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PubMed2026

Kinetic model of a determinate legume root nodule reveals plant metabolic characteristics for more efficient nitrogen fixation symbiosis.

While nitrogen fertilizers are widely used in agricultural production, their application incurs significant environmental and energetic costs. In contrast, some crops are less dependent on these fertilizers because they engage in symbioses with rhizobia, nitrogen-fixing bacteria that provide ammonium to the plant in exchange for carbon. However, the carbon cost associated with nitrogen fixation can negatively impact crop yields. Improving the efficiency of this metabolic process could alleviate this impact on crop productivity. Mathematical models can help us quantitatively explore metabolic behavior and identify potential targets for metabolic engineering. In this work, we developed a kinetic model of determinate root nodule metabolism, where this symbiotic exchange of carbon from the plant and nitrogen from the bacteria occurs. We used this model to evaluate how the predicted metabolic behavior differs between inefficient and efficient nodules, and to identify potential engineering targets for improving nitrogen fixation efficiency and rate. We show that the enzymes phosphoenolpyruvate carboxylase and pyruvate kinase have significant influence on the predicted rate and efficiency of nitrogen fixation, especially when their expression is varied in combination with oxidative Pentose Phosphate Pathway enzymes like glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase. The model predicts that pairing a 3-fold decrease in glucose-6-phosphate dehydrogenase activity along with either a 3-fold increase in phosphoenolpyruvate carboxylase activity or decrease in pyruvate kinase activity could increase nitrogen fixation rate by 8.82% while improving nitrogen fixation efficiency by 10.99%.

Enzyme kinetics↗

PubMed2026

Trade-off between photosynthetic promotion and nitrogen fixation suppression induced by chloroplast-targeted Mo nanoparticles in soybean.

Organelle-targeted nanomaterials offer opportunities to improve crop photosynthesis, yet their unintended effects on symbiotic nitrogen fixation remain poorly understood. Here, we developed chloroplast-targeted molybdenum nanoparticles (Chl-Mo) and compared their effects with those of ionic Mo (IonMo) and non-targeted Mo nanoparticles in soybean. Chl-Mo preferentially accumulated in chloroplasts, enhancing photosynthetic carbon assimilation, thylakoid development, PSII performance, sucrose transport, and biomass accumulation. However, this growth promotion was accompanied by suppressed nodule nitrogenase activity, reduced nif gene expression, inhibited GS/GOGAT-mediated nitrogen assimilation, and disrupted microoxic and ROS homeostasis in nodules. Integrated nodule proteomics and metabolomics showed downregulation of sucrose transport, glycolysis, pyruvate metabolism, and amino acid biosynthesis, indicating a decoupling between enhanced carbon input and nitrogen utilization. Root transcriptomics further revealed oxidative stress, impaired nitrate assimilation, and attenuated early symbiotic signaling. These findings demonstrate that chloroplast-targeted Mo delivery can enhance photosynthesis while compromising symbiotic nitrogen fixation, highlighting the need to evaluate belowground symbiotic functions when developing organelle-targeted nanotechnologies for sustainable agriculture.

Chloroplast-targeted Mo↗

PubMed2026

Silicon-mediated alleviation of mercury toxicity requires coordinated regulation of antioxidant defense, metal homeostasis, and nodule function in mung bean.

Mercury (Hg) contamination and accumulation in agricultural soil represent a major hazardous environmental concern, posing serious threats to living organisms, including plants. Silicon (Si) has been widely recognized to mitigate heavy metal (loid) toxicity; however, the underlying mechanism of Si-mediated mitigation of Hg-stress in mung bean remains unclear. In this study, we addressed this research gap by thoroughly examining the potential effects of Si supplementation on Hg-stressed mung bean plants, with particular emphasis on investigating the possible effects of Si on plant biomass, nodulation traits, antioxidant defense, and expression of metal-transporter and detoxification genes. Our findings demonstrated that Hg stress significantly impaired plant growth by inducing oxidative stress and reducing biological nitrogen fixation efficiency whereas Si application significantly alleviated the Hg-induced toxicity. Specifically, Si increased shoot dry biomass by +113% (2.13-fold), root dry biomass by +60% (1.60-fold), nodule number by +152% (2.52-fold), and nodule dry weight by +273% (3.73-fold) under Hg stress compared to Hg treated plants only. Furthermore, Si enhanced antioxidant defense system, restricted the uptake and accumulation of Hg in different plant tissues, and regulated the expression of genes related to metal transport and detoxification, contributing to improved nodulation and nitrogen fixation under Hg stress. Overall, our findings demonstrate that Si application mitigates the Hg-induced toxicity in mung bean plants by enhancing antioxidant defense, improving nitrogen fixation, regulation of genes involved in metal transport and detoxification, and limiting Hg accumulation.

