Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: (a) Maximum likelihood phylogenetic tree based on the concatenation of 120 single‐copy genes. Different colours represent different families (GTDB r220). The tree scale bar represents 0.1 substitutions per site. The numbers in nodes represent bootstrap values, and accession numbers are given in parentheses. Thermoanaerobacter kivui was used as an outgroup and root of the tree. (b) Average nucleotide identity comparisons between publicly available Thermincola strains and strain AZ34E. (c) Average nucleotide identity comparisons between publicly available Carboxydocella strains and strain AZ29I.

Article Snippet: In addition, digital DNA–DNA hybridisation (dDDH) values (and confidence intervals) between the genomes of AZ29I, AZ34E, Thermincola carboxydiphila (DSM 17129 T ) and their closest relatives were calculated using the Type (Strain) Genome Server ( https://tygs.dsmz.de ) and the recommended settings of GGDC v4.0 (Meier‐Kolthoff et al. , ; Yoon et al. ).

Techniques:

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: Phylogenetic comparison of CODHs detected in the Themincola and Carboxydocella genomes. The tree was constructed with the LG + G4 model in IQ‐TREE v2.0.6 and visualised in iTOL v6.8.1. CODH sequences of Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ29I are depicted in bold. The CODHs of Carboxydothermus hydrogenoformans were used as reference points for functional predictions. The tree scale bar represents 1 substitution per site. The circles in nodes represent bootstrap values > 80. The genomic structure of cooS gene clusters encoding the different CODHs in Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ291 are shown in the boxes on the top right corner. Gene abbreviations: acsB, Acetyl‐CoA synthase; acsC, corrinoid iron–sulfur protein large subunit; acsD, corrinoid iron–sulfur protein small subunit; acsE, methyltransferase A; ATPase, AAA family ATPase; cooA, CO‐dependent transcriptional activator; cooC, CODH chaperone; cooF, ferredoxin‐like electron transfer Fe‐S protein; cooMKLXUH, sub‐units of the energy‐converting hydrogenase; cooS, CO‐dehydrogenase; FNOR, NAD/FAD oxidoreductase; hp, hypothetical protein; hypA, hydrogenase maturation protein; nqrF, Na(+)‐translocating NADH‐quinone reductase subunit F; TR, transcription regulator; YlmC, YlmC/YmxH family sporulation protein; YpiB, YpiB family protein.

Article Snippet: In addition, digital DNA–DNA hybridisation (dDDH) values (and confidence intervals) between the genomes of AZ29I, AZ34E, Thermincola carboxydiphila (DSM 17129 T ) and their closest relatives were calculated using the Type (Strain) Genome Server ( https://tygs.dsmz.de ) and the recommended settings of GGDC v4.0 (Meier‐Kolthoff et al. , ; Yoon et al. ).

Techniques: Comparison, Construct, Functional Assay