Organic anion exudation by ectomycorrhizal fungi and Pinus sylvestris in response to nutrient deficiencies

Sporocarp nutrition of ectomycorrhizal fungi indicates an important role for endemic species in a high productivity temperate rainforest

Endemic species of ectomycorrhizal fungi (EMF) are found throughout many biomes, but it is unclear whether their localized distribution is dictated by habitat filtering or geographical barriers to dispersal. We examined community composition (via long-read metabarcoding) and differences in sporocarp nutrition between endemic and cosmopolitan EMF species across perhumid temperate rainforests of British Columbia, characterized by soils with high nitrogen (N) supply alongside low phosphorus (P) and cation availability. Endemic EMF species, representing almost half of the community, had significantly greater sporocarp N (24% higher), potassium (+16%), and magnesium (+17%) concentrations than cosmopolitan species. Sporocarp P concentrations were comparatively low and did not differ by fungal range. However, sporocarp N% and P% were well correlated, supporting evidence for linkages in N and P acquisition. Endemics were more likely to occur on Tsuga heterophylla (a disjunct host genus) than Picea sitchensis (a circumpolar genus). The Inocybaceae and Thelephoraceae families had high proportions of endemic taxa, while species in Cortinariaceae were largely cosmopolitan, indicating some niche conservatism among genera. We conclude that superior adaptive traits in relation to perhumid soils were skewed toward the endemic community, underscoring the potentially important contribution of these localized fungi to rainforest nutrition and productivity.

Soil microbiome of shiro reveals the symbiotic relationship between Tricholoma bakamatsutake and Quercus mongolica

Tricholoma bakamatsutake is a delicious and nutritious ectomycorrhizal fungus. However, its cultivation is hindered owing to limited studies on its symbiotic relationships. The symbiotic relationship between T. bakamatsutake and its host is closely related to the shiro, a complex network composed of mycelium, mycorrhizal roots, and surrounding soil. To explore the symbiotic relationship between T. bakamatsutake and its host, soil samples were collected from T. bakamatsutake shiro (Tb) and corresponding Q. mongolica rhizosphere (CK) in four cities in Liaoning Province, China. The physicochemical properties of all the soil samples were then analyzed, along with the composition and function of the fungal and bacterial communities. The results revealed a significant increase in total potassium, available nitrogen, and sand in Tb soil compared to those in CK soil, while there was a significant decrease in pH, total nitrogen, total phosphorus, available phosphorus, and silt. The fungal community diversity in shiro was diminished, and T. bakamatsutake altered the community structure of its shiro by suppressing other fungi, such as Russula (ectomycorrhizal fungus) and Penicillium (phytopathogenic fungus). The bacterial community diversity in shiro increased, with the aggregation of mycorrhizal-helper bacteria, such as Paenibacillus and Bacillus, and plant growth-promoting bacteria, such as Solirubrobacter and Streptomyces, facilitated by T. bakamatsutake. Microbial functional predictions revealed a significant increase in pathways associated with sugar and fat catabolism within the fungal and bacterial communities of shiro. The relative genetic abundance of carboxylesterase and gibberellin 2-beta-dioxygenase in the fungal community was significantly increased, which suggested a potential symbiotic relationship between T. bakamatsutake and Q. mongolica. These findings elucidate the microbial community and relevant symbiotic environment to better understand the relationship between T. bakamatsutake and Q. mongolica.

Cadmium in the hyperaccumulating mushroom Thelephora penicillata: Intracellular speciation and isotopic composition

Thelephora penicillata is an ectomycorrhizal mushroom that can accumulate extraordinarily high concentrations of Cd, As, Cu, and Zn in its fruit-bodies. To better understand its element accumulation ability, we compared the element concentrations in T. penicillata with 10 distinct ectomycorrhizal mushroom species growing at the same site (Karlina Pila, Czech Republic). On average, T. penicillata accumulated 330, 2130, 26, and 4 times more Cd, As, Cu, and Zn, respectively, than other mushrooms. Size-exclusion chromatography and an electrophoretic analysis of T. penicillata cell extracts indicate that intracellular Cd may be present mainly in >1 kDa, presumably compartmentalized, Cd species, and partially binding with 6-kDa cysteinyl-containing peptide(s) resembling metallothioneins. The cadmium isotopic composition of mushroom fruit-bodies, soil digests, and soil extracts was investigated by thermal ionization mass spectrometry (TIMS) with double spike correction. The isotopic composition (δ^114/110Cd) of ectomycorrhizal mushrooms from Karlina Pila varied in a wide range of -0.37 to +0.14 ‰. However, remarkably low δ^114/110Cd values were observed in the majority of the investigated mushrooms when compared to the relatively homogeneous Cd isotopic composition of bulk soil (δ^114/110Cd = +0.09 ‰) and the comparatively heavy isotopic composition of soil extracts (mean δ^114/110Cd values of +0.11 ± 0.01 ‰ and +0.22 ± 0.01 ‰, depending on the extraction method). The isotopic composition of Cd hyperaccumulated in T. penicillata essentially matched the mycoavailable soil Cd fraction. However, most isotopic data indicates isotopic fractionation at the soil/fruit-body interface, which could be of environmental significance.

