Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth or provide nutrients, or pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and can assemble stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. This review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

The Haber–Bosch process made synthetic ammonia abundant and helped feed a growing population, but it also created a sustainability debt: Substantial fossil-energy demand, significant CO2 emissions, and pervasive nitrogen losses that drive eutrophication and N2O emissions. Biological nitrogen fixation (BNF) is attractive because nitrogenase reduces N2 to NH3 at ambient conditions, yet the enzyme’s oxygen lability, complex metallocluster biosynthesis, and high energy demand complicate implementation beyond its native microbial contexts. This review synthesises three routes to reduce fertiliser dependence: engineered nitrogen-fixing biofertilisers that excrete ammonium; plant-centred strategies that extend symbiosis or express nitrogenase components in organelles; and purified nitrogenase or biohybrid systems powered by renewable electricity or light. We emphasise biohybrid devices because they decompose the challenge into modular interfaces (enzyme, power, microreactor environment) but require credible solutions for wiring, stability, continuous operation, and product capture. Across routes, protein engineering for stability, interface tolerance, and electron delivery is a shared enabling lever for system-level impact. 

The early nodulin-like (ENODL) subfamily, part of the phytocyanin, arabinogalactan protein, and nodulin-like families, is involved in plant growth and stress resistance. However, its role in symbiotic nodulation remains poorly understood. In barrel medic (Medicago truncatula), we found MtENODL29 was strongly activated at the late stages of nodule development, particularly in the infection zone of nodules. Both RNA interference (RNAi) and mutation of MtENODL29 caused a considerable reduction in nodule numbers, an increase in cysteine protease activity, a dramatic decrease in leghemoglobin content, and signs of premature senescence in nodule cells, suggesting that disruption of MtENODL29 accelerates nodule aging. Transcriptome analysis of 7-dpi (day post inoculation) inoculated roots and 28-dpi nodules in enodl29 mutants showed significant downregulation of symbiotic genes, accompanied by differential expression of genes associated with lipid metabolism and transport. MtENODL29 mutation also negatively impacted plant growth and development. MtENODL29 bound to MtnsLTP (non-specific lipid transfer protein), MtKCR (very-long-chain 3-oxoacyl-CoA reductase), and MtSec61γ (gamma subunit of the translocase complex Sec61) through its ALR (arabinogalactan protein-like region) domain. MtENODL29 co-localized with these proteins in the plasma membrane and endoplasmic reticulum. Notably, MtnsLTP showed high expression in the nodules, similar to MtENODL29, while MtKCR and MtSec61γ were also highly expressed in the leaves and stems. These results suggest that MtENODL29 participates in membrane lipid modification and transport by interacting with MtnsLTP, MtKCR, and MtSec61γ, facilitating the formation of symbiosome membranes as alfalfa rhizobium (Sinorhizobium meliloti) strain 1021 are released into nodule cells. Moreover, MtENODL29 influences plant growth, highlighting its role in coordinating plant development and symbiosis.

In the current era of global climate change, agriculture is under extreme pressure due to variety of abiotic stresses (extreme temperature conditions, prolonged drought situations, unexpected flooding, soil salinization, luxurious use of agrochemicals, depleting micro flora, metal and metalloid toxicity and war or warlike situations) and biotic stress factors (pathogens, pests and weeds), all seriously challenging the global food security (Dervash et al. 2024; Lahlali et al. 2025; Jiang et al. 2025; Zhang et al. 2025; Manghwar and Zaman 2024; Lin et al. 2023). Abiotic and biotic stresses significantly disrupt the vital physiological processes like net photosynthetic rate, uptake of essential and beneficial nutrients, water uptake and overall health of the plants and lead to serious yield penalties (Ashraf et al. 2009, 2012; Hakeem et al. 2013; Hasanuzzaman et al. 2019; Ozturk and Gul 2020; Akhtar et al. 2024; Wang et al. 2025a, b).

Plant-associated microbial communities consist of plant holobiont and play an essential role in plant growth and development, yet their collective functions are not fully understood. Theoretically, microbiota can act as integrated consortia, conferring emergent properties beyond those of single species. Here, we show that the tomato rhizosphere microbiome, when stimulated by a Flavobacterium dauae, enhances plant growth by activating the phytosterol biosynthesis pathway in both the microbiota and the plant host, a function unattainable by individual microbial species. A reconstructed synthetic community, based on meta-transcriptome of plant microbiota, recapitulated this microbiome-driven activity upon stimulation by F. dauae. This synthetic community also restored the growth response in diverse sterol-deficient plant mutants. The microbial consortium exhibits multispecies biofilm formation and functional specialization among its members, constituting a microbial coalition that promotes plant growth. This study provides direct experimental evidence that plant microbiota function as a coordinated unit and orchestrate host plant development. We highlight this to be a plant holobiont function based on microbial community coalition in host plant.

