Mycetocola spongiae sp. nov., isolated from deep-sea sponge Cacospongia mycofijiensis

Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus

A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).

Paenibacillus spongiae sp. nov. isolated from deep-water marine sponge Theonella swinhoei

A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).

Brevibacterium spongiae sp. nov., isolated from marine sponge Hymeniacidon sp

A novel bacterial strain, designated as WHS-Z9^T, was isolated from marine sponge Hymeniacidon sp. collected from Weihai (37° 25' N, 121° 58' E), Shandong Province, PR China. Cells of strain WHS-Z9^T were Gram-stain-positive, non-spore-forming, non-motile, short-rod-shaped and light yellow-pigmented. The strain could grow at 10-40 °C (optimum, 20 °C), pH 4.5-9.5 (optimum, pH 8.5) and 2-14 % (w/v) NaCl (optimum, 4 %). The 16S rRNA gene sequence of strain WHS-Z9^T showed 98.7  % similarity to that of Brevibacterium epidermidis NBRC 14811^T, 98.5  % to Brevibacterium sediminis FXJ8.269^T and 98.4 % to Brevibacterium oceani BBH7^T. The phylogenetic tree based on 16S rRNA gene sequences revealed that strain WHS-Z9^T was clustered with Brevibacterium limosum o2^T. The whole genome of WHS-Z9^T was approximately 4 217 721 bp in size with a G+C content of 65.2  %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among WHS-Z9^T and other Brevibacterium type strains were 83.3-85.5 % (ANI based on blast), 86.4-87.9  % (ANI based on MUMmer) and 41.9-57.5 % (dDDH). Percentage of conserved protein values between the genomes of strain WHS-Z9^T and members of genera Brevibacterium were 76.8-82.9 %, while the average amino acid identity (AAI) values were 83.7-87.0  %. The dDDH, ANI, AAI and POCP values were below the standard cut-off criteria for the delineation of bacterial species. The sole respiratory quinone in strain WHS-Z9^T was MK-8(H₂), and the predominant fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0. The major polar lipids of WHS-Z9^T consisted of diphosphatidylglycerol and glycolipid. The diagnostic cell-wall diamino acid of strain WHS-Z9^T was meso-diaminopimelic acid. Based on the data obtained in this study, strain WHS-Z9^T (=MCCC 1K07845^T=KCTC 49848^T) should be classified as the type strain of a novel species of the genus Brevibacterium, for which the name Brevibacterium spongiae sp. nov. is proposed.

The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery

Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.