Tuber indicum and T. lijiangense colonization differentially regulates plant physiological responses and mycorrhizosphere bacterial community of Castanopsis rockii seedlings

Black truffles and white truffles are widely studied around the world, but their effects on plant growth and physiological responses, and on the mycorrhizosphere bacterial community of the host plant remain unclear. Here, mycorrhizal colonization of Castanopsis rockii by Tuber indicum (Chinese black truffle) and T. lijiangense (Chinese white truffle), respectively, was induced in a greenhouse study, and their effects on host growth, physiological responses and mycorrhizosphere bacterial communities were compared. The results show that colonization of both Tuber species significantly increased leaf photosynthetic rate, leaf P concentration and mycorrhizosphere acid phosphatase activity, as well as richness of mycorrhizosphere bacterial communities of C. rockii seedlings. However, T. indicum colonization on the one hand significantly decreased tartrate content, bacterial acid phosphatase, phoC gene abundance in the mycorrhizosphere, and peroxidase (POD) activity of ectomycorrhizal root tips, but on the other hand increased mycorrhizosphere pH and superoxide dismutase (SOD) of ectomycorrhizal root tips, compared to T. lijiangense colonization. Moreover, principal coordinate and β-diversity analyses show significant differences in mycorrhizosphere bacterial community composition between T. indicum and T. lijiangese colonized C. rockii seedlings. Finally, the relative abundance of the bacterium Agromyces cerinus significantly correlated to mycorrhizosphere acid phosphatase activity and leaf P concentration, suggesting that this bacterium might play an important role in P mobilization and acquisition. Overall, these results suggest that T. indicum and T. lijiangense differently regulate their host plant's physiological responses and mycorrhizosphere bacterial community.

Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics

Bioactivities of fungal peptides are of interest for basic research and therapeutic drug development. Some of these peptides are derived from "KEX2-processed repeat proteins" (KEPs), a recently defined class of precursor proteins that contain multiple peptide cores flanked by KEX2 protease cleavage sites. Genome mining has revealed that KEPs are widespread in the fungal kingdom. Their functions are largely unknown. Here, we present the first in-depth structural and functional analysis of KEPs in a basidiomycete. We bioinformatically identified KEP-encoding genes in the genome of the model agaricomycete Coprinopsis cinerea and established a detection protocol for the derived peptides by overexpressing the C. cinerea KEPs in the yeast Pichia pastoris. Using this protocol, which includes peptide extraction and mass spectrometry with data analysis using the search engine Mascot, we confirmed the presence of several KEP-derived peptides in C. cinerea, as well as in the edible mushrooms Lentinula edodes, Pleurotus ostreatus, and Pleurotus eryngii. While CRISPR-mediated knockout of C. cinerea kep genes did not result in any detectable phenotype, knockout of kex genes caused defects in mycelial growth and fruiting body formation. These results suggest that KEP-derived peptides may play a role in the interaction of C. cinerea with the biotic environment and that the KEP-processing KEX proteases target a variety of substrates in agaricomycetes, including some important for mycelial growth and differentiation. IMPORTANCE Two recent bioinformatics studies have demonstrated that KEX2-processed repeat proteins are widespread in the fungal kingdom. However, despite the prevalence of KEPs in fungal genomes, only few KEP-derived peptides have been detected and studied so far. Here, we present a protocol for the extraction and structural characterization of KEP-derived peptides from fungal culture supernatants and tissues. The protocol was successfully used to detect several linear and minimally modified KEP-derived peptides in the agaricomycetes C. cinerea, L. edodes, P. ostreatus, and P. eryngii. Our study establishes a new protocol for the targeted search of KEP-derived peptides in fungi, which will hopefully lead to the discovery of more of these interesting fungal peptides and allow a further characterization of KEPs.

Improved methods to assess the effect of bacteria on germination of fungal spores

Bacterial-fungal interactions (BFI) play a major role on ecosystem functioning and might be particularly relevant at a specific development stage. For instance, in the case of biological control of fungal pathogens by bacteria, a highly relevant kind of BFI, in-vitro experiments often assess the impact of a bacterium on the inhibition of actively growing mycelia. However, this fails to consider other stages of plant infection such as the germination of a spore or a sclerotium. This study aims to present novel experimental platforms for in-vitro experiments with fungal spores, in order to assess the effect of bacteria on germination and fungal growth control, to recover the metabolites produced in the interaction, and to enhance direct visualisation of BFI. Botrytis cinerea, a phytopathogenic fungus producing oxalic acid (OA) as pathogenicity factor, was used as model. Given that oxalotrophic bacteria have been shown previously to control the growth of B. cinerea, the oxalotrophic bacteria Cupriavidus necator and Cupriavidus oxalaticus were used as models. The experiments performed demonstrated the suitability of the methods and confirmed that both bacteria were able to control the growth of B. cinerea, but only in media in which soluble OA was detected by the fungus. The methods presented here can be easily performed in any microbiology laboratory and are not only applicable to screen for potential biocontrol agents, but also to better understand BFI.

