What impact the abiotic environment has on connections between microbes and host genetics, and whether those connections

The gap

Evidence profile

Sourced from the future work and stated research gap and abstract of the source papers, classified as general, drawn from work published between 2025 and 2026, spanning 5 journals. Those papers have been cited 12 times in total.

Supporting evidence — 8 representative gaps

• Breeding for beneficial microbial associations (2026) · Nature Communications · doi

  https://doi.org/10.1038/s41467-026-76260-6 Fig. 2 | Challenges of the dual ecological engineering approach. The left side outlines key challenges related to promoting beneficial microbial associations, while the right side presents challenges associated with manipulating beneficial microbial association strategies. The top row highlights interventions and limita- tions from the plant side (e.g., breeding and genetic engineering), and the bottom row focuses on microbial-side challenges, including inoculation practices, microbiome compatibility, and soil variability. Addressing these challenges is essential for the successful integration of beneficial microbial associations (BMA) into diverse agricultural systems. On the right side, we addressed the socio- economic and socio-political challenges to scale new technologies. On the bottom the challenges in addressing the potential synergies between the methods. Created in BioRender. Golan davydov, O. (2026) https:// BioRender.com/9nsp62e. the strong potential of BMA for sustainable agriculture, breeding efforts should continue to prioritize overall plant performance and agronomic fitness. New breeding technologies enhance beneficial associations In addition to leveraging natural selection for BMA from wild relatives, new breeding techniques (NBT) offer new opportunities to enhance BMA. The overall approach of harnessing the plant genome to shape the microbiota was demonstrated in the rice phyllosphere by targeting specific plant metabolites, resulting in increased protection against pathogens34. Subsequently, specific M genes were used to improve plant growth and productivity through the modulation of beneficial plant–microbe interactions35. For example, modifications in lignin precursor metabolism were shown to alter the endosphere bacterial microbiome36 in the rhizosphere37. While several studies have focused on individual M genes38,39, many of these traits are regulated by complex gene net- works, and the secretion of signaling compounds often involves additional genes, making breeding strategies considerably more complex. and enrich beneficial microorganisms One approach is to directly manipulate the small molecules involved in recruiting beneficial microbes. Plants release approxi- mately 20–40% of their assimilated carbon into the rhizosphere as a complex blend of signaling compounds, including amino acids, fatty acids, and other metabolites40. These exudates not only attract beneficial microbial groups but also help repel pathogenic organisms41,42 (Fig. 2). Mutation within some metabolic pathways has been shown to alter the composition of the root exudate (Supple- mentary Table 1), thereby also reshape the microbial community43,44. Parallel to the innovation in pathways elucidation, technological advancements have improved the ability to detect and analyze root exudates, even under field conditions45, although the detection of microbiota recruitment signals remains challenging as they are pro- duced in low concentrations46. Through the application of NBT, it is now becoming feasible to modify specific metabolic pathways and possibly enhance the recruitment of targeted beneficial microbial groups. The second approach, complementary to root exudation, is root system architecture and molecular structure, which are crucial to BMA. Architectural traits, such as root depth and root density, along with morphological features like root diameter and root hairs, determine the root’s capacity to engage with beneficial microbes47,48. At the molecular level, nutrient transporter expression is essential for sym- biotic interactions. For instance, phosphate transporters are strongly expressed during AMF associations49, while ammonium and nitrate transporters play crucial roles in rhizobia symbiosis50. In addition, the transfer of organic carbon to symbionts, either in the form of sugars (e.g., via sugar transporters51) or fatty acids52, is a key molecular trait supporting mutualism. Moreover, it is important to mention that root exudates comprise thousands of different substances, and the inclu- sion or exclusion of specific compounds provides opportunities to Nature Communications | (2026) 17:7695

  generalfuture work
  Keywords: bene cial root challenges microbial plant side breeding approach associations speci enhance genes complex compounds
• Breeding for beneficial microbial associations (2026) · Nature Communications · doi

  https://doi.org/10.1038/s41467-026-76260-6 support or suppress specific groups of microbes. This plant-microbe morphological crosstalk offers an opportunity to enhance BMAs through targeted intervention. To date, only two genetically engineered traits, herbicide toler- ance and insect resistance, have been widely adopted in crops, both demonstrating substantial environmental and economic impacts globally53. In contrast, NBT plants targeting BMA traits have received limited attention, despite their significant potential to improve soil health and promote sustainable agriculture. Enhancing naturally occurring traits within the plant genome—rather than introducing entirely new gene loci—may also increase the likelihood of acceptance among farmers, policymakers and the public. The application of CRISPR-Cas9 and related gene-editing technologies enables precise manipulation of signaling pathways involved in microbe recruitment. By enhancing the production of specific signaling molecules or mod- ifying the composition of root exudates, it is now feasible to develop NBT genotypes that optimize BMA46. Several signaling compounds, including strigolactones, flavonoids, and benzoxazinoids, have already been identified as key mediators in the recruitment of beneficial microbes. However, most of this research remains confined to laboratory or greenhouse conditions, and comprehensive field trials and long-term studies are still lacking. Future research should focus on testing and refining NBT genotypes under field conditions to ensure agronomic viability and cost-effectiveness for real-world agricultural systems. Management practices improving beneficial microbial associations Scientists and farmers have developed a variety of management practices to enhance crop yields and soil health, many of which directly or indirectly improve conditions for BMA. In recent years, two over- arching systems of agricultural management have emerged—organic and conventional practices. Organic farming has become one of the most widely adopted approaches to improving soil multifunctionality, primarily through the use of natural pesticides and fertilizers instead of synthetic inputs54,55. In addition, organic practices often incorporate cover cropping and more diverse crop rotations, which can sig- nificantly influence soil functions and microbial dynamics56 (Supple- mentary Table 2). While current agricultural management tends to focus heavily on abiotic factors such as soil organic carbon and nutrient availability, greater emphasis should be placed on practices that foster the abundance and activity of beneficial microbial asso- ciations. Promoting BMA can play a crucial role in enhancing long-term soil health, plant resilience, and sustainable productivity. Microbial diversity—and in particular, BMA—has been shown to enhance primary productivity19. However, it remains unclear whether increasing microbial diversity through specific agricultural practices can directly improve soil functioni

