Microbacterium abyssi sp. nov. and Microbacterium limosum sp. nov., two new species of the genus Microbacterium, isolated from deep-sea sediment samples.

Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241T and Y20T, were isolated from deep-sea sediment samples collected from the Southwest Indian Ocean and Western Pacific Ocean, respectively. Both of the isolates were able to grow within the temperature range of 5-40 °C, NaCl concentration range of 0-7  % (w/v) and at pH 6.0-12.0. The two most abundant cellular fatty acids of both strains were anteiso-C15  :  0 and anteiso-C17  :  0. The major polar lipid contents of the two strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified glycolipid. These two strains shared common chemotaxonomic features comprising MK-10 and MK-12 as the respiratory quinones. The genomic DNA G+C contents of the two strains were 68.1 and 70.4  mol%, respectively. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus Microbacterium. Strain A18JL241T was most closely related to the type strain of Microbacterium tenebrionis KCTC 49593T (98.8 % sequence similarity), whereas strain Y20T formed a tight cluster with the type strain of Microbacterium schleiferi NBRC 15075T (99.0 %). The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the type strains of related Microbacterium species were in the range of 74.1-89.1  % and 19.4-36.9  %, respectively, which were below the recognized thresholds of 95-96 % ANI and 70 % dDDH for species definition. Based on the results obtained here, it can be concluded that strains A18JL241T and Y20T represent two novel species of the genus Microbacterium, for which the names Microbacterium abyssi sp. nov. (type strain A18JL241T=JCM 33956T=MCCC 1A16622T) and Microbacterium limosum sp. nov. (type strain Y20T=JCM 33960T=MCCC 1A16747T) are proposed.

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.

Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment.

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0-12.0, 5.0-11.0 and 5.0-11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0-93.1 % average nucleotide identity and 21.3-50.0 % DNA-DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides, for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Use of biexponential and stretched exponential models of intravoxel incoherent motion and dynamic contrast-enhanced magnetic resonance imaging to assess the proliferation of endometrial carcinoma.

Background: It is important to assess the proliferation of endometrial carcinoma (EC) noninvasively using imaging methods. This prospective diagnostic study investigated the value of biexponential and stretched exponential models of intravoxel incoherent motion (IVIM) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in predicting the Ki-67 status of EC. Methods: In all, 70 patients with EC underwent pelvic MRI. The diffusion coefficient (D), pseudo diffusion coefficient (D*), perfusion fraction (f), distributed diffusion coefficient (DDC), water molecular diffusion heterogeneity index (α), volume transfer constant (Ktrans), rate transfer constant (Kep), and volume of extravascular extracellular space per unit volume of tissue (Ve) were compared. The area under the receiver operating characteristic (ROC) curve (AUC) was used to quantify diagnostic efficacy. Multivariate logistic regression and bootstrap (1,000 samples) analyses were used to establish and evaluate, respectively, the optimal model to predict Ki-67 status. Results: D, Ktrans, and Kep were lower while α was higher in the high-proliferation group as compared with low-proliferation group (all P values<0.05). D and Kep were independent predictors of Ki-67 status in EC, and the combination of these parameters had optimal diagnostic efficacy (AUC =0.920; sensitivity 85.71%; specificity 89.29%), which was significantly better than that of D (AUC =0.753; Z=2.874; P=0.004), α (AUC =0.715; Z=3.505; P=0.001), Ktrans (AUC =0.808; Z=2.741; P=0.006), and Kep (AUC =0.832; Z=2.147; P=0.032) alone. The validation model showed good accuracy (AUC =0.882; 95% confidence interval 0.861-0.897) and consistency (C-statistic =0.902). D, Kep, Ktrans, and α showed a slightly negative (r=-0.271), moderately negative (r=-0.534), slightly negative (r=-0.409), and slightly positive (r=0.488) correlation with the Ki-67 index, respectively (all P values <0.05). Conclusions: IVIM- and DCE-MRI-derived parameters, including D, α, Ktrans, and Kep, were associated with Ki-67 status in EC, and the combination of D and Kep may serve as a superior imaging marker for the identification of low- and high-proliferation EC.

