Paola Bonfante

• University of Turin

Mycorrhizal associations, established between approximately 90% of land plants and soil fungi from diverse fungal taxa—ranging from early-diverging groups to Dikarya—represent a cornerstone of terrestrial ecosystems. Despite substantial advances in knowledge, driven by an increasingly broad and interdisciplinary scientific community, translational...

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 cent...

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 extra...

To understand whether domestication had an impact on susceptibility and responsiveness to arbuscular mycorrhizal fungi (AMF) in tomato ( Solanum lycopersicum ), we investigated two tomato cultivars (“M82” and “Moneymaker”) and a panel of wild relatives including S. neorickii, S. habrochaites and S. pennellii encompassing the whole Lycopersicon clad...

Mycorrhizas are mutualistic interactions that the majority of land plants establish with a heterogeneous group of soil fungi; their distribution and diversity have supported the success of plants on the planet. Among all different types of mycorrhizas, arbuscular mycorrhiza (AM) is the most ancient and the most common in host plants of all major cr...

Endosymbiotic bacteria are commonly inhabitants of environmental isolates of Mucoromycota fungi. Described bacterial endosymbionts of Mucoromycota are related to Burkholderia and Mycoplasma lineages. Bacterial endosymbionts of Mucoromycota tend to be obligately dependent on their fungal host for nutrition, but bacterial endosymbionts are not always...

Arbuscular mycorrhizal fungi (AMF) have accompanied the majority of land plants since their evolution in the Devonian period with a symbiotic alliance centered on nutrient exchanges. The exploration of AMF genomes is providing clues to explain major questions about their biology, evolution, and ecology. The dynamics of nuclei across the fungal life...

Alternate wetting and drying (AWD) system, in which water has been reduced by approximately 35% with an increased occurrence of beneficial arbuscular mycorrhizal (AM) symbiosis and no negative impact on rice yield, was proposed to utilize water and nutrients more sustainable. In this study, we selected six rice cultivars (Centauro, Loto, Selenio, V...

The beneficial symbiosis between plants and arbuscular mycorrhizal (AM) fungi leads to a deep reprogramming of plant metabolism, involving the regulation of several molecular mechanisms, many of which are poorly characterized. In this regard, proteomics is a powerful tool to explore changes related to plant–microbe interactions. This study provides...

Metagenomics approaches have revealed the importance of Mucoromycota in the evolution and functioning of plant microbiomes. Comprised of three subphyla (Glomeromycotina, Mortierellomycotina, and Mucoromycotina), this early diverging lineage of fungi encompasses species of mycorrhizal fungi, root endophytes, plant pathogens, and many decomposers of...

Gigaspora margarita is a cosmopolitan arbuscular mycorrhizal fungus, which - as an obligate symbiont- requires being associated to a host plant to accomplish its life cycle. It is characterized by huge white spores, the development of extraradical auxiliary cells, and the lack of intraradical vesicles. Its genome is dominated by transposable elemen...

Biodiversity drives the maintenance and stability of ecosystem functioning as well as many of nature’s benefits to people, yet people cause substantial biodiversity change. Despite broad consensus about a positive relationship between biodiversity and ecosystem functioning (BEF), the underlying mechanisms and their context-dependencies are not well...

Plants growing in nature live in association with beneficial, commensal, and pathogenic microbes, which make up the plant microbiota. The close interaction between plants and their microbiotas has raised fundamental questions about plant responses to these microbes and the identity of the main factors driving microbiota structure, diversity, and fu...

As other arbuscular mycorrhizal fungi, Gigaspora margarita contains unculturable endobacteria in its cytoplasm. A cured fungal line has been obtained and demonstrated to be capable of establishing a successful mycorrhizal colonization. However, previous OMICs and physiological analyses have demonstrated that the cured fungus is impaired in some fun...

Due to global warming, the cultivation range of many crops is extending at higher altitudes and latitudes exposing plants to new climatic and environmental conditions, as early spring frosts. To face these issues in a sustainable agriculture context, new innovative technologies, as the use of biostimulants and the manipulation of plant microbiota,...

Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In legumes, they are typically the first cells to become infected by nitrogen-fixing soil bacteria during root nodule symbiosis. Here we report a role for the Cellulose Synthase-Like D1 (CSLD1) gene in root hair de...

Plants rely on their microbiota for improving the nutritional status and environmental stress tolerance. Previous studies mainly focused on bipartite interactions (a plant challenged by a single microbe), while plant responses to multiple microbes have received limited attention. Here, we investigated local and systemic changes induced in wheat by...

As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of...