Bacterial pathogens and most nitrogen-fixing rhizobia employ type III effectors (T3Es) as potent tools to manipulate plant signaling pathways, thereby facilitating infection and colonization. However, how rhizobial T3Es regulate legume symbiosis remains elusive. Here, we show that NopM, a T3E from Sinorhizobium fredii NGR234, contributes to infection and nodulation in Lotus japonicus Gifu. The loss of nopM in an NGR234ΔnopT mutant reduced infection and nodulation in L. japonicus, and expression of NopM under the control of L. japonicus NIN promoter enhanced these processes. NopM associated with the NF receptors NFR1 and NFR5 and physically interacted with their cytosolic domains in vitro, and selectively mediated ubiquitination of NFR5. Expression of NopM in hairy roots of NFR5-HA transgenic plants correlated with increased NFR5 protein abundance relative to the inactive NopM variant. Taken together, our work suggests that NopM-dependent effects on symbiosis are associated with increased NFR5 abundance, expanding our understanding of rhizobial T3E functionality and the co-evolution of legume-rhizobium symbiosis.

The specific partnership between legumes and rhizobia relies on a chemical dialogue. Plant flavonoids activate the bacterial transcription factor NodD, which triggers production of Nod factors that are recognized by the plant. Structural studies of the Pisum sativum (pea) symbiont Rhizobium leguminosarum NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of Sinorhizobium medicae, the symbiont of Medicago truncatula, revealed that this specificity is determined by the shape of the pocket and by specific amino acids. A chimeric NodD containing the flavonoid recognition residues from S. medicae NodD1 in the R. leguminosarum NodD backbone was sufficient to complement nitrogen fixation in M. truncatula by an S. medicae nodD1 mutant, confirming the critical role of flavonoid recognition in host range.

During host-microbe symbioses, the fitness of mutualistic microbes is determined by the interactions that concurrently occur, throughout their life cycle, with their host and other members of the surrounding microbial community. Disentangling how these multiple interactions shape the fitness of microbial symbionts is challenging, but is essential to understand the diversity and functioning of mutualisms. Here we examined the different fitness components of rhizobial symbionts of the legume plant Mimosa pudica across the multiple stages of their symbiotic life cycle. By comparing rhizobial symbiotic fitness in single and pairwise inoculations, we found that inter-bacterial interactions causing significant fitness effects are common, transitive and can have major consequences, sometimes leading to the extinction of a strain. These interactions predominantly occur at the root infection (nodulation) step, but smaller post-infection interaction effects, involving yet uncharacterized mechanisms, were also detected. Furthermore, considering pairwise interactions was sufficient to predict fitness ranks in more complex rhizobial communities consisting of 6 or 8 strains, indicating that higher-order interaction effects do not play a significant role in these communities. Overall, our results provide a quantitative framework to describe the main drivers of rhizobial symbiotic fitness in a simple community context.

Legume nodulation enables biological nitrogen fixation but is strongly repressed by nitrate. NIN-like proteins (NLPs) mediate this nitrate response, yet how their activity is regulated remains unclear. Here, we demonstrate that SUMOylation—a reversible posttranslational modification—is essential for the transcriptional activity and protein–protein interactions of MtNLP1 in Medicago truncatula, independently of its nitrate-induced nuclear localization. This modification is conserved in other NLPs, including Arabidopsis thaliana NLP7. Moreover, knockdown of SUMOylation-machinery components disrupts nodulation, suggesting that additional regulators in the symbiotic pathway also depend on SUMOylation. This work identifies SUMOylation as a conserved regulatory mechanism integrating nitrate signaling with root nodule symbiosis, with broad implications for improving plant nitrogen use efficiency.

The cell surface localized lysin motif (LysM) receptor-like kinases/proteins (RLKs/RLPs) function as sensors for pathogenic and symbiotic microbes in land plants, perceiving chitin, lipo-chitooligosaccharides (LCOs), and peptidoglycan. LysM-RLKs/RLPs play a crucial role in activating various responses that lead to defense against pathogens or the establishment of symbiosis. While the functions of LysM-RLKs/RLPs were well-studied in land plants, their evolutionary origin and broader functional roles remain less explored. Streptophyte algae are widely recognized as the sister lineage of land plants. Land plants are believed to have emerged from a streptophyte algal ancestor. Plant–pathogen interactions are ancient and have played a pivotal role in shaping the evolution and complexity of the plant innate immune system. Genomic analyses revealed the presence of LysM-RLKs in two streptophyte algal species, Charophyceae Chara braunii and Zygnematophyceae Spirogyra pratensis. The functional roles of LysM-RLKs in both species were subsequently characterized. Through phylogenetic analysis combined with sequence alignment, I propose that LysM-RLKs originated from the last common ancestor of Charophyceae, Zygnematophyceae, and land plants. A conserved CXC motif within the LysM ectodomains (ECDs) was identified in streptophyte algal LysM-RLKs, like those present in land plants. Structural predictions using AlphaFold2 and three-dimensional modeling revealed that the overall architecture of LysM ECD is conserved, including a chitin-binding groove within the LysM2 domain. In vitro binding assays further demonstrated the chitin-binding capability of LysM ECDs from both streptophyte algae and bryophytes, suggesting an ancestral role of LysM ECDs in chitin recognition. Intriguingly, however, chitin treatment did not trigger downstream transcriptional responses in streptophyte algae, pointing to a functional divergence in LysM-RLKs during evolution. Furthermore, genetic and interaction studies demonstrated that heterodimerization and the formation of higher-order oligomeric complexes of LysM receptors are essential for proper function in bryophytes. In contrast to bryophytes, chitin treatment did not promote homodimerization of algal LysM receptors. Overall, this study new provides an insight into the evolutionary origin and functional diversification of LysM RLKs/RLPs in plants.

