The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.

中文翻译：

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将土壤微生物组解构为复杂性降低的功能模块。

土壤微生物组代表了地球上最复杂的微生物群落之一，涵盖了成千上万的生物分类和代谢途径，使整体分析在计算上变得十分繁琐且困难。在这里，我们开发了一种替代方法，其中根据代谢能力将复杂的土壤微生物组分解为各个组成部分（“功能模块”），以进行个性化表征。我们假设可以通过有针对性的富集获得代表功能模块的可再现的，低复杂性的社区，并且这些社区组合起来将包含很大范围的土壤微生物组多样性。在起始土壤接种物上进行富集，并在厌氧条件下根据特定的碳底物，抗生素，替代电子受体，使用确定的培养基，或反映共同场应力的替代生长条件。通过16S rRNA扩增子测序评估所得的群落。较宽松的模块（无氧条件，复杂的多糖和某些压力）导致群落特征更加鲜明，具有更高的丰富度和重复之间的变异性，而具有简单底物的模块则以较少的物种为主，并且具有更高的可重复性。总体上，在功能模块中发现了液态土壤提取物对照中存在的约27％的独特分类群。原始模块中未被充分代表或未被发现的分类单元也被整个模块丰富。在模块的一个子集上进行了转录组分析，以研究功能基因表达的差异。