Mycorrhizal associations， established between approximately 90% of land plants and soil fungi from diverse fungal taxa—ranging from early-diverging groups to Dikarya—represent a cornerstone of terrestrial ecosystems. Despite substantial advances in knowledge， driven by an increasingly broad and interdisciplinary scientific community， translational research in this area remains in its infancy. To bridge this gap， new approaches and ideas are needed.
From a broad perspective， narrowing down to specific priorities， we suggest the following：
（1） Setting a clear discrimination between mycorrhizal fungi and other beneficial endophytic fungi；
（2） Developing markers to assess benefits in field conditions；
（3） Advancing knowledge on the biology of arbuscular mycorrhizal （AM） fungi.
1 Mycorrhizal fungi versus other beneficial fungi
The term “mycorrhiza” acts as a broad umbrella encompassing a bunch of diverse biological interactions. The four major mycorrhizal types （arbuscular， ericoid， orchid， and ectomycorrhizas） involve partners with vastly different physiological， molecular， and phenotypic characteristics， often yielding varying outcomes. Nevertheless， a few shared and characteristic traits set them apart.
First， the presence of unique and well characterized morphological features， such as intracellular arbuscules， coils and pelotons， in endomycorrhizas， or complex extracellular structures such as Hartig nets and fungal sheaths in ectomycorrhizas （ECMs）.
Second， a major physiological dependency， based on consistent nutrient exchange and leading one or both partners to become heavily dependent on the symbiotic relationship for their survival. In most cases， fungi provide plants with mineral nutrients while plants feed mycorrhizal fungi with fixed carbon. Less frequently， such as in orchid mycorrhizas， fungal-mediated carbon supply to non-autotrophic plants may be part of the trade.
However， recent metagenomic analyses have unveiled the presence of a growing number of endophytic fungi， such as Fusarium， Trichoderma， Chaetomium， and Piriformospora in root tissues. Due to their beneficial effects on the host plants—including enhanced tolerance to biotic and abiotic stresses， improved nutrient acquisition， and defense modulation—these fungi are often misclassified as mycorrhizal fungi.
However， unlike canonical mycorrhizal interactions， the differentiation of root colonization structures in fungal endophytes is quite limited， leading in most cases to a loose system of simple intercellular/intracellular hyphae. An exception is given by the so-called ‘fine root endophytes’ （MFRE）， which belong to the Mucoromycota and produce very thin little arbuscule-like structures in the root cortical cells. Furthermore， the formation of a perifungal membrane， a hallmark of all endomycorrhizas， is not consistently documented in the case of endophytes.
Under a physiological perspective， such endophytes display a far less marked dependence on their host plants and frequently have saprobic capabilities thanks to their powerful sets of hydrolytic enzymes （e.g.， many Trichoderma strains）.
Related to this， their association with plants appears more random； they also colonize plant species that do not host mycorrhizal fungi， such as Arabidopsis， indicating that they do not rely on the specific signal transduction pathways governing mycorrhizal symbioses.
Considering advancements in barcoding and metagenomics studies， it is essential to establish the traits that differentiate harmless endophytes and beneficial endophytes from actual mutualistic symbionts such as mycorrhizal fungi. While these categories can be listed in a biological continuum， identifying phenotypic and molecular markers would help integrate data from metagenomic and transcriptomic studies into a broader ecological context. Such efforts could enhance our understanding of the biodiversity of plant-interacting fungi， facilitate the discovery of novel beneficial associations， and enable the development of more efficient microbial inoculants. In this frame， detailed meta-analyses could shed light on the ecological and functional roles of endophytes， as well as their potential synergistic interactions with mycorrhizal fungi.
2 Bridging mycorrhizal research with natural environments
From an ecological perspective， arbuscular（AM） and ECMs are among the most critical plant-fungal associations. They play a pivotal role in vegetation dynamics within both forest and agricultural systems， which are increasingly affected by global changes.
