Genomic characterisation of Actinospongicola halichondriae gen. nov., sp. nov., the first sponge-derived cultivated representative of a new genus within the class Acidimicrobiia

Abstract

A new strain (named Hal317^T) of class Acidimicrobiia was isolated from the marine breadcrumb sponge Halichondria panicea sampled in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the 16S rRNA gene sequence revealed similarities from 84.86 to 91.54% to all known type strains of the class Acidimicrobiia. Genome comparisons of strain Hal317^T with type strains of the family Iamiaceae exhibited average nucleotide identities (ANI) < 71.49% and percentage of conserved proteins (POCP) values < 50.30%. Strain Hal317^T was determined to be microaerophilic. Optimal growth occurred at 30–35 °C, 1–2% sea salt, and pH 6–7. Major fatty acids identified were C_18:1 ω7c, C_16:1 ω7c, C_17:1 ω8c, and C_16:0. The major respiratory menaquinone was MK-9(H₈). The G + C content of strain Hal317^T was 68.70%. Based on the polyphasic approach of bacterial classification, strain Hal317^T could be distinguished from known genera of the family Iamiaceae, and we propose the name Actinospongicola halichondriae gen. nov., sp. nov. (= DSM 114536^T = LMG 32795^T). Genomic features indicated that strain Hal317^T was characteristic of a sponge-associated lifestyle, such as the potential to metabolise diverse sponge-derived carbohydrates (e.g. chitin, l-fucose) and sulfur compounds (e.g. taurine). Moreover, the genome of strain Hal317^T contained stress response-related genes, including those involved in ectoine synthesis and toxin-antitoxin systems. Within the family Iamiaceae strain Hal317^T revealed unique genomic features, including a non-phosphorylated l-fucose pathway. Our study sheds light on the Acidimicrobiia, a class typified by few cultured representatives. Additionally, the new sponge-derived isolate offers valuable insights into the host-bacteria association.