Correlations among several screening methods used for identifying wood-decay fungi that can degrade toxic chemicals

Summary Several established screening methods were evaluated to examine enzyme production and toxic-chemical-degrading ability of four wood-decay fungi, includingPhanerochaete chrysosporium, Pleurotus ostreatus, Auricularia auriculajudae, andLentinus edodes. A correlation among various measured parameters for each fungal strain was established. This correlation may be used as a basis to simplify screening programs for wood-decay fungi that are capable of degrading toxic organic compounds.     

Proteomics of industrial fungi: trends and insights for biotechnology

Filamentous fungi are widely known for their industrial applications, namely, the production of food-processing enzymes and metabolites such as antibiotics and organic acids. In the past decade, the full genome sequencing of filamentous fungi increased the potential to predict encoded proteins enormously, namely, hydrolytic enzymes or proteins involved in the biosynthesis of metabolites of interest. The integration of genome sequence information with possible phenotypes requires, however, the knowledge of all the proteins in the cell in a system-wise manner, given by proteomics. This review summarises the progress of proteomics and its importance for the study of biotechnological processes in filamentous fungi. A major step forward in proteomics was to couple protein separation with high-resolution mass spectrometry, allowing accurate protein quantification. Despite the fact that most fungal proteomic studies have been focused on proteins from mycelial extracts, many proteins are related to processes which are compartmentalised in the fungal cell, e.g. β-lactam antibiotic production in the microbody. For the study of such processes, a targeted approach is required, e.g. by organelle proteomics. Typical workflows for sample preparation in fungal organelle proteomics are discussed, including homogenisation and sub-cellular fractionation. Finally, examples are presented of fungal organelle proteomic studies, which have enlarged the knowledge on areas of interest to biotechnology, such as protein secretion, energy production or antibiotic biosynthesis.     

LaeA在丝状真菌次级代谢、生长发育和其他重要生物过程中的作用

LaeA是在构巢曲霉中首次鉴定的一种全局调控因子,其同源蛋白在丝状真菌中广泛存在,具有高度的保守性。LaeA及其同源蛋白序列存在S-腺苷甲硫氨酸结合基序,是一种甲基转移酶,可能影响组蛋白修饰,导致染色体结构的改变,进而调控一系列基因的表达。大量研究表明,LaeA及其同源蛋白参与调控丝状真菌多种次级代谢产物的生物合成,影响丝状真菌的生长发育和形态分化,甚至在丝状真菌生产有机酸和一些工业酶的过程中也发挥着重要作用。本文综述了LaeA及其同源蛋白的作用机制,以及该蛋白在丝状真菌次级代谢、生长发育和其他重要生物过程中的作用,并对存在的问题及应用前景进行讨论与展望。     

NAD+/NADH homeostasis affects metabolic adaptation to hypoxia and secondary metabolite production in filamentous fungi*

Filamentous fungi are used to produce fermented foods, organic acids, beneficial secondary metabolites and various enzymes. During such processes, these fungi balance cellular NAD⁺:NADH ratios to adapt to environmental redox stimuli. Cellular NAD(H) status in fungal cells is a trigger of changes in metabolic pathways including those of glycolysis, fermentation, and the production of organic acids, amino acids and secondary metabolites. Under hypoxic conditions, high NADH:NAD⁺ ratios lead to the inactivation of various dehydrogenases, and the metabolic flow involving NAD⁺ is down-regulated compared with normoxic conditions. This review provides an overview of the metabolic mechanisms of filamentous fungi under hypoxic conditions that alter the cellular NADH:NAD⁺ balance. We also discuss the relationship between the intracellular redox balance (NAD/NADH ratio) and the production of beneficial secondary metabolites that arise from repressing the HDAC activity of sirtuin A via Nudix hydrolase A (NdxA)-dependent NAD⁺ degradation.     