Vigna radiata↗

PubMed2025

ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans.

All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans , also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans , but other factor(s) are likely involved in directly sensing Mo.

Methanosarcina↗

PubMed2026

Isolation of rhizobia from Ontario soils that are effective at fixing nitrogen with common bean (Phaseolus vulgaris).

UNLABELLED: Common bean (Phaseolus vulgaris) is an important crop in Canada and globally. Like other legumes, common bean establishes symbiotic interactions with nitrogen-fixing bacteria called rhizobia. However, nitrogen fixation by rhizobia in association with common bean is often suboptimal, constraining its productivity and necessitating the application of nitrogen fertilizer. To support the development of high-performing, locally adapted rhizobial inoculants for Ontario common bean growers, we isolated 216 common bean-nodulating rhizobia from southern Ontario soils using a nodule trapping approach with four common bean cultivars. Whole genome sequencing followed by phylogenomic analyses of all rhizobial isolates revealed substantial diversity, assigning them to 11 Rhizobium species, including two novel species. Nearly all isolates belong to the symbiovar phaseoli, spanning the nodC γ-a, γ-b, and α alleles, with four isolates belonging to the symbiovar gallica. Soil origin had a significant impact on the species-level community composition recovered during the nodule trapping experiments. In contrast, host trapping cultivar had only a minor influence on the recovered Rhizobium population. Greenhouse assays demonstrated that one of the novel Rhizobium species exhibited the highest average symbiotic effectiveness, although high-quality isolates were found across multiple species. Together, these results revealed a diverse and genomically variable Rhizobium community capable of forming effective symbioses with common bean in southern Ontario soils. Importantly, our genome-sequenced Rhizobium collection will serve as a valuable resource for identifying competitive and high-quality strains for the development of inoculants tailored to Ontario common bean production. IMPORTANCE: Common bean is a globally important food crop, yet its productivity is often limited by suboptimal nitrogen fixation, forcing growers to rely on synthetic fertilizers. Consequently, identifying high‑performing, locally adapted inoculant strains is essential for reducing dependence on synthetic nitrogen fertilizers and improving the sustainability of temperate agroecosystems. Our study provides a genome‑sequenced collection of common bean-nodulating Rhizobium from southern Ontario, revealing substantial species and genomic diversity across sampling locations. Greenhouse studies allowed us to identify multiple isolates that consistently fix nitrogen with, and enhance the growth of, common bean plants. Our findings highlight strong biogeographical structuring of the effective and competitive subpopulations of rhizobial communities and demonstrate that Ontario soils already harbor strains with high symbiotic potential. In addition, our Rhizobium collection represents a foundational resource to support future inoculant development and enables future work on the ecology, evolution, and applied optimization of legume-rhizobium symbioses.

Nanopore↗

PubMed2026

Whole-genome sequencing and characterization of Pseudomonas stutzeri P1 endophyte isolated from potato unveils plant growth-promoting and other traits.

Endophytic bacteria play an important role in plant growth promotion and stress tolerance, offering sustainable alternatives to chemical inputs in agriculture. In this study, an endophytic bacterial strain P1 was isolated and identified as Pseudomonas stutzeri, a plant-associated bacterium exhibiting multiple plant growth-promoting traits (PGPTs). Biochemical (qualitative and quantitative) and in vitro analyses demonstrated nitrogen fixation, phosphate solubilization, ammonia production, indole-3-acetic acid (IAA) production, biofilm formation, and tolerance to abiotic stresses, including salinity and drought. Furthermore, the P1 strain displayed strong biocontrol activity against the fungal pathogen Fusarium oxysporum f. sp. cumini, indicating its potential to mitigate biotic stress. Whole-genome sequencing generated a high-quality complete genome of 4,758,235 bp. Functional annotation showed enrichment of metabolic pathways associated with plant-microbe interactions and environmental adaptation. Further analyses using KEGG and PGPT-pred data confirmed the presence of genes associated with direct and indirect PGPT, such as nitrogen fixation, phosphate solubilization, biofilm formation, and stress tolerance. The genome also contained genes related to CAZymes, adhesion, and motility, highlighting a strong plant association, whereas the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain. Overall, these findings demonstrate the potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector.

