Untapped potential: exploiting fungi in bioremediation of hazardous chemicals

Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source

BACKGROUND

Lipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both plant pathogenic and saprophytic fungi. Regardless of numerous reports on fungal degradation of emulsified fatty acids or cutin, and on fungi-plant interactions, the pathways involved in the degradation and utilisation of suberin remain largely overlooked. As a structural component of the plant cell wall, suberin isolation, in general, uses harsh depolymerisation methods that destroy its macromolecular structure. We recently overcame this limitation isolating suberin macromolecules in a near-native state.

RESULTS

Suberin macromolecules were used here to analyse the pathways involved in suberin degradation and utilisation by Aspergillus nidulans. Whole-genome profiling data revealed the complex degrading enzymatic machinery used by this saprophytic fungus. Initial suberin modification involved ester hydrolysis and ω-hydroxy fatty acid oxidation that released long chain fatty acids. These fatty acids were processed through peroxisomal β-oxidation, leading to up-regulation of genes encoding the major enzymes of these pathways (e.g. faaB and aoxA). The obtained transcriptome data was further complemented by secretome, microscopic and spectroscopic analyses.

CONCLUSIONS

Data support that during fungal growth on suberin, cutinase 1 and some lipases (e.g. AN8046) acted as the major suberin degrading enzymes (regulated by FarA and possibly by some unknown regulatory elements). Suberin also induced the onset of sexual development and the boost of secondary metabolism.

Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L.) planting

Phytoremediation is a potentially inexpensive alternative to chemical treatment of hydrocarbon-contaminated soils, but its success depends heavily on identifying factors that govern the success of root-associated microorganisms involved in hydrocarbon degradation and plant growth stimulation. Arbuscular mycorrhizal fungi (AMF) form symbioses with many terrestrial plants, and are known to stimulate plant growth, although both species identity and the environment influence this relationship. Although AMF are suspected to play a role in plant adaptation to hydrocarbon contamination, their distribution in hydrocarbon-contaminated soils is not well known. In this study, we examined how AMF communities were structured within the rhizosphere of 11 introduced willow cultivars as well as unplanted controls across uncontaminated and hydrocarbon-contaminated soils at the site of a former petrochemical plant. We obtained 69 282 AMF-specific 18S rDNA sequences using 454-pyrosequencing, representing 27 OTUs. Contaminant concentration was the major influence on AMF community structure, with different AMF families dominating at each contaminant level. The most abundant operational taxonomic unit in each sample represented a large proportion of the total community, and this proportion was positively associated with increasing contamination, and seemingly, by planting as well. The most contaminated soils were dominated by three phylotypes closely related to Rhizophagus irregularis, while these OTUs represented only a small proportion of sequences in uncontaminated and moderately contaminated soils. These results suggest that in situ inoculation of AMF strains could be an important component of phytoremediation treatments, but that strains should be selected from the narrow group that is both adapted to contaminant toxicity and able to compete with indigenous AMF species.

Use of stable isotope probing to assess the fate of emerging contaminants degraded by white-rot fungus

The widespread of emerging contaminants in the environment and their potential impact on humans is a matter of concern. White-rot fungi are cosmopolitan organisms able to remove a wide range of pharmaceuticals and personal care products (PPCP) through cometabolism (i.e. laccases and peroxidases) or detoxification mechanisms (i.e. cytochrome P450 system). However, the use of PPCP as carbon source for these organisms is largely unexplored. Here, we used carbon stable isotope tracer experiments to assess the fate of anti-inflammatory diclofenac (DCF) and UV filter benzophenone-3 (BP3) during degradation by Trametes versicolor. The comparison between carbon isotopic composition of emitted carbon dioxide from 13C-labelled DCF ([acetophenyl ring-13C6]-DCF) and 13C-BP3 ([phenyl-13C6]-BP3) versus their 12C-homologue compounds showed mineralization of about 45% and 10% of the 13C contained in their respective molecules after 9 days of incubation. The carbon isotopic composition of the bulk biomass and the application of amino acid-stable isotope probing (SIP) allowed distinguishing between incorporation of 13C from BP3 into amino acids, which implies the use of this emerging contaminant as carbon source, and major intracellular accumulation of 13C from DCF without implying the transformation of its labelled phenyl ring into anabolic products. A mass balance of 13C in different compartments over time provided a comprehensive picture of the fate of DCF and BP3 across their different transformation processes. This is the first report assessing biodegradation of PPCP by SIP techniques and the use of emerging contaminants as carbon source for amino acid biosynthesis.

Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives

Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter metaproteomics studies.

Biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a wood-rotting fungus

Biotransformation of 6:2 FTOH [F(CF2)6CH2CH2OH] by the white-rot fungus, Phanerochaete chrysosporium, was investigated in laboratory studies. 6:2 FTOH is a raw material increasingly being used to replace products that can lead to long-chain perfluoroalkyl carboxylic acids (PFCAs, ≥ 8 carbons). During a product's life cycle and after final disposal, 6:2 FTOH-derived compounds may be released into the environment and potentially biotransformed. In this study, P. chrysosporium transformed 6:2 FTOH to perfluorocarboxylic acids (PFCAs), polyfluorocarboxylic acids, and transient intermediates within 28 days. 5:3 Acid [F(CF2)5CH2CH2COOH] was the most abundant transformation product, accounting for 32-43 mol % of initially applied 6:2 FTOH in cultures supplemented with lignocellulosic powder, yeast extract, cellulose, and glucose. PFCAs, including perfluoropentanoic (PFPeA) and perfluorohexanoic (PFHxA) acids, accounted for 5.9 mol % after 28-day incubation. Furthermore, four new transformation products as 6:2 FTOH conjugates or 5:3 acid analogues were structurally confirmed. These results demonstrate that P. chrysosporium has the necessary biochemical mechanisms to drive 6:2 FTOH biotransformation pathways toward more degradable polyfluoroalkylcarboxylic acids, such as 5:3 acid, with lower PFCA yields compared to aerobic soil, sludge, and microbial consortia. Since bacteria and fungi appear to contribute differently toward the environmental loading of FTOH-derived PFCAs and polyfluorocarboxylic acids, wood-rotting fungi should be evaluated as potential candidates for the bioremediation of wastewater and groundwater contaminated with fluoroalkyl substances.

New branches in the degradation pathway of monochlorocatechols by Aspergillus nidulans: a metabolomics analysis

A collective view of the degradation of monochlorocatechols in fungi is yet to be attained, though these compounds are recognised as key degradation intermediates of numerous chlorinated aromatic hydrocarbons, including monochlorophenols. In the present contribution we have analysed the degradation pathways of monochlorophenols in Aspergillus nidulans using essentially metabolomics. Degradation intermediates herein identified included those commonly reported (e.g. 3-chloro-cis,cis-muconate) but also compounds never reported before in fungi revealing for 4-chlorocatechol and for 3-chlorocatechol unknown degradation paths yielding 3-chlorodienelactone and catechol, respectively. A different 3-chlorocatechol degradation path led to accumulation of 2-chloromuconates (a potential dead-end), notwithstanding preliminary evidence of chloromuconolactones and protoanemonin simultaneous formation. In addition, some transformation intermediates, of which sulfate conjugates of mono-chlorophenols/chlorocatechols were the most common, were also identified. This study provides critical information for understanding the role of fungi in the degradation of chlorinated aromatic hydrocarbons; furthering their utility in the development of innovative bioremediation strategies.

The role of root exuded low molecular weight organic anions in facilitating petroleum hydrocarbon degradation: current knowledge and future directions

Rhizoremediation is a bioremediation technique whereby enhanced microbial degradation of organic contaminants occurs within the plant root zone (rhizosphere). It is considered an effective and affordable 'green technology' for remediating soils contaminated with petroleum hydrocarbons (PHCs). This paper critically reviews the potential role of root exuded compounds in rhizoremediation, with emphasis on commonly exuded low molecular weight aliphatic organic acid anions (carboxylates). The extent to which remediation is achieved shows wide disparity among plant species. Therefore, plant selection is crucial for the advancement and widespread adoption of this technology. Root exudation is speculated to be one of the predominant factors leading to microbial changes in the rhizosphere and thus the potential driver behind enhanced petroleum biodegradation. Carboxylates can form a significant component of the root exudate mixture and are hypothesised to enhance petroleum biodegradation by: i) providing an easily degradable energy source; ii) increasing phosphorus supply; and/or iii) enhancing the contaminant bioavailability. These differing hypotheses, which are not mutually exclusive, require further investigation to progress our understanding of plant-microbe interactions with the aim to improve plant species selection and the efficacy of rhizoremediation.

Characterization of Cd-, Pb-, Zn-resistant endophytic Lasiodiplodia sp. MXSF31 from metal accumulating Portulaca oleracea and its potential in promoting the growth of rape in metal-contaminated soils

The aim of this study was to characterize the features of a Cd-, Pb-, and Zn-resistant endophytic fungus Lasiodiplodia sp. MXSF31 and to investigate the potential of MXSF31 to remove metals from contaminated water and soils. The endophytic fungus was isolated from the stem of Portulaca oleracea growing in metal-contaminated soils. The maximum biosorption capacities of MXSF31 were 3.0 × 10(3), 1.1 × 10(4), and 1.3 × 10(4) mg kg(-1) for Cd, Pb, and Zn, respectively. The biosorption processes of Cd, Pb, and Zn by MXSF31 were well characterized with the pseudo-second-order kinetic model. The biosorption isotherm processes of Pb and Zn by the fungus were fitted better with the Langmuir model, while the biosorption processes of Cd was better fitted with the Freundlich model. The biosorption process of MXSF31 was attributed to the functional groups of hydroxyl, amino, carbonyl, and benzene ring on the cell wall. The active biomass of the strain removed more Cd, Pb, and Zn (4.6 × 10(4), 5.6 × 10(5), and 7.0 × 10(4) mg kg(-1), respectively) than the dead biomass. The inoculation of MXSF31 increased the biomass of rape (Brassica napus L.), the translocation factor of Cd, and the extraction amount of Cd by rape in the Cd+Pb-contaminated soils. The results indicated that the endophytic fungus strain had the potential to remove heavy metals from water and soils contaminated by multiple heavy metals, and plants accumulating multiple metals might harbor diverse fungi suitable for bioremediation of contaminated media.

