Recent Advances in Adaptation Genomics in Fumarole Fields: An Overlooked Extreme Environment

Extreme environments and plants thriving in them, known as extremophytes, offer promising platforms for studying the diverse adaptive mechanisms that have evolved in plants. However, research on adaptation to extreme environments is still limited to those environments where model species or their relative can survive. Fumarole fields, an extreme environment often overlooked, are characterized by multi-hazardous abiotic stressors, including atmospheric contamination (high concentration of H2S, SO2 and CO2), high soil temperature (∼60°C) and strong soil acidification (pH = 2-3). These conditions make fumarole fields a rich source for studying stress tolerance mechanisms in plants. In this review, we highlight the recent ecological, physiological and genomic advances involved in fumarole field adaptation and discuss the forward avenues. The studies outlined in this paper demonstrate that the extreme levels of abiotic stressors found in fumarole fields make them unparalleled field laboratories for studying the unknown stress tolerance mechanisms, warranting further genomic assessments. Some studies succeeded in identifying genes associated with fumarole field adaptation and shedding light on evolutionary implications; however, they have also encountered challenges such as limited genome resources and high genetic differentiation from related species and/or neighboring populations. To overcome such difficulties, we propose integrating ecophysiological and genomic approaches, drawing from the recent studies in other extreme environments. We expect that further studies in the fumarole fields will contribute to broadening our general knowledge of the limits of life.

Fungal Endophytes: An Insight into Diversity, Stress Tolerance, Biocontrol and Plant Growth-Promoting Potentials

Food and human health are closely related to each other. A healthy diet contributes to excellent health. However, chemical-based agricultural products delivered the poisons in our tray, which cause fatal illnesses like cancer. Overuse of chemical-based fertilizer, herbicides, insecticides, pesticides, etc. is responsible for decreasing soil health status and the development of resistant variants of phytopathogens. Endophytes may overcome such issues effectively without showing any harmful effects. Endophytes are microorganisms that invade intercellular or intracellular parts of host plants without causing any apparent symptoms of infection. Endophytes are broad groups of microorganisms; they may be algae, fungi, bacteria, or ascomycetes. Among them, endophytic fungi are a major group of endophytes that reside inside the host plant body. Types and biodiversity of fungal endophytes make them a potent biological agent for sustainable agricultural management because of their vast geographical distribution. Historically fungal endophytes are broadly categorized into two groups as clavicipitaceous and non-clavicipitaceous based on phylogeny and life history traits. Based on various criteria such as in planta biodiversity, colonization, transmission and fitness to the host, non-clavicipitaceous fungi classified into three distinct classes. They promote plant growth and development by overcoming biotic and abiotic stress and by accelerating systematic inducing resistance (SIR) in plants. They harbor a variety of bioactive compounds like., alkaloids, terpenoids, phenolic acid, steroids, tannins, and saponins that act as antifungal, antibacterial, anticancer, antioxidant, and insecticidal agents. These bioactive compounds have a great potential role in sustainable agricultural management. This review highlights the potential role of fungal endophytes in the field of sustainable agricultural practices to overcome biotic and abiotic stress along with plant growth-promoting activities rather than the use of chemicals in agro-ecosystems.

Mycoviruses and their ecological impacts on fungi

Mycoviruses, as components of the endohyphal microbiome, have been extensively identified in major fungal and oomycetous groups. While most mycoviral infections are asymptomatic, quite a few mycoviruses significantly affect biological characteristics of their hosts. This review emphasizes the roles of mycoviruses in the ecological adaptation of host fungi and oomycetes. Traditional views suggest that mycoviruses are primarily transmitted vertically through spores or horizontally among different individuals via hyphal fusion or anastomosis. However, recent studies have documented instances of mycoviral transmission between species, even across different kingdoms, as well as through specific vectors, suggesting the presence of additional transmission pathways. Although the majority of mycoviruses exert little to no influence on host phenotypes, certain mycoviral infections can significantly impact host fitness. Notably, recent research indicates that mycoviruses can alter interactions between fungi and plants. These findings may offer innovative strategies for the application of mycoviruses in management of plant diseases caused by fungi and oomycetes.

The four Ws of viruses: Where, Which, What and Why - A deep dive into viral evolution

For centuries, humanity has been captivated by evolution, seeking to unravel the origins of life and identify past patterns with future applications. Viruses, despite their obligate parasitic nature, are the most adaptable biological entities, surpassing cellular life in their variability and adaptability. While many theories about viral evolution exist, a consensus on their origins remains elusive. The quasispecies theory, however, has emerged as a leading framework for understanding viral evolution and, indirectly, their variability and adaptability. This theory illuminates how viruses regulate behaviours such as host range and their symbiotic or antagonistic interactions with hosts. This review delves into the most substantiated theories of viral evolution, addressing four fundamental questions relevant to virus ecology: Where did viruses originate? What factors drive viral evolution? What determines the virus host range? And why do viruses adopt pathogenic or mutualistic strategies? We will provide a comprehensive and up-to-date analysis that integrates diverse theoretical perspectives with empirical data, providing a holistic view of viral evolution and its implications for viral behaviour.