Despite recent laboratory advances， the integration of cell， genetic， and molecular insights into ecological contexts remains uneven. While genomics and transcriptomics analyses of ECM fungi are relatively well-developed， the responses of host plants—apart from limited studies on Populus， a host for both AM and ECM fungi—remain understudied. For ECM trees， some researchers have identified significant changes in hormone metabolism and secondary metabolites such as vitamins. However， fundamental gaps remain， particularly regarding the molecular recognition processes between plants and ECM fungi.
While functional markers of established symbioses are available for AM fungi （e.g.， nutrient transporter genes induced during symbiosis）， equivalent markers for ECM fungi remain elusive. Such markers are critical for evaluating the efficiency of AM and ECM associations under natural conditions， as well as for understanding whether these symbioses facilitate beneficial interconnections among plants—an area currently under scrutiny following debates on the validity of the “Wood Wide Web” concept.
Additionally， lab experiments predominantly focus on young seedlings， whereas natural forests are typically dominated by mature AM and ECM plants. Understanding the role of tree age could provide insights into whether mycorrhizal plants act as more effective carbon sinks than their non-mycorrhizal counterparts.
3 Arbuscular mycorrhizas： Expanding beyond plant-centered research
Despite the genomic era， limited progress has been made in the study of AM fungal genomes. According to MYCOcosm， only 15 AM fungal genomes have been sequenced so far， seven of which belong to different strains of Rhizophagus irregularis. Expanding genomic studies to include diverse strains could enable the development of a comprehensive pangenome， revealing critical insights into their ecology， saprobic capabilities， and applications in field inoculants.
Further research into cross-kingdom RNA interference mechanisms and the expression of fungal small RNAs during interactions with plants could also open new frontiers. However， other significant gaps in basic knowledge remain. Detailed biochemical analyses of fungal cell wall composition across developmental stages （e.g.， spores， extraradical mycelium， appressoria， intraradical hyphae， arbuscules） would offer keys to understand plant-fungal interactions， defense responses， accommodation processes， as well as the production of chitin-like molecules that are crucial in the plant-fungus dialogue. The biological causes of arbuscule collapse and the cellular mechanisms involved remain largely unknown. Single cell transcriptomics approaches are promising to shed light on these poorly understood processes. Lastly， novel metabolomics studies will help understanding the role of fungal exudates in shaping root-associated bacterial communities and maintaining enigmatic endobacteria， which are particularly present in Glomeromycotina and other Mucoromycota groups.
4 Conclusion
To address the challenges posed by global changes and fully harness the benefits of mycorrhizal fungi， a dual approach is required：
1. Deepen our understanding of basic ECM and AM biology.
2. Develop innovative tools and methods to study complex natural systems where interactions often involve multiple partners.
Incorporating AI-based strategies to simulate the intricate microbial ecosystems surrounding roots could provide a critical first step toward unraveling these complexities and leveraging the full potential of mycorrhizal symbioses， always avoiding exagerate optimistc and unrealistic expections.
Suggested further reading
BONFANTE P， VENICE F. Mucoromycota： going to the roots of plant interacting fungi. Fungal Biology Reviews， 2020， 34（2）：100-113.
DUAN S H， FENG G， LIMPENS E， et al. Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum. Nature Reviews Microbiology， 2024， 22： 773-790.
EISENHAUER N， BONFANTE P， BUSCOT F， et al. Biotic interactions as mediators of context-dependent biodiversity-ecosystem functioning relationships. Research Ideas and Outcomes， 2022， 8： e85873.
GENRE A， LANFRANCO L， PEROTTO S， et al. Unique and common traits in mycorrhizal symbioses. Nature Reviews Microbiology， 2020， 18： 649-660.
GIOVANNETTI M， BINCI F， NAVAZIO L， et al. Nonbinary fungal signals and calcium-mediated transduction in plant immunity and symbiosis. New Phytologist， 2024， 241（4）： 1393-1400.
LIANG S， ZOU Y N， SHU B， et al. Arbuscular mycorrhizal fungi and endophytic fungi differentially modulate polyamines or proline of peach in response to soil flooding. Pedosphere， 2023， 34（2）： 460-472.
