Plant agriculture contributes substantially to global greenhouse gas emissions, yet it also offers powerful opportunities for climate change mitigation. Here, we focus on how to identify and prioritize synthetic biology strategies to reduce emissions and sequester carbon through plant-based interventions. Effective solutions must process large volumes of carbon, be scalable, yield a positive life-cycle balance, and be economically viable, technically feasible, and deployable in field conditions without undue damage to what remains of nature on Earth. Using Fermi estimation, we quantify the per-hectare, annual, and 100-year CO2-equivalent (CO2e) drawdown potential of emerging synthetic biology strategies—including improved CO2 fixation, reduced yield losses, root-deposited biopolymers, engineered nitrogen fixation, and methane reduction—and benchmark them against nonengineered approaches such as biochar, forestation, and fast-growing biomass crops. We used a 100-year horizon to allow for both development and implementation of high-risk but high-impact synthetic biology strategies. We integrate factors such as per-hectare effectiveness, year-on-year sequestration, deployment area, and storage durability. We demonstrate that while per-hectare impacts vary by orders of magnitude (<1 to >30 t CO2e/ha/year), deployment scale is the dominant factor determining total impact. Targeted synthetic biology strategies implemented across existing agricultural systems could deliver ∼120 Gt CO2e drawdown over a century and contribute to an additional ∼140 Gt CO2e drawdown. Decreasing synthetic nitrogen fertilizer use and biochar implementation have the biggest CO2e impact potential. Early-stage quantitative evaluation is critical to guide R&D toward climate-relevant solutions and deliver a prioritized portfolio of near- and long-term strategies. A transdisciplinary approach—linking synthetic biology, agronomy, engineering, and social systems—is essential to realize impact. This work offers a framework for evaluating plant agriculture-based climate mitigation strategies and highlights a key role for synthetic biology in mitigation pathways. Regular re-evaluation of strategies should be performed to ensure that they are meaningful for climate change mitigation as other factors evolve.

Understanding how plant-associated microbiomes resist phytopathogen invasion remains a key challenge in natural ecosystems. Here we combined genome-scale metabolic models with synthetic community experiments, both in vitro and in planta, to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization profiles to fully capture their metabolic capacities. Trophic interactions inferred from models effectively predicted pathogen invasion outcomes across diverse microbial communities and nutrient environments. Importantly, considering both substrate and metabolite features provided a more holistic understanding of pathogen suppression. In particular, cross-feeding metabolites within the native community emerged as crucial yet often overlooked predictors of community resistance, disproportionally favouring native species over invaders. This study lays the foundation for designing disease-resistant microbiomes, with broad implications for mitigating pathogen exposure in diverse environments.

Background and aims
Intercropping has been demonstrated to enhance crop productivity and phosphorus (P) uptake, in which root-microbe interactions played crucial roles. Our previous results showed that this beneficial effect of intercropping depends largely on a match between root traits and rhizosphere processes. However, little is known about the role of soil microbial communities in underground processes.

Methods
Using a long-term field experiment with three P-fertilizer application rates and five cropping systems of maize, we integrated crop productivity, root physiological traits, root morphological traits and microbial amplicon sequencing data.

Results
Our findings revealed that intercropping significantly enhanced maize crop productivity and P uptake, accompanied by increased plasticity of morphological and physiological root traits compared with monoculture. Additionally, intercropping with different companion crops significantly altered the soil microbial community structure of maize, while P-fertilizer application rates had minimal effect. Network analysis showed that intercropping promoted more complex and stable microbial networks characterized with increased cooperative relationships, relative to monoculture. The relative abundance of keystones enriched in intercropping systems were positively correlated with crop productivity and P uptake, explaining 41.11% of the variation in maize grain yield. Structural equation modeling (SEM) further indicated that keystones enhanced grain yields of maize by inducing carboxylate secretion and fostering more acquisitive root morphological traits.

Conclusion
Our study elucidates how intercropping optimizes root-microbe synergies to improve P efficiency, highlighting the potential for targeted manipulation of keystone microbial taxa to enhance P acquisition and crop performance in sustainable agricultural systems.

