Harnessing Plant-Bacteria Interactions for Applications in Agriculture Plants exist as complex holobionts, whose health and productivity depend on dynamic interactions with diverse microbial partners. This chapter explores the ecological, molecular, and biotechnological dimensions of plant-microbe relationships, tracing the continuum from natural symbioses to their translation into microbe-based agricultural applications. It examines how plants actively structure their microbial communities across distinct yet interconnected compartments, such as the rhizosphere, phyllosphere, and endosphere, and how these microorganisms in turn modulate plant physiology, nutrient acquisition, and defense. Moving beyond the study of individual strains, we discuss the growing relevance of community-level approaches and synthetic microbial consortia as frameworks to decipher and replicate the ecological principles that sustain beneficial interactions. Finally, this chapter reflects on how the integration of ecological knowledge with emerging technologies such as synthetic biology, systems modeling, and artificial intelligence offers new opportunities to design resilient, predictable, and sustainable microbe-based solutions. By learning from these naturally optimized alliances, we can guide the transition to more adaptive and sustainable agricultural systems while sustaining plant health and productivity.

Ouch... The game in this review is to find all the inaccuracies. It's a peer-review version of "Where's Waldo/Wally?"... Harnessing Plant-Bacteria Interactions for Applications in Agriculture | Springer Nature Link

Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation | bioRxiv

Identification of nodule number-related loci and the candidate gene GmbHLH135 in soybean under low phosphorus stress Soybean plays a crucial role in meeting nitrogen demands through biological nitrogen fixation (BNF), a process highly dependent on phosphorus availability. Low-phosphorus (LP) stress significantly impairs nodule development, thereby affecting soybean growth and productivity. Genome-wide association study (GWAS) was conducted using the ratio of the nodule numbers (RNNs) under normal phosphorus condition and low-phosphorus condition in a natural population with 272 soybean accessions grown in three environments. A total of 21 novel single nucleotide polymorphisms (SNPs) related to nodule-related traits located on soybean chromosome 5 and chromosome 6 were repeatedly detected in two environments. Among them, 18 SNPs related to the ratio of the nodule number to the total plant weight under the normal phosphorus (NP) condition to that under the LP condition (RNP) formed a SNP cluster, and one SNP (AX-94275075) in this SNP cluster was detected simultaneously for multiple traits. A candidate gene, named GmbHLH135, which encodes a member of the basic helix-loop-helix (bHLH) family of transcription factors, was functionally characterized. The expression of GmbHLH135 was affected by low-phosphorus stress. Overexpressing and suppressing GmbHLH135 in soybean hairy roots resulted in a decreased and increased nodule number, respectively. GmbHLH135-overexpressing transgenic soybean lines presented decreased nodule number, brassinosteroids (BR) contents, plant biomass and yields. These findings could highlight the role of identified significant SNPs and the candidate gene GmbHLH135 in regulating nodule development under LP stress, provide valuable insights into the molecular mechanisms underlying phosphorus-mediated nodule growth and offer potential targets for soybean breeding.

@oswaldovaldesl.bsky.social this one is for you! -> Identification of nodule number-related loci and the candidate gene GmbHLH135 in soybean under low phosphorus stress

Great paper from @poolelaboxford.bsky.social on the sanctions of rhizobial cheaters and how rhizobia can evade them. -> Resource allocation to pea plant nodules impacted by nitrogen fixation potential of infecting rhizobia

Frontiers | Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis in legumes

Inoculation with indigenous nitrogen-fixers enhances seedling growth and nutrient uptake in a greenhouse bioassay  Desert ecosystems in Kuwait are increasingly affected by land degradation, resulting in nutrient-limited soils that constrain native plant establishment. Harnessing indigenous diazotrophic bacteria adapted to arid environments may provide a sustainable strategy to improve plant growth and nutrient acquisition. Free-living and root-associated nitrogen-fixing bacteria contribute substantially to nitrogen inputs in arid ecosystems and may enhance plant growth, performance and nutrient acquisition under nutrient-poor conditions. This study evaluated the growth performance and nutrient uptake ability of four native plant species of Kuwait following inoculation with a consortium of selected indigenous putative diazotrophs isolated from the Kuwait desert soils. The seedlings of Vachellia pachyceras were inoculated with both indigenous root-nodule bacteria isolated from Kuwait desert and a commercial inoculum to evaluate their symbiotic efficiency. The seedlings were cultivated under greenhouse conditions using either native desert soils or a potting mix substrate to assess the influence of growth medium or inoculation response. Across species, inoculation significantly enhanced plant dry mass and nutrient uptake compared to the non-inoculated controls. The magnitude of improvement varied among bacterial density, host plants, and growth substrate. These findings support the potential use of indigenous diazotrophs as biofertilizers to enhance plant growth and nutrient uptake of native plant species, and for restoration and revegetation efforts in arid environments. However, direct measurements of nitrogen fixation were not conducted and should be addressed in future field-based studies. This study represents the first evaluation of Kuwait’s native seedlings inoculated with indigenous diazotrophs, highlighting their potential for sustainable ecosystem restoration.

