Isolation, identification, and characterization of cadmium-tolerant endophytic fungi isolated from barley (Hordeum vulgare L.) roots and their role in enhancing phytoremediation

Eco-friendly management of Meloidogyne incognita in cadmium-contaminated soil by using nematophagous fungus Purpureocillium lavendulum YMF1.683: Efficacy and mechanism

Root-knot nematodes (RKNs) are distributed globally, including in agricultural fields contaminated by heavy metals (HM), and can cause serious crop damages. Having a method that could control RKNs in HM-contaminated soil while limit HM accumulation in crops could provide significant benefits to both farmers and consumers. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum YMF1.683 exhibited a high nematocidal activity against the RKN Meloidogyne incognita and a high tolerance to CdCl2. Comparing to the P. lavendulum YMF1.838 which showed low tolerance to Cd2+, strain YMF1.683 effectively suppressed M. incognita infection and significantly reduced the Cd2+ uptake in tomato root and fruit in soils contaminated by 100 mg/kg Cd2+. Transcriptome analyses and validation of gene expression by RT-PCR revealed that the mechanisms contributed to high Cd-resistance in YMF1.683 mainly included activating autophagy pathway, increasing exosome secretion of Cd2+, and activating antioxidation systems. The exosomal secretory inhibitor GW4869 reduced the tolerance of YMF1.683 to Cd2+, which firstly demonstrated that fungal exosome was involved in HM tolerance. The up-regulation of glutathione synthesis pathway, increasing enzyme activities of both catalase and superoxide dismutase also played important roles in Cd2+ tolerance of YMF1.683. In Cd2+-contaminated soil, YMF1.683 limited Cd2+-uptake in tomato by up-regulating the genes of ABCC family in favor of HM sequestration in plant, and down-regulating the genes of ZIP, HMA, NRAMP, YSL families associated with HM absorption, transport, and uptake in plant. Our results demonstrated that YMF1.683 could be a promising bio-agent in eco-friendly management of M. incognita in Cd2+ contaminated soils.

Mycorrhizal fungal communities associated with three metal accumulator plants growing in an abandoned Pb smelting factory

Plants associated with mycorrhizal fungi has the ability to establish on metal-contaminated soils playing an important role in phytoremediation programs. The objective of this study was to examine the presence of arbuscular mycorrhizal fungi (AMF) (spores density, diversity, indicator species, and root colonization) and dark septate endophytic fungi (DSE fungal root colonization) in three metal accumulator plants (Sorghum halepense, Bidens pilosa, and Tagetes minuta) growing in soils with high Pb content. The Pb content in AMF spores and plant biomass were also assessed. Rhizosphere soil samples were taken from the three dominant plant species at six study sites surrounding the abandoned Pb smelter and one uncontaminated site. The three studied plants were colonized by AMF and DSE fungi. A total of 24 AMF morphospecies were present in the Pb-contaminated areas. The AMF indicator species in the control site (non-contaminated area) was Funneliformis mosseae and in the most contaminated site were Gigaspora decipiens and Denticustata biornata. There was an increase in mycorrhizal variables such as the number of AMF vesicles, spore number, Pb content in AMF spores and plant biomass and DSE colonization (in Sorghum) with increasing soil Pb contamination, but a decrease in AMF diversity and richness was found. For upcoming soil restoration projects, it is crucial to understand the mycorrhizal fungi as well as the plant community that has adapted to the highly contaminated environment.

Physiological response mechanism of heavy metal-resistant endophytic fungi isolated from the roots of Polygonatum kingianum