Aspergillus as a versatile cell factory for organic acid production

Filamentous fungi from the genus Aspergillus are of high importance for biobased organic acid production. So far, a number of Aspergillus strains belonging to phylogenetically distantly related species have been successfully applied in industrial production of organic acids due to their excellent capabilities of secreting high amounts of desired organic acids. For the past decades, numerous efforts have been made to reveal the mechanisms of organic acid biosynthesis in several Aspergillus species and to improve the production of desired organic acids via genetic engineering. This review summarizes the recent breakthroughs in the fundamental understanding of physiological aspects of organic acid accumulation by fungal biocatalysts and highlights the progress in genetic engineering of aspergilli for organic acid production. The challenges for the future applications of aspergilli as commercial cell factories for organic acid production are also discussed.     

Microbial production of organic acids: expanding the markets

Microbial production of organic acids is a promising approach for obtaining building-block chemicals from renewable carbon sources. Although some acids have been produced for some time and in-depth knowledge of these microbial production processes has been gained, further microbial production processes seem to be feasible, but large-scale production has not yet been possible. Citric, lactic and succinic acid production exemplify three processes in different stages of industrial development. Although the questions being addressed by current research on these processes are diverging, a comparison is helpful for understanding microbial organic acid production in general. In this article, through analysis of the current advances in production of these acids, we present guidelines for future developments in this fast-moving field.     

Production of long-chain hydroxy fatty acids by microbial conversion

Hydroxy fatty acids (HFAs) are very important chemicals for versatile applications in biodegradable polymer materials and cosmetic and pharmaceutical industries. They are difficult to be synthesized via chemical routes due to the inertness of the fatty acyl chain. In contrast, these fatty acids make up a major class of natural products widespread among bacteria, yeasts, and fungi. A number of microorganisms capable of producing HFAs from fatty acids or vegetable oils have been reported. Therefore, HFAs could be produced by biotechnological strategies, especially by microbial conversion processes. Microorganisms could oxidize fatty acids either at the terminal carbon or inside the acyl chain to produce various HFAs, including α-HFAs, β-HFAs, mid-position HFAs, ω-HFAs, di-HFAs, and tri-HFAs. The enzymes and their encoded genes responsible for the hydroxylation of the carbon chain have been identified and characterized during the past few years. The involved microbes and catalytic mechanisms for the production of different types of HFAs are systematically demonstrated in this review. It provides a better view of HFA biosynthesis and lays the foundation for further industrial production.     

Soil acidification and adaptations of plants and microorganisms in Bornean tropical forests

In tropical forest ecosystems, a paradoxical relationship is commonly observed between massive biomass production and low soil fertility (low pH). The loss and deficiency of soil phosphorus (P) and bases generally constrain biomass production; however, high productivity on nutrient-deficient soils of Bornean tropical forests is hypothesized to be maintained by plant and microorganism adaptation to an acidic soil environment. Proton budgets in the plant–soil system indicated that plants and microorganisms promote acidification to acquire bases, even in highly acidic tropical soils. The nitric and organic acids they produce contribute to the mobilization of basic cations and their uptake by plants. In response to soil P deficiency and the recalcitrance of lignin-rich organic matter, specific trees and fungi can release organic acids and enzymes for nutrient acquisition. Organic acids exuded by roots and rhizosphere microorganisms can promote the solubilization of P bonded to aluminum and iron oxides and its uptake by plants from P-poor soils. Lignin degradation, a rate-limiting step in organic matter decomposition, is specifically enhanced in acidic organic layers by lignin peroxidase, produced by white-rot fungi, which may solubilize recalcitrant lignin and release soluble aromatic substances into the soil solution. This dissolved organic matter functions in the transport of nitrogen, P, and basic cations in acidic soils without increasing leaching loss. In Bornean tropical forests, soil acidification is promoted by plants and microorganisms as a nutrient acquisition strategy, while plant roots and fungi can develop rhizosphere and enzymatic processes that promote tolerance of low pH.     

