OmZnT1 and OmFET, two metal transporters from the metal-tolerant strain Zn of the ericoid mycorrhizal fungus Oidiodendron maius, confer zinc tolerance in yeast

Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Backgorund

The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods

In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results

Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion

This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Isolation and identification of mycorrhizal helper bacteria of Vaccinium uliginosum and their interaction with mycorrhizal fungi

Mycorrhizal helper bacteria (MHB) can promote mycorrhizal fungal colonization and form mycorrhizal symbiosis structures. To investigate the effect of interactions between mycorrhizal beneficial microorganisms on the growth of blueberry, 45 strains of bacteria isolated from the rhizosphere soil of Vaccinium uliginosum were screened for potential MHB strains using the dry-plate confrontation assay and the bacterial extracellular metabolite promotion method. The results showed that the growth rate of mycelium of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was increased by 33.33 and 77.77% for bacterial strains L6 and LM3, respectively, compared with the control in the dry-plate confrontation assay. In addition, the extracellular metabolites of L6 and LM3 significantly promoted the growth of O. maius 143 mycelium with an average growth rate of 40.9 and 57.1%, respectively, the cell wall-degrading enzyme activities and genes of O. maius 143 was significantly increased. Therefore, L6 and LM3 were preliminarily identified as potential MHB strains. In addition, the co-inoculated treatments significantly increased blueberry growth; increased the nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activities in the leaves; and promoted nutrient uptake in blueberry. Based on the physiological, and 16S rDNA gene molecular analyses, we initially identified strain L6 as Paenarthrobacter nicotinovorans and LM3 as Bacillus circulans. Metabolomic analysis revealed that mycelial exudates contain large amounts of sugars, organic acids and amino acids, which can be used as substrates to stimulate the growth of MHB. In conclusion, L6 and LM3 and O. maius 143 promote each other's growth, while co-inoculation of L6 and LM3 with O. maius 143 can promote the growth of blueberry seedlings, providing a theoretical basis for further studies on the mechanism of ericoid mycorrhizal fungi-MHB-blueberry interactions. It laid the technical foundation for the exploitation of biocontrol strain resources and the development of biological fertilizer.

Heterologous Expression of Full-Length and Truncated Human ZIP4 Zinc Transporter in Saccharomyces cerevisiae

The human (h) transporter hZIP4 is the primary Zn²⁺ importer in the intestine. hZIP4 is also expressed in a variety of organs such as the pancreas and brain. Dysfunction of hZIP4 can result in the Zn²⁺ deficiency disease acrodermatitis enteropathica (AE). AE can disrupt digestive and immune system homeostasis. A limited number of hZIP4 expression strategies have hindered increasing knowledge about this essential transmembrane protein. Here, we report the heterologous expression of hZIP4 in Saccharomyces cerevisiae. Both a wild-type and a mutant S. cerevisiae strain, in which the endogenous Zn²⁺ transporters were deleted, were used to test the expression and localization of an hZIP4–GFP fusion protein. A full-length hZIP4–GFP and a truncated membrane-domain-only (mhZIP4–GFP) protein were observed to be present in the plasma membrane in yeast.

The transfer of trace metals in the soil-plant-arthropod system

Essential and non-essential trace metals are capable of causing toxicity to organisms above a threshold concentration. Extensive research has assessed the behaviour of trace metals in biological and ecological systems, but has typically focused on single organisms within a trophic level and not on multi-trophic transfer through terrestrial food chains. This reinforces the notion of metal toxicity as a closed system, failing to consider one trophic level as a pollution source to another; therefore, obscuring the full extent of ecosystem effects. Given the relatively few studies on trophic transfer of metals, this review has taken a compartment-based approach, where transfer of metals through trophic pathways is considered as a series of linked compartments (soil-plant-arthropod herbivore-arthropod predator). In particular, we consider the mechanisms by which trace metals are taken up by organisms, the forms and transformations that can occur within the organism and the consequences for trace metal availability to the next trophic level. The review focuses on four of the most prevalent metal cations in soil which are labile in terrestrial food chains: Cd, Cu, Zn and Ni. Current knowledge of the processes and mechanisms by which these metals are transformed and moved within and between trophic levels in the soil-plant-arthropod system are evaluated. We demonstrate that the key factors controlling the transfer of trace metals through the soil-plant-arthropod system are the form and location in which the metal occurs in the lower trophic level and the physiological mechanisms of each organism in regulating uptake, transformation, detoxification and transfer. The magnitude of transfer varies considerably depending on the trace metal concerned, as does its toxicity, and we conclude that biomagnification is not a general property of plant-arthropod and arthropod-arthropod systems. To deliver a more holistic assessment of ecosystem toxicity, integrated studies across ecosystem compartments are needed to identify critical pathways that can result in secondary toxicity across terrestrial food-chains.