Characterization of plant growth-promoting endophytic fungi from Aegle marmelos Corr. and their role in growth enhancement and yield in rice

Plant growth-promoting endophytes (PGPE) are microorganisms which reside in plant tissues and are beneficial to the host in plant growth promotion and pathogen resistance. They are the eco-friendly and sustainable alternative to chemical fertilizers and pesticides. This study aimed to analyze the plant growth-promoting properties of the five endophytic fungal strains from the medicinal plant Aegle marmelos Corr. and evaluate their effects on Oryza sativa plants. Firstly, endophytes were isolated from the different parts of A. marmelos and identified by ITS sequencing. Phosphate solubilization ability was checked in Pikovskaya's agar medium, IAA secretion was measured by the Salkowski colourimetric method, and ACC deaminase activity was checked by Penrose's method. Four endophytic fungal strains with promising PGP activities were inoculated into rice seeds to check their growth promotion in rice. The strain Purpureocillium lilacinum (AMR2) enhanced the seed vigour of rice seeds and demonstrated excellent root colonization ability. Periconia byssoides (AML2) and Medicopsis romeroi (AMS3) were the most effective plant growth-promoting agents, leading to both crop yield improvement and enhanced plant morphological growth due to their great ability to solubilize inorganic phosphate, ACC deaminase activity and production of IAA and Gibberellin A3 (GA3). These endophytic strains could serve as microbial inoculants to enhance crop production, offering an eco-friendly alternative.

Uncovering the Host Range-Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic Genus Colletotrichum

Colletotrichum includes agriculturally and scientifically important pathogens that infect numerous plants. They can also adopt an endophytic lifestyle, refraining from causing disease and/or even promoting plant growth when inoculated on a non-susceptible host. In this manner, the host range of a Colletotrichum fungus can shift, depending on whether it exhibits endophytic or pathogenic lifestyles. Some fungi, such as Colletotrichum tofieldiae, can even shift between pathogenicity and endophytism within the same host depending on the environmental conditions. Here, we aim to disentangle the relationship between lifestyle and host range in Colletotrichum. Specifically, we aim to demonstrate that lifestyle is dependent on the host colonized in many Colletotrichum fungi. We discuss the ways in which pathogenic Colletotrichum species may act endophytically on alternative hosts, how comparative genomics has uncovered candidate molecules (namely effectors, CAZymes, and secondary metabolites) underlying fungal lifestyle, and the merits of using endophytic fungi alongside pathogenic fungi in research, which facilitates the use of reverse genetics to uncover molecular determinants of lifestyle. In particular, we reference the Arabidopsis thaliana-Colletotrichum tofieldiae study system as a model for elucidating the dual roles of plant-fungus interactions, both endophytic and pathogenic, through integrative omics approaches and reverse genetics. This is because C. tofieldiae contains closely related pathogens and endophytes, making it an ideal model for identifying candidate determinants of lifestyle. This approach could identify key molecular targets for effective pathogen management in agriculture. Lastly, we propose a model in which pathogenic lifestyle occupies a different host range than the endophytic lifestyle. This will enhance our understanding of pathogenicity and endophytism in a globally significant fungal genus and lay the groundwork for future research examining molecular determinants of lifestyle in plant-associated fungi.

Study of endophytic fungi of Ipomoea pes-caprae reveals the superiority of in situ plant conservation over ex situ conservation from a mycological view

In nature conservation, ex situ and in situ conservation strategies are discussed for protecting endangered species of plants and animals. However, the impacts of these strategies on the microbes associated with these species are rarely considered. In our study, we chose the endophytic fungi of the pantropical creeping plant Ipomoea pes-caprae as representative coastal plant in two natural coastal populations and two botanical gardens in Taiwan as collection sites in order to investigate the potential effect of ex situ plantation on the biodiversity of microbes intimately associated with this plant. In a culture-dependent approach, endophytic fungi were isolated under axenic conditions and identified to species, genus, or higher taxonomic ranks with DNA barcodes and morphology. In addition to yielding ca. 800 strains and over 100 morphospecies, a principal component analysis (PCA) of the distribution of the dominant fungal species showed clear differences in the composition of endophytic fungal species depending on the sampling sites. We conclude that the endophytic fungi from the original site are replaced by other species in the ex situ plantations. Due to the limitations of ex situ conservation of microbes and from a mycological and microbial perspective, in situ conservation should outweigh ex situ approaches.

Jurassic Osmundaceous Landscapes in Patagonia: Exploring the Concept of Ecological Stasis in the Deseado Massif, Argentina

Herein, we report the presence of a plant paleocommunity, dominated by ferns of the family Osmundaceae, structurally preserved from the only known Mesozoic, fossiliferous geothermal deposits, from the La Matilde Formation (Middle-Upper Jurassic) in the Deseado Massif of Southern Patagonia, Argentina. A total of 13 siliceous chert blocks sampled in an area of approximately 250 m2, preserving a monotypic assemblage dominated by Osmundaceae embedded within its original swampy substrate, are documented. Additional Osmundaceae and fewer ferns and conifers are present in the stratigraphically continuous, adjacent chert levels. This association is comparable to those dominated by Osmundaceae in modern swampy settings, such as in high-altitude lagoons in the Paraná Forest in Northeastern Argentina. In addition, a diverse community of mutualistic, parasitic, and saprotrophic microorganisms associated with the ferns and conifers in the assemblage is present. These compositional, paleoenvironmental, and trophic characteristics of the Jurassic Osmundaceae suggest a possible case of ecological stasis, where Osmundaceae-dominated plant communities apparently persisted in swamps of comparable structures, functions, and physical characteristics for over 150 million years. This suggests that Osmundaceae formed similar communities in compatible settings in the Jurassic, becoming preserved in analogous configurations.

