Influence of bioaugmented fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora Sw. DC in heavy metal-polluted landfill soil

The research aimed to determine the influence of endophytic fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora in heavy metal-polluted landfill soil. A consortium of 13 fungal isolates as well as Prosopis juliflora Sw. DC was used to decontaminate heavy metal-polluted landfill soil. Enhanced plant growth (biomass and root and shoot lengths) and production of carotenoids, chlorophyll and amino acids L-phenylalanine and L-leucine that are known to enhance growth were found in the treated P. juliflora. Better accumulations of heavy metals were observed in fungi-treated P. juliflora over the untreated one. An upregulated activity of peroxidase, catalase and ascorbate peroxidase was recorded in fungi-treated P. juliflora. Additionally, other metabolites, such as glutathione, 3,5,7,2',5'-pentahydroxyflavone, 5,2'-dihydroxyflavone and 5,7,2',3'-tetrahydroxyflavone, and small peptides, which include Lys Gln Ile, Ser Arg Ala, Asp Arg Gly, Arg Ser Ser, His His Arg, Arg Thr Glu, Thr Arg Asp and Ser Pro Arg, were also detected. These provide defence supports to P. juliflora against toxic metals. Inoculating the plant with the fungi improved its growth, metal accumulation as well as tolerance against heavy metal toxicity. Such a combination can be used as an effective strategy for the bioremediation of metal-polluted soil.

Diversity of endophytic bacteria isolated from leguminous agroforestry trees in western Kenya

Plants have diverse and vast niches colonized by endophytic microorganisms that promote the wellbeing of host plant. These microbes inhabit internal plant tissues with no signs of ill health. Bacterial endophytes from many plants have been isolated and characterized due to their beneficial roles however their diversity in leguminous plants still remain unexploited. Diversity of bacterial endophytes isolated from Sesbania sesban, Leucaena diversifolia and Calliandra calothyrsus was assessed using morphological and molecular characteristics. A total of 27 pure isolates were recovered from C. Calothyrsus, L. diversifolia and S. sesban constituting 44.4%, 33.3% and 22.2% from the leaves, stems and roots respectively. The isolates differentiated into Gram positive and negative with rods and spherical shapes. Analysis of 16S rRNA gene sequences revealed 8 closely related bacterial genera that consisted of Bacillus (33.3%), Staphylococcus (22.2%), Alcaligens (11.1%), Pantoea (11.1%), Xanthomonas,and Sphingomonas (7.4%) each. Others included Acinetobacter, and Pseudomonas at 3.7% each. Bacterial endophytes of genus bacillus were isolated from all the three plants. These results indicate the presence of high diversity of endophytic bacteria associated with the different parts of L. diversifolia, S. sesban and C. salothyrsus growing in western Kenya.

The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity

Organic debris accumulated in bird nests creates a unique environment for organisms, including microbes. Built from various plant materials that are typically enriched by animal residues, bird nest favours the development of various fungal groups. The aim of this study was to investigate the chemical properties of the material deposited in the white stork Ciconia ciconia nests and the link between extracellular enzyme activity and the diversity and composition of culturable fungi. Our findings revealed low C/P and N/P ratio values in the nest materials, which indicate a high P availability. Nest material C/N/P ratio ranged from 67/8/1 to 438/33/1. Enzymatic activity strongly correlated with the content of carbon, nitrogen, and pH of the material deposited in the nests. A total of 2726 fungal isolates were obtained from the nests, from which 82 taxa were identified based on morphology and DNA sequence data. The study indicates that white stork nests are microhabitat characterised by diverse chemical and biochemical properties. We found relationship between the fungal richness and diversity and the C/P and N/P ratios of materials from the nests. Our study showed that culturable fungi occurred frequently in materials with high levels of C, N, and P, as well as high concentrations of base alkaline elements (Ca, Mg, and K).

How does metal soil pollution change the plant mycobiome?