Discovery of New Siderophores from a Marine Streptomycetes sp. via Combined Metabolomics and Analysis of Iron-Chelating Activity.

The marine-derived Streptomyces sp. FIMYZ-003 strain was found to produce novel siderophores with yields negatively correlated with the iron concentration in the medium. Mass spectrometry (MS)-based metabolomics coupled with metallophore assays identified two novel α-hydroxycarboxylate-type siderophores, fradiamines C and D (3 and 4), together with two related known siderophores, fradiamines A and B (1 and 2). Their chemical structures were elucidated by nuclear magnetic resonance (NMR) and MS experiments. The annotation of a putative fra biosynthetic gene cluster enabled us to propose the biosynthetic pathway of fradiamines A-D. Furthermore, the solution-phase iron-binding activity of fradiamines was evaluated using metabolomics, confirming them as general iron scavengers. Fradiamines A-D exhibited Fe(III) binding activity equivalent to that of deferoxamine B mesylate. Growth analysis of pathogenic microbes demonstrated that fradiamine C promoted the growth of Escherichia coli and Staphylococcus aureus, but fradiamines A, B, and D did not. The results indicate that fradiamine C may serve as a novel iron carrier applicable to antibiotic delivery strategies to treat and prevent foodborne pathogens.

Malfilanol C, a new sesquiterpenoid isolated from the deep-sea-derived Aspergillus puniceus A2 fungus.

The chemical examination of the rice solid fermentation products of the deep-sea-derived fungus Aspergillus puniceus A2 resulted in the isolation of one new sesquiterpenoid malfilanol C (1), together with a rare analogue malfilanol B (2). The planar structure of 1 was resolved on the basis of the extensive analyses of the spectroscopic data (HRESIMS and NMR spectra), and its absolute configuration was assigned by quantum chemical calculation of the ECD data. Compound 1, featuring a bicyclo[5.4.0]-undecane nucleus skeleton, was the third example of this subclass sesquiterpenoids found from nature. Additionally, the subclass sesquiterpenoids 1 and 2 were discovered from marine-derived-fungi for the first time. All the isolated metabolites were evaluated the antibacterial activities against Staphylococcus aureus ATCC 29213 and Escherichia coli ATCC 25922. Compound 1 exhibited weak antibacterial activity against S. aureus ATCC 29213.

Phenolic Metabolites from a Deep-Sea-Derived Fungus Aspergillus puniceus A2 and Their Nrf2-Dependent Anti-Inflammatory Effects.

Four undescribed phenolic compounds, namely asperpropanols A-D (1-4), along with two known congeners 5 and 6, were isolated from Aspergillus puniceus A2, a deep-sea-derived fungus. The gross structures of the compounds were established by detailed analyses of the HRESIMS and NMR data, and their absolute configurations were resolved by modified Mosher's method and calculations of ECD data. Compounds 1-6 were found to have excellent anti-inflammatory effect on lipopolysaccharide (LPS)-induced RAW264.7 cells at 20 µM, evidenced by the reduced nitric oxide (NO), tumor necrosis factor α, and interleukin 6 production. Among them, 5 and 6 showed inhibitory effects on NO production comparable with the positive control (BAY11-7083 at 10 µM). Additionally, the LPS-induced mRNA expressions of inducible nitric oxide synthase and cyclooxygenase-2 were also decreased. Interestingly, mRNA expression of nuclear factor erythroid 2-related factor 2 (Nrf2) was downregulated by LPS and recovered by 1-6, suggesting a vital role of Nrf2 in their effect. We further found that pharmacological inhibition of Nrf2 by ML385 largely abrogated the effects of 1-6 on RAW264.7 cells. Therefore, 1-6 may share a common anti-inflammatory mechanism via Nrf2 upregulation and activation.

Antiviral Cyclopropane Acids from Deep-Sea-Derived Fungus Aspergillus sydowii.