PGPT-associated genes↗

PubMed2026

Genetic legacy effects in a mungbean-wheat rotation reveal potential to breed for system-level yield gains.

Legume crops provide protein-rich food, serve as critical disease breaks in cereal rotations, and contribute to soil fertility through symbiotic nitrogen fixation. However, crop improvement programs typically focus on within-crop performance rather than system-level benefits. We hypothesize that legacy effects (the influence of one crop's genotype on subsequent crop performance) are under genetic control and could be targeted in breeding programs. To test this, we evaluated how 309 genetically diverse mungbean genotypes influenced subsequent wheat performance. The mungbean panel was grown, followed by a single wheat cultivar sown in the same plots. Remarkably, wheat yield varied by nearly 1 t ha-1 (2.52-3.49 t ha-1), depending solely on the preceding mungbean genotype. Legacy effects showed moderate heritability (H2: 0.43-0.65), suggesting untapped genetic potential for breeding. However, these estimates were derived from a single site and season and require validation across environments. Analyses of mungbean traits, soil properties, and volatile organic compounds identified root architecture, symbiotic nitrogen fixation, and the soil microbiome as potential contributors to legacy effects, although these mechanisms remain to be tested directly. Haplotype mapping identified genomic regions in mungbean associated with wheat yield and, to a lesser extent, grain protein, revealing trade-offs between within-crop performance and legacy effects. Genetic simulations based on empirically derived marker effects compared genomic selection strategies targeting mungbean yield, wheat yield, or both simultaneously. A selection strategy placing equal weight on mungbean yield and subsequent wheat yield (50:50 weighting) achieved simultaneous gains in both crops (19.5% and 7.6%), highlighting the potential to breed for system-level productivity with reduced input requirements.

crop rotations↗

PubMed2026

Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments.

Acidobacteriota, one of the most abundant and ubiquitous bacterial phyla in soils, are well recognized for their role in carbon cycling. In contrast, their roles in soil nitrogen cycling remain largely unexplored, although recent metagenome-assembled genome (MAG) analyses suggest that Acidobacteriota may harbor genes involved in nitrogen cycling. Here, we provide culture-based evidence of diazotrophy within this phylum and demonstrate the widespread occurrence of nitrogen-fixing Acidobacteriota across diverse soil types. From grassland and agricultural soils, we isolated five Acidobacteriota strains representing novel taxonomic lineages, four of which harbor functional nitrogenase (nif) gene clusters. These strains were capable of fixing atmospheric nitrogen in vitro and/or in soil microcosms, as evidenced by acetylene reduction, N2-dependent growth, transcription of nif genes, incorporation of 15N into biomass and soil, and inhibition of nitrogenase activity by ammonium. Furthermore, global-scale meta-analysis of soil metagenomes revealed that nif-harboring Acidobacteriota are widely distributed and locally dominant across soil types. These results demonstrate the nitrogen-fixing capability of Acidobacteriota at the organismal level, complementing MAG-based inferences, and underscore their adaptive capacity in nitrogen-limited environments and their potential contribution to terrestrial nitrogen fixation. We also propose novel taxa within the class Terriglobia of the phylum Acidobacteriota, including diazotrophic strains, comprising one novel family, three novel genera, and four novel species: Koromonadaceae fam. nov., Koromonas soli gen. nov., sp. nov., Koromonas humicola sp. nov., Oryzophilus luti gen. nov., sp. nov., and Humiphilus diazotrophicus gen. nov., sp. nov.

Soil Microbiology↗

PubMed2025

A rhamnose-rich O-antigen of Paraburkholderia phymatum MP20 is required for symbiosis with Mimosa pudica.

