Biotransformation of biphenyl by the filamentous fungus Talaromyces helicus

A compartmentalized microsystem helps understanding the uptake of benzo[a]pyrene by fungi during soil bioremediation processes

Hydrophobic organic soil contaminants such as polycyclic aromatic hydrocarbons (PAH) are poorly mobile in the aqueous phase and tend to sorb to the soil matrix, resulting in low bioavailability. Some filamentous fungi are efficient in degrading this kind of pollutants. However, the mechanism of mobilization of hydrophobic compounds by non-motile microorganisms such as filamentous fungi needs investigations to improve pollutant bioavailability and bioremediation efficiency. Usual homogeneous media for microbial growth in the lab are poorly suited to model the soil, which is a compartmentalized and heterogeneous habitat. A microfluidic device was designed to implement a compartmentalization of the fungal inoculum and the source of the pollutant benzo[a]pyrene (BaP) as a deposit of solid crystals in order to gain a further insight into the mechanisms involved in the access to the contaminant and its uptake in soils. Thus in this device, two chambers are connected by an array of parallel microchannels that are wide enough to allow individual hyphae to grow through them. Macro-cultures of Talaromyces helicus in direct contact with BaP have shown its uptake and intracellular storage in lipid bodies despite the low propensity of BaP to cross aqueous phases as shown by simulation. Observations of T. helicus in the microfluidic device through laser scanning confocal microscopy indicate preferential uptake of BaP at a close range and through contact with the cell wall. However faint staining of some hyphae before contact with the deposit also suggests an extracellular transport phenomenon. Macro-culture filtrates analyses have shown that T. helicus releases extracellular non-lipidic surface-active compounds able to lower the surface tension of culture filtrates to 49.4 mN/m. Thus, these results highlight the significance of active mechanisms to reach hydrophobic contaminants before their uptake by filamentous fungi in compartmentalized micro-environments and the potential to improve them through biostimulation approaches for soil mycoremediation.

Fermentation Enhanced Biotransformation of Compounds in the Kernel of Chrysophyllum albidum

Chrysophyllum albidum Linn (African star apple) is a fruit with extensive nutritional and medicinal benefits. The fruit and kernel in the seed are both edible. Strains of lactic acid bacteria (LAB) were isolated from fermented seeds and assessed for probiotic characteristics. The extracts in both the unfermented and the fermented aqueous extracts from the kernels obtained from the seeds of C. albidum were subjected to analysis using the gas chromatography/mass spectrometry (GC-MS) method. This analysis identified the bioactive compounds present as possible substrate(s) for the associated organisms inducing the fermentation and the resultant biotransformed products formed. Three potential probiotic LAB strains identified as Lactococcus raffinolactis (ProbtA1), Lactococcus lactis (ProbtA2a), and Pediococcus pentosaceus (ProbtA2b) were isolated from the fermented C. albidum seeds. All strains were non hemolytic, which indicated their safety, Probt (A1, A2a, and A2b) grew in an acidic environment (pH 3.5) during the 48-h incubation time, and all three strains grew in 1% bile, and exhibited good hydrophobicity and auto-aggregation properties. Mucin binding proteins was not detected in any strain, and bile salt hydrolase was detected in all the strains. l-lactic acid (28.57%), norharman (5.07%), formyl 7E-hexadecenoate (1.73%), and indole (1.51%) were the four major constituents of the fermented kernel of the C. albidum, while 2,5-dimethylpyrazine (C1, 1.27%), 3,5-dihydroxy-6-methyl-2,3-dihydropyran-4-one (C2, 2.90%), indole (C3, 1.31%), norharman (C4, 3.01%), and methyl petroselinate (C5, 4.33%) were the five major constituents of the unfermented kernels. The isolated LAB are safe for consumption. The fermenting process metabolized C1, C2, and C5, which are possible starter cultures for the growth of probiotics. Fermentation is an essential tool for bioengineering molecules in foods into safe and health beneficial products.