Four novel monocyclic cyclopropane acids, namely, sydocyclopropanes A-D (1-4), along with one known congener hamavellone B (5), were isolated from the Aspergillus sydowii MCCC 3A00324 fungus, which was isolated from the deep-sea sediment. The gross structures of novel compounds were established by detailed analyses of the spectroscopic data (HRESIMS and NMR spectra), and their absolute configurations were resolved on the basis of the quantum chemical calculations of ECD and NMR data, in association with DP4+ probability analyses. Sydocyclopropanes A-D, featuring the 1,1,2,3-tetrasubstituted cyclopropane nucleus with different lengthy alkyl side chains, were discovered in nature for the first time. All compounds exhibited antiviral activities against A/WSN/33 (H1N1), with IC50 values ranging from 26.7 to 77.2 µM, of which compound 1 exhibited a moderate inhibitory effect (IC50 = 26.7 µM).

Evaluation of Amide Proton Transfer-Weighted Imaging for Risk Factors in Stage I Endometrial Cancer: A Comparison With Diffusion-Weighted Imaging and Diffusion Kurtosis Imaging.

Background: Endometrial cancer (EC) is one of the most common gynecologic malignancies in clinical practice. This study aimed to compare the value of diffusion-weighted imaging (DWI), diffusion kurtosis imaging (DKI), and amide proton transfer-weighted imaging (APTWI) in the assessment of risk stratification factors for stage I EC including histological subtype, grade, stage, and lymphovascular space invasion (LVSI). Methods: A total of 72 patients with stage I EC underwent pelvic MRI. The apparent diffusion coefficient (ADC), mean diffusivity (MD), mean kurtosis (MK), and magnetization transfer ratio asymmetry (MTRasym at 3.5 ppm) were calculated and compared in risk groups with the Mann-Whitney U test or independent samples t-test. Spearman's rank correlation was applied to depict the correlation of each parameter with risk stratification. The diagnostic efficacy was evaluated with receiver operating characteristic (ROC) curve analysis and compared using the DeLong test. A multivariate logistic regression was conducted to explore the optimal model for risk prediction. Results: There were significantly greater MTRasym (3.5 ppm) and MK and significantly lower ADC and MD in the non-adenocarcinoma, stage IB, LVSI-positive, high-grade, and non-low-risk groups (all p < 0.05). The MK and MTRasym (3.5 ppm) were moderately positively correlated with risk stratification as assessed by the European Society for Medical Oncology (EMSO) clinical practice guidelines (r = 0.640 and 0.502, respectively), while ADC and MD were mildly negatively correlated with risk stratification (r = -0.358 and -0.438, respectively). MTRasym (3.5 ppm), MD, and MK were identified as independent risk predictors in stage I EC, and optimal predictive performance was obtained with their combinations (AUC = 0.906, sensitivity = 70.97%, specificity = 92.68%). The results of the validation model were consistent with the above results, and the calibration curve showed good accuracy and consistency. Conclusions: Although similar performance was obtained with each individual parameter of APTWI, DWI, and DKI for the noninvasive assessment of aggressive behavior in stage I EC, the combination of MD, MK, and MTRasym (3.5 ppm) provided improved predictive power for non-low-risk stage I EC and may serve as a superior imaging marker.

Acremolin D, a new acremolin alkaloid from the deep-sea sediment derived Aspergillus sydowii fungus.

Chemical investigation of the deep-sea-derived fungus Aspergillus sydowii MCCC 3A00324 led to the isolation of one new acremolin type alkaloid (acremolin D, 1) and five known alkaloids (2‒6). The planar structure of 1 was established by the extensive analyses of the NMR and HRESIMS data, while its absolute configuration was assigned by the comparison of the experimental and calculated ECD data. Acremolin D (1) represented the second analogue of acremolin found in nature. All compounds were evaluated for their cytotoxic activities against six human cancer cell lines (A549, Hela-S3, MCF-7, HepG2, K562, and SF-268). As a result, compounds 1 and 2 exhibited a certain inhibitory effects against the proliferation of the A549, Hela-S3, HepG2, and K562 cell lines at the concentration of 20 µM.[Formula: see text].

