Abstract
Streptomyces thermoautotrophicus UBT1T has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether ‘S. thermoautotrophicus’ represents a higher taxonomic rank, ‘S. thermoautotrophicus’ strains UBT1T and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1T and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1T and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between ‘S. thermoautotrophicus’ and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1T and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the ‘S. thermoautotrophicus’ proteomic profiles and KEGG orthology demonstrated that UBT1T and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1T, = DSM 100163T = KCTC 49540T) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.
Highlights
The genus Streptomyces Waksman and Henrici 1943, belonging to order Streptomycetales, family Streptomycetaceae within the class Actinomycetia, is one of largest bacterial genera as currently defined, with more than 600 validly named species according to the List of Prokaryotic names with Standing in Nomenclature
The presence of intragenomic heterogeneity of 16S rRNA !6% was reported in some thermophiles, such as the Firmicutes members Desulfotomaculum kuznetsovii DSM 6115T and Thermoanaerobacter tengcongensis MB4T, and the Actinobacteria member Thermobispora bispora DSM 43833T [53,54]
Based on the genetic and phenotypic distinctness presented above, we conclude that the chemolithotrophic strains ‘S. thermoautotrophicus’ UBT1T and H1 represent a novel genus, consistent with previous observations [11,19], and for which we propose the name Carbonactinospora thermoautotrophica gen. nov., comb. nov. (Table 2)
Summary
The genus Streptomyces Waksman and Henrici 1943, belonging to order Streptomycetales, family Streptomycetaceae within the class Actinomycetia (former Actinobacteria [1]), is one of largest bacterial genera as currently defined, with more than 600 validly named species according to the List of Prokaryotic names with Standing in Nomenclature (https://lpsn.dsmz.de/genus/streptomyces). Given the size of the genus Streptomyces, attempts have been made to determine internal structure of the genus through phylogenetic characterization of species groups, and its relationships to other taxa within the family Streptomycetaceae [8,9,10,11], more comprehensive phylogenomic studies are required to resolve interspecies and suprageneric structure [6,11]. The use of phylogenetic analyses in addition to Average Amino acid Identity (AAI), Percentage of Conserved Proteins (POCP), and whole-genome ANI (gANI) coupled with Alignment Fractions (AF) metrics have been proposed to demarcate genus and higher taxa [13,16,17,18]
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