Growth, Rhizosphere Carboxylate Exudation, and Arbuscular Mycorrhizal Colonisation in Temperate Perennial Pasture Grasses Varied with Phosphorus Application

Phosphorus (P) fertiliser is applied regularly to the nutrient-poor sandy soils in southwestern Australia to elevate and/or maintain pasture production. This study aimed to characterise differential growth, root carboxylate exudation, and mycorrhizal responses in three temperate perennial pasture grasses at variable P supply. Tall fescue (Festuca arundinacea L. cv. Prosper), veldt grass (Ehrharta calycina Sm. cv. Mission), and tall wheatgrass (Thinopyrum ponticum L. cv. Dundas) with five P rates varying from 0 to 100 mg P kg−1 soil were evaluated in a controlled environment. Rhizosphere carboxylate exudation and mycorrhizal colonisation were assessed. Veldt grass produced the maximum shoot dry weight, highest agronomic phosphorus-use efficiency at low P supply, as well as the highest specific root length and shoot P content at all P rates. Across species, the maximum shoot weight was obtained at 20 and 50 mg P kg−1 soil, which differed significantly from the two lowest P rates (0 and 5 mg P kg−1 soil). Phosphorus application influenced carboxylate exudation, with plants exuding acetate only in the zero P treatment, and citrate and malonate in the P-supplemented treatments. In all three species, acetate and malonate were the major carboxylates exuded (37–51% of the total). Only tall wheatgrass released trans-aconitate. Citrate and malonate concentrations in the rhizosphere increased with P supply, suggesting their important role in P acquisition. Phosphorus applications reduced arbuscular mycorrhizal colonisation and increased root diameter as the P rate increased. Root carboxylate exudation in low-P soil played a role in mobilisation of P via P solubilisation, but the role of exuded carboxylate in soils well supplied with P might be diminished.

Insight into the mechanism of low molecular weight organic acids-mediated release of phosphorus and potassium from biochars

A crucial mechanism for the application of biochar in soil improvement is the direct release of nutrients from biochar. Low molecular weight organic acids (LMWOAs) ubiquitously exist in soil. However, the mechanism of LMWOAs-mediated release of nutrients from biochars remains little known. Ten biochars with different mineral element stoichiometric ratio were produced, and four LMWOAs [acetic (HAc), glycolic (GA), tartaric (TA), and citric acids (CA)] were employed, to enunciate the influence mechanism of LMWOAs on the release of phosphorus and potassium from biochar. The results showed that HAc suppressed the release of P from biochars, while TA and CA facilitated the release of P from biochars with high ratios of polyvalent metals to P. A new mechanism was proposed that the deprotonated HAc combined with the dissolved HPO₄^2- or H₂PO₄^- to form a complex through hydrogen bond and cation bridging. The hydrophobic methyl group of HAc was exposed outside of the complex, which decreased the water-solubility of phosphate. Meanwhile, a high ratio of polyvalent metals to P benefited more P to combine with polyvalent metals, which decreased the water-solubility of P, but the deprotonated TA and CA are polyvalent anions that could substitute this part of P by anion exchange. Also, LMWOAs promoted the release of K from biochars with low K/(P + S) ratios, possibly due to unionized carboxyl of LMWOAs served as a hydrogen bond donor to displace K out of biochars. This study gives a deep understanding of the fate of biochar originated nutrients response to LMWOAs.

Disentangling the factors of contrasting silver and copper accumulation in sporocarps of the ectomycorrhizal fungus Amanita strobiliformis from two sites

Amanita strobiliformis (European Pine Cone Lepidella) is an ectomycorrhizal fungus of the Amanitaceae family known to hyperaccumulate Ag in the sporocarps. Two populations (ecotypes) of A. strobiliformis collected from two urban forest plantations in Prague, Czech Republic, were investigated. The concentrations of Ag, Cu, Cd, and Zn were determined in the mushrooms. The metal mobility and fractionation in the soils was investigated by single extractions and sequential extraction. The soil distribution of A. strobiliformis mycelium was assessed by quantitative polymerase chain reaction (qPCR). The metal uptake from the soil into the mushroom sporocarps was traced by Pb isotopic fingerprinting. The findings suggested that A. strobiliformis (i) accumulates primarily Ag from the topsoil layer (circa 12cm deep) and (ii) accumulates Ag associated with the "reducible soil fraction". The concentrations of all metals, particularly Ag and Cu, were significantly higher in the A. strobiliformis sporocarps from one of the investigated sites (Klíčov). The elevated concentrations of Ag in the sporocarps from Klíčov can possibly be attributed to the higher Ag content in the topsoil layer found at this site. However, the simultaneously elevated concentrations of Cu in A. strobiliformis from Klíčov cannot be explained by the differences in the geochemical background and should be attributed to biological factors.

Effects of Nutrient Deficiency on Root Morphology and Nutrient Allocation in Pistacia chinensis Bunge Seedlings

Plant growth depends on soil mineral elements, a lack of which results in reduced nutrient accumulation leading to poor growth and resistance in plants. Therefore, more information is needed about the response of Pistacia chinensis Bunge (P. chinensis) seedlings to nutrient deficiency. In this study, we investigated how soil nutrient availability affects the nutrient accumulation and root system of P. chinensis seedlings. Seedlings were cultivated under five different nutrient treatments (500 mg, 400 mg, 300 mg, 200 mg, and 100 mg N). Various indices, including seedling growth, nutrient accumulation and root morphology, were analyzed at the end of the growing season. Nutrient deficiency (300 mg, 200 mg, and 100 mg N) reduced the accumulation of nitrogen (N), phosphorus (P) and potassium (K) in roots and stems, while the nutrient proportion of N, P, and K stored in the roots and root to shoot ratio (R/S) was increased at the end of growing season. Root length, root surface area, and root volume of very fine roots (<0.5 mm in diameter) and coarse roots (>3.0 mm in diameter) of the three lower nutrient treatments were significantly lower than those of the two highest nutrient treatments, while no significant difference was detected in the fine roots (1.0–3.0 mm in diameter). Instead, foliar N and K contents in seedlings treated with the two highest treatments were significantly greater than those of the three lower nutrient treatments, resulting in a greater nutrient loss ratio. However, seedlings treated with 100 mg N had significantly higher foliar P content than those treated with 500 mg. Seedlings treated with 300 mg and 200 mg N did not have restricted root nutrient accumulation but did have reduced nutrient accumulation in the stems. The 100 mg N treatment significantly reduced the root nutrient accumulation of N and K. The 500 mg N treatment did not increase the accumulation of nutrients in the storage organs compared with the 400 mg N treatment, but did increase the loss of N and K due to defoliation in autumn. In conclusion, there is a threshold for nutrient accumulation in storage organs at the nursery stage under a specific environment. P. chinensis seedlings reduced the negative effects of nutrient deficiency by promoting root growth, particularly fine roots, and increasing N and K allocation in storage organs.

Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes

Mycorrhizal fungi benefit plants by improved mineral nutrition and protection against stress, yet information about fundamental differences among mycorrhizal types in fungi and trees and their relative importance in biogeochemical processes is only beginning to accumulate. We critically review and synthesize the ecophysiological differences in ectomycorrhizal, ericoid mycorrhizal and arbuscular mycorrhizal symbioses and the effect of these mycorrhizal types on soil processes from local to global scales. We demonstrate that guilds of mycorrhizal fungi display substantial differences in genome-encoded capacity for mineral nutrition, particularly acquisition of nitrogen and phosphorus from organic material. Mycorrhizal associations alter the trade-off between allocation to roots or mycelium, ecophysiological traits such as root exudation, weathering, enzyme production, plant protection, and community assembly as well as response to climate change. Mycorrhizal types exhibit differential effects on ecosystem carbon and nutrient cycling that affect global elemental fluxes and may mediate biome shifts in response to global change. We also note that most studies performed to date have not been properly replicated and collectively suffer from strong geographical sampling bias towards temperate biomes. We advocate that combining carefully replicated field experiments and controlled laboratory experiments with isotope labelling and -omics techniques offers great promise towards understanding differences in ecophysiology and ecosystem services among mycorrhizal types.

In vitro selection of ecologically adapted ectomycorrhizal fungi through production of fungal biomass and metabolites for use in reclamation of biotite mine tailings

Mineral weathering plays an important role in poor-nutrient environments such as mine spoils and tailings. Ectomycorrhizal (ECM) fungi are able to enhance mineral weathering through different mechanisms, thereby increasing the availability of minerals and nutrients to plants. Six ECM fungi (Cadophora finlandia, Cenococcum geophilum, Hebeloma crustuliniforme, Lactarius aurantiosordidus, Paxillus involutes, and Tricholoma scalpturatum) were tested here for their tolerance to biotite-quartz-rich mine tailings. Either solid- or liquid-medium methods were used for in vitro selection of ECM fungi for their ability to grow on mine tailings. ECM fungi were selected based on their mycelial radial growth and metabolite production (ergosterol and low-molecular-mass organic acids, LMMOAs). We found a strong correlation between fungal ergosterol content and mycelial radial growth using the solid-medium method. However, the liquid-medium method was more appropriate for ergosterol synthesis and permitted direct measurement of organic acid production. We found that LMMOAs were exuded by ECM fungi, which solubilized mine tailings for their own growth and nutrition. Finally, we concluded that the ECM fungi C. finlandia and T. scalpturatum are the species most tolerant to tailings and could potentially improve the survival rate, growth, and health of white spruce seedlings planted on biotite mine spoils and tailings.

Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hyphosphere soils

Macro-fungi play important roles in the soil elemental cycle in terrestrial ecosystems. Many researchers have focused on the interactions between mycorrhizal fungi and host plants, whilst comparatively few studies aim to characterise the relationships between macro-fungi and bacteria in situ. In this study, we detected endophytic bacteria within fruit bodies of ectomycorrhizal and saprophytic fungi (SAF) using high-throughput sequencing technology, as well as bacterial diversity in the corresponding hyphosphere soils below the fruit bodies. Bacteria such as Helicobacter, Escherichia-Shigella, and Bacillus were found to dominate within fruit bodies, indicating that they were crucial in the development of macro-fungi. The bacterial richness in the hyphosphere soils of ectomycorrhizal fungi (EcMF) was higher than that of SAF and significant difference in the composition of bacterial communities was observed. There were more Verrucomicrobia and Bacteroides in the hyphosphere soils of EcMF, and comparatively more Actinobacteria and Chloroflexi in the hyphosphere of SAF. The results indicated that the two types of macro-fungi can enrich, and shape the bacteria compatible with their respective ecological functions. This study will be beneficial to the further understanding of interactions between macro-fungi and relevant bacteria.