Inoculation with indigenous nitrogen-fixers enhances seedling growth and nutrient uptake in a greenhouse bioassay | PLOS One

Specialised root hair cells facilitate rhizobial infection | bioRxiv

Calreticulin modulates the infection process and nodule organogenesis in the Phaseolus vulgaris-Rhizobium symbiosis | bioRxiv

I am concerned that this study is entirely based on relative, not absolute, abundances and compares microbial communities between very different plant species -> Co-occurrence networks reveal candidate AMF–microbe assemblages for generalist and crop-specific inocula

WOX5 expression stimulated by the transcription factor NF-YAc reprograms cortical cells for nodule primordium initiation in soybean Reprogramming of differentiated root cortical cells into proliferative stem cells is a prerequisite for legume nodule organogenesis, yet the molecular trigger that confers stem-cell identity upon these cortical cells remains elusive. Here we demonstrate that, in soybean (Glycine max), the canonical root stem-cell regulator WUSCHEL-RELATED HOMEOBOX gene WOX5 is activated by rhizobia specifically in cortical cells that will give rise to nodule primordia. CRISPR–Cas9-mediated knockout of the three WOX5 homologs, wox5abc mutants, reduced nodule number and attenuated nitrogenase activity, attributable to a decrease in primordium density rather than impaired rhizobial infection. Promoter dissection identified a 442 bp legume-specific promoter fragment within the WOX5a promoter that is both necessary and sufficient for primordium-specific expression. Chromatin immunoprecipitation and dual-luciferase assays revealed that this promoter fragment is directly bound by the symbiosis-responsive transcription factor NF-YAc to activate expression of WOX5a. Loss of NF-YAc phenocopied wox5abc, and NF-YAc overexpression failed to rescue nodulation in wox5abc mutants. Collectively, our findings reveal that NF-YAc-mediated activation of WOX5 initiates a de novo stem-cell niche in root cortical cells, providing the critical developmental trigger for nodule primordium initiation in soybean.

WOX5 expression stimulated by the transcription factor NF-YAc reprograms cortical cells for nodule primordium initiation in soybean | Journal of Experimental Botany | Oxford Academic

The microbes within: what happens inside Acacia longifolia nodules during development Plant-microbe interactions are important for plant development, particularly mutualisms where host promiscuity allows associations with diverse microbial partners. This flexibility is crucial for adaptation, especially in invasive species. Understanding microbial community dynamics is therefore key to explain invasion success. Acacia longifolia, a member of the Fabaceae family, is an aggressive invader capable of establishing symbioses with several microorganisms including rhizobia within root nodules. These interactions promote growth and play a role in its invasive capacity. However, the nodulation process remains poorly understood, regarding microbial succession and the dynamics of these communities, following nodule development. We assessed microbial profiles in root nodules from 1-year-old saplings in two habitats using Next-Generation Sequencing, targeting 16 S and 25-28 S rRNA genes. Nodules were classified by size as a proxy for developmental stage. Our findings show that (i) different developmental stages have a characteristic microbial community; (ii) there is a shift in dominance (i.e., abundance) from early to fully developed stage, with nodules containing respectively more microbes from seed or from soil; (iii) microbial partners change in each habitat. The microbial succession indicates a shift in abundance over time, highlighting mostly the changes in recruitment: while several genera that dominate early-stage nodules are mostly found in seeds, fully developed nodules have a community mostly acquired from the surrounding soils and showed a much more specialized fungal community. Our study shows a dynamic assembly of root nodules communities within invasive range that might contribute to the plasticity and adaptative strategy of A. longifolia in these new habitats.

