Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.

中文翻译：

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将不可触摸的命名-环境序列和生态位划分作为真菌中的分类学证据

由于其淹没和隐秘的生活方式，绝大多数真菌物种很难通过形态学来观察和描述，许多真菌物种仍然仅根据从环境样品中检测到的序列而为科学所知。缺乏界定和命名大多数真菌物种的方法，这是对真菌界生态学和进化的交流和解释的一个巨大限制。在这里，我们使用环境序列数据作为分类学证据，并将系统发育和生态学数据相结合，以生成和检验类古细菌属（Taphrinomycotina，Ascomycota）中的物种假设。根据对瑞典松树林Podzol土壤进行深入研究的环境扩增子测序，我们生成了68种不同的假古菌物种假说，其中两个对应于该类别中唯一描述的物种。九种物种假说代表了78％的测序古生菌群落，并得到了长期阅读的数据的支持，这些数据构成了基于系统发生分支长度界定物种假说的基础。土壤真菌群落是通过环境过滤和竞争性排斥而形成的，因此，如果进化性适应性特征得以保留，密切相关的物种就不太可能在生态位中同时发生。在土壤剖面中，不同的垂直水平线代表着可测的生态位尺寸，并且我们发现，在一对姐妹物种假设得到良好支持的情况下，样品之间的分布存在明显差异。基于系统发育和生态学证据的结合，我们确定了两个新物种，我们为其提供分子诊断并提出名称。尽管环境序列不能自动翻译为物种，但可以将其用于系统发育上不同的物种假设，可以使用序列作为生态证据对其进行进一步测试。我们得出的结论是，在物种数量丰富且经常观察的情况下，环境序列可以在没有物理标本的情况下支持物种识别，而在我们的采样和测序强度下，稀有的分类单元仍无法捕获。