Paraburkholderia phymatum, a β-proteobacterium, forms a nitrogen-fixing symbiosis with many species of the large legume genus Mimosa as well as with common bean (Phaseolus vulgaris L.). Paraburkholderia are considered to have evolved nodulation independently from the well-studied α-proteobacteria symbionts of legumes. However, the detailed mechanisms important for β-rhizobia-legume symbiosis have not yet been determined. In this manuscript, we have sequenced the genome of P. phymatum MP20, a strain isolated from Mimosa pudica nodules, and utilized transposon mutagenesis to identify a mutant that showed delayed and ineffective nodulation of M. pudica. Further analysis revealed that the mutant strain produced an altered lipopolysaccharide lacking rhamnose containing O-antigen. Complementation with the wild-type gene restored the symbiosis. Microscopic analysis of the ineffective nodules showed that the mutant strain did not infect the cortical cells but was restricted to the endodermis. The results suggest that the O-antigen of P. phymatum is important for the bacterial infection of cortical cells and for nodule maturation. Further research will unveil the specific involvement of the glycosyltransferase gene in LPS biosynthesis and its impact on successful nodule formation by P. phymatum.IMPORTANCEThe nitrogen-fixing symbiosis between legumes and rhizobia is important for agricultural and environmental sustainability. The mechanisms of the symbiotic interactions are extensively studied using α-rhizobia. In contrast, mechanisms of symbiotic interactions important for β-rhizobia and their Caesalpinioid (mimosoid) legume hosts are not well known. Here, we describe the genome sequence of P. phymatum MP20, a β-rhizobia isolated from the nodules of M. pudica, and isolation and characterization of a transposon mutant defective in symbiosis. We demonstrate that the O-antigen of the LPS is required for nodulation and symbiotic nitrogen fixation. This study broadens our knowledge of symbiotic interactions in β-rhizobia and will lead to a better understanding of the wider rhizobial-legume symbiosis apart from the α-rhizobia.

Symbiosis↗

PubMed2026

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.

BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses. RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation. CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.

Rhizosphere↗

PubMed2026

Azotobacter vinelandii gene fitness following carbon shift from sucrose to acetate, succinate and glycerol.

Nitrogen-fixing microbes are a primary contributor of this important nutrient to the global nitrogen cycle. Biological nitrogen fixation (BNF) through the enzyme nitrogenase requires extensive energy that in whole cells is generally studied during the oxidation of carbohydrates such as sugars. The nitrogen-fixing bacterium Azotobacter vinelandii is a model diazotroph for the study of aerobic BNF. Much is known about metabolism in A. vinelandii when cultured on a simple medium where energy is provided primarily in the form of sucrose or glucose. Outside of the laboratory, this soil bacterium grows on metabolites primarily derived from plant root exudates or from the degradation of dead plant matter. In this work, we expand on previous studies looking at genes that are essential to BNF in A. vinelandii when grown on sucrose medium using transposon sequencing (Tn-seq). We applied Tn-seq to determine the genes essential to growth when the medium was shifted to acetate, succinate or glycerol as the primary carbon and energy source to fuel both growth and BNF. A global overview of the genes of central metabolism and those directing substrates toward central metabolism, along with a selection of unexpected genes that were essential for specific growth substrates, is provided.

Azotobacter vinelandii↗

PubMed2026

Complete genome sequences of three effective nitrogen-fixing strains of Bradyrhizobium ottawaense from Canada.

We report complete genome sequences of three nitrogen-fixing Bradyrhizobium ottawaense strains isolated from soybeans in Canada. Each ~9.0 Mb genome (chromosome and plasmid) harbors predicted genes for nodulation, nitrogen fixation, N2O mitigation, phosphate solubilization, iron acquisition, phytohormone production, and stress tolerance, highlighting their potential for sustainable agriculture.

Bradyrhizobium ottawaense↗

PubMed2026

PGPR inoculation and growth enhancement of crops cultivated in hydroponic systems.