Fenton-Mediated Biodegradation of Chlorendic Acid - A Highly Chlorinated Organic Pollutant - By Fungi Isolated From a Polluted Site

Chlorendic acid is a recalcitrant, highly chlorinated organic pollutant for which no microbial degrader has yet been identified. To address this knowledge gap, fungi were isolated from bulk soil, rhizosphere, and roots of the common bent (Agrostis capillaris) and the hybrid poplar [Populus deltoides × (Populus trichocarpa × P. deltoides) cv. Grimminge], both of which grow on a chlorendic acid polluted site in Belgium. Isolates were taxonomically identified and phenotypically screened for chlorendic acid degradation. Several fungal isolates could degrade chlorendic acid in liquid media up to 45%. The chlorendic acid degrading fungal isolates produced higher levels of hydroxyl radicals when exposed to the pollutant when compared to non-exposed controls, suggesting that the oxidative degradation of chlorendic acid occurs through production of Fenton-mediated hydroxyl radicals. In addition, the isolated Ascomycete Penicillium sp. 1D-2a degraded 58% of the original chlorendic acid concentration in the soil after 28 days. This study demonstrates that the presence of fungi in a chlorendic acid polluted soil can degrade this highly chlorinated organic pollutant. These results indicate that recalcitrant, seemingly non-biologically degradable organic pollutants, such as chlorendic acid, can be remediated by using bioremediation, which opens new perspectives for in situ bioremediation.

Contrasting dynamics of polychlorinated biphenyl dissipation and fungal community composition in low and high organic carbon soils with biochar amendment

Biochar amendment has been advocated as an effective method to remediate organic pollutant-contaminated soils through adsorption and stimulating microbial degradation. However, such effects can vary depending on soil properties and biochar physiochemical characteristics. The objective of this study was to compare the dynamic variations of polychlorinated biphenyls (PCBs) in low and high soil organic carbon (SOC) soils both amended with biochar and to investigate its linkage with fungal community composition. Two soils having the same texture and soil type but varying in SOC contents were contaminated with PCBs to a final concentration of 60 mg kg^-1 and amended with 2% bamboo biochar. Temporal changes of PCB remaining in soils and adsorbed on biochar particles were determined during a 2-month incubation. Diversity and composition of fungal communities in both low and high SOC soils were investigated with Illumina MiSeq sequencing. The results showed that the PCB concentrations in low SOC soil were significantly lower than those in high SOC soil during the incubation. In the low SOC soil, the biochar particle adsorbed higher amounts of PCB, tetra-, and penta-chlorobiphenyls (CBs) than those in high SOC soil, and stimulated the dissipation of di- and tri-CBs. The nonmetric multidimensional scaling profile showed significant (p < 0.05) differences in the fungal community composition between the low and high SOC soils. The relative abundances of Eurotiomycetes were gradually increased, whereas those of Sordariomycetes and Dothideomycetes were decreased with increasing incubation time in the low SOC soils. In contrast, the fungal communities in high SOC soils were relatively stable. The relative abundances of Eurotiomycetes and Sordariomycetes were positively correlated with PCB dissipation in low and high SOC content soils, respectively. Our results suggest that SOC content affects PCB dissipation and fungal community composition in biochar-amended soils, and biochars have a high remediation potential of PCB in soils with low SOC contents.

A novel metabolite (1,3-benzenediol, 5-hexyl) production by Exophiala spinifera strain FM through dibenzothiophene desulfurization

