The state of food security is achieved if no one has to worry whether or how they can acquire—typically purchase—healthy and nutritious meals. In theory, food security could be addressed from two sides: increasing households’ purchasing power or lowering food prices. However, in practice, food insecurity is a by-product of prevailing political and economic systems. Agriculture produces more calories and nutrients than needed to feed humanity, so it is fundamentally an issue of distributive justice, where geography, education, ethnicity, gender, and other mechanisms of marginalization determine one’s food security—through access to wealth. Yet humanity has failed to eliminate poverty and instead of addressing socioeconomic causes of food insecurity, agricultural research and practice are called upon to compensate. This is not only unfair but bound to fail. It also diverts muchneeded scientific capacity from the long list of sustainability challenges that agricultural production systems must address.

The widespread use of plant protection products (PPPs) may lead to soil contamination, potentially compromising the symbiotic integrity of arbuscular mycorrhizal fungi (AMF) in agricultural systems. However, the effects of PPPs on AMF are underexplored due to the absence of standardized methodology for ecotoxicological assessments. The objective of this study was to introduce an in vivo method for assessing the effects of PPP pollutants on the AMF symbiotic phase and to evaluate the suitability of this method as an intermediate-tier protocol in risk assessment frameworks. Four tests were conducted using combinations of: (1) Gigaspora albida + Glycine max; (2) G. albida + Urochloa brizantha; (3) Rhizophagus clarus + G. max; (4) R. clarus + U. brizantha). All assays were performed in tropical artificial soil (TAS) under a gradient of chlorothalonil concentrations (0, 12, 18, 24, 36, 48, and 72 mg a.i. kg⁻1). The evaluated endpoints included total root colonization, percentage of arbuscules colonization, total extraradical mycelial length (ERM), and spore number. All endpoints were sensitive to the presence of PPPs in TAS, with mycorrhizal colonization and ERM being the most sensitive, meeting the validity criteria (CV < 30%). The Inhibitory concentration (IC50) values for all endpoints were higher than the predicted environmental concentrations (PECs). Therefore, this method can be considered suitable as an intermediate-tier protocol, as it exhibits key characteristics of a standardized approach and can be applied to ecotoxicological studies involving other potentially contaminating PPPs, as well as additional classes of environmental contaminants.

Colonization of plant roots by symbionts requires substantial morphodynamic reorganization. Examples are actin-scaffolded microcompartments called infection pockets formed during root nodule symbiosis (RNS) by legumes. We demonstrate that the actin-binding formin SYFO2 is indispensable for rhizobial infection in Medicago truncatula, where it drives actin polymerization in phase-separated and symbiosis-specific nanodomains. SYFO2 also regulates symbiotically active arbuscules formed during mycorrhizal symbiosis in plants outside the nodulating clade, indicating that it was additionally recruited to promote rhizobial infections in legumes. As part of our aim to enable nitrogen fixation in nonlegumes, we activated endogenous SYFO2 by stably introducing the RNS master regulator NODULE INCEPTION (NIN) into the natural nonhost tomato. This demonstrates the possibility of recruiting arbuscular mycorrhizae–related genes into an engineered nodulation-specific pathway.

