Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific.

Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The presence of rich categories related to catalytic activity, membrane part and metabolic process highlights their involvement in cellular component, biological process, and molecular function. The genome sequence of strain R16 also revealed the presence of 13 putative biosynthetic gene clusters for secondary metabolites, including those for ε-Poly-L-lysine, ectoine, heterobactin, isorenieratene and corynecin, suggesting its potential for antibiotic production and warranting further exploration.

Brevibacterium profundi sp. nov., isolated from deep-sea sediment of the Western Pacific Ocean.

A new Gram-stain-positive, aerobic, non-motile and rod-shaped actinobacterium, designated O1T, was isolated from a deep-sea sediment of the Western Pacific Ocean. Strain O1T showed optimal growth at 30 °C, between pH 6.0 and 8.0, and in the presence of 1-5 % (w/v) NaCl. The predominant menaquinone was MK-8 (H2), and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid. The DNA G+C content of strain O1T was 64.9 mol% and the genome size was 4.17 Mb. Based on a similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain O1T belonged to the genus Brevibacterium. The values of average nucleotide identity and in silico DNA-DNA hybridization between strain O1T and its close relatives were well below the thresholds used for the delineation of a new species. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain O1T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium profundi sp. nov. is proposed. The type strain is O1T (=JCM 33845T=MCCC 1A16744T).

Diversity and novelty of actinobacteria in Arctic marine sediments.

The actinobacterial diversity of Arctic marine sediments was investigated using culture-dependent and culture-independent approaches. A total of 152 strains were isolated from seven different media; 18 isolates were selected for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 18 isolates belonged to a potential novel genus and 10 known genera including Actinotalea, Arthrobacter, Brachybacterium, Brevibacterium, Kocuria, Kytococcus, Microbacterium, Micrococcus, Mycobacterium, and Pseudonocardia. Subsequently, 172 rDNA clones were selected by restriction fragment length polymorphism analysis from 692 positive clones within four actinobacteria-specific 16S rDNA libraries of Arctic marine sediments, and then these 172 clones were sequenced. In total, 67 phylotypes were clustered in 11 known genera of actinobacteria including Agrococcus, Cellulomonas, Demequina, Iamia, Ilumatobacter, Janibacter, Kocuria, Microbacterium, Phycicoccus, Propionibacterium, and Pseudonocardia, along with other, unidentified actinobacterial clones. Based on the detection of a substantial number of uncultured phylotypes showing low BLAST identities (<95 %), this study confirms that Arctic marine environments harbour highly diverse actinobacterial communities, many of which appear to be novel, uncultured species.