Phenolic root exudate and tissue compounds vary widely among temperate forest tree species and have contrasting effects on soil microbial respiration

Root-soil interactions fundamentally affect the terrestrial carbon (C) cycle and thereby ecosystem feedbacks to climate change. This study addressed the question of whether the secondary metabolism of different temperate forest tree species can affect soil microbial respiration. We hypothesized that phenolics can both increase and decrease respiration depending on their function as food source, mobilizer of other soil resources, signaling compound, or toxin. We analyzed the phenolic compounds from root exudates and root tissue extracts of six tree species grown in a glasshouse using high-performance liquid chromatography. We then tested the effect of individual phenolic compounds, representing the major identified phenylpropanoid compound classes, on microbial respiration through a 5-d soil incubation. Phenolic root profiles were highly species-specific. Of the eight classes identified, flavonoids were the most abundant, with flavanols being the predominating sub-class. Phenolic effects on microbial respiration ranged from a 26% decrease to a 46% increase, with reduced respiration occurring in the presence of compounds possessing a catechol ring. Tree species variation in root phenolic composition influences the magnitude and direction of root effects on microbial respiration. Our data support the hypothesis that functional group rather than biosynthetic class determines the root phenolic effect on soil C cycling.

Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during inter-kingdom interactions

Production of basidiomycete atromentin-derived pigments like variegatic acid (pulvinic acid-type) and involutin (diarylcyclopentenone) from the brown-rotter Serpula lacrymans and the ectomycorrhiza-forming Paxillus involutus, respectively, is induced by complex nutrition, and in the case of S. lacrymans, bacteria. Pigmentation in S. lacrymans was stimulated by 13 different bacteria and cell-wall-damaging enzymes (lytic enzymes and proteases), but not by lysozyme or mechanical damage. The use of protease inhibitors with Bacillus subtilis or heat-killed bacteria during co-culturing with S. lacrymans significantly reduced pigmentation indicating that enzymatic hyphal damage and/or released peptides, rather than mechanical injury, was the major cause of systemic pigment induction. Conversely, no significant pigmentation by bacteria was observed from P. involutus. We found additional putative transcriptional composite elements of atromentin synthetase genes in P. involutus and other ectomycorrhiza-forming species that were absent from S. lacrymans and other brown-rotters. Variegatic and its precursor xerocomic acid, but not involutin, in return inhibited swarming and colony biofilm spreading of Bacillus subtilis, but did not kill B. subtilis. We suggest that dissimilar pigment regulation by fungal lifestyle was a consequence of pigment bioactivity and additional promoter motifs. The focus on basidiomycete natural product gene induction and regulation will assist in future studies to determine global regulators, signalling pathways and associated transcription factors of basidiomycetes.

Mushrooms: from nutrition to mycoremediation

Mushrooms are well known as important food items. The uses of mushrooms in the cuisine are manifolds and are being utilized for thousands of years in both Oriental and Occidental cultures. Medicinal properties of mushrooms show an immense potential as drugs for the treatment of various diseases as they are rich in a great variety of phytochemicals. In this review, we attempted to encompass the recent knowledge and scientific advancement about mushrooms and their utilization as food or curative properties, along with their natural ability to accumulate (heavy) metals/radionuclides, which leads to an important aspect of bioremediation. However, accumulation of heavy metals and radionuclides from natural or anthropogenic sources also involves potential nutritional hazards upon consumption. These hazards have been pointed out in this review incorporating a selection of the most recently published literature.

Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions

In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime. In the system, B. terrae BS001 apparently perceived the presence of the fungal hyphae already at the early experimental stages (T1, T2), by strongly upregulating a suite of chemotaxis and flagellar motility genes. With respect to specific metabolism and energy generation, a picture of differential involvement in different metabolic routes was obtained. Initial (T1, T2) up- or downregulation of ethanolamine and mandelate uptake and utilization pathways was substituted by a strong investment, in the presence of the fungus, in the expression of putative metabolic gene clusters (T3). Specifically at T3, five clustered genes that are potentially involved in energy generation coupled to an oxidative stress response, and two genes encoding short-chain dehydrogenases/oxidoreductases (SDR), were highly upregulated. In contrast, the dnaE2 gene (related to general stress response; encoding error-prone DNA polymerase) was transcriptionally downregulated at this stage. This study revealed that B. terrae BS001, from a stress-induced state, resulting from the soil extract agar milieu, responds positively to fungal hyphae that encroach upon it, in a temporally dynamic manner. The response is characterized by phases in which the modulation of (1) chemotaxis, (2) metabolic activity, and (3) oxidative stress responses are key mechanisms.

Heavy metal bioaccumulation by wild edible saprophytic and ectomycorrhizal mushrooms

Heavy metals cause serious problems in the environment, and they can be accumulated in organisms, especially in the higher fungi. The concentration of Ni, Cr, Pb, Cd, and Hg in 10 species of edible mushrooms in Medvednica Nature Park, Croatia was therefore determined. In addition, the similarity between the studied species was determined by cluster analysis based on concentrations of the aforementioned metals in the fruiting bodies. The contents of nickel, chromium, lead, cadmium, and mercury in the fruiting bodies of mushrooms were obtained by X-ray fluorescence spectrometry. The highest concentrations of Ni (3.62 mg kg(-1)), Cr (3.01 mg kg(-1)), and Cd (2.67 mg kg(-1)) were determined in Agaricus campestris. The highest concentration of Pb (1.67 mg kg(-1)) was determined in Macrolepiota procera, and the highest concentration of Hg (2.39 mg kg(-1)) was determined in Boletus edulis. The concentration of all heavy metals significantly differed (p < 0.001) between examined saprophytic and ectomycorrhizal mushrooms. Considering anatomical part of the fruiting body (cap-stipe), a considerably higher concentration of the analyzed elements was found in the cap for all mushroom species. According to calculated bioconcentration factors, all the examined species were found to be bioexclusors of Ni, Cr, and Pb and bioaccumulators of Cd and Hg. Cluster analysis performed on the basis of the accumulation of the studied metals revealed great phenotypic similarity of mushroom species belonging to the same genus and partial similarity of species of the same ecological affiliation.

Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi

Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.

Involutin is an Fe3+ reductant secreted by the ectomycorrhizal fungus Paxillus involutus during Fenton-based decomposition of organic matter

Ectomycorrhizal fungi play a key role in mobilizing nutrients embedded in recalcitrant organic matter complexes, thereby increasing nutrient accessibility to the host plant. Recent studies have shown that during the assimilation of nutrients, the ectomycorrhizal fungus Paxillus involutus decomposes organic matter using an oxidative mechanism involving Fenton chemistry (Fe²⁺ + H₂O₂ + H⁺ → Fe³⁺ + ˙OH + H₂O), similar to that of brown rot wood-decaying fungi. In such fungi, secreted metabolites are one of the components that drive one-electron reductions of Fe³⁺ and O₂, generating Fenton chemistry reagents. Here we investigated whether such a mechanism is also implemented by P. involutus during organic matter decomposition. Activity-guided purification was performed to isolate the Fe³⁺-reducing principle secreted by P. involutus during growth on a maize compost extract. The Fe³⁺-reducing activity correlated with the presence of one compound. Mass spectrometry and nuclear magnetic resonance (NMR) identified this compound as the diarylcyclopentenone involutin. A major part of the involutin produced by P. involutus during organic matter decomposition was secreted into the medium, and the metabolite was not detected when the fungus was grown on a mineral nutrient medium. We also demonstrated that in the presence of H₂O₂, involutin has the capacity to drive an in vitro Fenton reaction via Fe³⁺ reduction. Our results show that the mechanism for the reduction of Fe³⁺ and the generation of hydroxyl radicals via Fenton chemistry by ectomycorrhizal fungi during organic matter decomposition is similar to that employed by the evolutionarily related brown rot saprotrophs during wood decay.

The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling

On million-year timescales, carbonate rock weathering exerts no net effect on atmospheric CO2 concentration. However, on timescales of decades-to-centuries, it can contribute to sequestration of anthropogenic CO2 and increase land-ocean alkalinity flux, counteracting ocean acidification. Historical evidence indicates this flux is sensitive to land use change, and recent experimental evidence suggests that trees and their associated soil microbial communities are major drivers of continental mineral weathering. Here, we review key physical and chemical mechanisms by which the symbiotic mycorrhizal fungi of forest tree roots potentially enhance carbonate rock weathering. Evidence from our ongoing field study at the UK's national pinetum confirms increased weathering of carbonate rocks by a wide range of gymnosperm and angiosperm tree species that form arbuscular (AM) or ectomycorrhizal (EM) fungal partnerships. We demonstrate that calcite-containing rock grains under EM tree species weather significantly faster than those under AM trees, an effect linked to greater soil acidification by EM trees. Weathering and corresponding alkalinity export are likely to increase with rising atmospheric CO2 and associated climate change. Our analyses suggest that strategic planting of fast-growing EM angiosperm taxa on calcite- and dolomite-rich terrain might accelerate the transient sink for atmospheric CO2 and slow rates of ocean acidification.

Copsin, a novel peptide-based fungal antibiotic interfering with the peptidoglycan synthesis

Fungi and bacteria compete with an arsenal of secreted molecules for their ecological niche. This repertoire represents a rich and inexhaustible source for antibiotics and fungicides. Antimicrobial peptides are an emerging class of fungal defense molecules that are promising candidates for pharmaceutical applications. Based on a co-cultivation system, we studied the interaction of the coprophilous basidiomycete Coprinopsis cinerea with different bacterial species and identified a novel defensin, copsin. The polypeptide was recombinantly produced in Pichia pastoris, and the three-dimensional structure was solved by NMR. The cysteine stabilized α/β-fold with a unique disulfide connectivity, and an N-terminal pyroglutamate rendered copsin extremely stable against high temperatures and protease digestion. Copsin was bactericidal against a diversity of Gram-positive bacteria, including human pathogens such as Enterococcus faecium and Listeria monocytogenes. Characterization of the antibacterial activity revealed that copsin bound specifically to the peptidoglycan precursor lipid II and therefore interfered with the cell wall biosynthesis. In particular, and unlike lantibiotics and other defensins, the third position of the lipid II pentapeptide is essential for effective copsin binding. The unique structural properties of copsin make it a possible scaffold for new antibiotics.

Getting rid of the unwanted: highlights of developments and challenges of biobeneficiation of iron ore minerals-a review

The quest for quality mineral resources has led to the development of many technologies that can be used to refine minerals. Biohydrometallurgy is becoming an increasingly acceptable technology worldwide because it is cheap and environmentally friendly. This technology has been successfully developed for some sulphidic minerals such as gold and copper. In spite of wide acceptability of this technology, there are limitations to its applications especially in the treatment of non-sulphidic minerals such as iron ore minerals. High levels of elements such as potassium (K) and phosphorus (P) in iron ore minerals are known to reduce the quality and price of these minerals. Hydrometallurgical methods that are non-biological involving the use of chemicals are usually used to deal with this problem. However, recent advances in mining technologies favour green technologies, known as biohydrometallurgy, with minimal impact on the environment. This technology can be divided into two, namely bioleaching and biobeneficiation. This review focuses on Biobeneficiation of iron ore minerals. Biobeneficiation of iron ore is very challenging due to the low price and chemical constitution of the ore. There are substantial interests in the exploration of this technology for improving the quality of iron ore minerals. In this review, current developments in the biobeneficiation of iron ore minerals are considered, and potential solutions to challenges faced in the wider adoption of this technology are proposed.