Degradation of diuron by Phanerochaete chrysosporium: role of ligninolytic enzymes and cytochrome P450

The white-rot fungus Phanerochaete chrysosporium was investigated for its capacity to degrade the herbicide diuron in liquid stationary cultures. The presence of diuron increased the production of lignin peroxidase in relation to control cultures but only barely affected the production of manganese peroxidase. The herbicide at the concentration of 7 μg/mL did not cause any reduction in the biomass production and it was almost completely removed after 10 days. Concomitantly with the removal of diuron, two metabolites, DCPMU [1-(3,4-dichlorophenyl)-3-methylurea] and DCPU [(3,4-dichlorophenyl)urea], were detected in the culture medium at the concentrations of 0.74 μg/mL and 0.06 μg/mL, respectively. Crude extracellular ligninolytic enzymes were not efficient in the in vitro degradation of diuron. In addition, 1-aminobenzotriazole (ABT), a cytochrome P450 inhibitor, significantly inhibited both diuron degradation and metabolites production. Significant reduction in the toxicity evaluated by the Lactuca sativa L. bioassay was observed in the cultures after 10 days of cultivation. In conclusion, P. chrysosporium can efficiently metabolize diuron without the accumulation of toxic products.

Hydrocarbon biodegradation in intertidal wetland sediments

Intertidal wetlands, primarily salt marsh, mangrove and mudflats, which provide many essential ecosystem services, are under threat on numerous fronts; a situation that is made worse by crude-oil pollution. Microbes are the main vehicle for remediation of such sediments, and new discoveries, such as novel biodegradation pathways, means of accessing oil, multi-species interactions, and community-level responses to oil addition, are helping us to understand, predict and monitor the fate of oil. Despite this, there are many challenges, not least because of the heterogeneity of these ecosystems and the complexity of crude oil. For example, there is growing awareness about the toxicity of the oxygenated products that result from crude-oil weathering, which are difficult to degrade. This review highlights how developments in areas as diverse as systems biology, microbiology, ecology, biogeochemistry and analytical chemistry are enhancing our understanding of hydrocarbon biodegradation and thus bioremediation of oil-polluted intertidal wetlands.

Genetic and functional investigation of Zn(2)Cys(6) transcription factors RSE2 and RSE3 in Podospora anserina

In Podospora anserina, the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase (aox) when the mitochondrial electron transport chain is impaired. In parallel, they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase (pck) and fructose-1,6-biphosphatase (fbp). Orthologues of these transcription factors are present in a wide range of filamentous fungi, and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organization of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of the aox gene. We identified 10 independent mutations in 9 positions in rse2 and 11 mutations in 5 positions in rse3. Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-terminal activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations in rse2 or rse3. It showed that in addition to aox, fbp, and pck, RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn2Cys6 transcription factor, a flavohemoglobin, and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both an rse2 gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids, and α-ketoglutarate pools.

Biodegradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin in liquid broth by brown-rot fungi

Dioxins are a class of extremely hazardous molecules that might pose a threat to the environment. This work evaluated the microbial degradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TCDD), in liquid broth using three brown-rot fungi and one white-rot fungi as control. A fast and reliable extraction method with recoveries of over 98% together with a validated GC-MS method was developed, and applied to quantify 1,2,3,4-TCDD in liquid broth, mycelia and reaction flask, with detection limits of 10 ppb. Among the four strains tested, brown-rot fungus Aspergillus aculeatus showed best results, removing up to 21% of dioxin after 30-day incubation. The results open both a path for biotechnological interest in bioremediation purposes and environmental behavior studies by using brown-rot fungus.

Bacterial farming by the fungus Morchella crassipes

The interactions between bacteria and fungi, the main actors of the soil microbiome, remain poorly studied. Here, we show that the saprotrophic and ectomycorrhizal soil fungus Morchella crassipes acts as a bacterial farmer of Pseudomonas putida, which serves as a model soil bacterium. Farming by M. crassipes consists of bacterial dispersal, bacterial rearing with fungal exudates, as well as harvesting and translocation of bacterial carbon. The different phases were confirmed experimentally using cell counting and (13)C probing. Common criteria met by other non-human farming systems are also valid for M. crassipes farming, including habitual planting, cultivation and harvesting. Specific traits include delocalization of food production and consumption and separation of roles in the colony (source versus sink areas), which are also found in human agriculture. Our study evidences a hitherto unknown mutualistic association in which bacteria gain through dispersal and rearing, while the fungus gains through the harvesting of an additional carbon source and increased stress resistance of the mycelium. This type of interaction between fungi and bacteria may play a key role in soils.

