Extended Data Fig. 1: The emergence of Ca. Heimdallarchaeum endolithica belonging to the Ancient Archaea Group of Heimdallarchaeota in a series of incubations derived from the same rock originated from Pescadero basin.
a. Maximum fraction of the AAG phylotype within the first-generation incubations from the rock detected within a 13-month period. b. Maximum fraction of the AAG phylotype within the serial dilution cultures of the initial lactate-fed culture. c. Amplicon sequencing of a hypervariable region in 16S rRNA gene showing the fraction of AAG phylotype in second-generation lactate-fed cultures. Mixed, mixture of rock and medium transferred from the first-generation incubation. Planktonic, only top-layer medium was transferred. d. Community complexity reduction over time as indicated by total operational taxonomic unit (OTU) counts (top) and the Shannon diversity index (bottom). e. Full-length 16S rRNA gene survey using universal archaea primers showing a single abundant AAG phylotype (Ca. Heimdallarchaeum endolithica) species above noise, and its 16S sequence dissimilarity (percent sequence identity difference) with other archaea in the community. Loki, a Lokiarchaeota phylotype; Thermopl, a Thermoplasmatota phylotype; Woese, a Woesearchaeia phylotype. f. Wide-field microscopy images of a large multispecies biofilm isolated from the lactate-fed 2nd-generation incubation, which was stained using DAPI (DNA), FM1-43 (membrane lipids), and concanavalin A (extracellular matrix). Imaging was repeated two times with similar observations. In c and d, error bars indicate SD. N=2, independent DNA samples extracted from the same incubation.