Microorganisms play a key role in plant adaptation to the environment. The aim of this study was to evaluate the effect of toxic metals present in the soil on the biodiversity of plant-related, endophytic mycobiota. The mycobiome of plants and soil from a Zn-Pb heap and a metal-free ruderal area were compared via Illumina sequencing of the ITS1 rDNA. The biodiversity of plants and fungi inhabiting mine dump substrate was lower than that of the metal free site. In the endosphere of Arabidopsis arenosa from the mine dump the number of endophytic fungal taxa was comparable to that in the reference population, but the community structure significantly differed. Agaricomycetes was the most notably limited class of fungi. The results of plant mycobiota evaluation from the field study were verified in terms of the role of toxic metals in plant endophytic fungi community assembly in a reconstruction experiment. The results presented in this study indicate that metal toxicity affects the structure of the plant mycobiota not by changing the pool of microorganisms available in the soil from which the fungal symbionts are recruited but most likely by altering plant and fungi behaviour and the organisms' preferences towards associating in symbiotic relationships.

Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants

The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.

Iron inactivation by Sporobolomyces ruberrimus and its potential role in plant metal stress protection. An in vitro study

The endophytic Basidiomycete Sporobolomyces ruberrimus protects its host Arabidopsis arenosa against metal toxicity. Plants inoculated with the fungus yielded more biomass and exhibited significantly fewer stress symptoms in medium mimicking mine dump conditions (medium supplemented with excess of Fe, Zn and Cd). Aside from fine-tuning plant metal homeostasis, the fungus was capable of precipitating Fe in the medium, most likely limiting host exposure to metal toxicity. The precipitated residue was identified by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), X-Ray Diffraction (XRD) and electron microscopy (SEM/TEM) with energy dispersive X-Ray analysis (EDX/SAED) techniques. The performed analyses revealed that the fungus transforms iron into amorphous (oxy)hydroxides and phosphates and immobilizes them in the form of a precipitate changing Fe behaviour in the MSR medium. Moreover, the complexation of free Fe ions by fungi could be obtained by biomolecules such as lipids, proteins, or biosynthesized redox-active molecules.

Endophytic yeast protect plants against metal toxicity by inhibiting plant metal uptake through an ethylene-dependent mechanism

Toxic metal pollution requires significant adjustments in plant metabolism. Here, we show that the plant microbiota plays an important role in this process. The endophytic Sporobolomyces ruberrimus isolated from a serpentine population of Arabidopsis arenosa protected plants against excess metals. Coculture with its native host and Arabidopsis thaliana inhibited Fe and Ni uptake. It had no effect on host Zn and Cd uptake. Fe uptake inhibition was confirmed in wheat and rape. Our investigations show that, for the metal inhibitory effect, the interference of microorganisms in plant ethylene homeostasis is necessary. Application of an ethylene synthesis inhibitor, as well as loss-of-function mutations in canonical ethylene signalling genes, prevented metal uptake inhibition by the fungus. Coculture with S. ruberrimus significantly changed the expression of Fe homeostasis genes: IRT1, OPT3, OPT6, bHLH38 and bHLH39 in wild-type (WT) A. thaliana. The expression pattern of these genes in WT plants and in the ethylene signalling defective mutants significantly differed and coincided with the plant accumulation phenotype. Most notably, down-regulation of the expression of IRT1 solely in WT was necessary for the inhibition of metal uptake in plants. This study shows that microorganisms optimize plant Fe and Ni uptake by fine-tuning plant metal homeostasis.