Novel endophytic fungus Leptosphaeria sp. strain T-2 improves plant growth and environmental stress tolerance

Drought and salinity stress pose threats to agricultural production in drylands. Although breeding and genetic modification techniques have been employed to develop drought- and salt-tolerant crops, these methods are costly and risky. Hence, the potential application of endophytic fungi in dryland agriculture is being explored as a novel approach in improving plant tolerance to environmental stress. In this study, endophytic fungi with growth-promoting effects were isolated, characterized, and evaluated in terms of their ability to confer drought and stress tolerance to their host plants. Seventy-seven growth-promoting endophytic fungi belonging to 20 genera were isolated from barley roots; of these, strain T-2 elicited remarkable effects on plant growth parameters. Phylogenetic analysis revealed that strain T-2 belongs to genus Leptosphaeria, whose members are generally known as plant pathogens. Thus, Leptosphaeria sp. strain T-2 is a novel endophytic fungus that promotes plant growth. Moreover, it alleviated growth inhibition caused drought and salinity stress, as evidenced by the survival and maintained health of lettuce plants inoculated with strain T-2. The results of this study suggest that strain T-2 can be applied as a biofertilizer to improve agricultural production in drylands.

Melanized root-associated fungi: key players in plant-soil systems

Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.

Phenological and Fungal Interactions of Malesherbia auristipulata Ricardi (Passifloraceae) in the Atacama Desert: Adaptations and Conservation in an Extreme Ecosystem

Malesherbia auristipulata is an endemic plant species of the Atacama Desert, with unique morphological and physiological adaptations. This research was conducted at Cuesta El Águila, Arica and Parinacota Region, Chile. Adult and juvenile plants were monitored, recording their growth, flowering, and fruiting phases. Additionally, plant community species were identified. For the study of endophytic mycoflora, samples of seeds, roots, stems, and leaves were collected, disinfected, and cultivated in specific media. The isolated fungi were analyzed morphologically and molecularly, determining their distribution in different plant organs. The diversity of endophytic fungi associated with M. auristipulata and the associated fungal community was determined. The presence of endophytic fungi varied depending on the organ studied, suggesting dynamic interactions in the structure of its fungal community. Among the identified endophytic fungi, Alternaria sorghi, A. alstroemeriae, and Fusarium nurragi stand out for their presence in the root and stem of the plant. Of particular interest is the presence of F. circinatum in the leaves. This study provides valuable information for the conservation of M. auristipulata and other organisms in the Atacama Desert, highlighting the importance of ecological interactions in the resilience of plants to extreme environmental conditions.

Genome-wide differentiation corresponds to climatic niches in two species of lichen-forming fungi

Lichens can withstand fluctuating environmental conditions such as hydration-desiccation cycles. Many species distribute across climate zones, suggesting population-level adaptations to conditions such as freezing and drought. Here, we aim to understand how climate affects population genomic patterns in lichenized fungi. We analysed population structure along elevational gradients in closely related Umbilicaria phaea (North American; two gradients) and Umbilicaria pustulata (European; three gradients). All gradients showed clear genomic breaks splitting populations into low-elevation (Mediterranean zone) and high-elevation (cold temperate zone). A total of 3301 SNPs in U. phaea and 138 SNPs in U. pustulata were driven to fixation between the two ends of the gradients. The difference between the species is likely due to differences in recombination rate: the sexually reproducing U. phaea has a higher recombination rate than the primarily asexually reproducing U. pustulata. Cline analysis revealed allele frequency transitions along all gradients at approximately 0°C, coinciding with the transition between the Mediterranean and cold temperate zones, suggesting freezing is a strong driver of population differentiation. Genomic scans further confirmed temperature-related selection targets. Both species showed similar differentiation patterns overall, but different selected alleles indicate convergent adaptation to freezing. Our results enrich our knowledge of fungal genomic functions related to temperature and climate, fungal population genomics, and species responses to environmental heterogeneity.

Role of grass endophytic fungi as a natural resource of bioactive metabolites

Grass endophytic fungi have garnered increasing attention as a prolific source of bioactive metabolites with potential application across various fields, including pharmaceticals agriculture and industry. This review paper aims to synthesize knowledge on the diversity, isolation, and bioactivity of metabolites produced by grass endophytic fungi. Additionally, this approach aids in the conservation of rare and endangered plant species. Advanced analytical techniques such as high-performance liquid chromatography, liquid chromatograpy-mass spectrometry and gas chromatography are discussed as critical tools for metabolite identification and characterization. The review also highlights significant bioactive metabolites discovered to date, emphasizing their antimicrobial, antioxidant, and insecticidal activities and plant growth regulation properties. Besides address the challenges and future prospects in harnessing grass endophytic fungi for sustainable biotenological applications. By consolidating recent advancements and identifying agaps in the current research, this paper provides a comprehensive overview of the potential grass endophytic fungi as a valuable resource for novel bioactive compounds.

Two +ssRNA mycoviruses cohabiting the fungal cultivar of leafcutter ants

Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.

Endosphere mycobiome in mature rice roots originate from both seedlings and soils

Plant-fungus symbioses have functional relevance during plant growth and development. However, it is still unknown whether the endosphere fungi in mature plants originated from soils or seeds. To elucidate the origination of endosphere fungi in mature rice roots, the fungal communities in surface sterilized roots and shoots of mature rice plants germinated in soils, rhizosphere soils and seedlings germinated under sterile conditions were analyzed by Illumina-based sequencing and compared. Total 62 fungal OTUs shared in the seedlings, shoots and roots, 126 OTUs shared in the rhizosphere soils, shoots and roots. Fungal OTUs coexisted in the four types of samples belonged to genera of Rhizophagus, Trichoderma, Fusarium, Atractiella, Myrmecridium, Sporothrix, Microdochium, Massariosphaeria, and Phialemonium. The principle component analysis (PCA) and NMDS plot suggested that the fungal community structure in rhizosphere soils was different from that in seedlings significantly. Rhizosphere soil, shoot and root contained more similar fungal community. The fungal community in seedling was similar to that in shoot and root of mature plants. The results suggested that endophytic fungal communities in mature rice plants originated from both seedlings and rhizosphere soils, and more fungal taxa originated from rhizosphere soils. Mature rice plants contain mycobiome transmitted vertically from seeds, which suggests that inoculation of endophytic fungi isolated from seedlings might be an effective way to introduce beneficial fungal inoculants into rice plants successfully.

