The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth’s habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.

在地球上绘制微生物组的巨大计划正在迅速推进，重点是单个微生物群。但是，在跨生态系统的水平上，仍缺少对掠夺性生物和其细菌猎物之间关联的全球评估。这些知识对于更好地理解自上而下的链接在构建微生物群落中的重要性至关重要。在这里，我们检查了38个基于序列的配对细菌和原生生物类群的数据集，涵盖了来自淡水，海洋和土壤等不同生境的3178个样本。我们显示，原生生物和细菌的群落概况在栖息地之间和栖息地之间密切相关，营养微生物组的结构在各个栖息地之间根本不同。土壤是最异质和多样的微生物群落。在水生环境中，原生动物群落以土壤中的食肉动物和光养动物为主。这导致总生物量与细菌丰富度的比率发生变化，在海洋中最高，而掠夺性生物体与细菌的比率在土壤中最高。捕食性生物的分类群丰富度和相对丰富度与海洋生境中细菌的丰富度呈正相关。这些联系在土壤，掠夺性原生生物丰富度和森林和草地土壤中细菌丰富度呈正相关的掠食性原生生物相对丰度上有所不同，而在农业土壤中则没有。我们的研究结果表明，人为压力对较高营养水平的影响比对较低营养水平的影响更大，从而导致微生物群落中营养结构解耦。一起，我们对全球细菌和原生生物的微生物组模式的累积概述揭示了整个地球栖息地中微生物群落营养结构的主要模式和差异，并表明人为因素可能会对微生物群落内部的营养结构产生负面影响。此外，人为因素对特别是较高营养水平的影响增加，这表明人为系统中经常观察到的生态系统功能下降可能部分归因于营养复杂性的降低。