The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1–2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50–280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.

真核细胞的起源是生物学中一个主要的悬而未决的问题。Asgard 古细菌是已知最接近真核生物的原核亲属，它们的基因组编码各种真核生物特征蛋白，表明在第一个真核细胞出现之前细胞复杂性的一些元素。然而，目前还缺乏证明环境中未培养的 Asgard 古细菌细胞结构的微观证据。我们使用无引物测序检索了 715 个几乎全长的 Loki- 和 Heimdallarchaeota 16S rRNA 序列，并设计了新型寡核苷酸探针，使用催化报告分子沉积-荧光原位杂交 (CARD-鱼）。超分辨率显微镜显示 1-2 µm 大的球状细胞，有时以聚集体形式出现。值得注意的是，DNA 染色在空间上与核糖体来源的 FISH 信号分离 50-280 nm。这表明基因组物质在特定位置是浓缩的并且在空间上是不同的，并且可能表明 Asgard 古菌细胞中的区室化或膜内陷。