Lessons from arbuscular mycorrhizal fungal genomes

Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests

Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.

Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches

The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques of roots sampled in bulk, with methods to capture subsets of cells such as laser microdissection. These approaches have revealed central regulators of this complex relationship, yet the requisite level of detail to effectively untangle the intricacies of temporal and spatial development remains elusive.The recent adoption of single-cell RNA sequencing (scRNA-seq) techniques in plant research is revolutionizing our ability to dissect the intricate transcriptional profiles of plant-microbe interactions, offering unparalleled insights into the diversity and dynamics of individual cells during symbiosis. The isolation of plant cells is particularly challenging due to the presence of cell walls, leading plant researchers to widely adopt nuclei isolation methods. Despite the increased resolution that single-cell analyses offer, it also comes at the cost of spatial perspective, hence, it is necessary the integration of these approaches with spatial transcriptomics to obtain a comprehensive overview.To date, few single-cell studies on plant-microbe interactions have been published, most of which provide high-resolution cell atlases that will become crucial for fully deciphering symbiotic interactions and addressing future questions. In AM symbiosis research, key processes such as the mutual recognition of partners during arbuscule development within cortical cells, or arbuscule senescence and degeneration, remain poorly understood, and these advancements are expected to shed light on these processes and contribute to a deeper understanding of this plant-fungal interaction.

Expanded trade: tripartite interactions in the mycorrhizosphere

Interactions between arbuscular mycorrhizal fungi (AMF), plants, and the soil microbial community have the potential to increase the availability and uptake of phosphorus (P) and nitrogen (N) in agricultural systems. Nutrient exchange between plant roots, AMF, and the adjacent soil microbes occurs at the interface between roots colonized by mycorrhizal fungi and soil, referred to as the mycorrhizosphere. Research on the P exchange focuses on plant-AMF or AMF-microbe interactions, lacking a holistic view of P exchange between the plants, AMF, and other microbes. Recently, N exchange at both interfaces revealed the synergistic role of AMF and bacterial community in N uptake by the host plant. Here, we highlight work carried out on each interface and build upon it by emphasizing research involving all members of the tripartite network. Both nutrient systems are challenging to study due to the complex chemical and biological nature of the mycorrhizosphere. We discuss some of the effective methods to identify important nutrient processes and the tripartite members involved in these processes. The extrapolation of in vitro studies into the field is often fraught with contradiction and noise. Therefore, we also suggest some approaches that can potentially bridge the gap between laboratory-generated data and their extrapolation to the field, improving the applicability and contextual relevance of data within the field of mycorrhizosphere interactions. Overall, we argue that the research community needs to adopt a holistic tripartite approach and that we have the means to increase the applicability and accuracy of in vitro data in the field.

Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum

The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.

Unraveling plant-microbe symbioses using single-cell and spatial transcriptomics

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.

Nutrient and mycoremediation of a global menace 'arsenic': exploring the prospects of phosphorus and Serendipita indica-based mitigation strategies in rice and other crops

KEY MESSAGE

Serendipita indica induced metabolic reprogramming in colonized plants complements phosphorus-management in improving their tolerance to arsenic stress on multifaceted biological fronts. Restoration of the anthropic damage done to our environment is inextricably linked to devising strategies that are not only economically sound but are self-renewing and ecologically conscious. The dilemma of heavy metal (HM) dietary ingestion, especially arsenic (As), faced by humans and animals alike, necessitates the exploitation of such technologies and the cultivation of healthy and abundant crops. The remarkable symbiotic alliance between plants and 'mycorrhizas' has evolved across eons, benefiting growth/yield aspects as well as imparting abiotic/biotic stress tolerance. The intricate interdependence of Serendipita indica (S. indica) and rice plant reportedly reduce As accumulation, accentuating the interest of microbiologists, agriculturists, and ecotoxicological scientists apropos of the remediation mechanisms of As in the soil-AMF-rice system. Nutrient management, particularly of phosphorus (P), is also praised for mitigating As phytotoxicity by deterring the uptake of As molecules due to the rhizospheric cationic competition. Taking into consideration the reasonable prospects of success in minimizing As acquisition by rice plants, this review focuses on the physiological, metabolic, and transcriptional alterations underlying S. indica symbiosis, recuperation of As stress together with nutritional management of P by gathering case studies and presenting successful paradigms. Weaving together a volume of literature, we assess the chemical forms of As and related transport pathways, discuss As-P-rice interaction and the significance of fungi in As toxicity mitigation, predominantly the role of mycorrhiza, as well as survey of the multifaceted impacts of S. indica on plants. A potential strategy for simultaneous S. indica + P administration in paddy fields is proposed, followed by future research orientation to expand theoretic comprehension and encourage field-based implementation.

The Application of Arbuscular Mycorrhizal Fungi as Microbial Biostimulant, Sustainable Approaches in Modern Agriculture

Biostimulant application can be considered an effective, practical, and sustainable nutritional crop supplementation and may lessen the environmental problems related to excessive fertilization. Biostimulants provide beneficial properties to plants by increasing plant metabolism, which promotes crop yield and improves the quality of crops; protecting plants against environmental stresses such as water shortage, soil salinization, and exposure to sub-optimal growth temperatures; and promoting plant growth via higher nutrient uptake. Other important benefits include promoting soil enzymatic and microbial activities, changing the architecture of roots, increasing the solubility and mobility of micronutrients, and enhancing the fertility of the soil, predominantly by nurturing the development of complementary soil microbes. Biostimulants are classified as microbial, such as arbuscular mycorrhizae fungi (AMF), plant-growth-promoting rhizobacteria (PGPR), non-pathogenic fungi, protozoa, and nematodes, or non-microbial, such as seaweed extract, phosphite, humic acid, other inorganic salts, chitin and chitosan derivatives, protein hydrolysates and free amino acids, and complex organic materials. Arbuscular mycorrhizal fungi are among the most prominent microbial biostimulants and have an important role in cultivating better, healthier, and more functional foods in sustainable agriculture. AMF assist plant nutrient and water acquisition; enhance plant stress tolerance against salinity, drought, and heavy metals; and reduce soil erosion. AMF are proven to be a sustainable and environmentally friendly source of crop supplements. The current manuscript gives many examples of the potential of biostimulants for the production of different crops. However, further studies are needed to better understand the effectiveness of different biostimulants in sustainable agriculture. The review focuses on how AMF application can overcome nutrient limitations typical of organic systems by improving nutrient availability, uptake, and assimilation, consequently reducing the gap between organic and conventional yields. The aim of this literature review is to survey the impacts of AMF by presenting case studies and successful paradigms in different crops as well as introducing the main mechanisms of action of the different biostimulant products.