Bacterial versus fungal laccase: potential for micropollutant degradation

Relatively high concentrations of micropollutants in municipal wastewater treatment plant (WWTP) effluents underscore the necessity to develop additional treatment steps prior to discharge of treated wastewater. Microorganisms that produce unspecific oxidative enzymes such as laccases are a potential means to improve biodegradation of these compounds. Four strains of the bacterial genus Streptomyces (S. cyaneus, S. ipomoea, S. griseus and S. psammoticus) and the white-rot fungus Trametes versicolor were studied for their ability to produce active extracellular laccase in biologically treated wastewater with different carbon sources. Among the Streptomyces strains evaluated, only S. cyaneus produced extracellular laccase with sufficient activity to envisage its potential use in WWTPs. Laccase activity produced by T. versicolor was more than 20 times greater, the highest activity being observed with ash branches as the sole carbon source. The laccase preparation of S. cyaneus (abbreviated L_Sc) and commercial laccase from T. versicolor (L_Tv) were further compared in terms of their activity at different pH and temperatures, their stability, their substrate range, and their micropollutant oxidation efficiency. L_Sc and L_Tv showed highest activities under acidic conditions (around pH 3 to 5), but L_Tv was active over wider pH and temperature ranges than L_Sc, especially at near-neutral pH and between 10 and 25°C (typical conditions found in WWTPs). L_Tv was also less affected by pH inactivation. Both laccase preparations oxidized the three micropollutants tested, bisphenol A, diclofenac and mefenamic acid, with faster degradation kinetics observed for L_Tv. Overall, T. versicolor appeared to be the better candidate to remove micropollutants from wastewater in a dedicated post-treatment step.

Insight into metabolic and cometabolic activities of autotrophic and heterotrophic microorganisms in the biodegradation of emerging trace organic contaminants

Many efforts have been made to understand the biodegradation of emerging trace organic contaminants (EOCs) in the natural and engineered systems. This review summarizes the current knowledge on the biodegradation of EOCs while having in-depth discussion on metabolism and cometabolism of EOCs. Biodegradation of EOCs is mainly attributed to cometabolic activities of both heterotrophic and autotrophic microorganisms. Metabolism of EOCs can only be observed by heterotrophic microbes. Autotrophic ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaeal (AOA) cometabolize a variety of EOCs via the non-specific enzymes, such as ammonia monooxygenase (AMO). Higher biodegradation of EOCs is often noted under nitrification at high ammonia loading rate. The presence of a growth substrate promotes cometabolic biodegradation of EOCs. Potential strategies for enhancing the biodegradation of EOCs were also proposed in this review.

Fungal hyphae stimulate bacterial degradation of 2,6-dichlorobenzamide (BAM)

Introduction of specific degrading microorganisms into polluted soil or aquifers is a promising remediation technology provided that the organisms survive and spread in the environment. We suggest that consortia, rather than single strains, may be better suited to overcome these challenges. Here we introduced a fungal-bacterial consortium consisting of Mortierella sp. LEJ702 and the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 into small sand columns. A more rapid mineralisation of BAM was obtained by the consortium compared to MSH1 alone especially at lower moisture contents. Results from quantitative real-time polymerase chain reaction (qPCR) demonstrated better spreading of Aminobacter when Mortierella was present suggesting that fungal hyphae may stimulate bacterial dispersal. Extraction and analysis of BAM indicated that translocation of the compound was also affected by the fungal hyphae in the sand. This suggests that fungal-bacterial consortia are promising for successful bioremediation of pesticide contamination.

Degradation of pharmaceuticals in non-sterile urban wastewater by Trametes versicolor in a fluidized bed bioreactor

The constant detection of pharmaceuticals (PhACs) in the environment demonstrates the inefficiency of conventional wastewater treatment plants to completely remove them from wastewaters. So far, many studies have shown the feasibility of using white rot fungi to remove these contaminants. However, none of them have studied the degradation of several PhACs in real urban wastewater under non-sterile conditions, where mixtures of contaminants presents at low concentrations (ng L(-1) to μg L(-1)) as well as other active microorganisms are present. In this work, a batch fluidized bed bioreactor was used to study, for the first time, the degradation of PhACs present in urban wastewaters at their pre-existent concentrations under non-sterile conditions. Glucose and ammonium tartrate were continuously supplied as carbon and nitrogen source, respectively, and pH was maintained at 4.5. Complete removal of 7 out of the 10 initially detected PhACs was achieved in non-sterile treatment, while only 2 were partially removed and 1 of the PhACs analyzed increased its concentration. In addition, Microtox test showed an important reduction of toxicity in the wastewater after the treatment.

Gains of bacterial flagellar motility in a fungal world

The maintenance of energetically costly flagella by bacteria in non-water-saturated media, such as soil, still presents an evolutionary conundrum. Potential explanations have focused on rare flooding events allowing dispersal. Such scenarios, however, overlook bacterial dispersal along mycelia as a possible transport mechanism in soils. The hypothesis tested in this study is that dispersal along fungal hyphae may lead to an increase in the fitness of flagellated bacteria and thus offer an alternative explanation for the maintenance of flagella even in unsaturated soils. Dispersal along fungal hyphae was shown for a diverse array of motile bacteria. To measure the fitness effect of dispersal, additional experiments were conducted in a model system mimicking limited dispersal, using Pseudomonas putida KT2440 and its nonflagellated (ΔfliM) isogenic mutant in the absence or presence of Morchella crassipes mycelia. In the absence of the fungus, flagellar motility was beneficial solely under conditions of water saturation allowing dispersal, while under conditions limiting dispersal, the nonflagellated mutant exhibited a higher level of fitness than the wild-type strain. In contrast, in the presence of a mycelial network under conditions limiting dispersal, the flagellated strain was able to disperse using the mycelial network and had a higher level of fitness than the mutant. On the basis of these results, we propose that the benefit of mycelium-associated dispersal helps explain the persistence of flagellar motility in non-water-saturated environments.