  generalfuture work
  Keywords: soil practices microbial agricultural management organic speci plant enhance traits improve health enhancing signaling bene
• Breeding for beneficial microbial associations (2026) · Nature Communications · doi

  https://doi.org/10.1038/s41467-026-76260-6 Fig. 3 | Schematic illustration of strategies to enhance beneficial microbial associations (BMA). The figure is organized along two axes: the horizontal axis separates plant-based interventions (top row) from microbial-based approaches (bottom row), while the vertical axis distinguishes strategies aimed at promoting beneficial associations (left) from those that manipulate associations (right). a Top left – Traditional breeding: Breeding programs that select crop genotypes with enhanced capacity to associate with beneficial microbes. In soils with very low health, beneficial microbes are scarce, and root traits that supposed to enhance BMA may have negative effects. Once soil health reaches a threshold, additional traits promoting beneficial associations show increasingly positive effects until they plateau. b Bottom left – Management practices: Agricultural practices that improve soil conditions and support native microbial communities. These follow a negative trend: in non-healthy soils, management practices can strongly boost beneficial interactions, whereas in already healthy soils, their effect is limited or neglectable. c Top right – New Breeding Technologies (NBTs): Approaches that enhance root traits or activate plant signaling pathways to attract specific microbial partners. These methods are especially effective for a large range of soil health gradients, where beneficial microbial populations are present. In poor soils, how- ever, beneficial microbial abundance is too low, and excessive exudation may cause neutral or negative effects. Compared to traditional breeding, NBTs exhibit a steeper positive slope due to their targeted enhancement of plant–microbe sig- naling and smaller negative effects. d Bottom right – Microbiome manipulation: Direct inoculation of soils with beneficial microbes. This strategy is most effective in low-quality soils where native microbial communities are absent or depleted, but in already healthy soils, it can be redundant or even disruptive (Adapted from Rog et al., 2025, based on field AMF inoculation studies). The figure highlights the potential synergistic effect of using multiple approaches. For example- Soil inoculation and selection of plant- enhancing BMA specifically under low soil health. initiation of this endosymbiosis (Supplementary Table 1). The transfer of the pathway of such signaling molecules into crop species opens exciting opportunities to manipulate and enhance plant-Rhizobia associations through genetic and biotechnological approaches. To date, more than 8000 flavonoid compounds have been iden- tified across various plant species90. These compounds are synthesized in multiple plant organs, and their core structures can be extensively modified to produce a wide array of products with diverse biological functions, mobility profiles, and signaling capacities. While the bio- synthesis of flavonoids is well understood in many crops, the exuda- tion of the molecules to the rhizosphere is less well understood, although some progress has been made recently in identifying transporters91. The flavonoids could play a role in the selection of compatible rhizobia species by the host92 and lead to modification of the associated microbial community. The host plant attempts to select the most beneficial symbiotic nitrogen-fixing bacteria93. At the same time, some studies found beneficial effects with multi-strain associations94, while others present more efficient symbiosis interac- tion with individual strains95. Flavonoids are not restricted to attracting N-fixing bacteria but also to attracting AMF, PGPB, and acting as defense molecules against root pathogens. Since nodule formation is a relatively simple pheno- typic trait for breeders to evaluate, it could be used for large-scale selection, while flavonoid profiling could be reserved for a smaller subset of selected genotypes. Given that flavonoids also participate in complex signaling interactions within the rhizosphere, their broader ecological roles warrant further research. Attraction of plant-promoting bacteria by benzoxazinoids Benzoxazinoids are secondary metabolites that regulate beneficial associations, specifically PGPB. These signaling compounds are exu- ded by grasses and cereal crops commonly used in agriculture. In addition to functioning as a chemoattractant, benzoxazinoids con- tribute to pathogen defense and modulate the structure and function Nature Communications | (2026) 17:7695

  generalfuture work
  Keywords: bene cial plant microbial associations soils effects soil signaling enhance approaches breeding health negative based
• Breeding for beneficial microbial associations (2026) · Nature Communications · doi