This study aims to evaluate the tolerance of endophytic fungi isolated from the fibrous roots of Polygonatum kingianum to arsenic (As) and cadmium (Cd) and their physiological response mechanisms. Five isolated strains were obtained with EC50 values for As(V) ranging from 421 to 1281 mg/L, while the other three strains tolerated Cd(II) with an EC50 range of 407-1112 mg/L. Morphological and molecular identification indicated that these eight strains were Cladosporium spp. belonging to dark septate endophytes (DSEs). The contents of metal ions in mycelium sharply increased, reaching 38.87 mg/kg for strain MZ-11 under As(V) stress and 0.33 mg/kg for fungus PR-2 under Cd(II). The physiological response revealed that the biomass decreased with increasing concentrations of As(V) or Cd(II), and the activity of superoxide dismutase significantly improved under the corresponding EC50 -concentration As/Cd of the strains, as well as the contents of antioxidant substances, including metallothionein, glutathione, malondialdehyde, melanin, and proline. Taken together, the filamentous fungi of Cladosporium spp. accounted for a high proportion of fungi isolated from the fibrous roots of P. kingianum and had a strong capacity to tolerate As(V) or Cd(II) stress by improving antioxidase activities and the content of antioxidant substances, and immobilization of metal ions in hyphae.

Impact of Iron Mining Activity on the Endophytic Fungal Community of Aspilia grazielae

Aspilia grazielae (J. U. Santos) is an endemic plant species in Morro do Urucum in the Pantanal wetland (Brazil). A. grazielae is used for the restoration of areas impacted by iron mining activities. This study evaluates the diversity (composition, value and abundance) of endophytic fungal communities, considering parts of the plant and soil condition. The leaves and roots of A. grazielae were collected from native vegetation areas (NVA) and recovery areas (RCA) in Morro do Urucum. Illumina sequencing technology was used to investigate variation in endophytic fungal biodiversity. The operational taxonomic units detected in NVA ranged from 183 to 263 (leaf) and 115 to 285 (root), while RCA samples ranged from 200 to 282 (leaf) and 156 to 348 (root). Ascomycota phylum was the most common species among all plant samples. The most significant classes identified were Lecanoromycetes and Dothideomycetes that differed significantly (p ≤ 0.05) according to their plant hosts and soil stress. The relative abundance of Pestalotiopsis (Sordariomycetes class) and Stereocaulon (Lecanoromycetes class) genera was influenced by the iron mining activities according to the leaf samples analysed. However, the abundance and wealth of endophytic fungal communities in A. grazielae from RCA were evidence that could explain their high resilience to environmental disturbances and the source-sink dynamics of fungal propagules.

Arbuscular Mycorrhizal Fungi as an Important Factor Enabling the Adaptation of Anthyllis vulneraria L. to Zn-Pb-Polluted Tailings

The old Zn-Pb-contaminated (calamine) tailings in southern Poland are spontaneously colonized by metal-tolerant Anthyllis vulneraria L. (Fabaceae), which can form simultaneously symbiotic association with nitrogen-fixing rhizobia and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). So far, fungal colonization and the AMF diversity of calamine-inhabiting legumes have been poorly studied. Thus, we determined AMF spore density in the substratum and the mycorrhizal status of nodulated A. vulneraria plants occurring on calamine tailings (M) and on a reference non-metallicolous (NM) site. The results indicate the presence of the Arum-type of arbuscular mycorrhiza in the roots of both Anthyllis ecotypes. Despite the presence of AM fungi in M plant roots, the dark septate endophyte (DSE) fungi (hyphae and microsclerotia) were occasionally also detected. Metal ions were accumulated mainly in the nodules and intraradical fungal structures rather than thick plant cell walls. Mycorrhization parameters (frequency of mycorrhization and intensity of root cortex colonization) for M plants were markedly higher and differed in a statistically significant manner from the parameters for NM plants. Heavy metal excess had no negative effect on the number of AMF spores, the amounts of glomalin-related soil proteins and AMF species composition. Molecular identification of AMF using PCR-DGGE analysis based on the 18S rDNA ribosomal gene by nested-PCR with primers AM1/NS31 and NS31-GC/Glo1 revealed similar genera/species of AMF in the roots of both Anthyllis ecotypes: Rhizophagus sp., R. fasciculatus, and R. iranicus. The results of this work indicate the presence of unique fungal symbionts, which may enhance A. vulneraria tolerance to heavy metal stress and plant adaptation to extreme conditions on calamine tailings.