Exploring extremophilic fungi in soil mycobiome for sustainable agriculture amid global change

As the Earth warms, alternatives to traditional farming are crucial. Exploring fungi, especially poly extremophilic and extremotolerant species, to be used as plant probiotics, represents a promising option. Extremophilic fungi offer avenues for developing and producing innovative biofertilizers, effective biocontrol agents against plant pathogens, and resilient enzymes active under extreme conditions, all of which are crucial to enhance agricultural efficiency and sustainability through improved soil fertility and decreased reliance on agrochemicals. Yet, extremophilic fungi's potential remains underexplored and, therefore, comprehensive research is needed to understand their roles as tools to foster sustainable agriculture practices amid climate change. Efforts should concentrate on unraveling the complex dynamics of plant-fungi interactions and harnessing extremophilic fungi's ecological functions to influence plant growth and development. Aspects such as plant's epigenome remodeling, fungal extracellular vesicle production, secondary metabolism regulation, and impact on native soil microbiota are among many deserving to be explored in depth. Caution is advised, however, as extremophilic and extremotolerant fungi can act as both mitigators of crop diseases and as opportunistic pathogens, underscoring the necessity for balanced research to optimize benefits while mitigating risks in agricultural settings.

Aspergillus brasiliensis E_15.1: A Novel Thermophilic Endophyte from a Volcanic Crater Unveiled through Comprehensive Genome-Wide, Phenotypic Analysis, and Plant Growth-Promoting Trails

Thermophilic fungi have been seldom studied despite the fact that they can contribute to understanding ecological mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano "El Chichonal" in Mexico. This strain was capable of surviving in soil with a temperature of 60 °C and a pH of neutral acidity, which preluded a high thermostability and a potential in industrial application. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in 37 Mb of genomic DNA. We performed a comprehensive phylogenomic analysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasiliensis. Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. A. brasiliensis E_15.1 was found to degrade chitin, chitooligosaccharides, xylan, and cellulose. The genes to biosynthesize clavaric acid (a triterpene with antitumor activity) were found, thus probably having antitumor activity. In addition to the genomic analysis, a set of enzymatic assays confirmed the thermostability of extracellular xylanases and cellulases of A. brasiliensis E_15.1. The enzymatic repertoire of A. brasiliensis E_15.1 suggests that A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.

Interactions of Melanin with Electromagnetic Radiation: From Fundamentals to Applications

Melanin, especially integumentary melanin, interacts in numerous ways with electromagnetic radiation, leading to a set of critical functions, including radiation protection, UV-protection, pigmentary and structural color productions, and thermoregulation. By harnessing these functions, melanin and melanin-like materials can be widely applied to diverse applications with extraordinary performance. Here we provide a unified overview of the melanin family (all melanin and melanin-like materials) and their interactions with the complete electromagnetic radiation spectrum (X-ray, Gamma-ray, UV, visible, near-infrared), which until now has been absent from the literature and is needed to establish a solid fundamental base to facilitate their future investigation and development. We begin by discussing the chemistries and morphologies of both natural and artificial melanin, then the fundamentals of melanin-radiation interactions, and finally the exciting new developments in high-performance melanin-based functional materials that exploit these interactions. This Review provides both a comprehensive overview and a discussion of future perspectives for each subfield of melanin that will help direct the future development of melanin from both fundamental and applied perspectives.

Fungal endophytes from saline-adapted shrubs induce salinity stress tolerance in tomato seedlings

To meet the food and feed demands of the growing population, global food production needs to double by 2050. Climate change-induced challenges to food crops, especially soil salinization, remain a major threat to food production. We hypothesize that endophytic fungi isolated from salt-adapted host plants can confer salinity stress tolerance to salt-sensitive crops. Therefore, we isolated fungal endophytes from shrubs along the shores of saline alkaline Lake Magadi and evaluated their ability to induce salinity stress tolerance in tomato seeds and seedlings. Of 60 endophytic fungal isolates, 95% and 5% were from Ascomycetes and Basidiomycetes phyla, respectively. The highest number of isolates (48.3%) were from the roots. Amylase, protease and cellulase were produced by 25, 30 and 27 isolates, respectively; and 32 isolates solubilized phosphate. Only eight isolates grew at 1.5 M NaCl. Four fungal endophytes (Cephalotrichum cylindricum, Fusarium equiseti, Fusarium falciforme and Aspergilus puniceus) were tested under greenhouse conditions for their ability to induce salinity tolerance in tomato seedlings. All four endophytes successfully colonized tomato seedlings and grew in 1.5 M NaCl. The germination of endophyte-inoculated seeds was enhanced by 23%, whereas seedlings showed increased chlorophyll and biomass content and decreased hydrogen peroxide content under salinity stress, compared with controls. The results suggest that the the four isolates can potentially be used to mitigate salinity stress in tomato plants in salt-affected soils.

Fungi beyond limits: The agricultural promise of extremophiles

Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges.

