Wu Bing, Hussain Muzammil, Zhang Weiwei, Stadler Marc, Liu Xingzhong, Xiang Meichun
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Mycology. 2019 May 7;10(3):127-140. doi: 10.1080/21501203.2019.1614106. eCollection 2019.
The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded "unculturable fungi" could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the "digital type" could be assigned as the "clade" name + species name. The "clade" name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.
真菌的全球生物多样性已得到广泛研究，其物种数量也已得到估计。值得注意的是，分子系统发育学的发展揭示了意想不到的真菌多样性，并且利用包括高通量扩增子测序在内的非培养方法极大地增加了真菌操作分类单元的数量。在过去十年中，已经建立了许多新的分类群，包括新的门、纲、目和新科。通过分子系统发育学鉴定出了许多隐性物种。根据最近对相同样本进行的依赖培养和非依赖培养调查所产生的数据，地球上的真菌物种估计有1200万（1170万 - 1320万）种，而最近通过各种估计技术估计的物种数量为220万 - 380万种。此外，有人推测，目前高通量测序技术的应用将揭示出比我们目前估计更高的多样性。最近，有人提议对环境序列进行正式分类，并允许将DNA序列数据作为真菌名称的模式，但遭到了真菌学家群体的强烈反对。对特殊生态位中的真菌进行的调查表明，许多以前被认为“不可培养的真菌”在特定条件下可以在某些底物上培养。此外，高通量扩增子测序、鸟枪法宏基因组学和单细胞基因组学可能是检测新分类群的有力手段。在这里，我们建议将真菌类型分为基于标本的物理类型、基于可培养和不可培养真菌标本完整基因组序列的基因组DNA（gDNA）类型以及基于环境DNA序列数据的数字类型。物理类型和gDNA类型应具有优先权，而数字类型可以在物理类型和gDNA类型可用之前作为临时补充。基于“数字类型”的真菌名称可以指定为“分支”名称 + 物种名称。“分支”名称可以是数字类型序列所属的属、科或目等的名称。应鼓励促进未来的培养工作。此外，由于新检测技术的快速发展，关于栖息在各种环境中的真菌的知识不断进步，预计我们星球上真菌多样性的更多信息将会出现。