  https://doi.org/10.1038/s41467-026-76260-6 of the rhizosphere microbiome96,97. Remarkably, benzoxazinoid exu- dation in cereals has been shown to shift microbial community com- position toward a higher abundance of BMA, even influencing the microbiome of subsequent crops in a rotation system. This legacy effect not only enhances plant performance but can also influence plant–herbivore interactions98. Breeding programs should consider crop rotation cycles, including the sequence of different crops, during both candidate selection and the design of breeding strategies. Other morphological traits can enhance association with PGPB, such as increased numbers and lengths of lateral roots. Manipulating the levels of Benzoxazinoids using NBT presents a promising strategy to pro- mote BMA in both current and future cropping cycles. pathogens (e.g., Fusarium tritici in wheat) and species-specific devel- opmental traits. To address this complexity, artificial intelligence (AI) and machine learning approaches offer powerful tools for analyzing large, multidimensional datasets. These models can predict microbial inoculation outcomes across both short- and long-term scales and under a variety of environmental conditions102. Such an application should allow users to input field-specific data, such as soil nutrient profiles, microbial community composition, pathogen loads, and environmental conditions, and return a prediction of BMA effectiveness103. Next-generation prediction tools can help farmers anticipate outcomes, optimize BMA use, and ensure more consistent soil and crop health across diverse agroecosystems.

  generalfuture work
  Keywords: microbial microbiome community crops rotation plant breeding crop cycles traits speci tools outcomes across environmental
• Optimizing Nitrogen Fixation in Vicia sativa: The Role of Host Genetic Diversity (2025) · Agronomy · cited 12× · doi

  Our results offer novel perspectives into the role of the host genotype on symbiotic interaction and BNF efficiency. However, several important questions remain to be ex- plored. Thus, future research could explore the genetic factors and molecular mechanisms underlying the genotype-dependent differences in nodulation and nitrogen fixation. Tran- scriptomic analysis, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) could be used to identify candidate genes involved in these processes. Further studies are needed to investigate the specificity of the interaction between the host genotype and the rhizobial strain in determining BNF efficiency. Understanding the molecular mechanisms behind host–rhizobia specificity is essential to developing more effective inoculation strategies. This can help optimize legume-based nitrogen fixation, supporting long-term soil health and reducing reliance on chemical inputs. Examining how environmental factors, like soil composition and climatic conditions, interact with the host genotype to influence BNF will provide a more comprehensive understanding of the Agronomy 2025, 15, 1479 13 of 16 factors driving the efficiency of nitrogen fixation in vetch. This study serves as an initial exploratory analysis of the role of BNF among a diverse set of V. sativa genotypes under controlled symbiotic conditions. By employing a single, well-characterized Rhizobium strain, we were able to focus specifically on the impact of host plant genetic diversity, minimizing the complex effects from microbial variability. While our findings highlight the importance of the host genotype in BNF, we must be aware that future research should incorporate multiple rhizobial strains to further elucidate host–bacteria specificity and opti- mize legume–rhizobium combinations. Our work has been carried out under controlled experimental conditions, considering the enormous difficulty of performing this work under field conditions. Translating these results to agronomic practice will require field trials that consider the complexity of natural environments, including competition among native rhizobia, soil composition, and climatic factors. Addressing these challenges will be essential for fully realizing the potential of genetic diversity to improve nitrogen fixation in legume-based agricultural systems. In any case, we strongly believe that our work aims to contribute an additional factor to be considered in breeding programs: the selection of accessions with good BNF ability for optimizing symbiotic interactions.

  generalfuture work
  Keywords: host genotype factors nitrogen fixation conditions symbiotic efficiency genetic specificity legume soil role interaction future
• Editorial: Microbial solutions for soil health and remediation: from natural diversity to engineered communities (2026) · Frontiers in Microbiology · doi

  The effects of microbial interventions on soil health and remediation are not fully understood. The local agroecological context and native microbial assemblages can influence the effects of microbial interventions.

  generalstated research gapevidence 5/5
  Keywords: effects microbial interventions soil health remediation fully understood
• Barley genetic architecture conditionally impacts recruitment of rhizosphere microorganisms and crop performance has been submitted (2026) · bioRxiv · doi

  However, what impact the abiotic environment has on connections between microbes and host genetics, and whether those connections in turn impact crop performance in realistic agricultural scenarios remains unclear.

  generalabstractevidence 2/5
  Keywords: impact connections abiotic environment microbes host genetics whether turn crop performance realistic agricultural scenarios remains
• Soil pH and nitrate shape deterministic assembly of microbial communities in agricultural soils via Nitrososphaeria (2025) · Applied and Environmental Microbiology · doi

  IMPORTANCE: Agricultural soil microbiomes are essential for element cycling, fertility maintenance, and crop productivity, yet how key functional taxa interact with environmental factors to shape community assembly remains poorly understood.

  generalabstractevidence 2/5
  Keywords: importance agricultural soil microbiomes essential element cycling fertility maintenance crop productivity functional taxa interact environmental

Questions about this gap