Starke Robert, Fernandes Maysa Lima Parente, Morais Daniel Kumazawa, Odriozola Iñaki, Baldrian Petr, Jehmlich Nico
Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech Republic.
Molecular Systems Biology, Helmholtz-Center for Environmental Research, UFZ, 04318 Leipzig, Germany.
Microorganisms. 2021 Feb 13;9(2):381. doi: 10.3390/microorganisms9020381.
Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.
揭示微生物群落中分类学与功能之间的关系对于发现它们对生态系统功能的贡献至关重要。然而，虽然细菌和真菌的分类学多样性与功能多样性之间的关系已为人所知，但古菌的情况并非如此。在这里，我们对417个完全注释的现存且分类学上独特的古菌基因组进行了荟萃分析，使用京都基因与基因组百科全书（KEGG）直系同源关系所有已知三级功能的累积曲线来预测古菌基因组中包含的地球上微生物群落功能的程度。我们发现，多个基因组中存在的功能作为基因组间冗余与一个基因组中一个基因的多个拷贝作为基因组内冗余呈负相关，这意味着在功能重要基因的额外拷贝或更多不同基因之间存在权衡。对数模型比不饱和模型和饱和模型都能更好地描述功能多样性与物种丰富度之间的关系，这表明与细菌和真菌无限的潜力形成对比，古菌的功能总数有限。使用全球古菌物种丰富度估计值13159，对数模型预测有4164.1±2.9个KEGG三级功能。非参数自举估计得出KEGG三级功能的下限为2994±57个。我们的方法不仅突出了功能冗余的相似性，还突出了古菌与其他生命领域在功能潜力上的差异。