A Dark Septate Endophyte Improves Cadmium Tolerance of Maize by Modifying Root Morphology and Promoting Cadmium Binding to the Cell Wall and Phosphate

Dark septate endophytes (DSEs) can improve the performance of host plants grown in heavy metal-polluted soils, but the mechanism is still unclear. A sand culture experiment was performed to investigate the effects of a DSE strain (Exophiala pisciphila) on maize growth, root morphology, and cadmium (Cd) uptake under Cd stress at different concentrations (0, 5, 10, and 20 mg·kg^-1). The results indicated that the DSE significantly improved the Cd tolerance of maize, causing increases in biomass, plant height, and root morphology (length, tips, branch, and crossing number); enhancing the Cd retention in roots with a decrease in the transfer coefficient of Cd in maize plants; and increasing the Cd proportion in the cell wall by 16.0-25.6%. In addition, DSE significantly changed the chemical forms of Cd in maize roots, resulting in decreases in the proportions of pectates and protein-integrated Cd by 15.6-32.4%, but an increase in the proportion of insoluble phosphate Cd by 33.3-83.3%. The correlation analysis revealed a significantly positive relationship between the root morphology and the proportions of insoluble phosphate Cd and Cd in the cell wall. Therefore, the DSE improved the Cd tolerance of plants both by modifying root morphology, and by promoting Cd binding to the cell walls and forming an insoluble phosphate Cd of lower activity. These results of this study provide comprehensive evidence for the mechanisms by which DSE colonization enhances Cd tolerance in maize in root morphology with Cd subcellular distribution and chemical forms.

Global Situation of Bioremediation of Leachate-Contaminated Soils by Treatment with Microorganisms: A Systematic Review

This systematic review presents the current state of research in the last five years on contaminants in soils, especially in leachates from solid waste landfills, with emphasis on biological remediation. In this work, the pollutants that can be treated by microorganisms and the results obtained worldwide were studied. All the data obtained were compiled, integrated, and analyzed by soil type, pollutant type, bacterial type, and the countries where these studies were carried out. This review provides reliable data on the contamination of soils worldwide, especially soils contaminated by leachate from municipal landfills. The extent of contamination, treatment objectives, site characteristics, cost, type of microorganisms to be used, and time must be considered when selecting a viable remediation strategy. The results of this study can help develop innovative and applicable methods for evaluating the overall contamination of soil with different contaminants and soil types. These findings can help develop innovative, applicable, and economically feasible methods for the sustainable management of contaminated soils, whether from landfill leachate or other soil types, to reduce or eliminate risk to the environment and human health, and to achieve greater greenery and functionality on the planet.

Metal-tolerant and siderophore producing Pseudomonas fluorescence and Trichoderma spp. improved the growth, biochemical features and yield attributes of chickpea by lowering Cd uptake

Industrialization and human urbanization have led to an increase in heavy metal (HM) pollution which often cause negative/toxic effect on agricultural crops. The soil-HMs cannot be degraded biologically however, microbe-mediated detoxification of toxic HMs into lesser toxic forms are reported. Considering the potentiality of HMs-tolerant soil microbes in metal detoxification, Pseudomonas fluorescence PGPR-7 and Trichoderma sp. T-4 were recovered from HM-affected areas. Under both normal and cadmium stress, the ability of both microorganisms to produce different plant hormones and biologically active enzymes was examined. Strains PGPR-7 and T-4 tolerated cadmium (Cd) an up-to 1800 and 2000 µg mL^-1, respectively, and produced various plant growth regulating substances (IAA, siderophore, ACC deaminase ammonia and HCN) in Cd-stressed condition. The growth promoting and metal detoxifying ability of both strains were evaluated (either singly/combined) by applying them in chickpea (Cicer arietinum L.) plants endogenously contaminated with different Cd levels (0-400 µg kg^-1 soils). The higher Cd concentration (400 µg kg^-1 soils) negatively influenced the plant parameters which, however, improved following single/combined inoculation of P. fluorescence PGPR-7 and Trichoderma sp. T-4. Both microbial strains increased the growth of Cd-treated chickpeas however, their combined inoculation (PGPR-7 + T-4) caused the most positive effect. For instance, 25 µg Cd Kg^-1 + PGPR-7 + T4 treatment caused maximum increase in germination percentage (10%), root dry biomass (71.4%) and vigour index (33%), chl-a (38%), chl-b (41%) and carotenoid content (52%). Furthermore, combined inoculation of P. fluorescence PGPR-7 and Trichoderma sp. T-4 maximally decreased the proline, MDA content, POD and CAT activities by 50%, 43% and 62%, respectively following their application in 25 µg Cd kg^-1 soils-treated chickpea. Additionally, microbial strains lowered the plant uptake of Cd. For example, Cd-uptake in root tissues was decreased by 42 and 34% when 25 µg Cd Kg^-1- treated chickpea plants were inoculated with P. fluorescence PGPR-7, Trichoderma sp. T-4 and co-inoculation (PGPR-7 + T4) of both strains, respectively. Therefore, from the current observation, it is suggested that dual inoculation of metal tolerant P. fluorescence and Trichoderma sp. may potentially be used in detoxification and reclamation of metal-contaminated soils.