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray-Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg(-1) hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.

Differential gene expression in Pycnoporus coccineus during interspecific mycelial interactions with different competitors

Fungi compete against each other for environmental resources. These interspecific combative interactions encompass a wide range of mechanisms. In this study, we highlight the ability of the white-rot fungus Pycnoporus coccineus to quickly overgrow or replace a wide range of competitor fungi, including the gray-mold fungus Botrytis cinerea and the brown-rot fungus Coniophora puteana. To gain a better understanding of the mechanisms deployed by P. coccineus to compete against other fungi and to assess whether common pathways are used to interact with different competitors, differential gene expression in P. coccineus during cocultivation was assessed by transcriptome sequencing and confirmed by quantitative reverse transcription-PCR analysis of a set of 15 representative genes. Compared with the pure culture, 1,343 transcripts were differentially expressed in the interaction with C. puteana and 4,253 were differentially expressed in the interaction with B. cinerea, but only 197 transcripts were overexpressed in both interactions. Overall, the results suggest that a broad array of functions is necessary for P. coccineus to replace its competitors and that different responses are elicited by the two competitors, although a portion of the mechanism is common to both. However, the functions elicited by the expression of specific transcripts appear to converge toward a limited set of roles, including detoxification of secondary metabolites.

Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria

Mycelia have been recently shown to actively transport polycyclic aromatic hydrocarbons (PAH) in water-unsaturated soil over the range of centimeters, thereby efficiently mobilizing hydrophobic PAH beyond their purely diffusive transport in air and water. However, the question if mycelia-based PAH transport has an effect on PAH biodegradation was so far unsolved. To address this, we developed a laboratory model microcosm mimicking air-water interfaces in soil. Chemical analyses demonstrated transport of the PAH fluorene (FLU) by the mycelial oomycete Pythium ultimum that was grown along the air-water interfaces. Furthermore, degradation of mycelia-transported FLU by the bacterium Burkholderia sartisoli RP037-mChe was indicated. Since this organism expresses eGFP in response to a FLU flux to the cell, it was also as a bacterial reporter of FLU bioavailability in the vicinity of mycelia. Confocal laser scanning microscopy (CLSM) and image analyses revealed a significant increase of eGFP expression in the presence of P. ultimum compared to controls without mycelia or FLU. Hence, we could show that physically separated FLU becomes bioavailable to bacteria after transport by mycelia. Experiments with silicon coated glass fibers capturing mycelia-transported FLU guided us to propose a three-step mechanism of passive uptake, active transport and diffusion-driven release. These experiments were also used to evaluate the contributions of these individual steps to the overall mycelial FLU transport rate.

Biotransformation of Trichoderma spp. and their tolerance to aromatic amines, a major class of pollutants

Trichoderma spp. are cosmopolitan soil fungi that are highly resistant to many toxic compounds. Here, we show that Trichoderma virens and T. reesei are tolerant to aromatic amines (AA), a major class of pollutants including the highly toxic pesticide residue 3,4-dichloroaniline (3,4-DCA). In a previous study, we provided proof-of-concept remediation experiments in which another soil fungus, Podospora anserina, detoxifies 3,4-DCA through its arylamine N-acetyltransferase (NAT), a xenobiotic-metabolizing enzyme that enables acetyl coenzyme A-dependent detoxification of AA. To assess whether the N-acetylation pathway enables AA tolerance in Trichoderma spp., we cloned and characterized NATs from T. virens and T. reesei. We characterized recombinant enzymes by determining their catalytic efficiencies toward several toxic AA. Through a complementary approach, we also demonstrate that both Trichoderma species efficiently metabolize 3,4-DCA. Finally, we provide evidence that NAT-independent transformation is solely (in T. virens) or mainly (in T. reesei) responsible for the observed removal of 3,4-DCA. We conclude that T. virens and, to a lesser extent, T. reesei likely utilize another, unidentified, metabolic pathway for the detoxification of AA aside from acetylation. This is the first molecular and functional characterization of AA biotransformation in Trichoderma spp. Given the potential of Trichoderma for cleanup of contaminated soils, these results reveal new possibilities in the fungal remediation of AA-contaminated soil.