Nitrogenase catalyzes atmospheric nitrogen fixation, a critical biological process that depends on an intricate organometallic cofactor assembled by a dedicated multiprotein system. Here we uncover the structural basis for the function of NifEN, the scaffold protein that mediates the final stages of cofactor biosynthesis before its incorporation into nitrogenase. High-resolution structural analyses reveal that the cofactor precursor initially binds at a surface docking site before being transferred into a specialized cavity for further maturation. This process involves dynamic structural rearrangements, including coordinated domain motions and partial unfolding, enabling the scaffold to alternate between open and closed states. Additionally, a rear channel extends to the precursor-binding cavity, likely facilitating the entry of the modifying components molybdenum and homocitrate. These findings illuminate the dynamic mechanisms underlying FeMo-cofactor assembly and underscore the functional divergence between NifEN, the biosynthetic scaffold, and NifDK, the catalytic component of nitrogenase.

Agriculture has intensified the presence of chemical stressors in the rhizosphere—the region surrounding roots where critical plant-microbe interactions occur, such as those between leguminous plants and nitrogen-fixing rhizobial bacteria. Particularly, rhizospheric pesticide exposure can disrupt the efficacy of the plant-rhizobia mutualism and reduce plant productivity. However, it is unknown whether genetic variation in plants (GP), rhizobia (GR), or interactions between them and the pesticide environment (E), i.e., GP or R  ×E, or GP  ×GR  ×E, could mitigate these negative outcomes. We grew two genotypes of the leguminous plant Trifolium pratense in symbiosis with each of eight genetic strains of its rhizobial partner Rhizobium spp. symbiovar trifolii. We exposed symbionts to the contemporary synthetic auxin herbicide dicamba or a control in the rhizosphere, and evaluated the symbiotic interaction and plant growth. Our results provide new evidence that rhizobial genetic variation drives herbicide impacts on mutualism outcomes through GR  × E interactions. Rhizospheric herbicide delayed rhizobial colonization of plants via root nodule formation, but its effects on the number of nodules and fixed nitrogen produced varied depending on rhizobial strain. Similarly, while herbicide exposure reduced plant size on average, the degree of this effect was mediated by rhizobial partner, suggesting that rhizobia could potentially function as an “extended genotype” for defense against herbicide damage. As the use of herbicides, particularly synthetic auxins, continues to escalate, our findings have important implications for how certain rhizobia could be selected to improve plant fitness in the face of these anthropogenically-released chemicals.

Nodule senescence in barrel medic (Medicago truncatula) can occur as a natural, developmentally regulated process or be triggered prematurely by environmental stress or ineffective symbiotic interactions. In this study, we examined five M. truncatula Fix⁻ mutants (dnf4, dnf7-2, TR183, TRV36, and TR36) that fail to fix nitrogen to determine whether they share common senescence-related traits. Our findings reveal that, despite distinct genetic defects, all mutants exhibit similar hallmarks of premature senescence: a rapid decline in the transcription of nitrogen-fixation-related genes (as indicated by DINITROGENASE REDUCTASE (NifH) expression), early degradation of bacteroids and symbiotic cells, recolonization of nodules by saprophytic rhizobia, premature closure of the nodule endodermis, impaired postmitotic differentiation of the symbiotic cells, and upregulation of senescence marker genes (CYSTEINE PROTEASE 2 (CP2), CYSTEINE PROTEASE 6 (CP6), CHITINASE 2, and PURPLE ACID PHOSPHATASE 22 (PAP22). Neither symbiotic maintenance genes (DEFECTIVE IN NITROGEN FIXATION 2 (DNF2), Symbiotic CYSTEINE-RICH RECEPTOR-LIKE KINASE (SymCRK), and REGULATOR OF SYMBIOSOME DIFFERENTIATION (RSD)) that inhibit plant defense responses nor the defense-related gene PATHOGENESIS-RELATED PROTEIN 10.1 (PR10.1) were upregulated, suggesting that premature senescence in these mutants is driven primarily by proteolytic activities rather than immune responses. These results indicate that early nodule senescence is a common feature of ineffective M. truncatula–Sinorhizobium medicae interactions, independent of the specific genetic mutation. Understanding nodule longevity and functionality may contribute to the development of strategies to enhance symbiotic efficiency in legumes for sustainable agriculture.

Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.

•Macroaggregate stability covaried most strongly with soil organic matter
•Actinobacteria moderately outperformed AMF as a predictor of soil macroaggregate stability
•Bacterial PLFAs more strongly covaried with stability than AMF in Appalachian pastures
•Penalized regression ranked bacterial groups as better predictors of stability over AMF
•Findings raise questions about long-held assumptions regarding AMF as primary soil stabilizers

The NIN-like protein 2 (NLP2) transcription factor is highly expressed in the infected cells of the N2 fixation zone of mature nodules in Medicago truncatula. In these cells, NLP2 directly activates the expression of leghemoglobin genes and is required for the full expression of nitrite reductase (NiR). Histological examination of nodules formed under different nitrate regimes revealed that the infected cells of nlp2 display abnormal vacuole morphology under high nitrate (5 mM KNO3). This phenotype is associated with starch accumulation, higher expression of starch biosynthesis genes, and increased levels of nitrite and nitric oxide. A transcriptomic comparison of nlp2 and wild-type nodules across nitrate concentrations revealed that under high nitrate, nlp2 shows lower expression of genes important for hypoxia adaptation, such as alcohol dehydrogenase and pyruvate decarboxylase (PDC), and increased expression of S-nitrosoglutathione reductase (GSNOR), which encodes a key enzyme for nitric oxide homeostasis. These changes in gene expression were associated with lower nodule ATP levels and a higher NAD+/NADH ratio, suggesting that energy metabolism is specifically compromised in nlp2 nodules under high nitrate. Transgenic expression of NiR in the nodules of nlp2-1 mutants grown under high nitrate rescued the vacuole phenotype and restored the expression of GSNOR and PDC to normal levels. Overall, our data indicate a role for NLP2 in the regulation of NiR in N2-fixing cells, suggesting a role for nitrate reduction in nodule energy homeostasis.

The root microbiota plays a vital role in plant growth and health. Recently, Zhang and colleagues demonstrated that the rhizobacterial strain Exiguobacterium R2567 produces cyclo(Leu-Pro), a cyclic dipeptide that regulates tillering by activating the rice strigolactone (SL) signaling pathway through binding to the SL receptor OsD14. This discovery provides an innovative strategy for optimizing crop architecture by harnessing the root microbiota for sustainable agriculture. It holds promise for achieving precision and environmentally friendly production through the application of synthetic microbial communities (SynComs) or functional metabolites. However, practical implementation faces challenges, including the field stability of cyclo(Leu-Pro), competition from native microbial communities, and potential long-term ecological risks, which require further study to realize its full potential.

Abiotic stresses affect the symbiotic relationship between legumes and rhizobia and nodule formation. Salt stress suppresses rhizobial infection, nodule development, and nitrogen fixation efficiency; however, the underlying genetic and molecular mechanisms remain unknown. In this study, we identified a GRAS transcription factor, designated MaGRAS51, that interacts with Nodulation Signaling Pathway 1 (MaNSP1) and jointly binds to the promoter of the Nodule Inception (MaNIN) gene to activate its expression. NSP1 and NIN genes are essential for rhizobial infection, nodule initiation, and symbiotic gene expression in legumes. Overexpression or knockdown of MaGRAS51 in Melilotus albus resulted in increased or decreased nodule number, respectively, which correspondingly led to the significant up- and downregulated expression of MaNIN. Interestingly, MaGRAS51 was highly induced by salt stress during nodulation and activated the expression of MaNIN by directly binding to its promoter independently, thereby maintaining symbiotic nodulation under salt stress. In conclusion, we identified a transcriptional activator of MaNIN and revealed the mechanism by which MaGRAS51 acts as a network node to coordinate the expression of MaNIN and symbiotic nodulation under salt stress conditions, providing insights to improve symbiotic nitrogen fixation in legumes under environmental stress conditions.