The responses and detoxification mechanisms of dark septate endophytes (DSE), Exophiala salmonis, to CuO nanoparticles

To understand the tolerance mechanisms of dark septate endophytes (DSE), Exophiala salmonis, to CuO nanoparticles (CuO-NPs) with different sizes (40 and 150 nm), we investigated the morphology, antioxidant response, Cu subcellular distribution, and the melanin gene expression in the mycelia of E. salmonis. E. salmonis was cultured in liquid and solid media under the stress of increasing CuO-NP concentrations (0, 50, 100, 150, and 250 mg/L). Results showed that (1) E. salmonis showed good CuO-NP tolerance, and the tolerance to CuO-NPs at 150 nm was stronger than that at 40 nm. A large number of agglomeration structures were observed on the mycelia surface with the exception of 50 mg/L CuO-NPs with a diameter of 150 nm. (2) CuO-NP stress significantly stimulated the production of antioxidant enzymes, particularly the CuO-NPs with small particle size (40 nm). (3) Cu uptaken by E. salmonis increased proportionally with the increase of CuO-NP concentration in the medium. More than 80% Cu was absorbed in cell wall of mycelia treated with a small particle size (40 nm). (4) FTIR analysis revealed that hydroxyl, amine, carboxyl, and phosphate groups were associated with CuO-NP binding regardless of particle size. (5) Fungal melanin content increased with the addition of CuO-NPs; the increase of melanin induced by CuO-NPs with small particle size (40 nm) was more significant. (6) The expression of 1,3,6,8-tetrahydroxynaphthalene reductase (Arp2) in the melanin synthesis pathway increased under the stress of CuO-NPs, and CuO-NPs with a small particle size (40 nm) caused a significant change in the expression level of Arp2 gene than those with a large particle size (150 nm). In conclusion, E. salmonis had a strong tolerance to CuO-NPs and mitigated the toxic effects of CuO-NPs through the antioxidant system, the expression of genes related to melanin synthesis, and the synthesis of melanin.

Augmented growth of Cd-stressed rice seedlings with the application of phytostimulating, root-colonizing, Cd-tolerant, leaf-endophytic fungi Colletotrichum spp. isolated from Eupatorium triplinerve

The potential of plant growth-promoting endophytic fungi (PGPEF) in mycoremediation has received notable attention in recent years. Unlike other root-colonizing microorganisms, PGPEF colonization under Cadmium (Cd) stress is a less-revealed phenomenon. Among eighteen fungal isolates from the leaves of Eupatorium triplinerve, twelve were found as the species of Colletotrichum and remaining six belong to Fusarium based on phenotypic characterization. However, only two PGPEF isolates (ALE15 and ALE18) were finally selected based on possession of ACCD activity (~0.84 and 0.47 nM/µg protein/h, respectively) and higher Cd tolerance (1000 and 750 µg/mL, respectively). Moreover, the said isolates showed IAA production (~248 and 289 µg/mL), GA production (~86 and 88 AUs), phosphate solubilization (~165 and 256 µg/mL, respectively) under Cd stress. ALE18 strain was found to produce siderophore too. Molecular identification through sequencing of ITS region of both isolates confirmed their identity as species of Colletotrichum. Furthermore, FESEM-EDAX and AAS analyses supported their Cd bioaccumulation ability in mycelial cells that directly impacted to assist rice seedlings' (IR-36 cultivar) growth under Cd stress. Successful root colonization was also observed through FESEM and fluorescence microscopic studies. Finally, the detached leaf experiment with six economically important crops assured their applicability on field-scale as non-pathogenic PGPEF candidates.

