Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov

Abstract

Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

“…Different CSIs which are part of our database were all considered specific or useful for the identification of indicated taxa in our published work [36, 52, 58, 64, 66, 75–77, 79, 80]. However, in these studies, the taxa specificities of the CSIs were generally assessed by examining the top 300–500 blast p hits [48, 52, 58, 64, 75].…”

“…For several taxa ( viz . families Borreliaceae , Caryophanaceae and Leuconostocaceae ; order Legionellales [64] and Chlorobiales [77]) , CSIs are present in the server’s database at more than one taxonomic level [47, 50, 62, 78, 81]. In these cases, analysis of a genome should identify CSIs present at different phylogenetic depths providing strong internally consistent evidence supporting the placement of a species/strain into a specific taxon.…”

“…Of these, >210 CSIs are specific for >30 Bacillaceae genera into which species from the genus Bacillus were recently reclassified [52, 58, 66], whereas 138 CSIs are specific for the families Caryophanaceae and Leuconostocaceae and multiple genera and clades within them [66, 75]. In addition, our database also includes information for >230 CSIs that are specific for members of several other prokaryotic taxa including members of the order Legionellales [64], Neisseriales [76], Chlorobiales [77], family Borreliaceae [36, 53, 78], as well as some species/genera belonging to the family Pseudomonadaceae [79, 80]. Presently, our database includes CSIs for only those clades/taxa whose specificities was examined within the past 2 years [36, 53, 64, 76–78, 81].…”

“…In addition, our database also includes information for >230 CSIs that are specific for members of several other prokaryotic taxa including members of the order Legionellales [64], Neisseriales [76], Chlorobiales [77], family Borreliaceae [36, 53, 78], as well as some species/genera belonging to the family Pseudomonadaceae [79, 80]. Presently, our database includes CSIs for only those clades/taxa whose specificities was examined within the past 2 years [36, 53, 64, 76–78, 81]. Of the CSIs present in our database, the genus Alkalihalobacillus [52] was subsequently split into eight genera ( viz .…”

Chimeric inheritance and crown-group acquisitions of carbon fixation genes within Chlorobiales: Origins of autotrophy in Chlorobiales and implication for geological biomarkers

“…The order Chlorobiales consists of a group of unclassified photoheterotrophic thermophiles and two families: Chlorobiaceae that contains five genera ( Chlorobium, Chlorobaculum, Chloroherpeton , and Prosthecochloris ) and the newly proposed family Chloroherpetonaceae with species of Chloroherpeton [ 30 , 31 ]. The 16S rRNA phylogenies of this group recover close relationships to Ignavibacterales (within the phylum Chlorobi) and the Bacteriodetes, which are often grouped together along with Firmicutes in a CFB superphylum [ 32 , 33 ] ( Fig 2 ).…”