Fig. 1: Phylogenomic tree of Thaumarchaeota and distinctive traits of Gagatemarchaeaceae and Heterotrophic Terrestrial Thaumarchaeota genomes.
From: Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
This tree comprises the major lineages of Thaumarchaeota, including 19 Gagatemarchaeaceae (previously Group I.1c Thaumarchaeota) genomes and two Heterotrophic Terrestrial Thaumarchaeota (HTT) genomes (Dataset 2). It was inferred by maximum likelihood reconstruction from 76 concatenated single-copy marker genes using the LG + C60 + G + F model. The 15 new genomes obtained in this study are labelled with the prefix “AcS” or “SubAcS” for topsoil and subsoil acidic soils, respectively. Dots indicate branches with 90% UFBoot and SH-aLRT support. The selected genes implicated in key ecosystem functions are: coxA (haem-copper oxygen reductases, subunit A; K02274), coxAC (haem-copper oxygen reductases, fused coxA and coxC subunit; K15408), coxB (haem-copper oxygen reductases, subunit B; K02275), ctaA (haem a synthase; K02259), ctaB (haem o synthase; K02257), cydA (cytochrome bd ubiquinol oxidase, subunit A; K00425), cydB (cytochrome bd ubiquinol oxidase, subunit B; K00426), rbcL (ribulose-bisphosphate carboxylase large chain; K01601), CBB (Calvin–Benson–Bassham) cycle, abfD (4-hydroxybutyryl-CoA dehydratase; K14534), apc (acetyl-CoA/propionyl-CoA carboxylase; K18603), amoABC (ammonia monooxygenase subunits A, B and C; K10944, K10945 and K10946), ATPase types (V/A-type ATPase, subunit A; K02117), arcA (arginine deiminase; K01478), kdpABC (K+ transporting ATPase subunits A, B and C; K01546, K01547 and K01548), F420-dep G6PD (F420-dependent glucose-6-phosphate dehydrogenase; K15510) and PQQ-dep DH (PQQ-dependent dehydrogenase; PF13360).