Arbuscular mycorrhizas (AMs) are the most widespread symbioses between plants and soil fungi. They play such a critical role in the nutrition of both partners that AM fungi cannot complete their life cycle in the absence of a host plant, and the existence of non-mycorrhizal individuals of AM host species is virtually unknown in natural ecosystems....

Zaxinone is an apocarotenoid regulatory metabolite required for normal rice growth and development. In addition, zaxinone has a large application potential in agriculture, due to its growth promoting activity and capability to alleviate infestation by the root parasitic plant Striga through decreasing strigolactone (SL) production. However, zaxinon...

Microbial communities associated to plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive area...

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF) may be effective in enhancing plant resilience to drought, one of the major limiting factors threatening crop productivity. AMF host their own microbiota and previous data demonstrated that endobacteria thriving in Gigaspora margarita modulate fungal antioxidant responses. Here,...

Mycorrhizas are among the most important biological interkingdom interactions, as they involve ~340,000 land plants and ~50,000 taxa of soil fungi. In these mutually beneficial interactions, fungi receive photosynthesis-derived carbon and provide the host plant with mineral nutrients such as phosphorus and nitrogen in exchange. More than 150 years...

RNA-seq is a powerful method for transcriptome profiling that allows the detection of total RNA present in a single cell, tissues, or organs. mRNA-seq is focused on protein-coding RNAs, and results in large datasets of reads, or portion of sequenced mRNA that can be assembled back to the original transcripts to reconstruct a virtual gene catalog. S...

Legumes interact with a wide range of microbes in their root systems, ranging from beneficial symbionts to pathogens. Symbiotic rhizobia and arbuscular mycorrhizal glomeromycetes trigger a so‐called common symbiotic signalling pathway (CSSP), including the induction of nuclear calcium spiking in the root epidermis. By combining gene expression anal...

RNA interference (RNAi) is a key regulatory pathway of gene expression in almost all eukaryotes. This mechanism relies on short non-coding RNA molecules (sRNAs) to recognize in a sequence-specific manner DNA or RNA targets leading to transcriptional or post-transcriptional gene silencing. To date, the fundamental role of sRNAs in the regulation of...

Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In addition, they are typically the first cells infected by nitrogen-fixing soil bacteria during the root nodule symbiosis. Here we report a role for the Cellulose Synthase-Like D1 ( CSLD1 ) gene in root hair devel...

Loss-of-function alleles of MLO (Mildew Resistance Locus O) confer broad-spectrum resistance to foliar infections by powdery mildew pathogens. Like pathogens, microbes that establish mutually beneficial relationships with their plant hosts, trigger the induction of some defense responses. Initially, barley colonization by the root endophyte Serendi...

Many fungi (from micro-to macromycetes) interact with plants as a relevant component of plant microbiota. The aim of the review is to focus on the early diverging fungi (Mucoromycota) whose members establish a wide range of beneficial or pathogenic interactions with their green hosts, depending on their phylogenetic position. While Mortierellomycot...

Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” appro...

Introduction: Arbuscular mycorrhizal (AM) symbiosis between soil fungi and the majority of plants is based on a mutualistic exchange of organic and inorganic nutrients. This takes place inside root cortical cells that harbor an arbuscule: a highly branched intracellular fungal hypha enveloped by an extension of the host cell membrane—the perifungal...

As members of the plant microbiota, Arbuscular Mycorrhizal Fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in th...

Plants utilize hormones and other small molecules to trigger and coordinate their growth and developmental processes, adapt and respond to environmental cues, and communicate with surrounding organisms. Some of these molecules originate from carotenoids that act as universal precursors of bioactive metabolites arising through oxidation of the carot...

Legumes interact with a wide range of microbes in their root system, ranging from beneficial symbionts to pathogens. Symbiotic rhizobia and arbuscular mycorrhizal glomeromycetes trigger a so-called common symbiotic signalling pathway (CSSP), including the induction of nuclear calcium spiking in the root epidermis. In our study, the recognition of a...

The ability of photosynthetic algae to enter the hyphae of a soil fungus could tell us more about the evolution of these species and their potential for applications in the production of biofuel.

Eukaryotes host numerous intracellular and associated microbes in their microbiota. Fungi, the so-called Mycobiota, are important members of both human and plant microbiota. Moreover, members of the plant mycobiota host their own microbiota on their surfaces and inside their hyphae. The microbiota of the mycobiota includes mycorrhizal helper bacter...

Plant cellular responses to endophytic filamentous fungi are scarcely reported, with the majority of described colonization processes in plant-fungal interactions referring to either pathogens or true symbionts. Fusarium solani strain K (FsK) is a root endophyte of Solanum lycopersicum, which protects against root and foliar pathogens. Here, we inv...