Perspectives and potential applications of endophytic microorganisms in cultivation of medicinal and aromatic plants

Ensuring food and nutritional security, it is crucial to use chemicals in agriculture to boost yields and protect the crops against biotic and abiotic perturbations. Conversely, excessive use of chemicals has led to many deleterious effects on the environment like pollution of soil, water, and air; loss of soil fertility; and development of pest resistance, and is now posing serious threats to biodiversity. Therefore, farming systems need to be upgraded towards the use of biological agents to retain agricultural and environmental sustainability. Plants exhibit a huge and varied niche for endophytic microorganisms inside the planta, resulting in a closer association between them. Endophytic microorganisms play pivotal roles in plant physiological and morphological characteristics, including growth promotion, survival, and fitness. Their mechanism of action includes both direct and indirect, such as mineral phosphate solubilization, fixating nitrogen, synthesis of auxins, production of siderophore, and various phytohormones. Medicinal and aromatic plants (MAPs) hold a crucial position worldwide for their valued essential oils and several phytopharmaceutically important bioactive compounds since ancient times; conversely, owing to the high demand for natural products, commercial cultivation of MAPs is on the upswing. Furthermore, the vulnerability to various pests and diseases enforces noteworthy production restraints that affect both crop yield and quality. Efforts have been made towards enhancing yields of plant crude drugs by improving crop varieties, cell cultures, transgenic plants, etc., but these are highly cost-demanding and time-consuming measures. Thus, it is essential to evolve efficient, eco-friendly, cost-effective simpler approaches for improvement in the yield and health of the plants. Harnessing endophytic microorganisms as biostimulants can be an effective and alternative step. This review summarizes the concept of endophytes, their multidimensional interaction inside the host plant, and the salient benefits associated with endophytic microorganisms in MAPs.

Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

Phytohormone based biostimulant combined with plant growth promoting endophytic fungus enhances Ni phytoextraction of Noccaea goesingensis

To improve the efficiency of Ni phytoextraction, the metal hyperaccumulator N. goesingensis was subject to treatment with a combination of a Ni uptake stimulating microorganism and the commercially available, IAA- based biostimulating seaweed extract - Kelpak. Additionally, we compared the plant growth promoting and Ni uptake capabilities of the two biofertilizers. Treatment with the Kelpak alone had no significant effect on plant growth or Ni accumulation. Inoculation of N. goesingensis with Phomopsis columnaris significantly improved the biomass of the hyperaccumulating plant and Ni yield per plant and improved several plant biometric features such as fresh and dry weight and several others related to leaf and root size. However, the combination of the two treatments yielded the best results; plants treated with the two growth promoting agents yielded 85% more biomass compared to not treated plants and accumulated 48% more Ni per plant. To verify plant inoculation with the fungus we generated a GFP expressing strain of P. columnaris and visualized the fungus in both plant leaves and roots. To trace the development of the fungus in planta and to evaluate the effect of biostimulant treatment on mycelium development fungal translational elongation factor 1α (tef1α) DNA was quantified with qPCR. Upon biofertilizer the abundance P. columnaris in plant leaves increased nearly 5-fold. The utilization of plant growth stimulating microorganisms, endophytic fungi in particular, can significantly improve Ni phytoextraction in hyperaccumulator N. goesingensis.

The Different Faces of Arabidopsis arenosa-A Plant Species for a Special Purpose

The following review article collects information on the plant species Arabidopsis arenosa. Thus far, A. arenosa has been known as a model species for autotetraploidy studies because, apart from diploid individuals, there are also tetraploid populations, which is a unique feature of this Arabidopsis species. In addition, A arenosa has often been reported in heavy metal-contaminated sites, where it occurs together with a closely related species A. halleri, a model plant hyperaccumulator of Cd and Zn. Recent studies have shown that several populations of A. arenosa also exhibit Cd and Zn hyperaccumulation. However, it is assumed that the mechanism of hyperaccumulation differs between these two Arabidopsis species. Nevertheless, this phenomenon is still not fully understood, and thorough research is needed. In this paper, we summarize the current state of knowledge regarding research on A. arenosa.

Stem endophytes increase root development, photosynthesis, and survival of elm plantlets (Ulmus minor Mill.)