Fungal-Metal Interactions: A Review of Toxicity and Homeostasis

Metal nanoparticles used as antifungals have increased the occurrence of fungal-metal interactions. However, there is a lack of knowledge about how these interactions cause genomic and physiological changes, which can produce fungal superbugs. Despite interest in these interactions, there is limited understanding of resistance mechanisms in most fungi studied until now. We highlight the current knowledge of fungal homeostasis of zinc, copper, iron, manganese, and silver to comprehensively examine associated mechanisms of resistance. Such mechanisms have been widely studied in Saccharomyces cerevisiae, but limited reports exist in filamentous fungi, though they are frequently the subject of nanoparticle biosynthesis and targets of antifungal metals. In most cases, microarray analyses uncovered resistance mechanisms as a response to metal exposure. In yeast, metal resistance is mainly due to the down-regulation of metal ion importers, utilization of metallothionein and metallothionein-like structures, and ion sequestration to the vacuole. In contrast, metal resistance in filamentous fungi heavily relies upon cellular ion export. However, there are instances of resistance that utilized vacuole sequestration, ion metallothionein, and chelator binding, deleting a metal ion importer, and ion storage in hyphal cell walls. In general, resistance to zinc, copper, iron, and manganese is extensively reported in yeast and partially known in filamentous fungi; and silver resistance lacks comprehensive understanding in both.

Mycoremediation of heavy metals: processes, mechanisms, and affecting factors

Industrial processes and mining of coal and metal ores are generating a number of threats by polluting natural water bodies. Contamination of heavy metals (HMs) in water and soil is the most serious problem caused by industrial and mining processes and other anthropogenic activities. The available literature suggests that existing conventional technologies are costly and generated hazardous waste that necessitates disposal. So, there is a need for cheap and green approaches for the treatment of such contaminated wastewater. Bioremediation is considered a sustainable way where fungi seem to be good bioremediation agents to treat HM-polluted wastewater. Fungi have high adsorption and accumulation capacity of HMs and can be potentially utilized. The most important biomechanisms which are involved in HM tolerance and removal by fungi are bioaccumulation, bioadsorption, biosynthesis, biomineralisation, bioreduction, bio-oxidation, extracellular precipitation, intracellular precipitation, surface sorption, etc. which vary from species to species. However, the time, pH, temperature, concentration of HMs, the dose of fungal biomass, and shaking rate are the most influencing factors that affect the bioremediation of HMs and vary with characteristics of the fungi and nature of the HMs. In this review, we have discussed the application of fungi, involved tolerance and removal strategies in fungi, and factors affecting the removal of HMs.

Unravelling the Role of Melanin in Cd and Zn Tolerance and Accumulation of Three Dark Septate Endophytic Species

Dark septate endophytes (DSEs) are often trace element (TE)-tolerant fungi and are abundant in TE-polluted environments. The production of melanin, a black polymer found in cell walls, was hypothesized by several authors to play a role in the TE tolerance of DSEs. To test this hypothesis, we established a series of experiments using albino strains and melanin inhibitors and examined the responses to Cd and Zn. Six DSEs belonging to genera Cadophora sp., Leptodontidium sp. and Phialophora mustea, were evaluated. The strains mainly produced 1,8-dihydroxynaphthalene (DHN) melanin whereas 3,4-dihydroxyphenylalanin melanin was also synthetized. Cd and Zn decreased melanin synthesis in most of the strains. A reduction in melanin concentration in hyphae through the use of tricyclazole, an inhibitor of DHN-melanin synthesis, did not reduce the tolerance of the strains to Cd and Zn. Similarly, albino mutants of Leptodontidium sp. were not more sensitive to Cd and Zn than the WT strain. Moreover, tricyclazole-treated colonies accumulated less Cd but more Zn compared to untreated colonies. The Cd and Zn contents of Leptodontidium albino strains were variable and similar to that of the WT. The results suggest that melanin production is not an important functional trait that contributes to Cd and Zn tolerance, but might contribute to Cd accumulation.

Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity

The contamination of soil with toxic metals is a worldwide problem, resulting in the disruption of plant vegetation and subsequent crop production. Thus, remediation techniques for contaminated soil and water remain a constant interest of researchers. Phytoremediation, which utilizes plants to remove or stabilize contaminants, is perceived to be a promising strategy. However, phytoremediation's use to date is limited because of constraints associated with such factors as slow plant growth rates or metal toxicity. Microbial-assisted phytoremediation serves as an alternative solution, since the impact of the microbial symbionts on plant growth and stress tolerance has frequently been described. Endophytic fungi occur in almost every plant in the natural environment and contribute to plant growth and tolerance to environmental stress conditions. Although this group of symbiotic fungi was found to form association with a wide range of hosts, including the non-mycorrhizal Brassicaceae metallophytes, their role in the response of plants to metal toxicity has not been thoroughly elucidated to date. This review summarizes the current knowledge regarding the role of endophytic fungi in the tolerance of plants to toxic metals and highlights the similarities and differences between this group of symbiotic fungi and mycorrhizal associations in terms of the survival of the plant during heavy metal stress.

Adsorption of heavy metal tolerance strains to Pb2+ and Cd2+ in wastewater

The functional strains with high tolerance to heavy metal Pb²⁺ and Cd²⁺ were screened from soil obtained in a heavy metal waste accumulation area. The immobilized biological adsorbent was made by embedding method and used for treatment of wastewater containing heavy metals. The effects of initial concentration of heavy metals, adsorption time, pH value of wastewater, and dosage of adsorbent on adsorption performance were investigated. The study showed (1) the strains tested were Brevibacterium and their maximum tolerable concentrations for Pb²⁺ and Cd²⁺ were 2200 and 700 mg/L, respectively; (2) the maximum adsorption rate for Pb²⁺ and Cd²⁺ was 87.77% and 57.50% respectively when the dosage of adsorbent was 10 g/L and the pH value of wastewater was 6; (3) Pb²⁺ and Cd²⁺ could be adsorbed in the equilibrium solution for 40 min and the maximum adsorption capacity reached 114.36 mg/g and 82.12 mg/g, respectively; and (4) when the initial pH value of the wastewater was 5-7, the adsorption rate decreased with the increase of the concentration, and the initial concentration of Pb²⁺ had a greater effect on the adsorption rate than Cd²⁺. Langmuir and Freundlich equation showed that the adsorption of Pb²⁺ and Cd²⁺ was mainly on the surface of monolayer. And the pseudo-second-order kinetic equation indicates that Cd²⁺ has a relatively greater adsorption rate than Pb²⁺ does.

Identification, evolution and functional characterization of two Zn CDF-family transporters of the ectomycorrhizal fungus Suillus luteus

Two genes, SlZnT1 and SlZnT2, encoding Cation Diffusion Facilitator (CDF) family transporters were isolated from Suillus luteus mycelium by genome walking. Both gene models are very similar and phylogenetic analysis indicates that they are most likely the result of a recent gene duplication event. Comparative sequence analysis of the deduced proteins predicts them to be Zn transporters. This function was confirmed by functional analysis in yeast for SlZnT1. SlZnT1 was able to restore growth of the highly Zn sensitive yeast mutant Δzrc1 and localized to the vacuolar membrane. Transformation of Δzrc1 yeast cells with SlZnT1 resulted in an increased accumulation of Zn compared to empty vector transformed Δzrc1 yeast cells and equals Zn accumulation in wild type yeast cells. We were not able to express functional SlZnT2 in yeast. In S. luteus, both SlZnT genes are constitutively expressed whatever the external Zn concentrations. A labile Zn pool was detected in the vacuoles of S. luteus free-living mycelium. Therefore we conclude that SlZnT1 is indispensable for maintenance of Zn homeostasis by transporting excess Zn into the vacuole.

Model systems to unravel the molecular mechanisms of heavy metal tolerance in the ericoid mycorrhizal symbiosis

Ericoid mycorrhizal plants dominate in harsh environments where nutrient-poor, acidic soil conditions result in a higher availability of potentially toxic metals. Although metal-tolerant plant species and ecotypes are known in the Ericaceae, metal tolerance in these plants has been mainly attributed to their association with ericoid mycorrhizal fungi. The mechanisms underlying plant protection by the fungal symbiont are poorly understood, whereas some insights have been achieved regarding the molecular mechanisms of heavy metal tolerance in the fungal symbiont. This review will briefly introduce the general features of heavy metal tolerance in mycorrhizal fungi and will then focus on the use of "omics" approaches and heterologous expression in model organisms to reveal the molecular bases of fungal response to heavy metals. Functional complementation in Saccharomyces cerevisiae has allowed the identification of several ericoid mycorrhizal fungi genes (i.e., antioxidant enzymes, metal transporters, and DNA damage repair proteins) that may contribute to metal tolerance in a metal-tolerant ericoid Oidiodendron maius isolate. Although a powerful system, the use of the yeast complementation assay to study metal tolerance in mycorrhizal symbioses has limitations. Thus, O. maius has been developed as a model system to study heavy metal tolerance mechanisms in mycorrhizal fungi, thanks to its high metal tolerance, easy handling and in vitro mycorrhization, stable genetic transformation, genomics, transcriptomic and proteomic resources.