Sulfur dioxide which is released from petroleum oil combustion causes pollution over the atmosphere and the soil. Biodesulfurization can be used as a complementary method of hydrodesulfurization, the common method of petroleum desulfurization in refineries. Many studies have been carried out to develop biological desulfurization of dibenzothiophene (DBT) with bacterial biocatalysts. However, fungi are capable to metabolize a wide range of aromatic hydrocarbons through cytochrome P450 and their extracellular enzymes. The aim of the present work was isolation and identification of fungi biocatalysts capable for DBT utilization as sulfur source and production of novel metabolites. DBT consumption and the related produced metabolites were analyzed by HPLC and GC-MS respectively. One of the isolated fungi that could utilize DBT as sole sulfur source was identified by both traditional and molecular experiments and registered in NCBI as Exophiala spinifera FM strain (accession no. KC952672). This strain could desulfurize 99 % of DBT (0.3 mM) as sulfur source by co-metabolism reaction with other carbon sources through the same pathway as 4S and produced 2-hydroxy biphenyl (2-HBP) during 7 days of incubation at 30 °C and 180 rpm shaking. However, the isolate was able to transform 2-HBP to 1,3-benzenediol, 5-hexyl. While biphenyl compounds are toxic to leaving cells, biotransformation of them can reduce their toxicity and the fungi will be more tolerant to the final product. These data are the first report about the desulfurization of DBT comparable to 4S-pathway and production of innovative metabolite by E. spinifera FM strain.

Granulomatous lymphadenitis caused by Talaromyces helicus in a Labrador Retriever

A 3-year-old spayed female Labrador Retriever was presented for right prescapular lymphadenomegaly. Examination of fine-needle aspirates and impression smears of the node revealed many short hyphal structures found within macrophages and extracellularly. Hyphae were approximately 3 μm in diameter, were irregularly septate with nonparallel walls, and had a small clear halo surrounding a partially stained basophilic internal structure. Hyphae were tapered on one end and had oval to pyriform swellings of 7-10 μm on the other, resulting in a bulbous appearance. Fungal elements stained positively with Gomori methenamine silver and Periodic acid-Schiff stains. The dog was euthanized at the owner's request, and necropsy revealed marked peripheral and visceral lymphadenomegaly. Histopathologic examination of lymph nodes confirmed granulomatous lymphadenitis with many fungal hyphae. Fungal culture yielded pure cultures of organisms that failed to produce ascospores or conidia precluding morphologic identification. PCR was performed using pan-fungal primers, ITS-1 and ITS-2, to amplify the intergenic spacer regions of ribosomal RNA; the PCR product was sequenced and a BLAST search of the GenBank databases at NCBI revealed 100% identity of the organism with Talaromyces helicus, the sexual form of Penicillium helicum. Talaromyces helicus has not previously been reported to cause disease in people or animals.

Biotransformation of 4-sec-butylphenol by Gram-positive bacteria of the genera Mycobacterium and Nocardia including modifications on the alkyl chain and the hydroxyl group

The environmental pollutant 4-sec-butylphenol (4-sec-BP) which possesses estrogenic properties was transformed by the aerobic Gram-positive bacteria Mycobacterium neoaurum and Nocardia cyriacigeorgica into three main products (P1-P3) which were isolated and structurally characterized in detail. Two of them were products of a process resembling anaerobic metabolism of alkylphenols based on modifications of the alkyl side chain of 4-sec-BP. The first product (P1) was identified as 4-(2-hydroxy-1-methylpropyl)-phenol. The second product P2 was isolated as a mixture of at least four structures which could be identified as I 4-sec-butylidenecyclohexa-2,5-dienone; II 4-(1-methylenepropyl)-phenol; III 4-(1-methylpropenyl)-phenol; and IV 4-(1-methylallyl)-phenol. In contrast to P1 and P2, the third product (P3) resulted from a modification of the hydroxyl group of 4-sec-BP. This product was only formed by M. neoaurum and was identified as the glucoside conjugate 4-sec-butylphenol-α-D-glucopyranoside. Since in general, fungi synthesize sugar conjugates to detoxify hazardous pollutants, the formation of this conjugate is a peculiarity of M. neoaurum. Thus, altogether, six products were formed from 4-sec-BP and different transformation pathways are introduced. The hydroxylating and glucosylating capacity of the characterized bacteria open up applications in environmental protection.

