Open research questions in Plant-Microbe Interactions and Immunity

What the literature leaves open

• Most race-specific resistance to P. infestans is rapidly overcome by evolving pathogen populations. The mechanisms underlying the durability of the R8 gene are not well understood. There is a need to identify and characterize R8 gene analogs that act as negative modulators of R8-mediated immunity.

  A built-in brake for plant immunity: Resistance (R) protein–mediated immunity is fine-tuned by R gene analogs · 2026 · DOI

• Little is known about the effect of Streptomyces on maize growth under water deficit. There is a need to investigate rhizospheric Streptomyces isolates as sustainable tools to mitigate drought-related constraints in maize.

  Streptomyces rhizobacteria enhance growth and drought tolerance in maize (Zea mays L.) under greenhouse conditions · 2026 · DOI

• The lack of understanding of how LRR-RKs specifically recognize their ligands. The need to define the minimal region of CTNIP4 required for high-affinity HSL3 interaction and signalling activation.

  A disulfide bond sculpts the CTNIP4 phytocytokine fold for recognition by the receptor kinase HSL3 · 2026 · DOI

• The lack of understanding of the biocontrol mechanisms of Pseudomonas strains against Geotrichum citri-aurantii. The need to explore the role of the T6SS in the antifungal activity of Pseudomonas strains.

  Plant growth-promoting traits and biocontrol mechanism of three Pseudomonas strains against Geotrichum citri-aurantii · 2026 · DOI

• The need to develop strategies to mitigate the effects of salinity on crops such as rapeseed. The lack of understanding of the mechanisms by which plant growth-promoting rhizobacteria (PGPR) mitigate salinity stress. The need to identify novel PGPR that can be used to improve crop productivity under salinity stress.

  Modulation of Physiological Responses and Salinity Tolerance in Rapeseed by Zhihengliuella halotolerans Isolated from the Rhizosphere of Alhagi persarum · 2026 · DOI

• The need to find an eco-friendly alternative for pest management. The challenge of scaling up the use of biological control methods for commercial agriculture.

  Biocontrol of Trialeurodes vaporariorum by Bacillus velezensis and Bacillus licheniformis through lipopeptide production and induction of tomato defense · 2026 · DOI

• The lack of eco-friendly alternatives for pest management. The need to investigate the effect of bacterial treatments on the nutrient content in the leaves of tomato plants. The importance of finding a biological control method for Trialeurodes vaporariorum.

  Biocontrol of Trialeurodes vaporariorum by Bacillus velezensis and Bacillus licheniformis through lipopeptide production and induction of tomato defense · 2026 · DOI

• The need for a deeper understanding of plant-microorganism interactions and their applications in agriculture. The lack of effective biotechnological strategies for replacing synthetic pesticides in pest and disease management. The limited understanding of the relationships between soil properties, microbial communities, and rhizosphere interactions.

  Editorial: Enhancing plant stress resilience: innovative roles of plant growth-promoting bacteria (PGPB) in sustainable agriculture and crop protection · 2026 · DOI

• The limited sample size is identified as a challenge, which prevented inferential statistical analysis.

  Microbial community structure of cigar tobacco leaves in Hunan production area and its regulatory mechanism on quality formation · 2026 · DOI

• The optimal concentration of methyl jasmonate for enhancing tuber peroxidase activity and increasing total flavonoid and saponin contents needed to be determined. The research required the development of a suitable experimental design to evaluate the effects of different methyl jasmonate concentrations.

  Effects of different concentrations of exogenous methyl jasmonate on tuber metabolism and rhizosphere bacterial community dynamics in Polygonatum cyrtonema Hua · 2026 · DOI

• The study notes that plant growth regulators can alter mycotoxin production, but NAA was not among the compounds tested. There is a lack of standardization in the measurement of NAA effects on microorganisms. The paper identifies inconsistencies in some of the source data.

  Direct Effects of Naphthaleneacetic Acid on Fungi, Bacteria and Microalgae: An Evidence Map with Dose–Response Synthesis and Its Implications for Plant-Associated Microbiology · 2026 · DOI

• The need for further research to fully explore the potential of plant-growth-promoting bacteria as natural alternatives to mineral fertilizers.

  Effect of Plant Growth-Promoting Bacteria on Photosynthetic Parameters of One-Year-Old Sessile Oak Seedlings · 2025 · DOI

• The study did not find statistically significant differences between the treatments. The study had a limited number of observations (four times during the growing season). The study used a specific type of seedling (one-year-old sessile oak seedlings).

  Effect of Plant Growth-Promoting Bacteria on Photosynthetic Parameters of One-Year-Old Sessile Oak Seedlings · 2025 · DOI

• Identification of the metabolites that accumulate in the F2-2 culture broth and determination of their biological activity - Further studies using purified trehalolipids to confirm or refute the hypothesis that the protective effect of the strain under phytopathogenic conditions is associated with stimulation of the plant immune system by these compounds - Analysis of the role of the phz genes in Rhodococcus spp.

  Phytostimulating Properties of the Oil-Degrading Strain Rhodococcus qingshengii F2-2 · 2025 · DOI

• The mechanisms of plant growth stimulation and phytopathogen biocontrol in Rhodococcus qingshengii F2-2 are not well understood. The potential of the strain for phytoremediation of oil-contaminated soils is not well assessed.