Arbuscular mycorrhizal fungi (AMF) establish a dynamic and asynchronous symbiosis with a wide range of land plants, involving distinct stages of root colonization and associated cellular responses that co-occur within the same root. Whilst decades of research have significantly advanced our understanding of the plant's symbiotic gene repertoire, this spatial and temporal complexity has hindered a detailed dissection of the molecular mechanisms underlying fungal accommodation. Here, we present the first single-nucleus RNA-sequencing (snRNA-seq) dataset of Solanum lycopersicum roots colonized by Rhizophagus irregularis. Unsupervised subclustering of an AM-specific cell population resolves AM-responsive root epidermal cells as well as a developmental gradient of cortical cells across distinct stages of arbuscule formation, unveiling stage-specific transcriptional signatures during AMF colonization. Moreover, using Motif-Informed Network Inference based on single-cell EXpression data (MINI-EX), we put forward candidate transcription factors orchestrating these stage-specific transcriptional programs. Together, our data support novel hypotheses on how diverse plant developmental and physiological processes – including localized cell cycle reactivation and the integration of multiple nutritional cues – are coordinated to facilitate the establishment of a functional symbiosis. As such, this high-resolution dataset serves as a valuable resource for candidate gene prioritization and future reverse genetic studies.

Legumes are important sources of dietary protein and are key crops for sustainable agriculture because they fix atmospheric nitrogen via symbiotic interactions with rhizobia bacteria. However, legume plants are particularly sensitive to salt stress, with salinity negatively affecting development of the root nodule symbiosis. Genes that control salt-symbiosis crosstalk or trade-offs are largely unknown and poorly characterised. To assess the role of symbiosis signalling genes in salt stress, we analysed wildtype and symbiosis signalling mutants of Medicago truncatula grown in the presence of NaCl, sorbitol and/or rhizobia bacteria. We assessed root growth, plant biomass, nodule number and gene expression responses in plants exposed to stress. Our findings demonstrate that several symbiosis signalling genes play a previously undescribed role in regulating root responses to salt stress, including a calcium- and calcium/calmodulin-dependent protein kinase (CCaMK) and its interacting partner and downstream transcription factor, IPD3. Our results also show that the identified responses to salt stress are due to sodium toxicity rather than osmotic stress. We conclude that symbiosis signalling genes, including the CCaMK-IPD3 signalling module, may mediate signalling crosstalk between salt stress and symbiosis. These findings open new research avenues to explore how the environment regulates the legume-Rhizobium symbiosis.

Arbuscular mycorrhizal fungi (AMF) are widespread plant symbionts that enhance nutrient acquisition and influence ecosystem productivity. Previous chromosome-level assemblies of a model species revealed a two-compartment genome architecture (active A and repressed B chromatin compartments), yet its conservation across evolutionarily distant AMF lineages remains unresolved. Here, we present a chromosome-scale and 3D genome assembly of Gigaspora margarita isolate BEG34—the largest and most repeat-rich AMF genome to date—alongside that of its obligate endobacterium, Candidatus Glomerobacter gigasporarum (CaGg), using PacBio HiFi and Hi-C sequencing. The G. margarita genome comprises 43 chromosomes (792 Mb) organized into stable A/B compartments and Topologically Associating Domains structures, irrespective of the presence of endobacteria. We uncover 21 divergent rDNA operons distributed across six chromosomes and show that these physically interact, suggesting conserved nucleolar organization. We also reveal that the CaGg genome is tripartite and mobilome-rich, encoding prophages, an orphan CRISPR array, and complete pathways for many novel and essential cofactors, including heme, which may enhance host bioenergetics. We also find that the endobacterium’s presence regulates transposable elements in G. margarita. These findings reveal conserved principles of chromatin architecture in AMF symbionts and highlight the tight molecular interplay between fungal hosts and their endosymbionts, offering new insights into genome evolution and symbiotic adaptation.