Functional analysis of two genes coding for distinct cation diffusion facilitators of the ectomycorrhizal Zn-accumulating fungus Russula atropurpurea

Russula atropurpurea can accumulate remarkably high concentrations of Zn in its sporocarps. We have previously demonstrated that 40 % of the intracellular Zn in this species is sequestered by MT-like RaZBP peptides. To see what other mechanisms for the handling of the accumulated Zn are available to R. atropurpurea, we searched its transcriptome for cDNAs coding for transporters of the cation diffusion facilitator (CDF) family. The transcriptome search enabled us to identify RaCDF1 and RaCDF2, which were further subjected to functional studies in metal sensitive Saccharomyces cerevisiae. The expression of RaCDF1 and its translational fusion with green fluorescent protein (GFP) protected the yeasts against Zn and Co, but not Cd or Mn, toxicity and led to increased Zn accumulation in the cells. The GFP fluorescence, observed in the RaCDF1::GFP-expressing yeasts on tonoplasts, indicated that the RaCDF1-mediated Zn and Co tolerance was a result of vacuolar sequestration of the metals. The expression of RaCDF2 supported Zn, but not Mn, tolerance in the yeasts and reduced the cellular uptake of Zn, which is congruent with the proposed idea of the Zn-efflux function of RaCDF2, supported by the localization of GFP-derived fluorescence on the plasma membrane of the yeasts expressing functional RaCDF2::GFP. Contrarily, RaCDF2 increased the sensitivity to Co and Cd in the yeasts and significantly promoted Cd uptake, which suggested that it can act as a bidirectional metal transporter. The notion that RaCDF1 and RaCDF2 are genuine CDF transporters in R. atropurputrea was further reinforced by the fact that the RaCDF-associated metal tolerance and uptake phenotypes were lost upon the replacement of histidyl (in RaCDF1) and aspartyl (in RaCDF2), which are highly conserved in the second transmembrane domain and known to be essential for the function of CDF proteins.

Common and metal-specific proteomic responses to cadmium and zinc in the metal tolerant ericoid mycorrhizal fungus Oidiodendron maius Zn

Although adaptive metal tolerance may arise in fungal populations in polluted soils, the mechanisms underlying metal-specific tolerance are poorly understood. Comparative proteomics is a powerful tool to identify variation in protein profiles caused by changing environmental conditions, and was used to investigate protein accumulation in a metal tolerant isolate of the ericoid mycorrhizal fungus Oidiodendron maius exposed to zinc and cadmium. Two-dimensional gel electrophoresis and shotgun proteomics followed by mass spectrometry lead to the identification of common and metal-specific proteins and pathways. Proteins selectively induced by cadmium exposure were molecular chaperons of the Hsp90 family, cytoskeletal proteins and components of the translation machinery. Zinc significantly up-regulated metabolic pathways related to energy production and carbohydrates metabolism, likely mirroring zinc adaptation of this fungal isolate. Common proteins induced by the two metal ions were the antioxidant enzyme Cu/Zn superoxide dismutase and ubiquitin. In mycelia exposed to zinc and cadmium, both proteomic techniques also identified agmatinase, an enzyme involved in polyamine biosynthesis. This novel finding suggests that, like plants, polyamines may have important functions in response to abiotic environmental stress in fungi. Genetic evidence also suggests that the biosynthesis of polyamines via an alternative metabolic pathway may be widespread in fungi.

Genome-wide analysis of copper, iron and zinc transporters in the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal fungi (AMF), belonging to the Glomeromycota, are soil microorganisms that establish mutualistic symbioses with the majority of higher plants. The efficient uptake of low mobility mineral nutrients by the fungal symbiont and their further transfer to the plant is a major feature of this symbiosis. Besides improving plant mineral nutrition, AMF can alleviate heavy metal toxicity to their host plants and are able to tolerate high metal concentrations in the soil. Nevertheless, we are far from understanding the key molecular determinants of metal homeostasis in these organisms. To get some insights into these mechanisms, a genome-wide analysis of Cu, Fe and Zn transporters was undertaken, making use of the recently published whole genome of the AMF Rhizophagus irregularis. This in silico analysis allowed identification of 30 open reading frames in the R. irregularis genome, which potentially encode metal transporters. Phylogenetic comparisons with the genomes of a set of reference fungi showed an expansion of some metal transporter families. Analysis of the published transcriptomic profiles of R. irregularis revealed that a set of genes were up-regulated in mycorrhizal roots compared to germinated spores and extraradical mycelium, which suggests that metals are important for plant colonization.