The microbes within: what happens inside Acacia longifolia nodules during development | Symbiosis | Springer Nature Link

Enhancement of fiber content and cannabinoids of hemp using arbuscular mycorrhizal fungi and endophytic fungi | Scientific Reports

Automated computer vision-based quantification of fluorescent root nodules in legume-rhizobia systems  Accurate quantification of root nodules is essential for understanding legume–rhizobia symbiosis and improving biological nitrogen fixation. Fluorescently labeled rhizobial strains enable clear visualization of nodules; however, automated segmentation and counting remain challenging under data-limited conditions. In this study, we present a systematic benchmarking framework to evaluate three complementary approaches for fluorescent root nodule segmentation and quantification: a rule-based computer vision pipeline with optimized color-space thresholding, supervised deep learning using YOLOv12-seg transfer learning, and the training-free Segment Anything Model (SAM). Experiments were conducted on a pilot-scale dataset comprising 16 fluorescent images of Pisum sativum roots with manually annotated blue and yellow nodules. To address instability associated with small test sets, a 4-fold cross-validation strategy was employed, and performance was reported as mean ± standard deviation across folds. Model performance was evaluated using pixel-level overlap metrics (IoU, Dice), instance-level precision, recall, and F1-score, and total nodule counting error (MAE and ). The rule-based approach achieved strong segmentation and counting accuracy when fluorescence provided clear chromatic separation, demonstrating near-zero bias in total counts. Among deep learning models, YOLOv12-m provided the most balanced performance, achieving high segmentation accuracy while minimizing counting error and inter-fold variability. Larger YOLO variants did not consistently improve quantitative outcomes, suggesting overfitting under data-scarce conditions. SAM produced stable segmentation masks without training, but systematically underestimated nodule counts and lacked intrinsic class discrimination. Overall, the results highlight that segmentation fidelity alone is insufficient for reliable biological phenotyping and that accurate nodule counting must be explicitly considered. While limited in scope, this study establishes a reproducible benchmarking framework for fluorescent nodule phenotyping and provides practical guidance on method selection under constrained data and computational resources. The findings are intended as a proof-of-concept and motivate future work on larger, publicly available fluorescent datasets and hybrid segmentation strategies.

Automated computer vision-based quantification of fluorescent root nodules in legume-rhizobia systems - ScienceDirect

CRISPR/Cas9-mediated knockout of PsLykX gene of pea (Pisum sativum L.) leads to loss of symbiotic nodules Pea (Pisum sativum L.) symbiosis with nodule bacteria supplying plants with additional nitrogen is a very specific plant-microbial interaction. Mutual recognition of the partners occurs through perception of bacterial signal molecules (Nod factors) by plant receptors, enabling bacterial entry via root hairs and formation of nitrogen-fixing nodules. The pea gene Sym2, described but not yet cloned, exists in different allelic forms defining the symbiotic specificity, and is therefore thought to encode a Nod factor receptor. The PsLykX gene is a strong candidate for the Sym2, since its alleles coincide with high or low symbiotic specificity; however, to date, no genetic evidence has been obtained for a role of PsLykX in symbiosis. Here, we knocked-out the PsLykX in European pea cultivar Caméor using Agrobacterium-mediated hairy root transformation and CRISPR-Cas9 editing. The roots with editing events confirmed by sequencing lost the ability to form nodules, providing direct functional evidence that PsLykX is essential, at least, for the symbiosis between pea cultivar Caméor and Rhizobium ruizarguesonis RCAM1026.

Expected but good to see! -> CRISPR/Cas9-mediated knockout of PsLykX gene of pea (Pisum sativum L.) leads to loss of symbiotic nodules | Transgenic Research | Springer Nature Link

Full article: Mycorrhizal specificity in orchids: a multidimensional filtering framework

Integrating microbial siderophores into concepts of plant iron nutrition Iron is a crucial micronutrient for plants, but its availability in soil is often limited. Iron deficiency compromises plant growth, and low iron content in crops contributes substantially to the ‘hidden hunger’ that affects human health globally. The elucidation of Strategy I (reduction-based) and Strategy II (phytosiderophore-based) for iron acquisition was a milestone in plant biology and enabled the development of biofortification concepts. However, recent genetic evidence reveals that the boundary between the two strategies is blurred, with many plants possessing elements of both. Here we show that plant iron uptake mechanisms are more complex and diverse than the classical dichotomy suggests. We review evidence for this integrative view and highlight the critical role of microbial siderophores. We explain how plants access iron from microbial siderophores not only indirectly through Strategy I and II pathways but also via the direct uptake of iron–siderophore complexes, an overlooked mechanism that we introduce as Strategy III. We propose three potential routes for this direct uptake and conclude that harnessing Strategy III holds great potential for novel agricultural interventions to enhance iron biofortification and improve human health.