Highways versus pipelines: contributions of two fungal transport mechanisms to efficient bioremediation

Based on experimental studies, two different fungus-mediated transport mechanisms have been suggested to facilitate the bacterial degradation of organic soil pollutants: bacteria may use liquid films around fungal hyphae for quick dispersal ('fungal highways'), and fungi may take up and translocate pollutants through their mycelial network ('fungal pipelines'). Both mechanisms are anticipated to enhance the bioavailability of pollutants to degrading bacteria. Using a microbial simulation model, we therefore investigated their respective efficiency in increasing biodegradation performance. We analysed networks that act either as bacterial dispersal vectors or as pollutant translocation vectors or as a combination of both. Our results suggest that each mechanism can improve biodegradation performance. The degree of improvement, however, varies distinctly depending on the environmental conditions, and is even negligible under certain conditions. Mycelial networks acting as 'highways' allow bacteria to overcome motility restrictions and reach remote areas, whereas networks acting as 'pipelines' may initiate degradation by bringing remote pollutants to bacteria. As a consequence, highest biodegradation improvements often emerge from the combination of both mechanisms. We conclude that 'fungal highways' as well as 'fungal pipelines' should be considered for developing novel bioremediation strategies based on fungus-mediated transport in soils.

Potential of autochthonous fungal strains isolated from contaminated soils for degradation of polychlorinated biphenyls

Up to now, most studies on polychlorinated biphenyl (PCB) bioremediation have examined the ability of model fungal strains to biodegrade PCBs. Yet, there is limited information concerning the potential of autochthonous filamentous fungal strains in the biodegradation of PCBs and their possible use in the environmental technologies. In this study, we investigated the capacity of autochthonous fungal strains in the biodegradation of PCBs by isolating 24 taxa from former industrial sites highly contaminated by PCBs. Microscopic and molecular analyses using the internal transcribed spacer (ITS) region revealed that the fungal strains belonged to the phyla Ascomycota (19 strains) and Zygomycota (five strains). The chromatography gas analysis revealed evidence of degradation of seven PCB congeners. With the exception of Circinella muscae which presented no degradation potential, the other fungal strains exhibited a rate of biodegradation ranging from 29 to 85 % after 7 d of incubation in liquid medium. Among these strains, Doratomyces nanus, Doratomyces purpureofuscus, Doratomyces verrucisporus, Myceliophthora thermophila, Phoma eupyrena, and Thermoascus crustaceus showed remarkable degradation ability (>70 %) regardless of the number of chlorine substituents on the biphenyl nucleus and a high tolerance towards PCBs. To our knowledge, this is the first study that demonstrates the ability of PCB degradation by these species and indicates the potential effectiveness of some autochthonous fungal strains in bioremediation systems.

Enhancement of phytoremediation of Cd- and Pb-contaminated soils by self-fusion of protoplasts from endophytic fungus Mucor sp. CBRF59

The aim of this study was to isolate protoplasts from endophytic fungi and to carry out self-fusion of protoplasts for their enhancement of metal resistance. Self-fusant CBRF59T3 with resistance to 25 mM Cd(II) was constructed by self-fusion of inactivated protoplasts from Mucor sp. CBRF59. The inoculation of CBRF59 and CBRF59T3 improved significantly the availability of Cd(II) and Pb(II) in the soil. Compared with CBRF59, CBRF59T3 inoculation increased the content of water-soluble Cd(II) by 24%. The dry weight of rape inoculated with CBRF59 and CBRF59T3 was both higher than that of the uninoculation rape. Inoculation of CBRF59T3 further increased the dry weight of rape by 62% than CBRF59 in the higher Cd(II)-+Pb(II)-contaminated soil. Compared with CBRF59, CBRF59T3 inoculation increased the concentration of Cd(II) in rape shoots by 35-189% in Cd(II)- and Cd(II)-+Pb(II)-contaminated soils. The inoculation of CBRF59T3 also enhanced the translocation of Cd(II) from roots to shoots and increased the amount of extracted Cd(II) by rape. The results indicated that the mutants constructed by protoplast fusion is a feasible and efficient method to improve stress tolerance of uncharacterized fungi for phytoremediation of soils contaminated by heavy metals.

Xenomic networks variability and adaptation traits in wood decaying fungi

Fungal degradation of wood is mainly restricted to basidiomycetes, these organisms having developed complex oxidative and hydrolytic enzymatic systems. Besides these systems, wood-decaying fungi possess intracellular networks allowing them to deal with the myriad of potential toxic compounds resulting at least in part from wood degradation but also more generally from recalcitrant organic matter degradation. The members of the detoxification pathways constitute the xenome. Generally, they belong to multigenic families such as the cytochrome P450 monooxygenases and the glutathione transferases. Taking advantage of the recent release of numerous genomes of basidiomycetes, we show here that these multigenic families are extended and functionally related in wood-decaying fungi. Furthermore, we postulate that these rapidly evolving multigenic families could reflect the adaptation of these fungi to the diversity of their substrate and provide keys to understand their ecology. This is of particular importance for white biotechnology, this xenome being a putative target for improving degradation properties of these fungi in biomass valorization purposes.

Can Stress Enhance Phytoremediation of Polychlorinated Biphenyls?

