Editorial: Cross-kingdom communications among plants, fungi, and bacteria: from molecules to ecological factors

In modern agriculture and forestry, the imperative for sustainable development demands innovative strategies that reduce chemical inputs while maintaining productivity. Central to this challenge is a deeper understanding of the complex, multi-trophic interactions occurring within the rhizosphere and plant tissues (Ling et al., 2022). The associations between plants and beneficial microbes particularly mycorrhizal fungi (Figure 1), and plant growth-promoting rhizobacteria, are well-recognized for their profound impacts on nutrient acquisition, stress tolerance, and overall ecosystem functioning (Trivedi et al., 2020; Ma et al., 2026). More recently, the conceptual framework has expanded to recognize the plant-arbuscular mycorrhizal (AM) fungus-bacterium continuum, wherein AM fungi-associated endobacteria or hyphosphere-associated bacteria actively modulate the outcome of plant-fungal symbioses (Duan et al., 2024). However, the molecular dialogues and ecological principles governing this cross-kingdom communication remain in their infancy (Silvestri et al., 2025; Usländer et al., 2026).

Figure 1.

WGA488 staining of a Medicago truncatula root colonized by the mycorrhizal fungus Rhizophagus irregularis showing the presence of arbuscules in the cortical parenchima.

This Research Topic, “Cross-Kingdom Communications Among Plants, Fungi and Bacteria: From Molecules to Ecological Factors”, brings together a compelling collection of 14 original research articles that collectively advance our understanding of how plants both shape and are shaped by their associated microbiomes across diverse environments, from deserts to subtropical forests and agricultural fields. The contributions herein underscore the intricate signaling networks, environmental drivers, and functional consequences of these interactions, while highlighting promising translational applications for sustainable agriculture and ecosystem conservation.

Signaling molecules and chemotaxis in the rhizosphere

The ability to locate and migrate toward plant roots is a fundamental prerequisite for microbes to establish either beneficial or pathogenic associations. Keren et al. demonstrate that root-secreted nucleosides act as potent chemoattractants for a diverse range of rhizobacteria, including both plant growth-promoting Bacillus strains and the pathogen Xanthomonas campestris. This work expands the repertoire of known rhizosphere signaling molecules beyond conventional nutrients and suggests that purinergic signaling may represent a conserved, cross-kingdom communication mechanism that shapes the assembly of the root microbiome.

Environmental and spatial drivers of microbial community assembly

A recurring theme across this Research Topic is the critical importance of environmental and spatial factors in structuring plant-associated microbial communities. Several studies leverage high-throughput sequencing to disentangle these complex relationships. Zhao et al. reveal that spatial variation, driven by geographic distance and contrasting soil properties such as pH and total nitrogen (N), exerts a stronger influence than seasonality on the assembly of fungal communities in Larix gmelinii forests. This spatial heterogeneity dictates the balance between deterministic and stochastic processes, with implications for forest health management.

This principle extends to the rhizocompartments of diverse plant species. Mo et al. demonstrate that the rhizocompartment (endosphere, rhizosphere, bulk soil) primarily drives fungal community structure across different life forms of halophytes in an arid wetland. They observe a clear niche differentiation, with endophytic compartments enriched for salt-tolerant genera such as Aporospora and Monosporascus, highlighting how plants filter and select specific fungal taxa from the surrounding soil matrix. Similarly, Xie et al. provide a detailed characterization of the microbiome associated with the medicinal orchid Dendrobium huoshanense, showing a marked decline in fungal diversity from the cultivation medium to the root endosphere. This gradient reflects the strong selective pressure exerted by the host plant (Liu et al., 2021), favoring specialist endophytic fungi while largely excluding saprotrophs and potential pathogens. The predominance of functionally uncharacterized fungi within the endosphere underscores a vast, unexplored reserve of biological diversity with potential implications for the orchid’s medicinal properties. Extending this theme, Tang et al. investigate the rhizosphere microbiomes of five Impatiens species across an elevational gradient. Their findings highlight pronounced interspecific variation, with endemic species harboring distinct fungal communities strongly correlated with elevation and soil nutrients.

The importance of geographic origin is further exemplified in the studies of Taheri et al. and Chen et al. Taheri et al. characterize the culturable endophytic fungal diversity of hairy vetch (Vicia villosa) across Japan, revealing that soil pH and geographic location significantly shape community composition. Their functional screening identifies numerous isolates with plant growth-promoting traits, including a novel strain of Penicillium griseofulvum with potential as a bioinoculant. Chen et al. link the rhizosphere bacterial community of the medicinal plant Zanthoxylum nitidum to its geographic origin, and, critically, establish a positive correlation between the abundance of specific bacterial genera (e.g., Rudaea, Bradyrhizobium) and the accumulation of the key bioactive compound, nitidine chloride. This study provides a tangible link between soil microbiota and the quality of medicinal plant materials.

Extending beyond the rhizosphere of annual crops, Quan et al. provide a compelling case study of plant-soil feedback in an extreme desert environment. Focusing on the endangered relict shrub Tetraena mongolica, a keystone species in the West Ordos region of China, the authors demonstrate that the plantation of T. mongolica profoundly ameliorates desert soil properties. These physicochemical improvements were paralleled by marked shifts in the soil microbiome, with increased bacterial and fungal diversity indices in the root-zone soil. Notably, this study revealed that T. mongolica simplified bacterial co-occurrence networks while increasing the complexity of fungal networks, suggesting a differential restructuring of microbial interactions. This work highlights the irreplaceable role of keystone relict plants in desert ecosystem stability and reveals how ancient plant lineages engineer their soil environment for long-term persistence.