Long-lived trees benefit from fungal symbiotic interactions in the adaptation to constantly changing environments. Previous studies revealed a core fungal endobiome in Ulmus minor which has been suggested to play a critical role in plant functioning. Here, we hypothesized that these core endophytes are involved in abiotic stress tolerance. To test this hypothesis, two core endophytes (Cystobasidiales and Chaetothyriales) were inoculated into in vitro U. minor plantlets, which were further subjected to drought. Given that elm genotypes resistant to Dutch elm disease (DED) tend to show higher abiotic stress tolerance than susceptible ones, we tested the endophyte effect on two DED-resistant and two DED-susceptible genotypes. Drought stress was moderate; endophyte presence attenuated stomata closure in response to drought in one genotype but this stress did not affect plant survival. In comparison, long-term in-vitro culture proved stressful to mock-inoculated plants, especially in DED-susceptible genotypes. Interestingly, no endophyte-inoculated plant died during the experiment, as compared to high mortality in mock-inoculated plants. In surviving plants, endophyte presence stimulated root and shoot growth, photosynthetic rates, antioxidant activity and molecular changes involving auxin-signaling. These changes and the observed endophyte stability in elm tissues throughout the experiment suggest endophytes are potential tools to improve survival and stress tolerance of DED-resistant elms in elm restoration programs.

The effect of endophytic fungi on growth and nickel accumulation in Noccaea hyperaccumulators

The role of endophytic fungi isolated from different populations of European Ni hyperaccumulators was investigated in regard to the microorganisms' ability to enhance the hyperaccumulation of Ni in Noccaea caerulescens. Effects of particular species of endophytic fungi on adaptation of N. caerulescens to excess Ni were tested by co-cultivation with single strains of the fungi. Seven of these had a positive effect on plant biomass production, whereas two of the tested species inhibited plant growth; biomass production of inoculated plants was significantly different compared to non-inoculated control. Inoculation with six fungal strains: Embellisia thlaspis, Pyrenochaeta cava, Phomopsis columnaris, Plectosphaerella cucumerina, Cladosporium cladosporioides and Alternaria sp. stimulated the plant to uptake and accumulate more Ni in both roots and shoots, compared to non-inoculated control. P. columnaris was isolated from all plant species sampled. Strains isolated from Noccaea caerulescens and Noccaea goesingensis increased Ni root and shoot accumulation of their native hosts (compared to non-inoculated control). Inoculation of different populations of Noccaea with P. columnaris of foreign origin did not cause its host to accumulate more Ni, with the exception of the Ni-unadapted ecotype of N. goesingensis. Inoculation with P. columnaris from N. caerulescens significantly improved Ni uptake, but the effect of the fungus was not as prominent as in the case of N. caerulescens. By comparing the transcriptomes of N. caerulescens and N. goesingensis from Flatz inoculated with P. columnaris, we showed that enhanced uptake and accumulation of Ni in the plants is accompanied by an upregulation of several genes mainly involved in plant stress protection and metal uptake and compartmentation.

Root fungal endophytes: identity, phylogeny and roles in plant tolerance to metal stress

Metal trace elements accumulate in soils mainly because of anthropic activities, leading living organisms to develop strategies to handle metal toxicity. Plants often associate with root endophytic fungi, including nonmycorrhizal fungi, and some of these organisms are associated with metal tolerance. The lack of synthetic analyses of plant-endophyte-metal tripartite systems and the scant consideration for taxonomy led to this review aiming (1) to inventory non-mycorrhizal root fungal endophytes described with respect to their taxonomic diversity and (2) to determine the mutualistic roles of these plant-fungus associations under metal stress. More than 1500 species in 100 orders (mainly Hypocreales and Pleosporales) were reported from a wide variety of environments and hosts. Most reported endophytes had a positive effect on their host under metal stress, but with various effects on metal uptake or translocation and no clear taxonomic consistency. Future research considering the functional patterns and dynamics of these associations is thus encouraged.

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner.

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.