  Phytostimulating Properties of the Oil-Degrading Strain Rhodococcus qingshengii F2-2 · 2025 · DOI

• Limited land resources hinder the implementation of traditional crop rotation, and the problem of Apple Replant Disease has become increasingly severe.

  Rhizosphere Soil Properties and Microbial Community Across an Apple Replanting Chronosequence · 2026 · DOI

• Investigating the regulatory layer where genetically linked RGAs control resistance (R) protein–mediated immunity - Exploring the potential for durable resistance…

  A built-in brake for plant immunity: Resistance (R) protein–mediated immunity is fine-tuned by R gene analogs · 2026 · DOI

• Investigate the mechanisms by which the plant and its microbiota respond to stress conditions, - Analyze the fungal microbiota associated with Cannabis sativa L., - Examine the effects of other environmental factors…

  Bacterial microbiota dynamics of Cannabis sativa L. under biotic stress induced by Tetranychus urticae · 2026 · DOI

• Further studies could investigate the mechanisms of microbial community structure on quality formation, - Research on the effects of different environmental factors on microbial communities could be…

  Microbial community structure of cigar tobacco leaves in Hunan production area and its regulatory mechanism on quality formation · 2026 · DOI

• Limited understanding of the specific functions of TLPs in leaf disease resistance - Limited characterization of the TLP gene family in Rosaceae - Need for further investigation of the role of TLPs in plant defense…

  Identification of the TLP gene family in Rosaceae and function of PbrTLP28 in leaf disease resistance · 2026 · DOI

• Further studies with increased replication are needed, - Investigation of the causal relationships between soil properties and microbial composition…

  Rhizosphere Soil Properties and Microbial Community Across an Apple Replanting Chronosequence · 2026 · DOI

• Investigate mycotoxin production by fungi in the presence of NAA, - Study the effects of NAA on named beneficial microorganisms in field trials, - Examine the implications of NAA for plant-associated…

  Direct Effects of Naphthaleneacetic Acid on Fungi, Bacteria and Microalgae: An Evidence Map with Dose–Response Synthesis and Its Implications for Plant-Associated Microbiology · 2026 · DOI

• The study only investigated the effects of As(V) on bacterial growth and viability, - The experiment used a limited number of bacterial strains, - The study did not investigate the long-term effects of As(V) exposure on peanut…

  Phosphate-Solubilizing Bacteria with Contrasting Arsenate Tolerance Sustain Phosphorus Nutrition and Restrict Arsenic Translocation in Peanut · 2026 · DOI

• Investigate the long-term effects of As(V) exposure on peanut plants, - Examine the effects of As(V) on other crop plants, - Develop microbial inoculants adapted to local agricultural…

  Phosphate-Solubilizing Bacteria with Contrasting Arsenate Tolerance Sustain Phosphorus Nutrition and Restrict Arsenic Translocation in Peanut · 2026 · DOI

• The use of advanced molecular techniques such as DNA and RNA sequencing to accurately identify and choose Trichoderma strains, - The potential of genetic engineering to improve the effectiveness of Trichoderma…

  Trichoderma in Sustainable Agriculture and the Challenges Related to Its Effectiveness · 2025 · DOI

Most-cited papers in Plant-Microbe Interactions and Immunity

• Plant pathogens and integrated defence responses to infection · Nature · 2001 · 3,239 citations
• Defining the core Arabidopsis thaliana root microbiome · Nature · 2012 · 2,588 citations
• Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria · Science · 2011 · 2,464 citations
• Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota · Nature · 2012 · 2,327 citations
• Pattern-recognition receptors are required for NLR-mediated plant immunity · Nature · 2021 · 1,218 citations
• Mutual potentiation of plant immunity by cell-surface and intracellular receptors · Nature · 2021 · 1,059 citations
• Thirty years of resistance: Zig-zag through the plant immune system · The Plant Cell · 2022 · 958 citations
• Plant Growth Promoting Rhizobacteria (PGPR) as Green Bioinoculants: Recent Developments, Constraints, and Prospects · Sustainability · 2021 · 812 citations
• Biological Control of Plant Pathogens: A Global Perspective · Microorganisms · 2022 · 776 citations
• Phosphate-Solubilizing Microorganisms: Mechanism and Their Role in Phosphate Solubilization and Uptake · Journal of soil science and plant nutrition · 2020 · 742 citations

Most recent work

• Exploring the Role of Root Exudates in Shaping Plant–Soil–Microbe Interactions to Support Agroecosystem Resilience · Horticulturae · 2026
• Engineering the plant microbiome: synthetic community approaches to enhance crop protection · Frontiers in Plant Science · 2026
• Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition · Nature Plants · 2026
• Microbial biocontrol agents and the rhizosphere microbiome: integrating ecological function and climate resilience in sustainable agriculture · Frontiers in Microbiology · 2026
• WRKY Transcription Factors: Integral Regulators of Defence Responses to Biotic Stress in Crops · Plant Biotechnology Journal · 2026
• Plant–soil–microbiome interactions: mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems · Frontiers in Microbiology · 2026
• Plant genomic and microbial interplay in the rhizosphere under salt stress: a review · Frontiers in Plant Science · 2026
• Progress in plant rhizosphere microbiome research for improved growth, nutrient uptake, and disease resistance · Plant Stress · 2026
• A regulatory network promotes apoplastic alkalinization to prime plant immunity in tissues distal to site of infection · Cell · 2026
• Calcium-dependent protein kinases in plant immunity: from calcium signaling to network integration · Frontiers in Plant Science · 2026

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