MARTIN F， KOHLER A， MURAT C， et al. Unearthing the roots of ectomycorrhizal symbioses. Nature Reviews Microbiology， 2016， 14： 760-773.
REDKAR A， SABALE M， ZUCCARO A， et al. Determinants of endophytic and pathogenic lifestyle in root colonizing fungi. Current Opinion in Plant Biology， 2022， 67： 102226.
SILVESTRI A， LEDFORD W C， FIORILLI V， et al. A fungal sRNA silences a host plant transcription factor to promote arbuscular mycorrhizal symbiosis. New Phytologist， 2025， 246（3）： 924-935.
约90%的陆地植物与不同真菌类群（从早期分化类群到Dikaria类群）的土壤真菌之间已建立了菌根共生关系，这是陆地生态系统的基石。得益于学术界日益广泛且跨学科的研究和探索，已在菌根共生的认知上取得了实质性进展，但在菌根共生机制和应用转化方面的研究仍处于起步阶段。因此，需要注入新的理念和方法，以弥补这一欠缺。
从宏观角度出发，具体到某些重点领域，我们建议关注以下几个方面：
（1）建立可区分丛枝菌根真菌和其他有益内生真菌的功能标签；
（2）研发可用于评估野外条件下菌根共生正效应的指标体系；
（3）深化对丛枝菌根真菌的生物学认识。
1 菌根真菌与其他有益真菌
“菌根”是一个广义的词汇，包含多种多样的生物互作。主要涉及4种菌根类型：丛枝菌根（arbuscular mycorrhiza，AM）、杜鹃花科菌根（ericoid mycorrhiza，ERM）、兰科菌根（orchid mycorrhiza，ORM）和外生菌根（ectomycorrhiza，ECM）。4种菌根类型所涉及的植物和菌根真菌共生伙伴在生理、分子和表型特征上迥然不同，基于此而产生的研究结果也有所不同。尽管如此，我们还是能够通过一些共同且独特的属性特征对不同菌根类型加以区分。
首先，内生菌根具有独特且明确的形态特征，例如胞内丛枝、菌丝圈和菌丝团；外生菌根（ECMs）则具有复杂的胞外结构，即哈氏网和真菌鞘。
其次，基于营养交换的生理依赖性，使植物与共生真菌中的一方或双方更加依赖于互惠共生关系以求得生存。在大多数情况下，真菌为植物提供矿质营养，对应地植物为菌根真菌提供其光合作用固定的碳。但也有特例，例如在某些兰科菌根中，真菌介导了向非自养植物的碳供应，这也是菌根营养交换的一部分。
然而，最近的宏基因组分析揭示了在根组织中存在大量的内生真菌，如镰刀菌属（Fusarium）、木霉属（Trichoderma）、毛菌属（Chaetomium）和梨形孢子菌属（Piriformospora）。由于这些真菌对宿主植物存在有益作用，包括增强对生物和非生物胁迫的耐受性，改善营养获取和防御调节，因而经常被错误地归为菌根真菌。
与典型的菌根相互作用不同，内生真菌在根系定殖结构的分化非常有限，在大多数情况下仅是简单的细胞间/细胞内菌丝的松散结构或系统。“细根内生菌根真菌”（MFRE）是一个例外，它们属于毛霉菌门（Mucoromycota），在根皮层细胞中产生非常细小的类似菌丝的结构。此外，所有内生菌根的一个标志性特征——真菌周膜的形成在内生菌的记录中并不一致。