Very clear review on plant iron acquisition in the context of plant-microbe interactions -> Integrating microbial siderophores into concepts of plant iron nutrition

US20260055423A1 - Methods, plants and compositions for overcoming nutrient suppression of mycorrhizal symbiosis - Google Patents

That's frustrating... I could not find the accession numbers of these MtLUX and MtRVE1 genes in the paper.

Exploring Azotobacter: a nitrogen-fixing microorganism as a powerhouse for sustainable and green ammonia synthesis Ammonia (NH₃) is a critical molecule for agriculture, industry, and emerging energy applications. However, current industrial production by the Haber–Bosch process is energy-intensive and environmentally damaging, accounting for a significant portion of global CO₂ emissions. In contrast, biological nitrogen fixation (BNF) offers a sustainable alternative by converting atmospheric nitrogen (N₂) into NH₃ under ambient conditions through the action of nitrogenase enzymes. Among diazotrophic microorganisms, Azotobacter vinelandii stands out due to its ability to fix nitrogen aerobically, supported by unique physiological and genetic adaptations that protect its oxygen-sensitive nitrogenase. This review presents a comprehensive overview of NH₃ synthesis with A. vinelandii, highlighting its biochemical mechanisms, nitrogenase structure and function, and the protective strategies that enable aerobic nitrogen fixation. We further examine the diversity and advantages of Azotobacter strains, with a focus on A. vinelandii’s potential for engineered NH₃ production through synthetic biology, metabolic engineering, and emerging bio-based technologies such as photobiocatalysis and bioelectrochemistry. Recent innovations aimed at improving nitrogenase expression, cellular stability, and overall system efficiency are discussed in the context of advancing A. vinelandii as a robust chassis for industrially scalable, carbon-neutral NH₃ synthesis. The review emphasizes the importance of free-living nitrogen fixers in addressing the challenges of sustainable NH₃ production and provides insights into future directions for research and application.

Good review on the superstar model of nitrogen fixation... Azotobacter! -> Exploring Azotobacter: a nitrogen-fixing microorganism as a powerhouse for sustainable and green ammonia synthesis

Rhizobial auxin activates transcription factors to orchestrate YUC2-dependent auxin biosynthesis for soybean nodule development] Establishing the symbiosis between legumes and nitrogen-fixing rhizobia requires the precise modulation of auxin levels. However, our understanding of auxin’s regulatory roles, particularly rhizobia-derived auxins, remains limited. Our study reveals that the auxin biosynthesis gene YUC2a is essential for the spatiotemporal control of nodule development in soybean (Glycine max). This process is orchestrated by three transcription factors: Nuclear Factor-YA9 (NF-YA9), Lateral Organ Boundaries Domain 41 (LBD41), and Nodule Inception 1a (NIN1a). In the early stages of nodulation, rhizobial auxin stimulates NF-YA9 expression, NF-YA9 then activates YUC2a expression in the cortical cell layer, establishing optimal auxin levels for nodule initiation. In the middle stages, rhizobial auxin elevates LBD41 expression, and LBD41 suppresses YUC2a to control auxin levels, ensuring proper rhizobia colonization. In the late stages, rhizobial auxin inhibits NIN1a expression, which increases YUC2a expression in nitrogen-fixing symbiosomes, fine-tuning optimal auxin levels for nodule maturation. Disruption of YUC2a and its homologs impairs cell division in nodule primordia, reducing nodule density and nitrogen fixation capacity. Conversely, cortex-specific overexpression of YUC2a promotes nodule formation but inhibits rhizobia colonization. This dynamic auxin regulation optimizes nodule development in soybean, revealing rhizobia-derived auxin's critical role in nitrogen-fixing symbiosis.

That's even more complicated than I anticipated... Rhizobial auxin activates transcription factors to orchestrate YUC2-dependent auxin biosynthesis for soybean nodule development

Role of the MtLUX-MtRVE1 Regulatory Module in Auxin-Mediated Root Development and Nodule Formation in Medicago truncatula The circadian clock synchronizes a multitude of biological events with environmental changes, thereby optimizing plant growth and development. In legumes, nodule formation, a pivotal process that sustains symbiotic nitrogen fixation, is one such event regulated by the circadian clock. Nevertheless, the mechanisms underlying the circadian clock's regulation of nodule formation and nitrogen fixation are still poorly elucidated. Herein, we unveil that the core clock gene LUX ARRHYTHMO (LUX) exerts a crucial role in modulating nodule formation and root development via auxin biosynthesis pathways in the model legume Medicago truncatula. Our findings indicate that MtLUX directly associates with the promoter of MtRVE1, a clock output gene involved in auxin biosynthesis, both in vivo and in vitro, thereby repressing its expression. Biochemical and genetic data further corroborate that the MtLUX-MtRVE1 regulatory module adjusts root architecture and nodule formation through the fine-tuning of auxin biosynthesis. These discoveries reveal a mechanism whereby the circadian clock integrates hormonal pathways to regulate nodule formation, thereby linking circadian regulation, auxin biosynthesis, and nitrogen fixation in legumes. This research lays the groundwork for enhancing legume growth and nitrogen acquisition under fluctuating environmental conditions.

