Fig. 5

Phylogenetic analysis and metabolism of bacteria represented by MAGs from the MS4 and MS11 sites. A The tree is based on 16 concatenated ribosomal proteins (rpL2, 3, 4, 5, 6, 14, 15, 16, 18, 22, 24, and rpS3, 8, 10, 17, 19) generated using iQ-TREE. An archaeon, Thermococcus alcaliphilus, was used as the outgroup. B The metabolic capacities for generalized biogeochemical pathways in Alum Rock genomes are represented by colored circles. A pathway is present if the core KEGG orthologs encoding that pathway are identified in each genome. Abbreviations are as follows: WLP, Wood–Ljungdahl pathway, rTCA, reductive tricarboxylic acid cycle; ANR, assimilatory nitrate reduction; DNRA, dissimilatory nitrate reduction to ammonia; thiosulfate oxidation by SOX complex; DSR, dissimilatory sulfate reduction; hydrogen oxidation, [NiFe]-hydrogenases, and NAD-reducing hydrogenase