Review: Research progress on seasonal succession of phyllosphere microorganisms

Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

New endophytic strains of Trichoderma promote growth and reduce clubroot severity of rapeseed (Brassica napus)

Rapeseed (Brassica napus L.) is the world's third most important edible oilseed crop after soybean and palm. The clubroot disease caused by Plasmodiophora brassicae poses a significant risk and causes substantial yield losses in rapeseed. In this study, 13 endophytic fungal strains were isolated from the healthy roots of rapeseed (B. napus) grown in a clubroot-infested field and molecularly identified. Based on germination inhibition of resting spores of P. brassicae, two endophytic fungal antagonists, Trichoderma spp. ReTk1 and ReTv2 were selected to evaluate their potential for plant growth promotion and biocontrol of P. brassicae. The Trichoderma isolates were applied as a soil drench (1×107 spore/g soil) to a planting mix and field soil, in which plants were grown under non-infested and P. brassicae-infested (2×106 spore/g soil) conditions. The endophytic fungi were able to promote plant growth, significantly increasing shoot and root length, leaf diameter, and biomass production (shoots and root weight) both in the absence or presence of P. brassicae. The single and dual treatments with the endophytes were equally effective in significantly decreasing the root-hair infection, root index, and clubroot severity index. Both ReTk1 and ReTv2 inhibited the germination of resting spores of P. brassicae in root exudates. Moreover, the endophytic fungi colonized the roots of rapeseed extensively and possibly induced host resistance by up-regulated expression of defense-related genes involved in jasmonate (BnOPR2), ethylene (BnACO and BnSAM3), phenylpropanoid (BnOPCL and BnCCR), auxin (BnAAO1) and salicylic acid (BnPR2) pathways. Based on these findings, it is evident that the rapeseed root endophytes Trichoderma spp. ReTk1 and ReTv2 could suppress the gall formation on rapeseed roots via antibiosis, induced systemic resistance (ISR), and/or systemic acquired resistance (SAR). According to our knowledge, this is the first report of the endophytic Trichoderma spp. isolated from root tissues of healthy rapeseed plants (B. napus.), promoting plant growth and reducing clubroot severity.

Tropical Trees Will Need to Acclimate to Rising Temperatures-But Can They?

For tropical forests to survive anthropogenic global warming, trees will need to avoid rising temperatures through range shifts and "species migrations" or tolerate the newly emerging conditions through adaptation and/or acclimation. In this literature review, we synthesize the available knowledge to show that although many tropical tree species are shifting their distributions to higher, cooler elevations, the rates of these migrations are too slow to offset ongoing changes in temperatures, especially in lowland tropical rainforests where thermal gradients are shallow or nonexistent. We also show that the rapidity and severity of global warming make it unlikely that tropical tree species can adapt (with some possible exceptions). We argue that the best hope for tropical tree species to avoid becoming "committed to extinction" is individual-level acclimation. Although several new methods are being used to test for acclimation, we unfortunately still do not know if tropical tree species can acclimate, how acclimation abilities vary between species, or what factors may prevent or facilitate acclimation. Until all of these questions are answered, our ability to predict the fate of tropical species and tropical forests-and the many services that they provide to humanity-remains critically impaired.

Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant-microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation.

The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia

Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.

Plants as the Extended Phenotype of Endophytes-The Actual Source of Bioactive Compounds

For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes.

Plant Seeds Commonly Host Bacillus spp., Potential Antagonists of Phytopathogens

In agriculture, horticulture and plantation forestry, Bacillus species are the most commonly applied antagonists and biopesticides, targeting plant pathogens and insect pests, respectively. Bacillus isolates are also used as bacterial plant biostimulants, or BPBs. Such useful isolates of Bacillus are typically sourced from soil. Here, we show that Bacillus - and other antagonistic microbes - can be sourced from a broad range of plant seeds. We found that culturable Bacillus isolates are common in the seeds of 98 plant species representing 39 families (i.e., 87% of the commonly cultured bacteria belonged to Bacillales). We also found that 83% of the commonly cultured fungi from the seeds of the 98 plant species belonged to just three orders of fungi-Pleosporales, Hypocreales and Eurotiales-that are also associated with antagonism. Furthermore, we confirmed antagonism potential in agaro with seed isolates of Bacillus from Pinus monticola as a representative case. Eight isolates each of seed Bacillus, seed fungi, and foliar fungi, all from P. monticola, were paired in a total of 384 possible pair-wise interactions (with seed and foliar fungi as the targets). Seed Bacillus spp. were the strongest antagonists of the seed and foliar fungi, with a mean interaction strength 2.8 times greater than seed fungi (all either Eurotiales or Hypocreales) and 3.2 times greater than needle fungi. Overall, our study demonstrates that seeds host a taxonomically narrow group of culturable, antagonistic bacteria and fungi.

Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with 'Ca. L. asiaticus'

Detection of new viruses or new virus hosts is essential for the protection of economically important agroecosystems and human health. Increasingly, metatranscriptomic data are being used to facilitate this process. Such data were obtained from adult Asian citrus psyllids (ACP) (Diaphorina citri Kuwayama) that fed solely on mandarin (Citrus ×aurantium L.) plants grafted with buds infected with 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium associated with the severe Asian variant of huanglongbing (HLB), the most destructive disease of citrus. Brassica yellows virus (BrYV), the causative agent of yellowing or leafroll symptoms in brassicaceous plants, and its associated RNA (named as BrYVaRNA) were detected in ACP. In addition, the porcine reproductive and respiratory syndrome virus (PRRSV), which affects pigs and is economically important to pig production, was also found in ACP. These viruses were not detected in insects feeding on plants grafted with CLas-free buds. Changes in the concentrations of insect-specific viruses within the psyllid were caused by coinfection with CLas. IMPORTANCE The cross transmission of pathogenic viruses between different farming systems or plant communities is a major threat to plants and animals and, potentially, human health. The use of metagenomics is an effective approach to discover viruses and vectors. Here, we collected buds from the CLas-infected and CLas-free mandarin (Citrus ×aurantium L. [Rutaceae: Aurantioideae: Aurantieae]) trees from a commercial orchard and grafted them onto CLas-free mandarin plants under laboratory conditions. Through metatranscriptome sequencing, we first identified the Asian citrus psyllids feeding on plants grafted with CLas-infected buds carried the plant pathogen, brassica yellows virus and its associated RNA, and the swine pathogen, porcine reproductive and respiratory syndrome virus. These discoveries indicate that both viruses can be transmitted by grafting and acquired by ACP from CLas+ mandarin seedlings.

