Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera

Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters

A novel actinomycete strain, designated S2-4^T, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene indicated that strain S2-4^T formed a unique clade next to that harboring Pseudonocardia dioxanivorans CB1190^T, which shared the highest sequence similarity (98.20%) with the new isolate. Phylogenetic analysis based on core genes of genomic sequences displayed a different scenario, exhibiting closer phylogenetic relationship of strain S2-4^T with several species with 16S rRNA gene sequence similarities ranging from 96.95 to 98.06%, which was confirmed by the phylogenetic tree reconstructed based on genomic sequences. Further, substantial differences between the genotypic properties of strain S2-4^T and its closest neighbors, including digital DNA-DNA hybridization, average nucleotide identity, and distribution patterns of biosynthetic gene clusters (BGC), indicated the taxonomic position of strain S2-4^T as a novel species of the genus Pseudonocardia. Accordingly, strain S2-4^T was observed to show a different distribution pattern of a predicted BGC encoding ectoine by comparative genomic analysis, which could be strongly linked to its unique habitat distinct from where its close neighbors were isolated. The major cellular fatty acids were iso-C_15:0, C_21:0, and iso-C_16:0. The predominant menaquinone was MK-8(H₄). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidyl-N-monomethylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, and two unidentified glycolipids. Here, we propose a novel species of the genus Pseudonocardia: Pseudonocardia humida sp. nov. with the type strain S2-4^T (= JCM 34291^T = CGMCC 4.7706^T).

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

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.