In the current context of climate change, there is a need to develop more sustainable agrifood strategies. As an alternative to the intensive use of chemically synthesized fertilizers and pesticides that pollute water and impact biodiversity, there is a growing interest in using beneficial microbes as biostimulants and/or bioprotection agents. However, their implementation in agriculture remains a challenge due to highly variable outcomes and benefits. Furthermore, there are major knowledge gaps about the molecular mechanisms that regulate different plant–microbe interactions. In the present review, we summarize current knowledge on the molecular mechanisms that control different beneficial plant root–microbe interactions; namely, arbuscular mycorrhiza, the rhizobium–legume symbiosis, ectomycorrhiza, and fungal and bacterial endophytic associations. This includes the signaling pathways required for recognition of microbes as beneficial, the metabolic pathways that provide nutritional benefits to the plant, and the regulatory pathways that modulate the extent of symbiosis establishment depending on soil nutrient availability and plant needs. Our aim is to highlight the main common mechanisms, as well as knowledge gaps, in order to promote the use of microbes, either individually or in consortia, within the framework of a sustainable agriculture that is less dependent on chemicals and more protective of biodiversity and water resources.

Background and aims
Mycorrhizal (AMF) benefits to ancient tetraploid and hexaploid wheats, particularly under saline conditions, are not sufficiently known.

Methods
A two-year field experiment and a pot experiment were carried out, where the field experiment encompassed non-saline and saline (120 mM NaCl) irrigation, presence and absence of AMF (Funneliformis mosseae) inoculation, and 10 wheat genotypes. The pot experiment encompassed four salinities (0, 40, 80, and 120 mM) and two levels of AMF inoculation (with and without of AMF inoculation) and 11 genotypes.

Results
Salinity suppressed the chlorophyll, carotenoids, K, and P, grains/m2, grain yield, harvest index, and dry mass. Though, it boosted the activities of antioxidative enzymes, Na, electrolyte leakage, Na/K, protein, wet gluten, and gluten index. Inoculation to AMF led to enhancement in the maximum quantum efficiency of photosystem II, chlorophyll, K, P, N, and total phenolic compounds concentrations, the activities of antioxidative enzymes, grains/m2, grain yield, dry mass, protein, wet gluten, and gluten index, while decreasing the Na concentration, Na/K, and electrolyte leakage, particularly in the salt-stricken plants; favorable responses to the AMF were more appreciable in the salt-stricken modern wheats, than the ancient emmer and spelt wheats.

Conclusion
Salinity and AMF exerted contrasting effects on physiological, growth, dry mass, and grain yield attributes of different genotypes, with a tendency of salt-induced suppressions and AMF-induced enhancements to be less notable in the ancient wheats, than the modern bread and durum wheats. Though, salinity and AMF inoculation shared a same trend in improving the grain and flour quality attributes.

Drought-induced stress is a significant constraint for crop yields in semi-arid and arid areas.
Yield assessments under water stress indicate that mycorrhizae can alleviate the detrimental impacts of drought, placing them as sustainable options for agricultural practices in affected areas. Thus, we executed a two-year study to examine the effects of root colonization by two AMF species (Diversispora epigaea and Diversispora versiformis) under different drought stress conditions, assessing maize morpho-physiological and biochemical characteristics, nutrient absorption, yield components, oil percentage, and irrigation water efficiency. The research was conducted in a desolate region of Pakistan during the 2023 and 2024 growing seasons. Drought-induced stress was generated at two levels by irrigating after 80 % and 60 % water loss, categorized as severe and mild drought stress. Irrigation after a 40 % reduction in water was considered normal (without stress). The findings demonstrated that regardless of AMF species and level of drought stress, inoculated plants yielded heavier seeds, higher dry matter, chlorophyll (37 %) and carotenoids (41 %), phytohormone (27 %), enhanced oil yields (32 %) and seeds (24.2 %) compared to uninoculated plants. Notably, the maize seed yields of Diversispora epigaea-treated plants under every irrigation treatment surpassed those of Diversispora versiformis inoculated plants and uninoculated plants. Drought stress reduced nitrogen levels in seeds and leaves, whereas AMF enhanced nitrogen levels, particularly when crops were treated with Diversispora epigaea. Moreover, seed phosphorus percentages were not influenced by AMF in 2023. Conversely, the highest phosphorus percentages in seeds and leaves were recorded in crops inoculated with Diversispora epigaea in 2023. Our findings indicate that Diversispora epigaea exhibits greater efficiency under water stress and provides superior support to maize plants.

