Plant-Microbe Symbiosis

Crops are increasingly exposed to drought and nutrient deficiencies, necessitating enhanced resistance to adverse conditions to meet the growing demands of the global population. While crop productivity has been greatly improved by integrating traits for high yield and stress tolerance through breeding, yield plateaus are now being observed. The rhizosheath, with physical and biological properties distinct from bulk soil, presents a promising target for enhanced tolerance to abiotic stresses such as drought and nutrient deficiencies. This multifunctional region contributes substantially to stress resistance and nutrient cycling, playing a pivotal role in the context of climate change and diminishing supplies of non-renewable fertilisers. We highlight the potential of the rhizosheath as a valuable breeding target to enhance crop productivity under diverse challenging environmental conditions.

Fungi are one of the most diverse and ecologically important groups of organisms on Earth. They exhibit remarkable diversity in their ecological roles, ranging from decomposers to mutualistic symbionts to parasites. They have a wide array of lifestyles, which reflect their diverse ecological roles and evolutionary adaptations to marine, aquatic, and terrestrial ecosystems. Fungi are osmotrophs that grow as filaments of cells (hyphae) into their food, secrete digestive enzymes across their cells’ chitinous walls, and absorb dissolved nutrients. The classification of fungal lifestyles is primarily based on how they obtain nutrients, with the major modes of nutrition being saprotrophy, parasitism, mutualism and commensalism. Here, we briefly explore these various lifestyles, illustrating their significance in ecosystems and their relationships with other organisms, and then discuss how comparative genomics provides novel insights into their evolutionary trajectories.

Arbuscular mycorrhizal (AM) fungi are ancient plant mutualists that are ubiquitous across terrestrial ecosystems. These fungi are unique among most eukaryotes because they form multinucleate, open-pipe mycelial networks, where nutrients, organelles, and chemical signals move bidirectionally across a continuous cytoplasm. AM fungi play a crucial role in ecosystem functioning by supporting plant growth, mediating ecosystem diversity, and contributing to carbon cycling. It is estimated that plant communities allocate ∼3.93 Gt CO2e to AM fungi every year, much of which is stored as lipids inside the fungal network. Despite their ecological significance, the cellular biology of AM fungi remains underexplored. Here, we synthesise the current knowledge on AM fungal cellular structure and organisation. We examine AM fungal development at different biological levels — the hypha and its content, hyphal networks and AM fungal spores — and explore key cellular dynamics. This includes cell wall composition, cytoplasmic contents, nuclear and lipid organisation and dynamics, network architecture, and connectivity. We highlight how their unique cellular arrangement enables complex cytoplasmic flow and nutrient exchange processes across their open-pipe mycelial networks. We discuss how both established and novel techniques, including microscopy, culturing, and high-throughput image analysis, are helping to resolve previously unknown aspects of AM fungal biology. By comparing these insights with established knowledge in other, well-studied filamentous fungi, we identify critical knowledge gaps and propose questions for future research to further our understanding of fundamental AM fungal cell biology and its contributions to ecosystem health.

Symbiotic nitrogen fixation represents a crucial yet energy-demanding strategy for legumes to survive in nutrient-poor soils. We highlight the multifaceted roles of NSP1 and NSP2 in this symbiosis and propose their function as ‘nutrient-responsive regulators’, integrating environmental signals, physiological status, and nutrient availability, to ensure nodulation occurs only under favorable conditions.

Root nodule symbiosis allows for plant acquisition of reactive nitrogen through fixation of atmospheric molecular dinitrogen by nitrogen-fixing bacteria. Nodulation is a complex trait, with diverse modes of bacterial infection and nodule morphologies across species, reflecting evolutionary adaptation. Understanding ancient forms of this trait may carry advantages for its current utilization, since basal states likely reflect the least complexity. In this review we focus on the evolution of nodule development, particularly on events that have led to increased complexity of this symbiosis in later adaptations. We hypothesize that the ancestral form of nodulation comprises of an evolutionary coupling of nutrient-dependent lateral root development with apoplastic intercellular bacterial growth, alongside the acquisition or evolution of an ancestral chitinaceous signaling molecule by the microbial symbiont. Uncovering the evolutionary adaptations underpinning the extant diversity of this trait allows for a better understanding of the simplest ancestral state.

