeast Candida maltosa is able to degrade monochlorophenols but cannot grow on these substrates. 3- and 4-chlorophenol were broken down very rapidly by phenol-grown cells under the formation of 4-chlorocatechol, 5-chloropyrogallol and 4-carboxymethylenebut-2-en-4-olide with concomitant release of chloride. 2-Chlorophenol was partially converted into cis,cis-2-chloromuconic acid via 3-chlorocatechol which was also obtained from 3-chlorophenol in low amounts. No further metabolites containing chloride were found. The dehalogenation step in the chlorophenol degradation is the cycloisomerization of the cis,cis-chloromuconic acid to 4-carboxymethylenebut-2-en-4-olide in the ortho fission pathway.

[Activities of gluconeogenetic enzymes in the yeast Candida maltosa during growth on glucose or ethanol]

The activities of fructose-1,6-bisphosphatase, malate dehydrogenase and PEP carboxykinase were tested during discontinuous growth of the n-alkane-assimilating yeast Candida maltosa on glucose or ethanol. As expected, the highest activities of the enzymes were measured in the early log phase of growth on ethanol and the lowest in the early log phase of growth on glucose. However, the differences in the activities are much smaller than in Saccharomyces cerevisiae and other yeasts under similar conditions. Therefore, we conclude that catabolite repression does not play an essential role in the control of gluconeogenesis in Candida maltosa.

Cyclic AMP-dependent phosphorylation of fructose-1,6-bisphosphatase and other proteins in the yeast Candida maltosa

In crude extracts of Candida maltosa, about 12 proteins are phosphorylated in the presence of cAMP or of a catalytic subunit of cAMP-dependent protein kinase. A strongly labelled protein spot occurred in the position of fructose-1,6-bisphosphatase both after electrophoresis of crude extracts incubated with cAMP and of a partially purified fructose-1,6-bisphosphatase incubated with a catalytic subunit of cAMP-dependent protein kinase. No phosphorylation of the cytoplasmic malate dehydrogenase could be detected. From these results it was concluded that cAMP-dependent phosphorylation plays an important role in the catabolite inactivation of fructose-1,6-bisphosphatase in Candida maltosa, as described for Saccharomyces cerevisiae.

Cyclic AMP, fructose-2,6-bisphosphate and catabolite inactivation of enzymes in the hydrocarbon-assimilating yeast Candida maltosa

The inactivation of fructose-1,6-bisphosphatase, isocitrate lyase and cytoplasmic malate dehydrogenase in Candida maltosa was found to occur after the addition of glucose to starved cells. The concentration of cyclic AMP and fructose-2,6-bisphosphate increased drastically within 30 s when glucose was added to the intact cells of this yeast. From these results it was concluded that catabolite inactivation, with participation of cyclic AMP and fructose-2,6-bisphosphate, is an important control mechanism of the gluconeogenetic sequence in the n-alkane-assimilating yeast Candida maltosa, as described for Saccharomyces cerevisiae.