•Glomalin is widely used as a soil health and mycorrhizal fungi indicator.
•The extraction method raises concerns about its specificity to mycorrhizal fungi.
•Glomalin content correlates with plant litter decomposition and added organic matter.
•High-temperature citrate extracts include diverse compounds, not just glomalin.
•Glomalin is unsuitable for standardized measurements of mycorrhizal fungi.

Climate change, a major threat to global food security, has been accelerated by increasing atmospheric CO2 levels over the last two centuries. Numerous studies indicate that high atmospheric CO2 (eCO2) enhances carbon (C) sequestration in plant biomass, potentially aiding in its mitigation. Plant root characteristics are critical regulators of underground C inputs, soil nutrient acquisition, and water uptake. Roots directly interface with soil, while shoots perceive atmospheric CO2 via β-carbonic anhydrase, triggering systemic signals, such as hormone pathways, that influence root functions, including strigolactone secretion and mycorrhizal colonization. Recent research has begun to elucidate how eCO2 influences root morphology, root system expansion, and overall root functionality, including increased root:shoot ratios, respiration rates, rhizodeposition, and fungal colonization. This review aims to synthesize the current understanding of eCO2 effects on plant roots, with a particular focus on arbuscular mycorrhizal (AM) symbiosis. We highlight novel findings regarding the interactions between eCO2 and plant hormones, which play a crucial role in the systemic regulation of AM symbiosis. Finally, we outline potential future research directions that could enhance crop resilience to climate change, emphasizing the importance of integrating root biology and mycorrhizal interactions in sustainable agricultural practices.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in promoting plant health. They assist plants in absorbing nutrients and enhance their resistance to diseases and environmental stressors. In contrast, plant-parasitic nematodes (PPNs) pose a significant threat to global crop production. Both AMF and PPNs inhabit the soil surrounding plant roots, yet their interactions are not fully understood. They may compete directly or influence plants in indirect ways. This review examines the relationship between AMF and PPNs, emphasizing their interactions and suggesting that AMF could serve as a natural method to control PPN populations. Unlike previous studies that have focused on these organisms separately, this review integrates insights on the impact of AMF and nematode interactions on plants through nutrient availability, spatial competition, and rhizosphere dynamics. Additionally, it explores the mechanisms of systemic resistance that AMF may provide against nematodes, creating a comprehensive framework for future research and sustainable agriculture.

Central to the legume–rhizobium symbiosis is the formation of organelle-like symbiosomes where nitrogen-fixing bacteroids are enclosed by a host-derived symbiosome membrane. This creates the symbiosome space, which topologically resembles an apoplastic compartment within the cell. While the apoplast of plant cells is largely occupied by the cell wall, symbiosomes are devoid of cell wall polymers. Here, we describe a mechanism that functions to protect and maintain effective nitrogen fixation through the action of cell-wall-degrading enzymes that prevent accumulation of un-esterified pectin within symbiosomes. We identify two symbiotically-induced polygalacturonase (PG) genes in Medicago truncatula, SyPG1 and SyPG2, that are secreted into the symbiosome space. Silencing the expression of SyPG1/2 or editing SyPG1/2 via CRISPR-Cas9 both lead to nodule senescence and trigger excessive accumulation of un-esterified pectin in symbiosome containing cells. Additionally, we show that un-esterified pectins inhibit rhizobial growth both in vivo and in vitro. Together, our results provide evidence for a host-controlled cell wall clearance mechanism that is essential for symbiosome maintenance.

Soil, the Earth's upper crust layer, is crucial for ecological processes, comprising mineral, organic, and biological components that determine fertility and multifuncionality. Human-induced degradation necessitates advancements in pedology and soil conservation. The rhizosphere, surrounding plant roots, houses a diverse microbial community, notably bacteria, which enhance plant growth and disease resistance. Root exudates fuel biological activity and nutrient cycling, supporting microbial growth, improving soil structure, and reducing plant stress. Plant-microorganism interactions in ecological and agricultural systems play a vital role for maintaining primary production and ecosystem sustainability. Moreover, arbuscular mycorrhizae and nitrogen-fixing bacteria are essential, influencing plant development, sustainability, and ecosystem health. Specific bacterial phyla populate the rhizosphere and endosphere, with Plant Growth-Promoting Rhizobacteria (PGPR), such as Pseudomonas spp. and Bacillus spp., playing a prominent role. PGPR employ direct and indirect mechanisms, including phytohormone production, mineral solubilization, systemic resistance induction, antibiosis, competition for resources, and ACC deaminase activity, The amalgamation of these traits underscores the conceptual foundation for comprehending the ecological and agricultural implications of employing microbes. This inquiry is particularly relevant to sustainable agriculture, where the use of microbes, including PGPR, plays a crucial role in biofertilization and mitigating environmental stressors. Thus, investigating the ecological and agricultural implications through multi-omics approaches such as genomics, transcriptomics, proteomics, and metabolomics offers valuable insights. The integration of these multi-omics data provides a comprehensive framework for understanding the complex interactions between plants, bacteria, and fungi. This holistic perspective not only deepens our understanding of soil ecology but also lays the groundwork for informed and sustainable agricultural practices, fostering resilience against environmental stresses.