Phytoremediation-plant-facilitated remediation of polluted soil and groundwater-is a potentially effective treatment technology for the remediation of heavy metals and certain organic compounds. However, contaminant attenuation rates are often not rapid enough to make phytoremediation a viable option when compared with alternative treatment approaches. Different strategies are being employed to enhance the efficacy of phytoremediation, including modification to the plant genome, inoculation of the rhizosphere with specialized and/or engineered bacteria, and treatment of the soil with supplementary chemicals, such as surfactants, chelators, or fertilizers. Despite these efforts, greater breakthroughs are necessary to make phytoremediation a viable technology. Here, we introduce and discuss the concept of integrating controlled environmental stresses as a strategy for enhancing phytoremediation. Plants have a diverse suite of defense mechanisms that are only induced in response to stress. Here, we examine some stress-response mechanisms in plants, focusing on defenses involving physiological changes that alter the soil microenvironment (rhizosphere), and outline how these defense mechanisms can be co-opted to enhance the effectiveness of phytoremediation of polychlorinated biphenyls and other contaminants.

Comparison of DNA and RNA, and cultivation approaches for the recovery of terrestrial and aquatic fungi from environmental samples

Estimates of fungal biodiversity from environmental samples are all subject to bias. Major issues are that the commonly adopted cultivation-based approaches are suitable for taxa which grow readily under laboratory conditions, while the DNA-based approaches provide more reliable estimates, but do not indicate whether taxa are metabolically active. In this study, we have evaluated these approaches to estimate the fungal diversity in soil and freshwater samples from a subtropical forest, and compared these to RNA-based culture-independent approach intended to indicate the metabolically active fungal assemblage. In both soil and freshwater samples, the dominant taxon recovered by all three approaches was the same (Anguillospora furtiva). This taxon was cultivable from all samples and comprised 85–86 % DNA libraries and 90–91 % RNA libraries. The remaining taxa were phylogenetically diverse and spanned the Ascomycota, Basidiomycota, and Fungi incertae sedis. Their recovery was not consistent among the three approaches used and suggests that less abundant members of the assemblage may be subjected to greater bias when diversity estimates employ a single approach.

Laccase immobilization and insolubilization: from fundamentals to applications for the elimination of emerging contaminants in wastewater treatment

Over the last few decades many attempts have been made to use biocatalysts for the biotransformation of emerging contaminants in environmental matrices. Laccase, a multicopper oxidoreductase enzyme, has shown great potential in oxidizing a large number of phenolic and non-phenolic emerging contaminants. However, laccases and more broadly enzymes in their free form are biocatalysts whose applications in solution have many drawbacks rendering them currently unsuitable for large scale use. To circumvent these limitations, the enzyme can be immobilized onto carriers or entrapped within capsules; these two immobilization techniques have the disadvantage of generating a large mass of non-catalytic product. Insolubilization of the free enzymes as cross-linked enzymes (CLEAs) is found to yield a greater volume ratio of biocatalyst while improving the characteristics of the biocatalyst. Ultimately, novel techniques of enzymes insolubilization and stabilization are feasible with the combination of cross-linked enzyme aggregates (combi-CLEAs) and enzyme polymer engineered structures (EPESs) for the elimination of emerging micropollutants in wastewater. In this review, fundamental features of laccases are provided in order to elucidate their catalytic mechanism, followed by different chemical aspects of the immobilization and insolubilization techniques applicable to laccases. Finally, kinetic and reactor design effects for enzymes in relation with the potential applications of laccases as combi-CLEAs and EPESs for the biotransformation of micropollutants in wastewater treatment are discussed.

Biodegradation of chlorpyrifos and its hydrolysis product 3,5,6-trichloro-2-pyridinol by a new fungal strain Cladosporium cladosporioides Hu-01

Intensive use of chlorpyrifos has resulted in its ubiquitous presence as a contaminant in surface streams and soils. It is thus critically essential to develop bioremediation methods to degrade and eliminate this pollutant from environments. We present here that a new fungal strain Hu-01 with high chlorpyrifos-degradation activity was isolated and identified as Cladosporium cladosporioides based on the morphology and 5.8S rDNA gene analysis. Strain Hu-01 utilized 50 mg·L⁻¹ of chlorpyrifos as the sole carbon of source, and tolerated high concentration of chlorpyrifos up to 500 mg·L⁻¹. The optimum degradation conditions were determined to be 26.8°C and pH 6.5 based on the response surface methodology (RSM). Under these conditions, strain Hu-01 completely metabolized the supplemented chlorpyrifos (50 mg·L⁻¹) within 5 d. During the biodegradation process, transient accumulation of 3,5,6-trichloro-2-pyridinol (TCP) was observed. However, this intermediate product did not accumulate in the medium and disappeared quickly. No persistent accumulative metabolite was detected by gas chromatopraphy-mass spectrometry (GC-MS) analysis at the end of experiment. Furthermore, degradation kinetics of chlorpyrifos and TCP followed the first-order model. Compared to the non-inoculated controls, the half-lives (t_1/2) of chlorpyrifos and TCP significantly reduced by 688.0 and 986.9 h with the inoculum, respectively. The isolate harbors the metabolic pathway for the complete detoxification of chlorpyrifos and its hydrolysis product TCP, thus suggesting the fungus may be a promising candidate for bioremediation of chlorpyrifos-contaminated water, soil or crop.