This study aimed to isolate and characterize nitrogen-fixing bacteria from the maize rhizosphere and evaluate their plant growth-promoting potential to reduce reliance on synthetic fertilizers and enhance soil fertility. Nitrogen-free selective media were used for bacterial isolation, followed by detection of the nifH gene and nitrogenase activity. Phylogenetic identification was conducted via 16S rRNA sequencing. Growth-promoting traits, stress tolerance, and pot-based plant inoculation effects were assessed. Genetic modification of strain GN8811 was performed to improve nitrogen fixation and growth promotion. Seven isolates possessed the nifH gene and nitrogenase activity, including Azotobacter chroococcum GN2001, A. vinelandii GN1202, Azospirillum brasilense GN1004, Kosakonia sacchari GN2003, Klebsiella michiganensis GN8799 and GN8801, and K. quasivariicola GN8811. Furthermore, GN8801 and GN2001 exhibited phosphate solubilization and iron chelation, while GN1004 and GN8811 showed strong IAA production and potassium solubilization. Additionally, GN2003 and GN8811 tolerated high salinity and variable pH. Maize inoculated with GN8811 showed biomass and root enhancement comparable to nitrogen-fertilized controls. The genetically modified GN8811 strain (ΔnifL::nifA) exhibited further improvement in ni-trogen fixation and plant growth, maintaining performance even under high nitrogen conditions. Diverse nitrogen-fixing bacteria were identified from the maize rhizo-sphere, possessing multiple growth-promoting functions and stress tolerance. K. quasivariicola GN8811 demonstrated the best performance, and its genetic enhancement further improved nitrogen fixation efficiency. These findings highlight the potential of combining microbial screening with genetic engineering to develop efficient bioinocu-lants for sustainable maize cultivation. Biological nitrogen fixation by plant-associated bacteria offers a promising route to reduce synthetic nitrogen fertilizer inputs in cere-al-based agroecosystems, yet its reliability is often constrained by environmental stress and nitrogen repression. In this study, we combined systematic isolation of native maize rhizosphere diazotrophs with targeted regulatory engineering of the NifL–NifA system to generate a high-performance nitrogen-fixing strain capable of promoting maize growth even under nitrogen-replete conditions. Our results demonstrate that precise genetic rewiring of indigenous plant-associated bacteria can substantially en-hance nitrogen fixation efficiency and plant growth promotion, highlighting a viable strategy for developing next-generation biofertilizers to support sustainable maize production.

The Medicago sativa-Sinorhizobium meliloti symbiotic plant-microbe interaction, which results in the formation of nitrogen-fixing root nodules, is subject to sophisticated genetic and metabolic regulation by both partners. S. meliloti is capable of inhibiting secondary plant infections via an adenosine 3′,5′-cyclic adenosine monophosphate (cAMP)-dependent regulatory pathway that depends on CHASE2 domain adenylate/guanylate cyclases (AC/GCs). This pathway likely responds to a plant signal of protein nature. Plant cytokinins (CKs) are adenine derivative phytohormones that control many aspects of plant development, including the symbiotic nodule formation. Classical CK receptors in plants and bacteria contain a CHASE domain. In our study, we present a novel, CK-dependent cAMP signaling pathway, specifically mediated by the AC/GC CyaB, which lacks any known receptor domains. The plant CKs N6(Δ2isopentenyl)-adenine (iP), trans-zeatin, kinetin, and 6-benzylaminopurine all promoted CyaB-dependent increase in cAMP levels detected through a genetic reporter construct. Among these four CKs, iP exerted the strongest effect. Metabolic profiling confirmed the CyaB-dependent accumulation of cAMP in S. meliloti cells, cultured in the presence of iP. The first enzyme in the terpenoid biosynthetic pathway, 1-deoxyxylulose-5-phosphate synthase Dxs, was identified as a CyaB interaction partner and is proposed to mediate the CK perception. CyaB homologs from closely related members of the Rhizobiaceae were able to interact with Dxs and to mediate cAMP signaling in response to iP.

Gibberellins have been reported to play both positive and negative roles in arbuscular mycorrhizal (AM) symbioses. Despite extensive characterisation of the role of DELLAs in AM colonisation, studies of gibberellin function have largely been restricted to chemical interventions. Few studies have examined how disruption to gibberellin biosynthesis affects AM symbioses. To explore this further, we obtained Lotus japonicus LORE1 transposon insertion mutants in four key gibberellin biosynthetic genes: CPS, KS, KO, and KAO. Through a characterisation of their developmental phenotypes, we determined that for each gene there is a single homolog which has a major role in gibberellin biosynthesis. We name these genes CPS1, KS1, KO1, and KAO1. Mutations in these genes affect AM colonisation in the overall distribution of arbuscules, but not in total colonisation levels. These results are consistent with previous studies indicating that DELLAs control the number of cortical cell layers, and therefore regulate the number of cells able to accommodate arbuscules.