Microbiota-mediated nutrient turnover in the rhizosphere determines nutrient bioavailability, thereby enhancing nutrient uptake, utilization, and ultimately crop productivity. Consequently, elucidating the functional core microbiota in rhizosphere nutrient turnover is of critical importance. In this study, we leveraged soybean germplasm core collections to investigate the tripartite relationship among host genotype, core microbiota and nutrient availability, with a focus on delineating the pivotal role of core microbiota in nutrient turnover. Our results suggest that phylogenetic variation significantly shape root-associated microbial communities and rhizosphere nutrient availability, explaining 11.75 % and 2.07 % of total variances, respectively. Core microbiota analysis identified 29 phylogenetic conserved core amplicon sequence variants (ASVs), the majority of which exhibited significant correlated with nutrient availability. Notably, three key core ASVs—ASV13, ASV14 and ASV12, positively correlated with alkali-hydrolyzed nitrogen, available phosphorus, and soil organic matter, respectively. These taxa were subsequently incorporated into a Bradyrhizobium-based synthetic bacterial community (SynCom) to validate their functional roles. Further experiments confirmed that core microbiota-driven nutrient turnover directly facilitates host plant, as evidenced by SynCom inoculation assays. Collectively, this study establishes that phylogenetically conserved core microbiota critically regulate nutrient turnover and acquisition efficiency in the rhizosphere. These insights advance our understanding the ecological function of core microbiota in the rhizosphere and provide a framework for harnessing the beneficial traits in sustainable agriculture.

Transmission electron microscopy was the key for revealing structural similarities between intracellular plant-microbe interactions.

Crop rotation enhances agroecosystem sustainability by reducing nutrient loss, improving soil fertility, and decreasing crop evapotranspiration. Arbuscular mycorrhizal fungi (AMF) inoculation further supports enhanced nutrient and water uptake by plants, potentially improving water use efficiency and soil health while reducing fertigation needs. However, crop species may respond differently to AMF inoculation under varying fertigation regimes. In this study, the response of four horticultural species to AMF inoculation was investigated under optimal (100 %) and deficit (25 % reduction) water and fertilizer (fertigation) availability. Leek, courgette, white bean, and celery were planted consecutively over the course of two years, with crop production and quality as well as leaf nutrients and soil parameters being measured at the end of each crop cycle. Mycorrhizal inoculation did not improve any agronomic parameter among the crops studied under either fertigation condition.

The symbiotic nitrogen fixation process between legume roots and rhizobia initiates at the root hairs. Rhizobia initially colonize the tip of the root hairs and induce its curling to become entrapped. However, the specific molecular mechanisms underlying root hair deformation and curling in response to rhizobial infection remain unclear. In this study, transcriptome analysis of wild-type JiMa389 and nodulation-deficient mutant jima61 of Melilotus albus, the Rho-like small GTPase MaROP10. Our results show that MaROP10 functions as an interacts with the Nod factor receptor NFR5 to regulate rhizobia-induced root hair deformation and infection thread formation during the early stages of rhizobial infection. To elucidate the mechanism of MaROP10, we further identified its downstream potential effector protein, MaRIC6, which positively regulates root hair deformation and infection thread formation. Taken together, MaROP10 likely integrates signals from the symbiotic receptor NFR5 to regulate downstream signaling pathways through its effector MaRIC6, thereby coordinating root hair deformation and infection thread development during the early stages of rhizobial infection.

Legume Nod Factor Receptors (NFRs) are LysM-Receptor-Like Kinases (LysM-RLKs) that initiate host nodulation signaling upon perception of Nod Factors produced by rhizobia. Structural and functional characterization of NFRs from the model legumes Medicago truncatula and Lotus japonicus have unravelled crucial domains/motifs that are indispensable for nodulation signaling. Due to a partial homology of NFRs with that of LysM-RLKs in cereals, the identified domains/motifs have helped in the engineering of these receptors in non-nodulating crop plants like barley.