Metal-chelating compounds produced by ectomycorrhizal fungi collected from pine plantations

AIMS: To investigate the in vitro production of metal-chelating compounds by ectomycorrhizal fungi collected from pine plantations in southern Chile. METHODS AND RESULTS: Scleroderma verrucosum, Suillus luteus and two isolates of Rhizopogon luteolus were grown in solid and liquid modified Melin-Norkans (MMN) media with and without iron addition and the production of iron-chelating compounds was determined by Chrome Azurol S (CAS) assay. The presence of hydroxamate and catecholate-type compounds and organic acids was also investigated in liquid medium. All isolates produced iron-chelating compounds as detected by CAS assay, and catecholates, hydroxamates as well as oxalic, citric and succinic acids were also detected in all fungal cultures. Scleroderma verrucosum produced the greatest amounts of catecholates and hydroxamates whereas the highest amounts of organic acids were detected in S. luteus. Nevertheless, the highest catecholate, hydroxamate and organic acid concentrations did not correlate with the highest CAS reaction which was observed in R. luteolus (Yum isolate). CONCLUSIONS: Ectomycorrhizal fungi produced a variety of metal-chelating compounds when grown in liquid MMN medium. However, the addition of iron to all fungi cultures reduced the CAS reaction, hydroxamate and organic acid concentrations. Catecholate production was affected differently by iron, depending on the fungal isolate. SIGNIFICANCE AND IMPACT OF THE STUDY: The ectomycorrhizal fungi described in this study have never been reported to produce metal-chelating compound production. Moreover, apart from some wood-rotting fungi, this is the first evidence of the presence of catecholates in R. luteolus, S. luteus and S. verrucosum cultures.     

Atomic Force Microscopy of the fungi-mineral interface: applications in mineral dissolution, weathering and biogeochemistry

The interaction between mycorrhizal fungi and minerals is of fundamental importance in affecting the geochemical carbon cycle and CO(2) concentration in the atmosphere, alongside roles in soil creation and the release of nutrients. The symbiosis between the fungi and the plant, supported by photosynthesis in the host plant, has as one of its key features the interfacial zone where mineral and fungi come into contact. At this interface, the organism exudes a complex mixture of organic acids, chelating molecules, protons, and extracellular polysaccharide. In this review, examples will be given of recent Atomic Force Microscopy experiments to monitor the colonization of phyllosilicate minerals in sterile controlled microcosm environments containing only tree seedlings, mineral chips and mycorrhizal fungi. The surface activity of the colonizing fungal hyphae is extensive and complex. In complementary experiments involving exposure of minerals surfaces to single organic acids, it has been possible to monitor dissolution at the unit cell level and to extract activation energies for specific dissolution processes, for example 49kJmol(-1) for 100mM oxalic acid acting upon a biotite sample. The link between these simpler model experiments and the whole microcosm studies is illustrated partly by observations of fungal-colonized mineral surfaces from microcosms after careful removal of the organism and biolayer. These mineral surfaces give clear indications of basal plane modification and fungal weathering.     

Improved molecular methods to characterise Serpula lacrymans and other Basidiomycetes involved in wood decay

Early detection of indoor wood-decay fungi is crucial to prevent building deterioration and thereby avoid considerable economic loss. Due to their increased sensitivity, two reliable DNA-based fingerprinting techniques, capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) and denaturing high-performance liquid chromatography (DHPLC), were used to identify Serpula lacrymans and to profile wood-rot Basidiomycetes in the built environment. Molecular fungal diversity was assessed on 74 environmental samples, collected from 2003 to 2009 from infected buildings in France. S. lacrymans, the most widespread, indoor wood-decay fungus accounted for 64% of total wood-rot Basidiomycetes. A number of other common wood-rot fungi such as Coniophora puteana, Trametes versicolor and Donkioporia expansa were identified. Other Basidiomycetes such as Phlebiopsis gigantea and Scleroderma verrucosum were detected for the first time in the built environment. Reliable diagnostic tools were developed using two PCR-based molecular typing techniques, one for routine diagnosis and another one for community inventories. Together they provided useful data for characterising the complexity of wood-decay ecosystems and helped reveal the coexistence of different wood-decay fungi within the same microbiotope.     