Arbuscular mycorrhiza (AM) with soilborne Glomeromycota fungi was pivotal in the conquest of land by plants almost half a billion years ago. In flowering plants, it is hypothesized that AM is initiated by the perception of AM fungi-derived chito- and lipochito-oligosaccharides (COs/LCOs) in the host via Lysin Motif Receptor-Like Kinases (LysM-RLKs). However, it remains uncertain whether plant perception of these molecules is a prerequisite for AM establishment and for its origin. Here, we made use of the reduced LysM-RLK complement present in the liverwort Marchantia paleacea to assess the conservation of the role played by this class of receptors during AM and in CO/LCO perception. Our reverse genetic approach demonstrates the critical function of a single LysM-RLK, MpaLYKa, in AM formation, thereby supporting an ancestral function for this receptor in symbiosis. Binding studies, cytosolic calcium variation recordings and genome-wide transcriptomics indicate that another LysM-RLK of M. paleacea, MpaLYR, is also required for triggering a response to COs and tested LCOs, despite being dispensable for AM formation. Collectively, our results demonstrate that the perception of symbionts by LysM-RLK is an ancestral feature in land plants, and suggest the existence of yet-uncharacterized AM fungi signals.

The environmental release of both engineered and non-engineered organisms for Biotechnologies Beyond Conventional Containment (BBCC) offers unique solutions to pressing global challenges, including the prevention of soil degradation, the attenuation of nitrogen pollution, the replacement of harmful pesticides and herbicides, the remediation of anthropogenic contaminants and ‘forever chemicals’ mitigation. An evaluation of impacts, both positive and negative, rather than arbitrary prohibitions, is crucial for advancing the responsible use of organisms intentionally released into the environment. The history of biological interventions demonstrates that organisms have successfully contributed to agriculture, pollution remediation, ecosystem restoration, waste upcycling, and pest control, yet their full potential remains constrained by regulatory hurdles that do not fully account for modern scientific advancements. At the same time, some releases serve as cautionary tales, having caused harm due to a lack of regulation and monitoring. Unlike chemicals released to the environment, organisms — particularly those designed or selected for specific functions — can be managed with built-in safeguards, ranging from physical and genetic containment strategies to controlled ecological interactions to mitigate risks while maximizing benefits. Advancements in precision engineering, computational modeling, and real-time monitoring technologies now allow for unprecedented accuracy in tracking, assessing, and controlling the environmental impact of released organisms — capabilities inaccessible when recombinant DNA technology first emerged 50 years ago. Many regulatory structures were developed decades before today’s explosion of biological knowledge and insight was even imaginable. This resulted in our current policies that have become restrictive, limiting the deployment of innovative and promising biological solutions. A new approach to risk analysis is now needed that accounts for changes in science, and in society, which assesses the environmental release of natural, evolved, and engineered organisms based on their functions rather than their origin or how they were developed. By modernizing these frameworks to emphasize continuous assessment, real-world data collection, and adaptive risk assessment and management, stakeholders can create a regulatory pathway for the sustainable, responsible, and evidence-based integration of environmental biological technologies.

While intracellular symbiosis with rhizobia relies on Nod factor signaling through the conserved common symbiosis signaling pathway (CSSP), it remains unclear how legumes simultaneously manage interactions with commensal soil microbes. Using single cell RNA-sequencing, we show that commensal soil bacteria induce a Nod factor-independent transcriptional response in specific root hairs. This response is similar to the rhizobium response in the CSSP-deficient cyclops mutant, which is unable to accommodate rhizobia in root hair infection threads. Both responses include the nodulation gene NSP2 and a transcription factor, which we name ROOT HAIR DEFECTIVE 6 LIKE A (RHD6LA). We show that RHD6LA is required for facilitating infection thread formation in response to rhizobia and for preventing exaggerated root hair responses to commensal soil bacteria. The overlap between commensal and symbiotic signaling highlights the complexity of legume-microbe interactions at the root hair interface and suggests new mechanisms for microbial discrimination in rhizobium-responsive root hairs.

Unraveling the mechanisms underlying the maintenance of species diversity is a central pursuit in ecology. It has been hypothesized that ectomycorrhizal (EcM) in contrast to arbuscular mycorrhizal fungi can reduce tree species diversity in local communities, which remains to be tested at the global scale. To address this gap, we analyzed global forest inventory data and revealed that the relationship between tree species richness and EcM tree proportion varied along environmental gradients. Specifically, the relationship is more negative at low latitudes and in moist conditions but is unimodal at high latitudes and in arid conditions. The negative association of EcM tree proportion on species diversity at low latitudes and in humid conditions is likely due to more negative plant-soil microbial interactions in these regions. These findings extend our knowledge on the mechanisms shaping global patterns in plant species diversity from a belowground view.