Plant growth-promoting rhizobacteria (PGPR) are ubiquitous rhizosphere microorganisms that promote plant health through various mechanisms. Although the study of PGPR inoculants in soil has been done for ages, their application in hydroponic systems has received relatively limited attention. This review identifies PGPR inoculants that are commonly used in hydroponics, methods of application, and their effects on plant growth and nutrient use efficiency. Literature shows that PGPR inoculants improve plant performance in controlled hydroponic systems through the production of growth-stimulating substances, nitrogen fixation, and improved nutrient acquisition. However, the plant growth responses are highly variable depending on the composition of nutrient solutions, environmental factors, crop and microbe species, and the type of hydroponic system. The review identifies various challenges of PGPR inoculation in hydroponic systems and future research directions to address the current gaps. Generally, the productivity of hydroponic systems can be enhanced through advanced inoculation strategies and the development of suitable carrier materials to improve inoculant survival, viability, and functions. Emphasis should also be placed on designing system-specific microbial consortia and Synthetic communities that are tailored to the unique ecological conditions of hydroponic systems.

Hydroponics↗

PubMed2026

Genomic and Molecular Interaction Analysis of NodD1 in a Novel Bradyrhizobium yuanmingense sp. B64 Isolate for Nodulation and Symbiosis of Legume Plants.

Rhizobial bacteria are known for their ability to fix nitrogen for leguminous plants and their essential function for sustainable agriculture. This study characterizes the taxonomic status and functional potential of the Bradyrhizobium B64 isolate using integrated genomic and molecular approaches. The whole genome of the B64 isolate was sequenced via Illumina paired-end technology. Species delimitation was performed using average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH). The NodD1 protein structure was modeled using AlphaFold3 and validated by Ramachandran plot analysis. Molecular docking was then conducted to evaluate interactions between NodD1 and four signaling flavonoids: Apigenin, Daidzein, Genistein, and Naringenin. Genomic analysis revealed a maximum ANI of 94.4% and dDDH values between 51.4 and 62.4%. Since these values fall below the standard prokaryotic thresholds (ANI < 95%; dDDH < 70%), the B64 isolate is identified as a novel species. Physiological assays confirmed nitrogen fixation (1.97 ppm), IAA production (3.67 ppm), and phosphate solubilization (26.10 ppm). Structural validation showed 100% of NodD1 residues in allowed regions, ensuring high model reliability. Docking simulations demonstrated strong binding affinities across all flavonoids, with binding free energies ranging from - 8.8 to - 9.0 kcal/mol. Daidzein exhibited the highest thermodynamic stability (- 9.0 kcal/mol), whereas apigenin showed the most extensive residue interaction network. The B64 isolate is a novel Bradyrhizobium species with a high symbiotic capacity. The stable NodD1-flavonoid interactions provide a molecular basis for efficient nodulation, positioning B64 as a promising candidate for developing lipo-chitooligosaccharide (LCO)-based biofertilizers.

Bradyrhizobium↗

PubMed2026

Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.

Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.

Seawater↗

PubMed2026

A conserved partner-switching system controls terminal differentiation in multicellular cyanobacteria.

UNLABELLED: Canonical partner-switching systems (PSSs) regulate sigma factor activity through reversible phosphorylation, but their established roles have been largely limited to stress responses and sporulation in Firmicutes. Whether this regulatory mechanism also controls developmental cell fate decisions in other bacterial phyla has remained unknown. Here, we identify a canonical PSS that governs heterocyst differentiation in the multicellular cyanobacterium Anabaena sp. PCC 7120. This system comprises the anti-sigma factor All2284 (NfsS) and the anti-anti-sigma factor All2283 (NfsR). Structural predictions and biochemical assays showed that NfsS phosphorylates NfsR on a conserved serine residue, whereas bacterial two-hybrid and co-purification assays demonstrated that NfsS binds the developmental sigma factors SigC and SigE. Deletion of nfsR abolished heterocyst formation and diazotrophic growth, and transcriptomic analysis revealed broad failure to induce late heterocyst genes, including nitrogen fixation functions such as nifHDK and fdxH. Phylum-wide comparative genomics further showed that PSS genes and putative functional clusters are strongly enriched in filamentous and heterocyst-forming taxa, indicating an association between the expansion of these signaling modules and the emergence of multicellularity and developmental specialization. Together, these findings establish a PSS as a direct regulator of terminal cell differentiation in a gram-negative bacterium and reveal partner switching as a conserved regulatory principle linking environmental signaling to developmental fate in a major bacterial phylum. IMPORTANCE: While partner-switching systems are classically associated with stress responses and sporulation control in Firmicutes, whether this regulatory logic governs developmental decisions in other bacterial phyla has remained unknown. Here, we establish that a related partner-switching mechanism operates in a distinct bacterial lineage, the cyanobacteria, where it controls a major developmental transition involving terminal cell differentiation. Specifically, we show that a phosphorylation-dependent checkpoint involving the anti-sigma factor NfsS and the anti-anti-sigma factor NfsR directly regulates heterocyst formation. Disruption of this switch abolishes cell differentiation and diazotrophic growth, revealing that this system is an obligate gatekeeper for terminal differentiation. Conceptually, these findings substantially extend the known functional repertoire of partner-switching circuits: rather than controlling stress adaptation or spore dormancy, this module has been co-opted to govern a complex, multicellular developmental program in an organism that underpins global carbon and nitrogen cycles. This work, therefore, establishes a new paradigm for phosphorylation-based control of developmental sigma factors and provides a tractable model for dissecting how conserved signaling modules are rewired to drive lineage-specific innovations across the bacterial domain.