Wood-decay fungi in fine living roots of conifer seedlings

The mycorrhizal basidiomycetes are known to have multiple, independent evolutionary origins from saprotrophic ancestors. To date, a number of studies have revealed functional resemblance of mycorrhizal fungi to free-living saprotrophs, but information on the ability of saprotrophic fungi to perform as mycorrhizal symbionts is scarce. Here, the objective was to investigate the ability of three wood-decay fungi, Phlebiopsis gigantea, Phlebia centrifuga and Hypholoma fasciculare, to colonize fine roots of conifer seedlings. For each fungus, mycorrhizal syntheses were attempted with Picea abies and Pinus sylvestris. After 24 wk, isolation of fungi and direct sequencing of fungal internal transcribed spacer (ITS) rDNA were carried out from healthy-looking surface-sterilized root tips that yielded both pure cultures and ITS sequences of each inoculated strain. Mycelial mantle of P. gigantea was frequently formed on root tips of P. abies, and microscopical examination has shown the presence of intercellular hyphae inside the roots. The results provide evidence of the ability of certain wood-decay fungi to colonise fine roots of tree seedlings.     

Involvement of Nitrogen-Containing Compounds in β -Lactam Biosynthesis and its Control

ABSTRACT

Biosynthesis of β -lactam antibiotics by fungi and actinomycetes is markedly affected by compounds containing nitrogen. The different processes employed by the spectrum of microbes capable of making these valuable compounds are affected differently by particular compounds. Ammonium ions, except at very low concentrations, exert negative effects via nitrogen metabolite repression, sometimes involving the nitrogen regulatory gene nre. Certain amino acids are precursors or inducers, whereas others are involved in repression and, in certain cases, as inhibitors of biosynthetic enzymes and of enzymes supplying precursors. The most important amino acids from the viewpoint of regulation are lysine, methionine, glutamate and valine. Surprisingly, diamines such as diaminopropane, putrescine and cadaverine induce cephamycin production by actinomycetes. In addition to penicillins and cephalosporins made by fungi and cephamycins made by actinomycetes, other β-lactams are made by actinomycetes and unicellular bacteria. These include clavams (e.g., clavulanic acid), carbapenems (e.g., thienamycin), nocardicins and monobactams. Here also, amino acids are precursors and inhibitors, but only little is known about regulation. In the case of the simplest carbapenem made by unicellular bacteria, i.e., 1-carba-2-em-3-carboxylic acid, quorum sensors containing homoserine lactone are inducers.     

Fungi in freshwaters: ecology, physiology and biochemical potential

Research on freshwater fungi has concentrated on their role in plant litter decomposition in streams. Higher fungi dominate over bacteria in terms of biomass, production and enzymatic substrate degradation. Microscopy-based studies suggest the prevalence of aquatic hyphomycetes, characterized by tetraradiate or sigmoid spores. Molecular studies have consistently demonstrated the presence of other fungal groups, whose contributions to decomposition are largely unknown. Molecular methods will allow quantification of these and other microorganisms. The ability of aquatic hyphomycetes to withstand or mitigate anthropogenic stresses is becoming increasingly important. Metal avoidance and tolerance in freshwater fungi implicate a sophisticated network of mechanisms involving external and intracellular detoxification. Examining adaptive responses under metal stress will unravel the dynamics of biochemical processes and their ecological consequences. Freshwater fungi can metabolize organic xenobiotics. For many such compounds, terrestrial fungal activity is characterized by cometabolic biotransformations involving initial attack by intracellular and extracellular oxidative enzymes, further metabolization of the primary oxidation products via conjugate formation and a considerable versatility as to the range of metabolized pollutants. The same capabilities occur in freshwater fungi. This suggests a largely ignored role of these organisms in attenuating pollutant loads in freshwaters and their potential use in environmental biotechnology.     

Low temperature enhances the ability of the termite-egg-mimicking fungus Athelia termitophila to compete against wood-decaying fungi

A unique symbiosis exists between subterranean termites and the sclerotium-forming fungus Athelia termitophila, which forms termite-egg-mimicking sclerotia called ‘termite balls’. While the sclerotia gain a competitor-free habitat by being harboured by termite eggs, A. termitophila mycelia have to compete with wood-decay fungi in the life stage without termites. To understand its relationship with termites, the factors that affect the ability of A. termitophila to compete with other wood-decay fungi must be clarified. Here, we show that A. termitophila is competitive against other wood-decay fungi at low temperatures. In Petri dish experiments to evaluate the effects of the physicochemical conditions, that A. termitophila experiences in termite nests, on its competitive ability, A. termitophila overcame surrounding fungi in the winter, when termites are less active. Further studies quantifying the effects of A. termitophila on termites in winter will help us to understand this relationship.     