Carotenoid cleavage dioxygenases (CCDs) form hormones and signaling molecules. Here we show that a member of an overlooked plant CCD subfamily from rice, that we name Zaxinone Synthase (ZAS), can produce zaxinone, a novel apocarotenoid metabolite in vitro. Loss-of-function mutants (zas) contain less zaxinone, exhibit retarded growth and showed elev...

Despite their importance in establishing mutualistic symbiosis with 72% of land plants, Arbuscular Mycorrhizal Fungi (AMF, Glomeromycotina) are still enigmatic from a biological point of view, since our knowledge on the genetic mechanisms regulating AM symbiosis mostly mirrors a plant-centric point of view. In addition to being members of the plant...

Modifications in cell wall composition, which can be accompanied by changes in its structure, were already reported during plant interactions with other organisms, such as the mycorrhizal fungi. Arbuscular mycorrhizal (AM) fungi are among the most widespread soil organisms that colonize the roots of land plants, where they facilitate mineral nutrie...

Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) an...

Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying context-dependency of mycor...

Strigolactones (SLs), a novel class of plant hormones, are key regulator of plant architecture and mediator of biotic interactions in the rhizosphere. Root-released SLs initiate the establishment of arbuscular mycorrhizal (AM) symbiosis by inducing spore germination and hyphal branching in AM fungi (AMF). However, these compounds also trigger the g...

More than 400 million years ago, before plants had leaves and roots, they had established intimate relationships with fungi. Fungi at that time may already have been key ecosystem players that recycled carbon, solubilized and redistributed minerals, and colonized plants and other organisms. We will assess fossil and phylogenetic evidence for the ki...

Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associatio...

Metabolomic profiling is becoming an increasingly important technique in the larger field of systems biology by allowing the simultaneous measurement of thousands of small molecules participating in and resulting from cellular reactions. In this way, metabolomics presents an opportunity to observe the physiological state of a system, which may prov...

Our knowledge of mycorrhizas dates back to at least 150 years ago, when the plant pathologists A. B. Frank and G. Gibelli described the surprisingly morphology of forest tree roots surrounded by a fungal mantle. Compared with this history, our molecular study of mycorrhizas remains a young science. To trace the history of mycorrhizal research, from...

Motivation Arbuscular mycorrhizal fungi (AMF) are important members of the plant micro- biota, being associated with the roots of 80% of land plants. As obligate symbionts, they are able to enhance their host’s fitness by improving mineral nutrition. AMF have their own microbiota, too (Desiro et al, 2014), since some of them possess un- cultivable...

Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mi...

Plants live in ecosystems where they interact with complex microbial communities instigating a wide range of relationships. These communities constitute the ‘microbiota’, a term initially coined to describe host-symbiont systems that has been extended to cover non-symbiotic, but mostly beneficial interactions. Through the development of innovative...

An increasing number of studies have investigated soil microbial biodiversity. However, the mechanisms regulating plant responses to soil microbiota are largely unknown. A previous work tested the hypothesis that tomato plants grown on native soils with their complex microbiotas respond differently from tomato growing in a sterile substrate. Two so...

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families are engaged in complex interactions that lead to critical behavioural shifts of the microorgani...

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato ( Solanum lycopersicum ), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics,...

Arbuscular Mycorrhizal Fungi (AMF) are key components of the plant microbiota. AMF genetic complexity is increased by the presence of endobacteria, which live inside many species. A further component of such complexity is the virome associated to AMF, whose knowledge is still very limited. Here, by exploiting transcriptomic data we describe the vir...

Strigolactones (SLs) first evolved as regulators of simple developmental processes in very ancient plant lineages, and then assumed new roles to sustain the increasing biological complexity of land plants. Their versatility is also shown by the fact that during evolution they have been exploited, once released in the rhizosphere, as a communication...

Arbuscular mycorrhizal (AM) fungi experience oxidative stress during the plant–fungal interaction, due to endogenous reactive oxygen species (ROS) produced by fungal metabolism and exogenous ROS produced by plant cells. Here, we examine the responses to H2O2 in Gigaspora margarita, an AM fungus containing the endobacterial symbiont Candidatus Glome...

ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared...

As very ancient and widespread in nature, arbuscular mycorrhizal fungi (AMF) are key com-ponents of the plant microbiota. Recent publication of genomic and transcriptomic data shed light on the biology and evolution of AMF. The genetic complexity of AMF is increased by the presence of endobacteria which live inside many AMF1. A further component of...