Phosphate (Pi) is one of the most important nutrients for plant growth and productivity, as it is an essential building block for a wide range of biomolecules. However, Pi is often poorly available in soils because of its low mobility and tendency to bind strongly to soil particles (Wang et al. 2025). This limitation poses a particular challenge for legumes, where symbiotic nitrogen fixation in root nodules demands high energy and phosphorus inputs. Under Pi limitation, nodules number is tightly regulated through the long-distance signaling pathway called autoregulation of nodulation (AON) to avoid an energetic imbalance (Isidra-Arellano and Valdes-López 2024). Although phosphate starvation responses (PSR) are well-characterized, the precise mechanisms by which Pi status is directly integrated into the genetic control of rhizobial nodulation have remained unclear.

Bacterial culture collections represent a valuable tool for mechanistic understanding of microbiome assemblies and are increasingly used to assemble tailored synthetic communities to characterize their microbe-microbe interactions and those with the environment. Given the size of these collections, short-read sequencing is primarily used to capture the encoded genetic information. Whilst sufficient for many microbiome studies, this approach is not amenable for understanding bacterial genome evolution or detailed genetic analyses at the entire genome level. Here we report the assembly of 152 full bacterial genomes from the Lj-SPHERE, the Lotus japonicus collection of root commensals. We performed long-read sequencing using Oxford Nanopore Technology and used this together with pre-existing Illumina sequences to de novo assemble these into high quality genomes with improved contiguity and quality. These genomes now provide a solid platform for detailed, mechanistic understanding of microbiome assembly, dynamics, and evolution in plants.

Bacteria have multiple mechanisms through which they sense changes in their environment and respond appropriately. In some instances, bacteria appear to retain an imprint of past events that can influence future behaviour, resembling a form of memory. This Perspective explores this concept of bacterial memory at the genetic, epigenetic, biochemical and ecological levels. We discuss how memory can prime bacteria to respond appropriately to recurring stimuli, providing fitness benefits in fluctuating environments. At the cellular level, there is evidence for memory storage mechanisms involving mutations, DNA methylation, or the inheritance of metabolites or proteins that provide a means of accessing past experiences. Complex bacterial communities can exhibit ecological memories of past environments, stored as microbiota population changes that persist or lag after acute environmental change. We review the emerging evidence supporting these concepts of microbial memory, outline some of the key molecular mechanisms, and identify research gaps and potential future applications.

Purpose
Fungi play a crucial role as soil microorganisms, mediating carbon and nitrogen dynamics while influencing nutrient availability for host plants. However, the regulatory effects of plants on fungal communities and the functional roles of soil fungi in plant-soil system dynamics, as well as the nitrogen transformation rates in different pH soils remain largely uncharacterized.

Methods
In this study, wheat (Triticum aestivum L.), a typical nitrate-preferring crop, was selected as the model plant in alkaline (AK) and acidic (AC) soils. After one month pot cultivation, the wheat planted soil (WS) and not planted (CK) soil samples were collected. Fungal community structure and diversity in soil samples were assessed through high-throughput sequencing of the ITS1 region. Plant samples were dried and sieved for nitrogen concentration and uptake rate analysis. The soil and plant nitrogen transformation rates were quantified using 15N isotope techniques.

Results
We observed divergent responses of fungal community structure and diversity to wheat cultivation between AK and AC. In AC, wheat cultivation increased fungal copies and Ascomycita abundance, while in AK, fungal community structure and diversity shifts were contingent on DOC and nitrogen content. Notably, the cultivation of wheat in AK and AC soils significantly reduced the concentration of soil NH4⁺ and NO3⁻, and significantly promoted the uptake rate of NO3⁻. FUNGuild functional classification revealed a dominant of endomycorrhizal across all treatments. As the abundance of endomycorrhizal fungi increased with the decreased soil inorganic nitrogen. In contrast, ectomycorrhizal fungi abundance decreased. The abundance of endomycorrhizal fungi showed a strong positive correlation with the gross mineralization rate (P < 0.05) and the nitrification rate (P < 0.05).

Conclusions
Our findings suggest that wheat cultivation promotes the recruitment of endomycorrhizal fungi while stimulating soil nitrogen mineralization and nitrification processes, ultimately enhancing nitrogen uptake efficiency in wheat plants. Those findings reveal the critical role of mycorrhizal fungi in mediating wheat nitrogen acquisition, underscoring the necessity of integrating endomycorrhizal fungi into nitrogen transformation models to refine the accuracy of simulating plant-soil nitrogen turnover dynamics.