Schulz Frederik, Yan Ying, Weiner Agnes K M, Ahsan Ragib, Katz Laura A, Woyke Tanja
DOE Joint Genome Institute, Berkeley, California, USA.
Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.
bioRxiv. 2024 Dec 30:2024.12.29.630703. doi: 10.1101/2024.12.29.630703.
Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae , and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.
微生物真核生物（又名原生生物）因其在不同生态系统的养分循环中发挥的重要作用而闻名。然而，与原生生物相关的微生物群落的组成和功能在很大程度上仍不清楚。在这里，我们采用不依赖培养的单细胞分离和基因组解析宏基因组学，以深入了解从不同环境中分离出的100多种目前无法培养的纤毛虫和变形虫中未被充分探索的微生物群落和病毒群落。我们的研究结果揭示了独特的微生物群落组成，并暗示了与细菌共生体和病毒之间复杂相互作用和关联的错综复杂网络。我们观察到纤毛虫和变形虫在微生物群落和病毒群落组成方面存在明显差异，突出了原生生物与微生物相互作用的特异性。回收的115多个微生物基因组与已知的真核生物内共生体有关，包括全孢菌目、立克次氏体目、军团菌目、衣原体目、依赖菌目的不同成员，还有250多个与可能的宿主相关细菌——候选门TM7有关。我们还鉴定出80多种属于不同病毒谱系的巨型病毒，其中一些在单细胞转录组中活跃表达基因，表明它们可能与所采样的原生生物有关。我们还发现了大量预计会感染真核生物或宿主相关细菌的其他病毒。我们的结果进一步证明，原生生物充当复杂微生物和病毒关联的介质，在生态网络中发挥关键作用。我们样本中巨型病毒和多种微生物共生体的频繁共存表明存在多部分关联，特别是在变形虫之间。我们的研究对与鲜为人知的原生生物谱系相关的微生物多样性进行了初步评估，为更深入了解原生生物生态学及其在环境和人类健康中的作用铺平了道路。