从生理学角度来看，这些内生菌对宿主植物的依赖程度并不高，反而因其强大的水解酶（例如许多木霉属菌株）使它们具有腐生能力。与此相关的是，它们与植物的共生关系有较大的随机性；它们也定殖于那些非菌根真菌宿主植物，如拟南芥，这表明它们不依赖于控制菌根共生的某些特定信号转导途径。
得益于基因条码和宏基因组学研究取得的重要进展，有必要建立一套分类性状以区分无害的和有益的内生菌与那些互惠共生体，比如菌根真菌。这些分类性状系统可以列入生物连续体中，所识别的表型和分子记号也有助于将基因组学和转录组学研究的数据整合到更广泛的生态背景中。这些努力可以增进我们对植物互作的真菌多样性的理解，有助于我们发现新的有益共生关系，并开发更有效的微生物接种剂。在这样的研究框架下，更加细化的大数据分析将有助于揭示内生菌的生态和功能作用，以及它们与菌根真菌之间潜在的协同作用。
2 连接菌根研究与自然环境
从生态学的角度来看，丛枝菌根（AM）和外生菌根（ECMs）是两类最重要的植物-真菌共生体。森林和农田系统的植被动态受到全球变化的影响，而菌根共生关系在植物动态变化中发挥着关键作用。
尽管最近室内研究在细胞、基因和分子层面对菌根共生的认知已取得进展，但这些微观层面的认知并未充分整合到生态环境背景下的菌根共生关系中。在菌根共生体的研究中，对ECM真菌的基因组学和转录组学分析已较为成熟，但对于宿主植物的组学研究尚且不足，仅对杨树（它同时是AM和ECM真菌的宿主）开展了较多的组学研究。一些研究已发现被ECM侵染的树种在激素代谢和次生代谢物（如维生素）方面发生了显著变化，但对一些根本性过程的认知依然存在空白，特别是植物和ECM真菌间分子识别过程仍然未知。
丛枝菌根真菌与植物建立共生关系的功能标记已被破解，例如，共生过程中诱导的营养转运基因，但ECM真菌的等效标记仍然未知。这些功能标记对于评估自然条件下AM和ECM共生效率至关重要。在经历了关于“Wood Wide Web”概念的有效性的辩论之后，这些功能标记对理解菌根共生是否有益于植物之间的内部联结也同样重要，这个植物之间的内部联结领域目前正受到密切关注。
此外，室内试验多是基于幼苗的研究，而在野外天然林多以成年AM和ECM林木为主。考虑树龄效应将有助于深刻理解菌根植物碳汇效率会否真的高于非菌根植物。
3 丛枝菌根：超越以植物为中心的研究
尽管已进入基因组时代，但AM真菌基因组的研究进展仍就有限。根据MYCOcosm，迄今为止仅有15个AM真菌基因组完成测序，其中7个来自异形根孢囊霉不同菌株。将基因组学方法应用到更多菌种，可促进泛基因组层面研究的发展，有助于深刻理解菌根共生的生态功能、腐生能力和在大田接种剂中的应用。
深入研究跨界RNA干扰机制及真菌-植物互作过程中真菌小RNA表达也将开辟新的前沿领域。然而，在基础研究中仍然存在诸多未解之谜。在真菌不同发育阶段（如孢子、根外菌丝体、附着胞、根内菌丝、丛枝），对真菌细胞壁组成进行生物化学详细解析，将帮助我们理解植物-真菌相互作用、防御反应、调节过程及在植物-真菌对话中至关重要的几丁质类分子的产生。丛枝塌陷的生物学原因及其细胞学机制仍然未知。单细胞转录组学的应用有望为我们提供新的方法破解这些谜团。再者，新的代谢组学研究将有助于我们了解真菌分泌物在塑造根际细菌群落和维持神秘的内生细菌中的作用，这些细菌尤其存在于小球菌门和其他毛霉门中。
4 结论
为应对全球变化带来的挑战，以及充分利用菌根真菌的益处，需要采取双重措施：
1.加深我们对基础ECM和AM生物学的理解。
2.开发创新的工具和方法来研究复杂的自然系统，其中的相互作用往往涉及多个合作伙伴。
结合基于人工智能的策略来模拟根部周围复杂的微生物生态系统，可以为解开这些复杂性和利用菌根共生的全部潜力提供关键的第一步，始终避免夸大的乐观和不切实际的期望。
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