RESUMEN
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
Asunto(s)
Composición de Base , ADN Bacteriano , Mucinas , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , ARN Ribosómico 16S/genética , Mucinas/metabolismo , ADN Bacteriano/genética , Genoma Bacteriano/genética , Técnicas de Tipificación Bacteriana , GenómicaRESUMEN
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94â%) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70â%. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
Asunto(s)
Alcanivoraceae , Análisis de Secuencia de ADN , Alcanivoraceae/genética , Filogenia , ARN Ribosómico 16S/genética , Ácidos Grasos/química , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Composición de BaseRESUMEN
The current genus Rhodopirellula consists of marine bacteria which belong to the family Pirellulaceae of the phylum Planctomycetota. Members of the genus Rhodopirellula are aerobic, mesophiles and chemoheterotrophs. The here conducted analysis built on 16S rRNA gene sequence and multi-locus sequence analysis based phylogenomic trees suggested that the genus is subdivided into four clades. Existing Rhodopirellula species were studied extensively based on phenotypic, genomic and chemotaxonomic parameters. The heterogeneity was further confirmed by overall genome-related indices (OGRI) including digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and percentage of conserved proteins (POCP). AAI and POCP values between the clades of the genus Rhodopirellula were 62.2-69.6% and 49.5-62.5%, respectively. Comparative genomic approaches like pan-genome analysis and conserved signature indels (CSIs) also support the division of the clades. The genomic incoherence of the members of the genus is further supported by variations in phenotypic characteristics. Thus, with the here applied integrated comparative genomic and polyphasic approaches, we propose the reclassification of the genus Rhodopirellula to three new genera: Aporhodopirellula gen. nov., Allorhodopirellula gen. nov., and Neorhodopirellula gen. nov.
Asunto(s)
Bacterias , ADN , Análisis de Secuencia de ADN , ARN Ribosómico 16S/genética , Filogenia , Bacterias/genética , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Ácidos Grasos/químicaRESUMEN
A shiny dark yellow pigmented, Gram-stain-negative, rod-shaped, non-motile bacterium, designated as strain JC631T, was isolated from the sediment ecosystem of Chilika lagoon, India. Strain JC631T tolerates up to pH 10 and NaCl up to 3% (w/v). MK6 is the only respiratory quinone. Predominant (> 10%) cellular fatty acids are anteiso-C11:0, anteiso-C13:0, and anteiso-C15:0. Major polar lipids are phosphatidylethanolamine, phosphatidylcholine, a few unidentified phospholipids, and a few unidentified aminolipids. 16S rRNA gene sequencing showed that strain JC631T shared the highest sequence identity (98.7%) with Arenibacter latericius KMM 426T followed by Arenibacter certesii CCUG 48006T (98.6%) and other members of the genus Arenibacter (< 97%). The genome size of strain JC631T is 4.16 Mb with a GC content of 40.8 mol%. Strain JC631T has ANI scores of 78.3% and 78.1%; dDDH values of 22.2% and 21.8%, respectively, with the type strains of A. latericius and A. certesii. The genomic distinction is well supported by chemotaxonomic characteristics and differential physiological properties. This supports strain JC631T to be described as a new species of the genus Arenibacter, named as Arenibacter lacus sp. nov. The type strain is JC631T (= KCTC 72002T = NBRC 114071T).