Role of the MtLUX-MtRVE1 Regulatory Module in Auxin-Mediated Root Development and Nodule Formation in Medicago truncatula | Horticulture Research | Oxford Academic

Ancestral functionality and symbiotic refinement of NIN in root nodule symbiosis | Nature Communications

Unraveling the Mysteries of Root Nodule Symbiosis An intriguing and intricate biological process, root nodule symbiosis is vital to the nitrogen cycle and potentially has far-reaching consequences for the long-term viability of agriculture. This chapter delves into the intricate mechanisms underlying root nodule symbiosis and explores the latest insights into its molecular, genetic, and ecological aspects. From the molecular signaling between host plants and nitrogen-fixing rhizobia to the environmental implications for plant–microbe interactions, we discuss the multifaceted nature of this symbiotic relationship. Furthermore, we highlight the practical applications of unraveling these mysteries, including developing sustainable agricultural practices, biofertilizers, and bioremediation strategies. By synthesizing the latest research findings, this chapter aims to comprehensively understand root nodule symbiosis and its potential implications for agriculture, ecology, and environmental sustainability. In this chapter, we will unravel the mysteries of root nodule symbiosis. We will explore the current landscape of plant–microbial–nanoparticle interactions better to understand the intricate relationships within root nodule symbiosis. This exploration will provide valuable insights and applications for furthering our knowledge in this fascinating field.

Unraveling the Mysteries of Root Nodule Symbiosis | 1 | Insights and A

Coevolution of plant–microbe interactions, friend–foe continuum, and microbiome engineering for a sustainable future

Presymbiotic activation of karrikin signaling creates a permissive state for arbuscular mycorrhizal symbiosis by derepressing the NSP1–NSP2–SLR1 transcriptional complex in rice

Kathrin Wippel (UvA): Bacterial interactions influencing microbiome composition and plant performance
#NIME2026

Yeah!

How Should Policymakers Respond to Rising Fertilizer Prices? The Iran war has driven up the cost of fertilizer, squeezing farmers in the developing world. Prof. Kevin Donovan says that governments can respond most effectively by shifting from broad subsidies to...

Good article making the point of why we need alternatives to synthetic nitrogen fertilizers like biological nitrogen fixation for smallholder farmers:
insights.som.yale.edu/insights/how...

How arbuscular mycorrhizal fungi maintain plant nitrogen acquisition under drought While arbuscular mycorrhizal fungi (AMF) influence plant nitrogen (N) acquisition and drought tolerance, the complex interactions governing N uptake under varying water deficits remain unclear. To addressing this, well-characterized mycorrhizal tomato type (MYC) and its mycorrhiza-defective mutant (referred to as rmc) were labeled with 15NH4Cl under normal and drought conditions in a greenhouse. We quantified 15N allocation in plant biomass and rhizosphere soil, while assessing shifts in activities of β-N-acetylglucosaminidase and leucine aminopeptidase. MYC increased tomato total biomass relative to rmc under both water regimes, with the most pronounced root biomass enhancement observed under drought (64–74%). Similarly, MYC increased tomato 15N uptake compared to rmc, with a greater increase under drought (80–104%) versus normal (55–94%) conditions. This phenomenon can be ascribed to elevated 15N enrichment in microbial biomass and increased activities of β-N-acetylglucosaminidase and leucine aminopeptidase. This was further supported by the positive correlations between tomato 15N acquisition and 15N incorporation into microbial biomass as well as activities of β-N-acetylglucosaminidase and leucine aminopeptidase. Collectively, AMF alleviated drought stress and improved plant productivity through enhanced root N-acquisition capacity, increased microbial biomass and enzyme secretion, and optimized soil N mineralization processes.

How arbuscular mycorrhizal fungi maintain plant nitrogen acquisition under drought | Biology and Fertility of Soils | Springer Nature Link

Medicago truncatula Iron-chaperone 1 (ICHAP1) is required for symbiotic nitrogen fixation | bioRxiv