Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean

Abstract

The actinomycetes strains KRD168T and KRD185T were isolated from sediments collected from the deep Southern Ocean and, in this work, they are described as representing two novel species of the genus Pseudonocardia through a polyphasic approach. Despite sharing >99 % 16S rRNA gene sequence similarity with other members of the genus, comparative genomic analysis allowed species delimitation based on average nucleotide identity and digital DNA–DNA hybridization. The KRD168T genome is characterized by a size of 6.31 Mbp and a G+C content of 73.44 mol%, while the KRD185T genome has a size of 6.82 Mbp and a G+C content of 73.98 mol%. Both strains contain meso-diaminopimelic acid as the diagnostic diamino acid, glucose as the major whole-cell sugar, MK-8(H4) as a major menaquinone and iso-branched hexadecanoic acid as a major fatty acid. Biochemical and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their status as distinct species. The names Pseudonocardia abyssalis sp. nov. (type strain KRD168T=DSM 111918T=NCIMB 15270T) and Pseudonocardia oceani (type strain KRD185T=DSM 111919T=NCIMB 15269T) are proposed.

Multi‐omics analysis of antagonistic interactions among free‐living Pseudonocardia from diverse ecosystems

“…As a model of free‐living Pseudonocardia , the whole‐genome sequence of three species ( Pseudonocardia abyssalis KRD168, Pseudonocardia oceani KRD185 and Pseudonocardia sp. KRD291) isolated previously from the deep Southern Ocean (Millán‐Aguiñaga et al, 2019; Parra et al, 2021) was selected and compared with Pseudonocardia strains from diverse ecological and geographical origins (Table S1). These strains correspond to two phylogenetically closely related species ( P. abyssalis and P. oceani ), and a third species ( Pseudonocardia KRD291), which is phylogenetically closely related to Pseudonocardia sediminis , another species of marine origin.…”

Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant

“…Certain strains that were considered during our phylogenetic analyses based on 16S rRNA gene sequences were omitted from the aforementioned investigations because of the unavailability of their protein sequences in the NCBI database [22]. Hence, despite the high sequence similarity (99.56 %) observed in the 16S rRNA gene between strain I65 T and N. yanshanensis CCBAU 05354 T , the whole-genome sequence analysis indicates that strain I65 T and N. yanshanensis CCBAU 05354 T represent two distinct novel species [23]. Additionally, our genomic analysis using the NCBI databases, Uniprot blast , and the dfast web-based tool revealed that only the genome of strain I65 T possesses heavy metal resistance genes, such as cusA , cusB , and merA () [24].…”

ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

“…Many Streptomyces species can be readily isolated from any soil, but less well studied genera of filamentous actinobacteria such as Amycolatopsis , Pseudonocardia , Saccharopolyspora , and Salinispora are often described as rare because they are recovered less frequently. Pseudonocardia species, for example, are slow-growing and difficult to culture, and have been most commonly found living in a mutually-beneficial symbiosis with attine ants in South and Central America but they have also been isolated from soil and deep-sea marine sediments, suggesting a combination of free-living and symbiotic species in this genus [23–28]. The marine environment is the natural niche of Salinispora species, which have been described as the ‘ Streptomyces of the sea’ because they are also prolific producers of SMs including molecules currently undergoing clinical trials [24].…”