Functional mechanisms of symbiosis: from nutrient exchange to disease resistance

The functional core of plant-microbe interactions lies in the exchange of resources and the modulation of host physiology (Trivedi et al., 2020). Zadegan et al. employ comparative transcriptomics to dissect the differential compatibility between Bradyrhizobium strains and soybean (cultivated versus wild). This study reveals that the formation of non-functional nodules is associated with the activation of defense-related and cell wall biogenesis genes, offering a molecular blueprint for understanding symbiotic specificity and domestication effects.

Mycorrhizal symbiosis is a central pillar of nutrient acquisition in terrestrial ecosystems (Duan et al., 2024). Li et al. provide a compelling demonstration of how arbuscular mycorrhizal (AM) fungi modulate the N nutrition of Eucalyptus seedlings. They show that mycorrhization shifts the plant preference from complex organic N sources (e.g., peptone) to simpler forms (e.g., glycine), and this is accompanied by the upregulation of specific organic N transporters (e.g., EgAAP3, EgLHT1). This work reveals a sophisticated level of metabolic coordination that enhances N use efficiency under low-fertilization regimes.

Beyond nutrition, beneficial microbes can prime plant defenses. Zhang et al. characterize the W-box binding (WRKY) transcription factor family in Eucalyptus grandis and demonstrate that colonization by the AM fungus Rhizophagus irregularis induces the expression of specific EgWRKY genes. This transcriptional reprogramming is associated with enhanced defense against the bacterial pathogen Ralstonia solanacearum, illustrating the role of AM symbiosis in bolstering the plant’s innate immune system.

The specificity of symbiotic dependency is elegantly contrasted in the work of Yang et al. on two medicinal orchids. Pleione bulbocodioides strictly depends on mycorrhizal fungi for complete development from germination to seedling, whereas Bletilla striata can germinate autonomously, with fungi greatly accelerating the process. This dichotomy highlights the evolutionary spectrum of symbiotic reliance and provides practical insights for the conservation and cultivation of these valuable species.

Translational applications for sustainable agriculture

The ultimate goal of understanding these fundamental plant-microbe interactions is to harness them for practical applications. Two studies in this Research Topic showcase innovative, technology-driven approaches to improving agricultural sustainability. Liu et al. demonstrate that optimizing nitrate supply can enhance rice resistance to bacterial leaf blight. Through transcriptomic analysis, they elucidate a molecular regulatory network wherein nitrate modulates defense gene expression, providing a rational basis for nutrient management strategies that reduce reliance on chemical pesticides.

Furthermore, Bian et al. (2025) explore a novel irrigation technique using micro-/nanobubble oxygenation. They show that this method significantly enhances soil phosphorus availability and maize yield by altering the structure and diversity of the rhizosphere bacterial community and increasing alkaline phosphatase activity. This study exemplifies how manipulating the soil physicochemical environment can indirectly steer the microbiome to improve nutrient cycling and crop productivity.

In conclusion, this Research Topic significantly advance our understanding of the intricate cross-kingdom communications among the plants, fungi, and bacteria. They illuminate the signaling molecules that initiate these interactions, the environmental and host genetic factors that sculpt microbial communities, and the functional mechanisms by which these associations enhance nutrient uptake and resilience to stress. As we move forward, integrating this knowledge into ecological models and agricultural practices will be essential for developing robust, microbiome-informed strategies that promote both ecosystem health and sustainable food and fiber production.

As we are writing this Editorial, less than 2 years after the acceptance of the first manuscript, this Research Topic has gained over 42,000 views and 9,500 downloads. This success mirrors a growing and widespread recognition within the scientific community of the fundamental importance of cross-kingdom communications in shaping plant health and ecosystem resilience. The enthusiastic reception of this Research Topic underscores the urgent need to move beyond single-organism perspectives and embrace the complexity of the plant symbiosis, as we collectively strive to translate these intricate ecological insights into practical solutions for a more sustainable agricultural and environmental future.

Editorial on the Research Topic: Cross-kingdom communications among plants, fungi and bacteria: from molecules to ecological factors

Funding Statement

The author(s) declared that financial support was received for this work and/or its publication. This study was funded by the National Natural Science Foundation of China (Grant Nos. 32301332, 32370108), the Jiangsu Funding Program for Excellent and Postdoctoral Talent (Grant No. 2022ZB357), the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions, the Guangdong Special Support Plan for Young Top-notch Talents Project (Grant No. 2024TQ08A220), the Natural Science Foundation of Fujian Province (Grant No. 2024J09028), the Young Talent Project of Yunnan (Grant No. C619300A101); the Yunnan International Joint Laboratory (R&D Center) of plateau woody vegetables development and utilization (Grant No. 202403AP140010).

Author contributions

XX: Writing – original draft, Writing – review & editing. FX: Writing – review & editing. LL: Writing – review & editing. J-JH: Writing – review & editing. KS: Writing – original draft, Writing – review & editing.

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The authors KS, XX declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Correction note

This article has been corrected with minor changes. These changes do not impact the scientific content of the article.

Generative AI statement

The author(s) declared that generative AI was not used in the creation of this manuscript.

Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.