Novel insights into the fungal oxidation of monoaromatic and biarylic environmental pollutants by characterization of two new ring cleavage enzymes

The phenol-degrading yeast Trichosporon mucoides can oxidize and detoxify biarylic environmental pollutants such as dibenzofuran, diphenyl ether and biphenyl by ring cleavage. The degradation pathways are well investigated, but the enzymes involved are not. The high similarity of hydroxylated biphenyl derivatives and phenol raised the question if the enzymes of the phenol degradation are involved in ring cleavage or whether specific enzymes are necessary. Purification of enzymes from T. mucoides with catechol cleavage activity demonstrated the existence of three different enzymes: a classical catechol-1,2-dioxygenase (CDO), not able to cleave the aromatic ring system of 3,4-dihydroxybiphenyl, and two novel enzymes with a high affinity towards 3,4-dihydroxybiphenyl. The comparison of the biochemical characteristics and mass spectrometric sequence data of these three enzymes demonstrated that they have different substrate specificities. CDO catalyzes the ortho-cleavage of dihydroxylated monoaromatic compounds, while the two novel enzymes carry out a similar reaction on biphenyl derivatives. The ring fission of 3,4-dihydroxybiphenyl by the purified enzymes results in the formation of (5-oxo-3-phenyl-2,5-dihydrofuran-2-yl)acetic acid. These results suggest that the ring cleavage enzymes catalyzing phenol degradation are not involved in the ring cleavage of biarylic compounds by this yeast, although some intermediates of the phenol metabolism may function as inducers.

Degradation pathway of pentachlorophenol by Mucor plumbeus involves phase II conjugation and oxidation-reduction reactions

Environmental pollution by pentachlorophenol (PCP) is a critical concern worldwide and fungal bioremediation constitutes an elegant and environment-friendly solution. Mucorales from the Zygomycota phylum are often observed to be competitive in field conditions and Mucor plumbeus, in particular, can efficiently deplete PCP from media. The pathway for PCP degradation used by this fungus has not been investigated. In this study, PCP-derived metabolites were identified by liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, including tetra- and tri-chlorohydroquinones and phase II-conjugated metabolites. Amongst the latter are the previously reported glucose, sulfate and ribose conjugates, and identified for the first time in fungi sulfate-glucose conjugates. A PCP transformation pathway for M. plumbeus is proposed, which excludes the involvement of cytochrome P-450 and extracellular ligninolytic enzymes.

Oxidative ring cleavage of low chlorinated biphenyl derivatives by fungi leads to the formation of chlorinated lactone derivatives

The yeast Trichosporon mucoides and the filamentous fungus Paecilomyces lilacinus as biphenyl oxidizing organisms are able to oxidize chlorinated biphenyl derivatives. Initial oxidation of derivatives chlorinated at C4 position started at the non-halogenated ring and went on up to ring cleavage. The products formed were mono- and dihydroxylated 4-chlorobiphenyls, muconic acid derivatives 2-hydroxy-4-(4-chlorophenyl)-muconic acid and 2-hydroxy-5-(4-chlorophenyl)-muconic acid as well as the corresponding lactones 4-(4-chlorophenyl)-2-pyrone-6-carboxylic acid and 3-(4-chlorophenyl)-2-pyrone-6-carboxylic acid. Altogether T. mucoides formed 12 products and P. lilacinus accumulated five products. Whereas the rate of the first oxidation step at 4-chlorobiphenyl seems to be diminished by the decreased bioavailability of the compound, no considerable differences were observed between the degradation of 4-chloro-4'-hydroxybiphenyl and 4-hydroxybiphenyl. Twofold chlorinated biphenyl derivatives did not serve as substrates for oxidation by either organism with the exception of 2,2'-dichlorobiphenyl, transformed by the yeast Trichosporon mucoides to two monohydroxylated derivatives. The results show, that soil fungi may contribute to the aerobic degradation of low chlorinated biphenyls accumulating from anaerobic dehalogenation of PCB by bacteria.