The Fungal Kingdom
The Fungal Kingdom
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发表时间：
2019
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通讯作者：
Sarah J. Araldi-Brondolo;Joseph E. Spraker;Justin P. Shaffer;Emma H. Woytenko;David A. Baltrus;Rachel E. Gallery;Elizabeth Arnold
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作者：
Sarah J. Araldi-Brondolo;Joseph E. Spraker;Justin P. Shaffer;Emma H. Woytenko;David A. Baltrus;Rachel E. Gallery;Elizabeth Arnold
从腐烂植物材料的腐养菌到在局部和区域尺度上塑造植物种群动态的病原体和共生菌，真菌是所有主要生物群系中生态系统健康、植物生产力和可持续性的主要驱动力（1-5）。这些真菌的生态作用是由它们自身的基因组和表观遗传结构以及它们的宿主驱动的，通常受到这种相互作用发生的环境背景的强烈影响（1-9）。真菌生物学的环境背景长期以来被定义为非生物因素，包括那些直接影响真菌生长和基因表达的因素，以及那些影响真菌与宿主或基质相互作用的健康、生长、结构或防御的因素（图1）。然而，越来越清楚的是，这些环境背景也包括生物成分，即额外的，相互作用的物种，直接或间接地改变真菌与宿主关联的结果。就主要影响而言，其中最重要的是菌丝内微生物共生体，包括存在于活真菌菌丝内并能深刻改变真菌表型的病毒和细菌（即，内生真菌微生物或微生物内生共生体）（10-13）。菌丝内微生物对真菌的表型调节可导致真菌底物利用、酶生产、耐热性、毒力和共生建立的早期阶段发生重大变化。就像水平基因转移（HGT）可以在生态时间内改变生物体表型的各个方面一样，微生物共生体的获得（或丢失）也可以将毒性真菌病原体改变为无毒的生活方式，将真菌的繁殖策略从有性改变为无性，增加真菌分泌激素和其他与植物相关的信号分子。或者通过改变真菌群落动态平衡的方式拓宽真菌的生态位空间和竞争能力（见参考文献11-19）。在这些方面，菌丝内微生物不仅在生态时间中很重要，而且在真菌的进化和宿主的相互协同进化反应中也很重要（图1）。因此，了解微生物共生调节真菌表型的机制不仅有可能为真菌生态学提供信息，也有可能为真菌进化的轨迹提供信息，特别是关于趋同表型或生态模式（例如内生作用），其中基因组标记和进化转变仍然难以捉摸。这些问题，加上对真菌微生物内共生体应用的兴趣日益浓厚，真菌学家在短期生态快照和进化时间内定义了塑造真菌功能特征的无数因素，这是一个激动人心的时刻。根据de Bary的概念，真菌和菌丝内微生物之间的共生关系被广泛定义为“不同生物的共同生活”（20），包括互惠、寄生和共生的相互作用，其中许多相互作用的重要性或效果可能与环境有关。作为菌丝内共生体出现的最著名的微生物代表了生命的两个领域。第一种是非细胞微生物，如分枝病毒。分枝病毒（感染真菌的病毒）通常是双链RNA病毒（约占已知分枝病毒的70%），正义单链RNA病毒（约占30%），很少是双链病毒（21）。
INTRODUCTION From the saprotrophs that decay plant material to the pathogens and mutualists that shape plant population dynamics at local and regional scales, fungi are major drivers of ecosystem health, plant productivity, and sustainability in all major biomes (1–5). The ecological roles of such fungi are driven by their own genomic and epigenetic architecture, as well as that of their hosts, often with strong influences from the environmental context in which such interactions occur (1–9). The environmental context of fungal biology has long been defined in terms of abiotic factors, including those that impact fungal growth and gene expression directly and those that influence the health, growth, structure, or defenses of hosts or substrates with which fungi interact (Fig. 1). Increasingly, however, it is clear that these environmental contexts also include biotic components—that is, additional, interacting species that directly or indirectly alter the outcomes of fungushost associations. Foremost among these in terms of major effects are endohyphal microbial symbionts, including viruses and bacteria that occur within living fungal hyphae and can profoundly alter fungal phenotypes (i.e., endofungal microbes or microbial endosymbionts) (10–13). Phenotypic modulation of fungi by endohyphal microbes can cause major shifts in fungal substrate use, enzyme production, thermotolerance, virulence, and the early phases of symbiotic establishment. Much like horizontal gene transfer (HGT) can alter diverse aspects of an organism’s phenotype in ecological time, so too can acquisition (or loss) of a microbial symbiont change a virulent fungal pathogen to an avirulent lifestyle, alter the reproductive strategy of the fungus from sexual to asexual, increase fungal secretion of hormones and other signaling molecules relevant to plants, or broaden the niche space and competitive ability of fungi in ways that change the balance of fungal community dynamics (see references 11–19). In these ways endohyphal microbes are important not only in ecological time, but also in the evolution of fungi and reciprocal coevolutionary responses from their hosts (Fig. 1). Thus, understanding the mechanisms underlying symbiotic modulation of fungal phenotypes by microbes has the potential to inform not only fungal ecology but also the trajectory of fungal evolution, especially with regard to convergent phenotypes or ecological modes (e.g., endophytism) for which genomic markers and evolutionary shifts remain elusive. Such questions, paired with growing interest in applications of microbial endosymbionts of fungi, frame an exciting time as mycologists define myriad factors that shape fungal functional traits in short-term ecological snapshots and over evolutionary time. Broadly defined under de Bary’s conceptualization as “the living together of unlike organisms” (20), symbioses between fungi and endohyphal microbes encompass mutualistic, parasitic, and commensal interactions, many of which may be context-dependent in terms of their importance or effects. The best known microbes that occur as endohyphal symbionts represent two domains of life. The first are acellular microbes such as mycoviruses. Mycoviruses (viruses that infect fungi) usually are double-stranded RNA viruses (ca. 70% of known mycoviruses), positive-sense, single-stranded RNA viruses (ca. 30%), and rarely, geminiviruses (21).