Starke Robert, Capek Petr, Morais Daniel, Jehmlich Nico, Baldrian Petr
Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.
Faculty of Science, University of South Bohemia, České Budějovice, Czechia.
Front Microbiol. 2020 Feb 6;11:143. doi: 10.3389/fmicb.2020.00143. eCollection 2020.
Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here, we used a meta-analysis of completely annotated extant genomes of 377 taxonomically distinct fungal species to predict the total fungal microbiome functionality on Earth with accumulation curves (ACs) of all known functions from the level 3 of KEGG Orthology using both parametric and non-parametric estimates in an explorative data-mining approach. The unsaturated model extrapolating functional diversity as a function of species richness described the ACs significantly better than the saturated model that assumed a limited total number of functions, which suggested the presence of widespread and rare functions. Based on previous estimates of 3.8 million fungal species on Earth, we propagated the unsaturated model to predict a total of 42.4 ± 0.5 million KEGG level 3 functions of which only 0.06% are known today. Our approach not only highlights the presence of widespread and rare functions but points toward the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.
揭示微生物群落的分类学与功能之间的关系对于确定其对生态系统功能的贡献至关重要。然而，尽管有大量关于微生物分类多样性的信息，但我们对其与功能多样性关系的理解仍然匮乏。在这里，我们使用对377种分类学上不同的真菌物种的完全注释的现存基因组进行的荟萃分析，通过探索性数据挖掘方法，使用参数估计和非参数估计，利用KEGG直系同源关系第3级的所有已知功能的累积曲线（ACs）来预测地球上真菌微生物群落的总功能。将功能多样性作为物种丰富度的函数进行外推的不饱和模型比假设功能总数有限的饱和模型能更好地描述ACs，这表明存在广泛和罕见的功能。基于之前对地球上380万种真菌物种的估计，我们推广了不饱和模型，预测共有4240±50万个KEGG第3级功能，而目前已知的仅占0.06%。我们的方法不仅突出了广泛和罕见功能的存在，还指出了需要新颖且更复杂的方法来揭示功能的全貌，以充分理解真菌微生物群落在生态系统功能中的作用。
