Quantifying microbial guilds.

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae042
Juan Rivas-Santisteban, Pablo Yubero, Semidán Robaina-Estévez, José M González, Javier Tamames, Carlos Pedrós-Alió
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Abstract

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

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量化微生物行会。
由于微生物与环境的多重相互作用,微生物的生态作用至关重要。然而,尽管有了高通量数据,评估各个分类群的贡献却很困难,这阻碍了我们对这种复杂系统的理解。在此,我们提出了一种适用于元基因组数据的行会定量定义。我们的框架侧重于蛋白质序列的功能特征及其多样化性质。首先,我们从与基因注释相对应的整个序列空间中分辨出功能序列,然后量化它们在不同环境中对行会组成的贡献。此外,我们还识别并区分了功能实现,即具有不同功能实现方式的序列空间。与此相反,我们发现选系的划分并不能始终与生态(或功能)上不同的功能实现方式保持一致。我们通过两个案例研究证明了我们方法的价值:马拉斯皮纳环游巡航中的氨氧化和多胺摄取行会,揭示了后者在海洋生态系统中的新生态动态。因此,行会的量化有助于我们评估不同分类群的功能作用,对微生物群落的研究具有深远影响。
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