The diversity of cultivable endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan

Background

Ipomoeapes-caprae is a plant of sand coasts and it can tolerate stresses, such as high salinity, strong wind and sand movements and lack of nutrients. It plays an important role in coast protection and preventing erosion. Fungal endophytes show high biodiversity and have a strong influence on the survival of plants under different stress factors. Although this plant is important for sand coast ecosystems, little is known about the associated fungi. In this study, we isolated and identified endophytic fungi of Ipomoeapes-caprae, a dominant plant along the shore of Taiwan. The dataset contains 896 records, which correspond to 177 species. The geographical scope of the dataset covers the northern subtropical area of the main island of Taiwan, with its sand coasts in New Taipei, Taoyuan, Hsinchu and Taichung and two botanical gardens in Taipei and Taichung. The detailed original data of fungal diversity are rarely publicly shared under strictly formalised and, thus, reusable standards. As an example for such an approach, the complete occurrence dataset was made available in the Darwin Core Archive format via the Global Biodiversity Information Facility (GBIF) under Version 1.13, Taiwan Biodiversity Information Facility (TaiBIF) https://doi.org/10.15468/9h9rcg. In this first data paper on endophytic fungi, the scientific name and associated DNA sequence in the dataset were directly linked to other free online resource (Index Fungorum, GenBank), which shows the potential of GBIF for linking together different online data repositories.

New information

We describe a dataset, in which the diversity of endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan was investigated.

Diversity, Lifestyle, Genomics, and Their Functional Role of Cochliobolus, Bipolaris, and Curvularia Species in Environmental Remediation and Plant Growth Promotion under Biotic and Abiotic Stressors

Cochliobolus, Bipolaris, and Curvularia genera contain various devastating plant pathogens that cause severe crop losses worldwide. The species belonging to these genera also perform a variety of diverse functions, including the remediation of environmental contaminations, beneficial phytohormone production, and maintaining their lifestyle as epiphytes, endophytes, and saprophytes. Recent research has revealed that despite their pathogenic nature, these fungi also play an intriguing role in agriculture. They act as phosphate solubilizers and produce phytohormones, such as indole acetic acid (IAA) and gibberellic acid (GAs), to accelerate the growth of various plants. Some species have also been reported to play a significant role in plant growth promotion during abiotic stresses, such as salinity stress, drought stress, heat stress, and heavy metal stress, as well as act as a biocontrol agent and a potential mycoherbicide. Similarly, these species have been reported in numerous industrial applications to produce different types of secondary metabolites and biotechnological products and possess a variety of biological properties, such as antibacterial, antileishmanial, cytotoxic, phytotoxic, and antioxidant activities. Additionally, some of the species have been utilized in the production of numerous valuable industrial enzymes and biotransformation, which has an impact on the growth of crops all over the world. However, the current literature is dispersed, and some of the key areas, such as taxonomy, phylogeny, genome sequencing, phytohormonal analysis, and diversity, are still being neglected in terms of the elucidation of its mechanisms, plant growth promotion, stress tolerance, and bioremediation. In this review, we highlighted the potential role, function, and diversity of Cochliobolus, Curvularia, and Bipolaris for improved utilization during environmental biotechnology.

Recent Advances in Using Natural Antibacterial Additives in Bioactive Wound Dressings

Wound care is a global health issue with a financial burden of up to US $96.8 billion annually in the USA alone. Chronic non-healing wounds which show delayed and incomplete healing are especially problematic. Although there are more than 3000 dressing types in the wound management market, new developments in more efficient wound dressings will require innovative approaches such as embedding antibacterial additives into wound-dressing materials. The lack of novel antibacterial agents and the misuse of current antibiotics have caused an increase in antimicrobial resistance (AMR) which is estimated to cause 10 million deaths by 2050 worldwide. These ongoing challenges clearly indicate an urgent need for developing new antibacterial additives in wound dressings targeting microbial pathogens. Natural products and their derivatives have long been a significant source of pharmaceuticals against AMR. Scrutinising the data of newly approved drugs has identified plants as one of the biggest and most important sources in the development of novel antibacterial drugs. Some of the plant-based antibacterial additives, such as essential oils and plant extracts, have been previously used in wound dressings; however, there is another source of plant-derived antibacterial additives, i.e., those produced by symbiotic endophytic fungi, that show great potential in wound dressing applications. Endophytes represent a novel, natural, and sustainable source of bioactive compounds for therapeutic applications, including as efficient antibacterial additives for chronic wound dressings. This review examines and appraises recent developments in bioactive wound dressings that incorporate natural products as antibacterial agents as well as advances in endophyte research that show great potential in treating chronic wounds.

The Role of Plant Growth-Promoting Microorganisms (PGPMs) and Their Feasibility in Hydroponics and Vertical Farming

There are many reasons for the increase in hydroponics/soil-free systems in agriculture, and these systems have now advanced to the form of vertical farming. The sustainable use of space, the reduction in water use compared to soil-based agriculture, the lack of pesticides, the ability to control nutrient inputs, and the implementation of user-friendly technology for environmental control and harvesting are all factors that have made the global market for vertical farming predicted to reach more than USD 10.02 billion by 2027. By comparison, soil-based agriculture consumes 20 times more water, and some agricultural practices promote soil deterioration and cause environmental pollution. Plant growth-promoting microorganisms (PGPMs) have been used extensively in traditional agriculture to enhance plant growth, environmental stress tolerance, and the efficacy of phytoremediation in soil-based farming. Due to the controlled atmosphere in hydroponics and vertical farms, there is strong potential to maximize the use of PGPMs. Here, we review the leveraging of plant growth-promoting microorganism mechanisms in hydroponics and vertical farming. We recommend a synchronized PGPM treatment using a biostimulant extract added to the hydroponic medium while also pre-treating seeds or seedlings with a microbial suspension for aquaponic and aeroponic systems.

