Fig. 1
Overview of Atribacterota in the hydrocarbon- and acetate-enriched environments. a The community structures of oil reservoir and acetate enrichment samples that were examined by Kaiju software [36] with high-quality reads. b, c Transmission electron microscope (TEM) observations of Thermatribacter velox B11T. The intracellular membrane is visible, as described in Atribacterota previously [2]. d Scanning electron microscope (SEM) observation of ultrathin sections of Thermatribacter velox B11T. Cells of strain B11 were fusiform rod or ovoid shape with 0.4–0.5 μm in width and 0.6–1.9 μm in length. e Phylogenetic analysis of Atribacterota. F1: Thermatribacteraceae fam. nov. (G1: Thermatribacter gen. nov.); F2: Caldatribacteriaceae (G2: Sordiicultor gen. nov., G3: Aquicavum gen. nov., G4: Caldatribacterium); F3: Atribacteraceae (G5: Nitricultor gen. nov., G6: Atribacter); F4: Stramentimicrobiaceae fam. nov. (G7: Stramentimicrobium gen. nov., G8: Oleincola gen. nov., G9: Oleihabitans gen. nov.); F5: Phoenicimicrobiiaceae fam. nov. (G10: Phoenicimicrobium gen. nov., G11: Immundihabitans gen. nov., G12: Sediminicultor gen. nov., G13: Infernicultor gen. nov.). The maximum-likelihood phylogenetic tree was constructed using the concatenated alignment of 16 ribosomal proteins identified by using AMPHORA2 [38, 65]. All marker genes were aligned using the MUSCLE program [39] with 100 iterations, respectively. The TrimAL software [40] was used to eliminate the poorly aligned regions, and finally, 2393 amino acid positions were kept for further analysis. The alignments were concatenated and then used for calculating a maximum-likelihood phylogeny by IQ-Tree [41]. The best-fit model LG+F+R5 is well supported by the Bayesian Information Criterion. Bootstrap values were based on 1000 replicates and nodes with percentages > 80% were indicated as black circles. The red circles listed on the right illustrate the genome sources. The lineages with red stars showed the phylogenetic placement of novel lineages from this study