The production of organic acids.

The production of organic acids covers two aspects: first, the metabolic pathways involved in the biosynthesis, and, second, the industrial process strategy adopted. The review seeks to show the underlying biochemical similarities in the biosynthesis of organic acids and the resulting similarities in the commercial processes. Two groups of acids are defined, those with a "long" biosynthetic path from glucose, involving much of the glycolytic pathway and the tricarboxylic acid cycle, and those acids with a "short pathway", essentially a biotransformation of glucose. The regulation of the pathways and the future developments in metabolic control theory and genetic manipulations relating to them are considered. The organisms used industrially are also limited, Aspergillus sp. and Candida yeasts; again the underlying metabolic similarities lead to similar strategies for all the acids discussed.     

Dual Purpose of ligninolytic- basidiomycetes: mycoremediation of bioethanol distillation vinasse coupled to sustainable bio-based compounds production

Agro-industrial wastes consist of various agriculture and food industry residues produced worldwide at an estimated rate of a thousand million tons per year. Vinasse is the main wastewater resulting from sugarcane bioethanol production. This agro-industrial effluent is highly polluting and, when discarded with no previous treatment, may cause nutrient imbalance and salt saturation in the soil as well as a reduction in photosynthesis in aquatic ecosystems. Environmentally safe vinasse disposal requires reliable mechanisms, preferably involving the production of goods or services. Various cleanup technologies have been implemented and different microorganisms are being studied as viable remediation agents. Ligninolytic basidiomycetes, which have the ability to store, release and mineralize a wide variety of toxic materials and compounds, are a source of valuable biochemicals for agricultural and industrial uses. This review discusses the use of filamentous fungi in the bioremediation of distillery vinasses, their main characteristics, the enzymes implicated and the transformation processes involved in the production of several high-value bio-based compounds.     

Living in a fungal world: impact of fungi on soil bacterial niche development

The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.     

Bioconversion of crude glycerol by fungi

The production of synthetic glycerol from petrochemical feedstocks has been decreasing in recent years. This is largely due to increasing supplies of crude glycerol derived as a co-product from the oleochemical industry, especially biodiesel production. The price of glycerol is at historic lows, and the supply of crude glycerol is projected to grow faster than its industrial uses. This oversupply is driving the transition from glycerol as a product to glycerol as a precursor for new industrial applications, including its use as a substrate for bioconversion. This article reviews the use of fungi for the bioconversion of crude glycerol to the value-added products 1,2-propanediol, ethanol, single cell oil, specialty polyunsaturated fatty acids, biosurfactants, and organic acids. Information on the impurities of crude glycerol from different industrial processes is also included.     

Spore sensitivity to sunlight and freezing can restrict dispersal in wood‐decay fungi

Assessment of the costs and benefits of dispersal is central to understanding species'' life-history strategies as well as explaining and predicting spatial population dynamics in the changing world. While mortality during active movement has received much attention, few have studied the costs of passive movement such as the airborne transport of fungal spores. Here, we examine the potential of extreme environmental conditions to cause dispersal mortality in wood-decay fungi. These fungi play a key role as decomposers and habitat creators in forest ecosystems and the populations of many species have declined due to habitat loss and fragmentation. We measured the effect of simulated solar radiation (including ultraviolet A and B) and freezing at −25°C on the spore germinability of 17 species. Both treatments but especially sunlight markedly reduced spore germinability in most species, and species with thin-walled spores were particularly light sensitive. Extrapolating the species'' laboratory responses to natural irradiance conditions, we predict that sunlight is a relevant source of dispersal mortality at least at larger spatial scales. In addition, we found a positive effect of spore size on spore germinability, suggesting a trade-off between dispersal distance and establishment. We conclude that freezing and particularly sunlight can be important sources of dispersal mortality in wood-decay fungi which can make it difficult for some species to colonize isolated habitat patches and habitat edges.