Bioactive compounds of Curvularia species as a source of various biological activities and biotechnological applications

Many filamentous fungi are known to produce several secondary metabolites or bioactive compounds during their growth and reproduction with sort of various biological activities. Genus Curvularia (Pleosporaceae) is a dematiaceous filamentous fungus that exhibits a facultative pathogenic and endophytic lifestyle. It contains ~213 species among which Curvularia lunata, C. geniculata, C. clavata, C. pallescens, and C. andropogonis are well-known. Among them, C. lunata is a major pathogenic species of various economical important crops especially cereals of tropical regions while other species like C. geniculata is of endophytic nature with numerous bioactive compounds. Curvularia species contain several diverse groups of secondary metabolites including alkaloids, terpenes, polyketides, and quinones. Which possess various biological activities including anti-cancer, anti-inflammatory, anti-microbial, anti-oxidant, and phytotoxicity. Several genes and gene factors are involved to carry and regulate the expression of these activities which are influenced by environmental signals. Some species of Curvularia also show negative impacts on humans and animals. Apart from their negative effects, there are some beneficial implications like production of enzymes of industrial value, bioherbicides, and source of nanoparticles is reported. Many researchers are working on these aspects all over the world but there is no review in literature which provides significant understanding about these all aspects. Thus, this review will provide significant information about secondary metabolic diversity, their biological activities and biotechnological implications of Curvularia species.

Many foliar endophytic fungi of Quercus gambelii are capable of psychrotolerant saprotrophic growth

Many endophytic fungi have the potential to function as saprotrophs when living host tissues senesce and enter the litter pool. The consumption of plant litter by fungi obviously requires moisture but, in the arid, western USA, the native range of Quercus gambelii Nutt., most of the precipitation occurs during the coldest months of the year. Therefore, we hypothesized that the endophytic fungi of Q. gambelii have the potential to function as psychrotolerant saprotrophs, which we defined in this study as an organism capable of significant growth on leaf litter at 5°C. We further hypothesized that a tradeoff exists between growth of endophytic fungi at 5°C and at 17°C such that fungal isolates are either cold- or warm-temperature specialists. Consistent with our first hypothesis, we found that 36 of our 40 isolates consumed leaf litter at 5°C, but there was a surprisingly high degree of variability among isolates in this ability, even among isolates of a given species. Contrary to our second hypothesis, there was no tradeoff between saprotrophic growth at 5°C and saprotrophic growth at 17°C. Indeed, the isolates that grew poorly as saprotrophs at 5°C were generally those that grew poorly as saprotrophs at 17°C. By virtue of being endophytic, endophytic fungi have priority in litter over decomposer fungi that colonize plant tissues only after they enter the litter pool. Moreover, by virtue of being psychrotolerant, some endophytic fungi may function as saprotrophs during the cold months of the year when moisture is temporarily available. Therefore, we suggest that some endophytic fungi of Q. gambelii could play significant ecosystem roles in litter decomposition and nutrient cycling.

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability

The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.

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.

Fungal communities in soils under global change

Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO₂ concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Use of Secondary Metabolites of Wood-Decaying Fungi to Reduce Damping off Disease

Phytopathogenic fungi can cause plant diseases that are difficult to control, including mass mortality of some tree species. The Fusarium oxysporum complex (sensu lato) is one of the most dangerous groups of phytopathogenic fungi, causing the death of conifer species, including Pinus sylvestris seedlings in forest and ornamental nurseries. Recently, non-chemical methods of plant protection have become the basis of integrated pest management (IPM) in the European Union (EC Directive). The possibility of protection of pine seedlings against the pathogen F. oxysporum using active substances from wood-destroying fungi commonly found in forests was examined. Methanolic extracts of Fomitopsis pinicola, Ganoderma applanatum, and Trametes versicolor were found to contain substances effective in both prevention and treatment of infected seedlings. G. applanatum and T. versicolor showed particular biological activity in increasing plant resistance. Efficacy, especially of the extract of F. pinicola, increased with concentration. Further field trials are needed to confirm the results obtained in laboratory tests on plant protection.

Culturable Endophytic Fungi in Fraxinus excelsior and Their Interactions with Hymenoscyphus fraxineus

The species diversity of culturable endophytic fungi was studied in the leaves and twigs of symptomatic and asymptomatic Fraxinus excelsior trees. Endophytic mycobiota was dominated by Ascomycota species, with Pleosporales (44.17%) and Diaporthales (23.79%) endophytes being the most frequently observed in the tree samples. The number of endophytic isolates and species richness varied depending on the sampling date (May and October) and tissue location. Of the 54 species identified based on ITS sequences, 14 were classified as dominant. The most frequently isolated species were Diaporthe eres, followed by Alternaria alternata, Dothiorella gregaria, and Fraxinicola fraxini. The inhibitory effect of 41 species (75 isolates) of endophytes on the radial growth of a Hymenoscyphus fraxineus isolate was studied under in vitro conditions (dual cultures). The radial growth of H. fraxineus was the most inhibited by four endophytic fungi from twigs (Fusarium lateritium, Didymella aliena, Didymella macrostoma, and Dothiorella gregaria). The inhibitory effect of the four isolates was also studied under in planta conditions. The isolates artificially inoculated into the trunks of ash trees reduced the length of necroses formed by H. fraxineus co-inoculated in the same trunks. This effect depended on the isolate, and the inhibition was most prominent only on trunks inoculated with F. lateritium and D. aliena. Although the total length of necrotic lesions formed by the H. fraxineus infection was shorter in the ash trunks co-inoculated with the endophytes, the difference was not significant.

