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(H-4). 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)).

Automated summary

A novel actinomycete strain was isolated from a mangrove soil sample and its taxonomic position was determined using a polyphasic approach. It was identified as a new species of the genus Pseudonocardia based on phylogenetic analysis and genotypic properties.