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests.

An update on magnesium homeostasis mechanisms in plants

Worldwide, nearly two-thirds of the population do not consume the recommended amount of magnesium (Mg) in their diet. Furthermore, low Mg status (hypomagnesaemia) is known to contribute to a number of human chronic disease conditions. Because the principal dietary Mg source is of plant origin, agronomic and genetic biofortification strategies are aimed at improving nutritional Mg content in food crops to overcome this mineral deficiency in humans. This update incorporates the contributions of annotated permeases involved in Mg uptake, storage and recycling with a schematic model of Mg movement at the organ and cellular levels in the model species Arabidopsis thaliana. Furthermore, approaches using mutagenesis or natural ionomic variation to identify loci involved in Mg homeostasis in roots, leaves and seeds will be summarised. A brief overview will be presented on how Arabidopsis research can help to develop strategies for biofortification of crops.

Macro and trace mineral constituents and radionuclides in mushrooms: health benefits and risks

This article reviews and updates data on macro and trace elements and radionuclides in edible wild-grown and cultivated mushrooms. A huge biodiversity of mushrooms and spread of certain species over different continents makes the study on their multi-element constituents highly challenging. A few edible mushrooms are widely cultivated and efforts are on to employ them (largely Agaricus spp., Pleurotus spp., and Lentinula edodes) in the production of selenium-enriched food (mushrooms) or nutraceuticals (by using mycelia) and less on species used by traditional medicine, e.g., Ganoderma lucidum. There are also attempts to enrich mushrooms with other elements than Se and a good example is enrichment with lithium. Since minerals of nutritional value are common constituents of mushrooms collected from natural habitats, the problem is however their co-occurrence with some hazardous elements including Cd, Pb, Hg, Ag, As, and radionuclides. Discussed is also the problem of erroneous data on mineral compounds determined in mushrooms.

Macro and trace mineral constituents and radionuclides in mushrooms: health benefits and risks

This article reviews and updates data on macro and trace elements and radionuclides in edible wild-grown and cultivated mushrooms. A huge biodiversity of mushrooms and spread of certain species over different continents makes the study on their multi-element constituents highly challenging. A few edible mushrooms are widely cultivated and efforts are on to employ them (largely Agaricus spp., Pleurotus spp., and Lentinula edodes) in the production of selenium-enriched food (mushrooms) or nutraceuticals (by using mycelia) and less on species used by traditional medicine, e.g., Ganoderma lucidum. There are also attempts to enrich mushrooms with other elements than Se and a good example is enrichment with lithium. Since minerals of nutritional value are common constituents of mushrooms collected from natural habitats, the problem is however their co-occurrence with some hazardous elements including Cd, Pb, Hg, Ag, As, and radionuclides. Discussed is also the problem of erroneous data on mineral compounds determined in mushrooms.

Fungal communities influence root exudation rates in pine seedlings

Root exudates are hypothesized to play a central role in belowground food webs, nutrient turnover, and soil C dynamics in forests, but little is known about the extent to which root-associated microbial communities influence exudation rates in trees. We used a novel experimental technique to inoculate loblolly pine (Pinus taeda L.) seedlings with indigenous forest fungi to examine how diverse fungal communities influence exudation. Surface-sterilized seeds were sown in intact, unsieved soil cores for 14 weeks to promote root colonization by fungi. After 14 weeks, we transferred seedlings and root-associated fungi into cuvettes and measured exudate accumulation in trap solutions. Both the abundance and identity of root-associated fungi influenced exudation. Exudation rates were greatest in root systems least colonized by ectomycorrhizal (ECM) fungi and most colonized by putative pathogenic and saprotrophic fungi. However, the ECM community composition was not a strong determinant of exudation rates. These results suggest that environmental conditions that influence the degree to which tree roots are colonized by pathogenic and saprotrophic vs. mutualistic fungi are likely to mediate fluxes of labile C in forest soils, with consequences for soil biogeochemistry and ecosystem processes.

The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry

Soils in boreal forests contain large stocks of carbon. Plants are the main source of this carbon through tissue residues and root exudates. A major part of the exudates are allocated to symbiotic ectomycorrhizal fungi. In return, the plant receives nutrients, in particular nitrogen from the mycorrhizal fungi. To capture the nitrogen, the fungi must at least partly disrupt the recalcitrant organic matter-protein complexes within which the nitrogen is embedded. This disruption process is poorly characterized. We used spectroscopic analyses and transcriptome profiling to examine the mechanism by which the ectomycorrhizal fungus Paxillus involutus degrades organic matter when acquiring nitrogen from plant litter. The fungus partially degraded polysaccharides and modified the structure of polyphenols. The observed chemical changes were consistent with a hydroxyl radical attack, involving Fenton chemistry similar to that of brown-rot fungi. The set of enzymes expressed by Pa. involutus during the degradation of the organic matter was similar to the set of enzymes involved in the oxidative degradation of wood by brown-rot fungi. However, Pa. involutus lacked transcripts encoding extracellular enzymes needed for metabolizing the released carbon. The saprotrophic activity has been reduced to a radical-based biodegradation system that can efficiently disrupt the organic matter-protein complexes and thereby mobilize the entrapped nutrients. We suggest that the released carbon then becomes available for further degradation and assimilation by commensal microbes, and that these activities have been lost in ectomycorrhizal fungi as an adaptation to symbiotic growth on host photosynthate. The interdependence of ectomycorrhizal symbionts and saprophytic microbes would provide a key link in the turnover of nutrients and carbon in forest ecosystems.