Symbiotic Modulation as a Driver of Niche Expansion of Coastal Plants in the San Juan Archipelago of Washington State

Modern evolutionary theory and population genetics posit that adaptation and habitat expansion of plants result from processes exclusive to their genomes. Here, we present studies showing that plants can grow across complex habitat gradients by modulating symbiotic associations with Class 2 fungal endophytes. Endophyte analysis of three native (Leymus mollis, Distichlis spicata, and Salicornia pacifica) and one invasive (Spartina anglica) plant growing across adjacent microhabitats in the San Juan Archipelago altered associations with Class 2 fungal endophytes in response to soil salinity levels. At the microhabitat interfaces where the gradation of salinity varied, the plants were colonized by endophytes from both microhabitats. A reciprocal transplant study along a salt gradient demonstrated that Leymus mollis (dunegrass) required endophytes indigenous to each microhabitat for optimal fitness and/or survival. In contrast, when dunegrass and Grindelia integrifolia (gumweed) were found growing in low salinity, but high drought habitats, these plant species had their own unique dominant endophyte association regardless of geographic proximity and conferred drought but not high salt stress tolerance. Modulation of endophyte abundance occurred in planta based on the ability of the symbiont to confer tolerance to the stress imposed on plants. The ability of an endophyte to confer appropriate stress tolerance resulted in a significant increase of in planta fungal abundance. Conversely, the inability of an endophyte to confer stress tolerance resulted in a decrease of in planta fungal abundance. Our studies indicate that Class 2 fungal endophytes can provide a symbiotic mechanism for niche expansion and phenotypic plasticity across environmental gradients.

A Comprehensive Overview of Nanotechnology in Sustainable Agriculture

Plant nutrition is crucial in crop productivity and providing food security to the ever-expanding population. Application of chemical/biological fertilizers and pesticides are the mainstays for any agricultural economy. However, there are unintended consequences of using chemical fertilizers and pesticides. The environment and ecological balance are adversely affected by their usage. Biofertilizers and biopesticides counter some undesired environmental effects of chemical fertilizers/pesticides; inspite of some drawbacks associated with their use. The recent developments in nanotechnology offer promise towards sustainable agriculture. Sustainable agriculture involves addressing the concerns about agriculture as well as of the environment. This review briefs about important nanomaterials used in agriculture as nanofertilizers, nanopesticides, and a combination called nanobiofertilizers. Both nanofertilizers and nanopesticides enable slow and sustained release besides their eco-friendly environmental consequences. They can be tailored to specific needs to crop. Nanofertilizers also offer greater stress tolerance and, therefore, of considerable value in the era of climate change. Furthermore, nanofertilizers/nanopesticides are applied in minute amounts, reducing transportation costs associated and thus positively affecting the economy. Their uses extend beyond such as if nanoparticles (NPs) are used at high concentrations; they affect plant pathogens adversely. Polymer-based biodegradable nanofertilizers and nanopesticides offer various benefits. There is also a dark side to the use of nanomaterials in agriculture. Nanotechnology often involves the use of metal/metal oxide nanoparticles, which might get access to human bodies leading to their accumulation through bio-magnification. Although their effects on human health are not known, NPs may reach toxic concentrations in soil and runoff into rivers, and other water bodies with their removal to become a huge economic burden. Nevertheless, a risk-benefit analysis of nanoformulations must be ensured before their application in sustainable agriculture.

A viewpoint on ecological and evolutionary study of plant thermal performance curves in a warming world

We can understand the ecology and evolution of plant thermal niches through thermal performance curves (TPCs), which are unimodal, continuous reaction norms of performance across a temperature gradient. Though there are numerous plant TPC studies, plants remain under-represented in syntheses of TPCs. Further, few studies quantify plant TPCs from fitness-based measurements (i.e. growth, survival and reproduction at the individual level and above), limiting our ability to draw conclusions from the existing literature about plant thermal adaptation. We describe recent plant studies that use a fitness-based TPC approach to test fundamental ecological and evolutionary hypotheses, some of which have uncovered key drivers of climate change responses. Then, we outline three conceptual questions in ecology and evolutionary biology for future plant TPC studies: (i) Do populations and species harbour genetic variation for TPCs? (ii) Do plant TPCs exhibit plastic responses to abiotic and biotic factors? (iii) Do fitness-based TPCs scale up to population-level thermal niches? Moving forward, plant ecologists and evolutionary biologists can capitalize on TPCs to understand how plasticity and adaptation will influence plant responses to climate change.

Thermo-Priming Mediated Cellular Networks for Abiotic Stress Management in Plants

Plants can adapt to different environmental conditions and can survive even under very harsh conditions. They have developed elaborate networks of receptors and signaling components, which modulate their biochemistry and physiology by regulating the genetic information. Plants also have the abilities to transmit information between their different parts to ensure a holistic response to any adverse environmental challenge. One such phenomenon that has received greater attention in recent years is called stress priming. Any milder exposure to stress is used by plants to prime themselves by modifying various cellular and molecular parameters. These changes seem to stay as memory and prepare the plants to better tolerate subsequent exposure to severe stress. In this review, we have discussed the various ways in which plants can be primed and illustrate the biochemical and molecular changes, including chromatin modification leading to stress memory, with major focus on thermo-priming. Alteration in various hormones and their subsequent role during and after priming under various stress conditions imposed by changing climate conditions are also discussed.

The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind

My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.