Purification and characterization of a novel chlorpyrifos hydrolase from Cladosporium cladosporioides Hu-01

Chlorpyrifos is of great environmental concern due to its widespread use in the past several decades and its potential toxic effects on human health. Thus, the degradation study of chlorpyrifos has become increasing important in recent years. A fungus capable of using chlorpyrifos as the sole carbon source was isolated from organophosphate-contaminated soil and characterized as Cladosporium cladosporioides Hu-01 (collection number: CCTCC M 20711). A novel chlorpyrifos hydrolase from cell extract was purified 35.6-fold to apparent homogeneity with 38.5% overall recovery by ammoniumsulfate precipitation, gel filtration chromatography and anion-exchange chromatography. It is a monomeric structure with a molecular mass of 38.3 kDa. The pI value was estimated to be 5.2. The optimal pH and temperature of the purified enzyme were 6.5 and 40°C, respectively. No cofactors were required for the chlorpyrifos-hydrolysis activity. The enzyme was strongly inhibited by Hg²⁺, Fe³⁺, DTT, β-mercaptoethanol and SDS, whereas slight inhibitory effects (5–10% inhibition) were observed in the presence of Mn²⁺, Zn²⁺, Cu²⁺, Mg²⁺, and EDTA. The purified enzyme hydrolyzed various organophosphorus insecticides with P-O and P-S bond. Chlorpyrifos was the preferred substrate. The Km and Vmax values of the enzyme for chlorpyrifos were 6.7974 μM and 2.6473 μmol·min⁻¹, respectively. Both NH2-terminal sequencing and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometer (MALDI-TOF-MS) identified an amino acid sequence MEPDGELSALTQGANS, which shared no similarity with any reported organophosphate-hydrolyzing enzymes. These results suggested that the purified enzyme was a novel hydrolase and might conceivably be developed to fulfill the practical requirements to enable its use in situ for detoxification of chlorpyrifos. Finally, this is the first described chlorpyrifos hydrolase from fungus.

Marine crude-oil biodegradation: a central role for interspecies interactions

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.

Mycelia promote active transport and spatial dispersion of polycyclic aromatic hydrocarbons

To cope with heterogeneous subsurface environments mycelial microorganisms have developed a unique ramified growth form. By extending hyphae, they can obtain nutrients from remote places and transport them even through air gaps and in small pore spaces, repectively. To date, studies have been focusing on the role that networks play in the distribution of nutrients. Here, we investigated the role of mycelia for the translocation of nonessential substances, using polycyclic aromatic hydrocarbons (PAHs) as model compounds. We show that the hyphae of the mycelial soil oomycete Pythium ultimum function as active translocation vectors for a wide range of PAHs. Visualization by two-photon excitation microscopy (TPEM) demonstrated the uptake and accumulation of phenanthrene (PHE) in lipid vesicles and its active transport by cytoplasmic streaming of the hyphae ('hyphal pipelines'). In mycelial networks, contaminants were translocated over larger distances than by diffusion. Given their transport capacity and ubiquity, hyphae may substantially distribute remote hydrophobic contaminants in soil, thereby improving their bioavailability to bacterial degradation. Hyphal contaminant dispersal may provide an untapped potential for future bioremediation approaches.

Microbial detoxification of bifenthrin by a novel yeast and its potential for contaminated soils treatment

Bifenthrin is one the most widespread pollutants and has caused potential effect on aquatic life and human health, yet little is known about microbial degradation in contaminated regions. A novel yeast strain ZS-02, isolated from activated sludge and identified as Candida pelliculosa based on morphology, API test and 18S rDNA gene analysis, was found highly effective in degrading bifenthrin over a wide range of temperatures (20–40°C) and pH (5–9). On the basis of response surface methodology (RSM), the optimal degradation conditions were determined to be 32.3°C and pH 7.2. Under these conditions, the yeast completely metabolized bifenthrin (50 mg·L⁻¹) within 8 days. This strain utilized bifenthrin as the sole carbon source for growth as well as co-metabolized it in the presence of glucose, and tolerated concentrations as high as 600 mg·L⁻¹ with a q_max, K_s and K_i of 1.7015 day⁻¹, 86.2259 mg·L⁻¹ and 187.2340 mg·L⁻¹, respectively. The yeast first degraded bifenthrin by hydrolysis of the carboxylester linkage to produce cyclopropanecarboxylic acid and 2-methyl-3-biphenylyl methanol. Subsequently, 2-methyl-3-biphenylyl methanol was further transformed by biphenyl cleavage to form 4-trifluoromethoxy phenol, 2-chloro-6-fluoro benzylalcohol, and 3,5-dimethoxy phenol, resulting in its detoxification. Eventually, no persistent accumulative product was detected by gas chromatopraphy-mass spectrometry (GC-MS) analysis. This is the first report of a novel pathway of degradation of bifenthrin by hydrolysis of ester linkage and cleavage of biphenyl in a microorganism. Furthermore, strain ZS-02 degraded a variety of pyrethroids including bifenthrin, cyfluthrin, deltamethrin, fenvalerate, cypermethrin, and fenpropathrin. In different contaminated soils introduced with strain ZS-02, 65–75% of the 50 mg·kg⁻¹ bifenthrin was eliminated within 10 days, suggesting the yeast could be a promising candidate for remediation of environments affected by bifenthrin. Finally, this is the first described yeast capable of degrading bifenthrin.