Calcium oxalate biomineralization by Piloderma fallax in response to various levels of calcium and phosphorus

Piloderma fallax is an ectomycorrhizal fungus commonly associated with several conifer and hardwood species. We examined the formation of calcium oxalate crystals by P. fallax in response to calcium (0.0, 0.1, 0.5, 1, and 5 mM) and phosphorus (0.1 and 6 mM) additions in modified Melin-Norkrans agar medium. Both calcium and phosphorus supplementation significantly affected the amount of calcium oxalate formed. More calcium oxalate was formed at high P levels. Concentrations of soluble oxalate in the fungus and medium were higher at low P levels. There was a strong positive linear relationship between Ca level and calcium oxalate but only under conditions of phosphorus limitation. Calcium oxalate crystals were identified as the monohydrate form (calcium oxalate monohydrate [COM] whewellite) by X-ray diffraction analysis. Prismatic, styloid, and raphide forms of the crystals, characteristic COM, were observed on the surface of fungal hyphae by scanning electron microscopy. P. fallax may be capable of dissolving hyphal calcium oxalate under conditions of limited Ca. The biomineralization of calcium oxalate by fungi may be an important step in the translocation and cycling of Ca and P in soil.

A pH signaling mechanism involved in the spatial distribution of calcium and anion fluxes in ectomycorrhizal roots

Mycorrhization is a typical example of a host-pathogen symbiotic interaction where the pathogen cell biology and the host immune response coevolved several functional links. Here, the role played by ion fluxes across the root concerning nutrient uptake, osmoregulation, growth and signaling events is addressed. An ion-selective vibrating probe system was used to determine the net fluxes of protons (H(+)), calcium (Ca(2+)) and anions (A(-)) along nonmycorrhizal and ectomycorrhizal (ECM) roots of Eucalyptus globulus colonized by Pisolithus sp. These data show that, from five root zones analyzed, the main effect of fungal colonization was localized to the elongation zone. Here, strong changes in ion dynamics and rhizosphere acidification capacity were observed. Additionally, ion fluxes exhibited periodic fluctuations. To verify whether these fluctuations corresponded to sustained oscillations, continuous wavelet time spectrum analysis was applied and it was determined that H(+) and A(-) fluxes from ECM roots had longer periods than nonmycorrhizal roots. By contrast, Ca(2+) oscillations were completely abolished following fungal interaction. These results are interpreted in the light of a working model in which nutrient uptake and stimulation of growth are mediated by ECM fungi and may be pH-dependent. Furthermore, the variations detected in ECM roots for H(+) and A(-) fluxes suggest a main contribution from the plant, while the results obtained for Ca(2+) point to a significant involvement of the fungus.

Efflux of hydraulically lifted water from mycorrhizal fungal hyphae during imposed drought

Apart from improving plant and soil water status during drought, it has been suggested that hydraulic lift (HL) could enhance plant nutrient capture through the flow of mineral nutrients directly from the soil to plant roots, or by maintaining the functioning of mycorrhizal fungi. We evaluated the extent to which the diel cycle of water availability created by HL covaries with the efflux of HL water from the tips of extramatrical (external) mycorrhizal hyphae, and the possible effects on biogeochemical processes. Phenotypic mycorrhizal fungal variables, such as total and live hyphal lengths, were positively correlated with HL efflux from hyphae, soil water potential (dawn), and plant response variables (foliar (15)N). The efflux of HL water from hyphae was also correlated with bacterial abundance and soil enzyme activity (P), and the moistening of soil organic matter. Such findings indicate that the efflux of HL water from the external mycorrhizal mycelia may be a complementary explanation for plant nutrient acquisition and survival during drought.

Ectomycorrhizal weathering of the soil minerals muscovite and hornblende

Ectomycorrhizal fungi are hypothesized to enhance mineral weathering in forest soils. Several studies have shown an increased uptake of mineral-derived nutrients by trees when in symbiosis with ectomycorrhizal fungi. However, it is difficult to determine from these studies if the improved nutrient uptake is the result of increased weathering or better exploitation of the substrate by the ectomycorrhizal fungi. In a pot experiment, Pinus sylvestris (Scots pine) seedlings were grown with or without ectomycorrhizal fungi, and with or without the mineral muscovite as the only potassium (K) source or the mineral hornblende as the only magnesium (Mg) source. After 27 wk, all pools of non-mineral-bound K or Mg were determined. The ectomycorrhizal fungus Paxillus involutus increased weathering of muscovite but not hornblende. The other ectomycorrhizal fungi tested, Piloderma croceum and Suillus bovinus, did not increase weathering of either muscovite or hornblende compared with the nonmycorrhizal trees. The P. involutus-mediated mobilization of K from muscovite resulted in increased K content of root plus adhering hyphae, but not of shoots. In conclusion, ectomycorrhizal fungi may increase weathering of minerals in response to nutrient deficiencies, but this response is species specific.