Globally, invasive plants, animals, and microbes are a dominant threat to biodiversity and ecosystems, inflicting over $1 trillion USD in damage annually. Hundreds of microbial invasive taxa are documented.
Currently, we are inoculating microbes into many environments in enormous numbers to fertilize agricultural soils, remediate contamination, control eutrophication, precipitate minerals, and restore ecosystem functions.
Given the astronomical numbers and myriad environments that are being inoculated with microbes, these manipulations risk creating microbial invasions in much the same way that catastrophic plant and animal invasions have been precipitated by intentional introductions by humans.
A mechanistic understanding and predictive framework for the potential for microbial inoculants to cause invasions is needed to balance their benefits with their risks of causing harmful effects.

Breakthroughs in DNA sequencing have upended our understanding of fungal diversity. Only ∼155,000 of the 2–3 million fungal species on the planet have been formally described and named, and ‘dark taxa’ — species known only from sequences — represent the vast majority of species within the fungal kingdom. The International Code of Nomenclature requires physical type specimens to officially recognize new fungal species, making it difficult to name dark taxa. This is a significant problem for conservation because, without names, species cannot be recognized for environmental and legal protection. Symbiotic ectomycorrhizal (EcM) fungi play a particularly important role in forest carbon drawdown, but at present we have little understanding of how many EcM fungal species exist, or where to prioritize research activities to survey and describe EcM fungal lineages. In this review, we use global soil metabarcoding databases (GlobalFungi and the Global Soil Mycobiome consortium) to evaluate current estimates of the total number of EcM fungal species on Earth, outline the current state of undescribed EcM dark taxa, and identify priority regions for future dark taxa exploration. The metabarcoding databases include up to 219,730 EcM fungal operational taxonomic units (OTUs) detected from almost 39,500 samples. Using Chao richness estimates corrected for extrapolating species numbers from metabarcoding datasets, we predict that the global diversity of EcM fungi could be ∼25,500–55,500 species. Dark taxa — those that do not match species-level identities — account for 79–83% of OTUs. Oceania contains the highest percentage of dark taxa (87%), and Europe the lowest (78%). Priority ‘darkspots’ for future research occur predominantly in tropical regions, but also in selected temperate forests at both southern and northern latitudes. We propose concrete steps to reduce the prevalence of EcM darkspots, including performing targeted field surveys, barcoding fungaria voucher specimens, and developing new ways to describe and conserve fungal taxa from DNA alone.

Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars—Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.

Many plants and animals, including humans, host diverse communities of microbes that provide many benefits. A key challenge in understanding microbiomes is that the species composition often differs among individuals, which can thwart generalization. Here, we argue that the key to identifying general principles for microbiome science lies in microbial metabolism. In the human microbiome and in other systems, every microbial species must find ways to harvest nutrients to thrive. The available nutrients in a microbiome interact with microbial metabolism to define which species have the potential to persist in a host. The resulting nutrient competition shapes other mechanisms, including bacterial warfare and cross-feeding, to define microbiome composition and properties. We discuss impacts on ecological stability, colonization resistance, nutrient provision for the host, and evolution. A focus on the metabolic ecology of microbiomes offers a powerful way to understand and engineer microbiomes in health, agriculture, and the environment.

Understanding the molecular basis of regulated nitrogen (N2) fixation is essential for engineering N2-fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system NifL-NifA controls the expression of nif genes that encode the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. Whilst genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-EM map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

The objective of this study was to characterize the arbuscular mycorrhizal fungi (AMF) community associated with local varieties of Pinot noir, Sauvignon blanc, and Chardonnay grown in the Malleco and Cautín valleys, in La Araucanía region, Chile. The research attempted to answer the following question: How do soil and climatic conditions, as well as cultivar characteristics could influence root colonization, spore abundance, and AMF composition in vineyards in this emerging region? Rhizosphere samples were collected from two locations and six grapevine cultivars. Root colonization rates and AMF spore abundance were measured, and the spores present were morphologically identified. In addition, differences in the AMF community were evaluated regarding cultivar and plant age. The results showed root colonization rates higher than 50%, with no significant differences between sites. However, variations in spore abundance and AMF community composition were observed among cultivars. Twelve AMF genera were identified, including Glomus, Sclerocystis, Dominikia, Rhizoglomus, Oehlia, and Paraglomus. Overall, Glomus rubiforme, Sclerocystis sp. CL1, Rhizoglomus irregulare, and Diversispora versiformis were the most abundant morphotypes. Additionally, R. irregulare, G. rubiforme, and Paraglomus occultum were consistently detected across nearly all analyzed rhizospheres. The presence of AMF genera varies according to cultivar, but not according to clones or plant age. It is hypothesized that differences in root architecture and root exudates of different grapevine cultivars are responsible for the observed variations in the composition of native AMF. These factors should be further investigated in future studies.