cell differentiation↗

PubMed2026

Plant-derived and microbial biostimulants in sustainable agriculture: mechanisms, applications, and challenges.

Plant biostimulants have emerged as transformative and sustainable tools for improving crop productivity, resource-use efficiency, and resilience under rapidly intensifying environmental stresses. Unlike conventional agrochemicals, biostimulants function by activating physiological, biochemical, and molecular processes that optimize plant performance without directly supplying nutrients or exerting pesticidal effects. This review comprehensively examines the integrated roles of plant-derived and microbial biostimulants in sustainable agriculture, with particular emphasis on microbial-mediated mechanisms underlying plant stress adaptation and rhizosphere functioning. Plant-derived biostimulants, including seaweed extracts, humic substances, protein hydrolysates, amino acids, and chitosan, enhance nutrient acquisition, root architecture, hormonal regulation, and antioxidant defense systems. More importantly, microbial biostimulants, such as plant growth-promoting rhizobacteria (PGPR), endophytic microorganisms, mycorrhizal fungi, actinomycetes, yeasts, and cyanobacteria, exert multifunctional effects through biological nitrogen fixation, mineral solubilization, phytohormone biosynthesis, volatile signaling, osmolyte accumulation, pathogen suppression, and modulation of stress-responsive genes. These beneficial microorganisms reshape rhizosphere microbial communities, improve nutrient cycling, and enhance plant tolerance to drought, salinity, heat, and heavy metal toxicity. Emerging evidence from genomics, transcriptomics, metabolomics, and microbiome-based investigations has further revealed the molecular networks and signaling pathways governing biostimulant-induced resilience and plant-microbe interactions. Despite their substantial promise, inconsistent field performance, formulation instability, regulatory limitations, and inadequate mechanistic understanding continue to restrict their large-scale adoption. This review highlights recent advances in microbial and plant-derived biostimulants while identifying critical knowledge gaps and future opportunities for precision biostimulant engineering, microbiome manipulation, and climate-resilient crop management. The integration of next generation biostimulant technologies into sustainable agricultural systems may significantly reduce dependence on agrochemicals while improving crop productivity, environmental sustainability, and global food security.

Agriculture↗

PubMed2026

Have we entered a 'post-model' era in plant biology?

Models such as arabidopsis (Arabidopsis thaliana) have underpinned genomic and physiological research in plant science. Advances in genome sequencing, pangenomics, and genome editing have prompted claims of a 'post-model' era, with model-crops and crops such as rice and bread wheat combining agricultural relevance with experimental tractability. We argue that the 'simplicity-to-complexity' approach remains valid, although model systems have evolved. Arabidopsis remains indispensable for interpreting multi-omics data, testing developmental hypotheses, and generating mechanistic insights difficult to obtain in crops. Linking these strengths to model-crops adds translational value by bridging discovery and breeding, while niche models such as Brachypodium distachyon and legumes address grass cell wall biology and nitrogen fixation. Future progress depends on diverse species with complementary strengths across fundamental and applied plant biology.

arabidopsis↗