The study of extracellular adenosine triphosphate (eATP) in plants has gained significant traction in recent years. Although plant responses to eATP were reported decades ago, the concept initially struggled to captivate widespread scientific interest, largely due to doubts about ATP’s role as a signal in plants. This perception shifted dramatically with the discovery of the plant purinoceptor P2K1, which has since become a cornerstone for research in this field, catalyzing the exploration of eATP-specific responses, the molecular components of its signaling pathways, and interactions with other key regulatory networks, such as plant hormone signaling. Today, the study of the plant purinergic system represents an advanced and dynamic research area, offering insights into how plants perceive and respond to environmental stimuli and internal cues. This chapter provides a comprehensive overview of the evolution of eATP research, beginning with its historical context and tracing the development of our understanding of plant purinergic signaling. Particular emphasis is placed on the mechanisms underlying eATP release, turnover, perception, and response, highlighting recent discoveries and their implications for plant physiology and cross-communication with other signaling pathways.

Ethylene is a well-established negative regulator of nodulation, yet how ethylene biosynthesis and perception are spatially coordinated during early symbiotic signalling remains unresolved. Here, we investigate the dynamics of ethylene responses in Medicago truncatula using transcriptomics, promoter–reporter analyses, loss-of-function approaches and a synthetic reporter. We show that the activity of the ethylene-responsive EBSn reporter shifts from inner root tissues under non-symbiotic conditions to the outer cortex and epidermis following rhizobial inoculation, revealing a spatial reprogramming of ethylene signalling. Among the eight Medicago 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes, upon rhizobia application MtACS3 is induced in outer root cell layers, while MtACS10 is repressed in the inner cortex and pericycle, mirroring the shift in ethylene perception. Functional analysis demonstrates that MtACS10 restricts nodule initiation, whereas MtACS3 modulates infection thread number, prevents nodule clustering, and contributes to radial positioning of nodule primordia. Rhizobial induced ectopic ACS expression in the root interior counteracts MtACS10 repression and blocks nodulation, highlighting the requirement for spatially confined downregulation of ethylene biosynthesis. Together, these findings establish a framework in which localized shift in ethylene biosynthesis, mediated by distinct Medicago ACS genes, balances infection and organogenesis while co-defining the spatial limits of the root susceptible zone.

Soybean can meet much of its nitrogen demand through biological nitrogen fixation (BNF). However, yields in sub-Saharan Africa (SSA) remain constrained by nitrogen deficiency and inconsistent responses to rhizobial inoculation. Despite widespread promotion of inoculation, the influence of host genotype on symbiotic effectiveness in African soybean cultivars remains is not well characterized. We assessed nodulation, nitrogen fixation, and growth responses of three widely cultivated Ghanaian soybean cultivars inoculated with ten phylogenetically diverse Bradyrhizobiumstrains under controlled, nitrogen-free conditions. Symbiotic performance was assessed using nodulation traits, acetylene reduction assay, shoot biomass, and relative symbiotic effectiveness (RSE) relative to mineral nitrogen treatment.
Symbiotic outcomes were strongly dependent on the host. Two cultivars exhibited high nitrogen fixation and growth with multiple strains, whereas one showed consistently weak fixation and growth despite nodulation, indicating host-imposed post-infection constraints. Nodule weight and nitrogenase activity, but not nodule number, reliably predicted symbiotic benefits. Notably, several non-classical soybean Bradyrhizobium strains performed comparably or better to recognized soybean symbionts when paired with compatible hosts. These results demonstate that host genotype is a key determinant of soybean BNF effectiveness and highlight the need to integrate symbiotic performance traits into breeding and inoculant design for reliable BNF in low-input SSA farming systems.

Rhizobia fix nitrogen in plant nodules. Notably, Rhizobium sp. ACO-34A (which could be reclassified as Paenirhizobium), recovered from the rhizosphere of Agave americana, is capable of fixing nitrogen in a defined medium in microaerobic conditions and carries nifHDKENBV genes in a 213 kb plasmid. ACO-34A failed to induce nodules in several leguminous hosts and does not have nod genes. ACO-34A NifH mutant did not fix nitrogen in pure cultures and did not promote stem growth in Lotus japonicum plants as the wild strain did. The plasmid harboring the nif genes contains repABC replication genes, genes for homocitrate synthesis, for toxin-antitoxin production and for plant colonization. Comparative phylogenomic analyses revealed that strain ACO-34A is close to Ciceribacter sichuanensis S101, which was isolated from soybean nodules and should be reclassified. According to ANI, AAI and dDDH parameters, ACO-34A may represent a novel species within the Rhizobiacea family.

Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiome⍰assisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genome⍰wide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiome⍰wide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial sub⍰communities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive population⍰level framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiome⍰informed breeding strategies.

Biological discoveries in plant and human systems have long advanced our understanding of how signaling, metabolism, and immunity shape cross-kingdom interactions. Building on this rich history of interdisciplinary insight, there is now a tremendous opportunity to strengthen connections between human and agricultural microbiome research. This perspective highlights key biological synergies across these systems that are essential for advancing human, agricultural, and ecosystem health. Focus is given to colonization, immune, and biosafety engineering strategies developed for microbiome therapeutics that can guide the design and development of next-generation agricultural bioproducts. Ultimately, greater knowledge exchange and collaboration across disciplines will be critical to translate microbiome discoveries into bioproducts with positive societal impact.

Drought is a major constraint on maize production worldwide, particularly in tropical regions where climate variability is intensifying. Arbuscular mycorrhizal fungi (AMF) have emerged as beneficial symbionts enhancing plant resilience to drought by improving water uptake, nutrient acquisition, and photosynthetic performance. This study evaluated the effects of Rhizoglomus clarum inoculation on maize growth, water status, osmotic adjustment, and chlorophyll a fluorescence under well-watered (WW) and water-deficit (WD) conditions in sterile and natural soils. The experiment was conducted in a greenhouse using a randomized complete block design in a 4 × 2 factorial scheme (soil treatment × water regime), with four replicates. Drought significantly reduced leaf area, shoot and root biomass, and water status. However, R. clarum inoculation attenuated these effects, increasing leaf dry mass by up to 45% and stem dry mass by 100% in under WD. Inoculated plants also showed higher photochemical efficiency (Fv/Fm and PIABS) under both water regimes. The strongest responses were observed in natural soil, suggesting synergistic interactions between R. clarum and indigenous microbiota. These results demonstrate that R. clarum enhances maize drought tolerance through coordinated morphological, physiological, and photochemical adjustments. This highlights the potential of species-specific AMF inoculation as a sustainable strategy to improve maize performance under water-limited conditions.

Rhizobia associate with legumes and induce the formation of nitrogen-fixing nodules. The regulation of bacterial redox state plays a major role in symbiosis, and reactive oxygen species produced by the plant are known to activate signaling pathways. However, only a few redox-sensing transcriptional regulators (TRs) have been characterized in the microsymbiont. Here, we describe SydR, a novel redox-sensing TR of Sinorhizobium meliloti that is essential for the establishment of symbiosis with Medicago truncatula. SydR, a MarR-type TR, represses the expression of the adjacent gene SMa2023 in growing cultures, and this repression is alleviated by NaOCl, tert-butyl hydroperoxide, or H2O2 treatment. Transcriptional psydR-gfp and pSMa2023-gfp fusions, as well as gel shift assays, showed that SydR binds two independent sites of the sydR-SMa2023 intergenic region. This binding is redox-dependent, and site-directed mutagenesis demonstrated that the conserved C16 is essential for SydR redox sensing. The inactivation of sydR did not alter the sensitivity of S. meliloti to NaOCl, tert-butyl hydroperoxide, or H2O2, nor did it affect the response to oxidants of the roGFP2-Orp1 redox biosensor expressed within bacteria. However, in planta, ΔsydR mutation impaired the formation of root nodules. Microscopic observations and analyses of plant marker gene expression showed that the ΔsydR mutant is defective at an early stage of the bacterial infection process. Altogether, these results demonstrated that SydR is a redox-sensing MarR-type TR that plays a key role in the regulation of nitrogen-fixing symbiosis with M. truncatula.

Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with cell growth, chemotaxis, plant immune suppression, biofilm formation, and stress responses, reflecting the coordinated physiological adaptation to the root environment. Additionally, we discovered that transcriptional activation of xanthine dehydrogenase and a lysozyme inhibitor is crucial for evading plant immune systems. This framework is scalable to other bacterial species and provides new opportunities for understanding rhizobacterial gene regulation in native environments.