Plant association with dark septate endophytes: When the going gets tough (and stressful), the tough fungi get going

Dark septate endophytes (DSEs) comprise a diverse and ubiquitous group of fungal generalists with broad habitat niches that robustly colonize the roots of plants in stressful environments. DSEs possess adaptation strategies that determine their high tolerance to heavy metal (HM) contamination, drought, and salinity. Most DSEs developed efficient melanin-dependent and melanin-independent mechanisms of HM detoxification and osmoprotection, including intracellular immobilization and extracellular efflux of HMs and excess ions, and the scavenging of reactive oxygen species. DSEs form mutualistic relationship with plants according to the hypothesis of "habitat-adapted associations", supporting the survival of their hosts under stressful conditions. As saprophytes, DSEs mineralize a complex soil substrate improving plants' nutrition and physiological parameters. They can protect the host plant from HMs by limiting HM accumulation in plant tissues and causing their sequestration in root cell walls as insoluble compounds, preventing further HM translocation to shoots. The presence of DSE in drought-affected plants can substantially ameliorate the physiology and architecture of root systems, improving their hydraulic properties. Plant growth-promoting features, supported by the versatility and easy culturing of DSEs, determine their high potential to enhance phytoremediation and revegetation projects for HM-contaminated, saline, and desertic lands reclamation.

Insights into the beneficial roles of dark septate endophytes in plants under challenging environment: resilience to biotic and abiotic stresses

Dark septate endophytes (DSE) exert a plethora of effects in regulating plant growth, signalling and stress tolerance. The advent of metagenomics has led to the identification of various species of DSE to be associated with plant organs. They are known to modulate growth, nutrient uptake, phytohormone biosynthesis and production of active bioconstituents in several plants. The interactions between the DSE and host plants are mostly mutualistic but they can also be neutral or exhibit negative interactions. The DSE has beneficial role in removal/sequestration of toxic heavy metals from various environmental sites. Here, we discuss the beneficial role of DSE in enhancing plant tolerance to heavy metal stress, drought conditions, high salinity and protection from various plant pathogens. Furthermore, the underlying mechanism of stress resilience facilitated by DSE-plant interaction has also been discussed. The article also provides insights to some important future perspectives associated with DSE-mediated phytoremediation and reclamation of polluted land worldwide thus facilitating sustainable agriculture.

Characterization of cadmium-tolerant endophytic fungi isolated from soybean (Glycine max) and barley (Hordeum vulgare)

Cadmium stress disrupts plant-microbial interactions and reduces plant growth and development. In plants, the tolerance to stress can be increased by inoculation with endophytic microorganisms. The aim of this study was to investigate the distribution of endophytic fungi in various plant organs of barley and soybean and evaluate their Cd removal ability. Two hundred fifty-three fungal strains were isolated from various organs of barley (Hordeum vulgare cv Arna) and soybean (Glycine max cv Almaty). The colonization rate ranged from 13.6% to 57.3% and was significantly higher in the roots. Ten genera were identified: Fusarium, Penicillium, Aspergillus, Metarhizium, Beauveria, Trichoderma, Rhodotorula, Cryptococcus, Aureobasidium and Metschnikowia. Twenty-three fungal strains have a Cd tolerance index from 0.24 to 1.12. Five strains (Beauveria bassiana T7, Beauveria bassiana T15, Rhodotorula mucilaginosa MK1, Rhodotorula mucilaginosa RH2, Metschnikowia pulcherrima MP2) with the highest level of Cd tolerance have minimum inhibitory concentrations from 290 to 2400 μg/ml. These fungi were able to remove Cd up to 59%. The bioaccumulation capacity ranged from 2.3 to 11.9 mg/g. Selected fungal strains could be considered as biological agents for their potential application in the bioremediation of contaminated sites.