As obligate biotrophs colonizing the roots of most land plants, arbuscular mycorrhizal fungi (AMF) are crucial members of the rhizosphere microbiota, being able to increase plant fitness through mineral nutrition.Some AMF species are at the center of a network which involves plants, fungi and bacteria, since they possess obligate endobacteria insid...

Grapevine, cultivated for both fruit and beverage production, represents one of the most economically important fruit crops worldwide. With the aim of better understanding how grape roots respond to beneficial microbes, a transcriptome sequencing experiment has been performed to evaluate the impact of a single arbuscular mycorrhizal (AM) fungal spe...

Arbuscular mycorrhizal fungi (AMF) are widespread root symbionts that perform important ecological services, such as improving plant nutrient and water acquisition. Some AMF from the Gigasporaceae family host a population of endobacteria, Candidatus Glomeribacter gigasporarum (Cagg). The analysis of the Cagg genome identified six putative toxin-ant...

Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endo...

Arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are symbionts of most terrestrial plants. They commonly harbour endobacteria of a largely unknown biology, referred to as MRE (Mollicutes/mycoplasma-related endobacteria). Here, we propose to accommodate MRE in the novel genus 'Candidatus Moeniiplasma.' Phylogeny reconstructions based on the...

The symbiosis established with arbuscular mycorrhizal (AM) fungi is one of the main and long-lasting strategies that plants have adopted to improve their nutrient uptake capacities. Carbon for mineral exchange between the two symbionts is regulated by the activities of fine-tuned plant and fungal transporter genes, some of which have been described...

The Mutualistic Interaction between Plants and Arbuscular Mycorrhizal Fungi, Page 1 of 2 Abstract Mycorrhizal fungi belong to several taxa and develop mutualistic symbiotic associations with over 90% of all plant species, from liverworts to angiosperms. While descriptive approaches have dominated the initial studies of these fascinating symbioses...

Arbuscular mycorrhizal fungi form a homogeneous group of soil fungi that are found in most terrestrial ecosystems. Glomeromycota are estimated to form symbiotic associations with about 80% of plants, from liverworts and ferns to gymnosperms and angiosperms. This ecological success is the result of the major selective advantages that arbuscular myco...

The majority of terrestrial vascular plants are capable of forming mutualistic associations with obligate biotrophic arbuscular mycorrhizal (AM) fungi from the phylum Glomeromycota. This mutualistic symbiosis provides the fungus with fixed carbohydrates, and reciprocally improves plant phosphate (Pi) uptake. AM fungal transporters can acquire Pi fr...

Main conclusion: A combined approach, using a carbohydrate microarray as a support for genomic data, has revealed subtle plant cell-wall remodelling during Tuber melanosporum and Corylus avellana interaction. Cell walls are involved, to a great extent, in mediating plant-microbe interactions. An important feature of these interactions concerns cha...

Functional divergence of paralogs following gene duplication is one of the mechanisms leading to evolution of novel pathways and traits. Here we show that divergence of Lys11 and Nfr5 LysM receptor kinase paralogs of Lotus japonicus has affected their specificity for lipochitooligosaccharides (LCOs) decorations, while the innate capacity to recogni...

Main conclusion: Systemic responses to an arbuscular mycorrhizal fungus reveal opposite phenological patterns in two tomato ripening mutants depending whether ethylene or light reception is involved. The availability of tomato ripening mutants has revealed many aspects of the genetics behind fleshy fruit ripening, plant hormones and light signal r...

As obligate biotrophs that colonize the roots of most land plants, arbuscular mycorrhizal fungi (AMF) are important members of the plant microbiota, since they are able to enhance host's nutrient acquisition. Some AMF possess endobacteria inside their cytoplasm, giving rise to a special type of endosymbiosis. Bacterial genome sequencing revealed a...

For some truffle species of the Tuber genus, the symbiotic phase is often associated with the presence of an area of scant vegetation, commonly known as the brûlé, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brûlé of a Tuber melanosporum truffle-ground, but the molecular mech...

Bacterial endosymbionts are critical to the existence of many eukaryotes. Among them, vertically transmitted endobacteria are uniquely typified by reduced genomes and molecular evolution rate acceleration relative to free-living taxa. These patterns are attributable to genetic drift-dominated degenerative processes associated with reproductive depe...

The Gram-negative bacterium Candidatus Glomeribacter gigasporarum is an obligate endobacterium living inside the cytoplasm of the arbuscular mycorrhizal fungus Gigaspora margarita. We sequenced its genome, leading to a 1.8-Mb final assembly. Phylogenetic analyses placed Ca. G. gigasporarum among Burkholderiaceae, whereas metabolic network analyses...