Nesterenkonia sedimenti sp. nov., isolated from marine sediment.

A Gram-staining-positive actinobacteria strain, designated MY13T, was isolated from deep-sea sediment of the western Pacific Ocean and subjected to a taxonomic polyphasic investigation. Based on the results, cells were aerobic, irregular short rod, non-motile and non-spore-forming. Colonies were cream, circular, smooth, convex, opaque and 1.0-2.0 mm in diameter after growth on MZ2 medium at 40 °C for 72 h. Strain MY13T grew at 4-50 °C (optimum, 40 °C), pH 7-12 (pH 9) and 0.5-15% (w/v) NaCl (3.5%). The 16S rRNA gene sequence analysis revealed that strain MY13T is affiliated with the genus Nesterenkonia and closely related to Nesterenkonia populi GP10-3T (96.6%). Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) differentiated it from its closest relatives, with values ranging from 19.8% to 22.4% and 72.6% to 78.0%, respectively. Chemotaxonomic analysis showed that the major menaquinone of strain MY13T was MK-7; major cellular fatty acids were anteiso-C17:0, anteiso-C15:0 and iso-C16:0; whole-cell sugars were galactose and xylose; the peptidoglycan type was L-Lys-Gly-D-Asp; and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, one unknown polar lipid and two unknown lipids. The G+C content of genomic DNA was 63.1 mol%. Based on the physiological, chemotaxonomic and phylogenetic data, strain MY13T is a novel species of the genus Nesterenkonia, for which the name Nesterenkonia sedimenti sp. nov. is proposed. The type strain is MY13T (= LMG 28111T = MCCC 1A09979T = JCM 19767T = CGMCC 1.12784T).

Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.

A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83T, was isolated from a marine sediment of Indian Ocean. Strain WY83T grew optimally at 30-35 °C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C19:1 ω9c/C19:1 ω11c, anteiso-C15:0, C17:0 3OH, and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730T, Chryseoglobus indicus CTD02-10-2T, Yonghaparkia alkaliphila JCM 15138T, Microcella alkaliphila DSM 18851T and Microcella putealis DSM 19627T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83T, Y. alkaliphila JCM 15138T, C. frigidaquae JCM 14730T, M. alkaliphila DSM 18851T and M. putealis DSM 19627T should belong to different species of the same genus. Strain WY83T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83T (= KCTC 39637T = MCCC 1A07099T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov., respectively.

Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments.

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5-99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains' ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.

Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria.

We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.

A rapid and efficient method for the extraction and identification of menaquinones from Actinomycetes in wet biomass.

BACKGROUND: Menaquinones are constituents of prokaryote cell membranes where they play important functions during electron transport. Menaquinone profiles are strongly recommended for species classification when proposing a new Actinomycetes taxon. Presently, the most widely used methods to determine menaquinones are based on freeze-dried cells. Taxonomic research in our lab has revealed that menaquinone concentrations are low for some species of the genus Microbacterium, leading to difficulties in identifying menaquinones. RESULTS: Menaquinones extracted using the novel lysozyme-chloroform-methanol (LCM) method were comparable in quality to those obtained using the Collins method, the most widely used method. All tested strains extracted via the LCM method showed higher concentrations of menaquinones than those extracted via the Collins method. For some Microbacterium strains, the LCM method exhibited higher sensitivity than the Collins method, and more trace menaquinones were detected with the LCM method than the Collins method. In addition, LCM method is faster than the Collins method because it uses wet cells. CONCLUSION: The LCM method is a simple, rapid and efficient technique for the extraction and identification of menaquinones from Actinomycetes.

Complete genome sequence of Streptomyces sp. HSG2 from rhizosphere soil of mangrove in Qingmei Gang, Sanya.

Streptomyces sp. HSG2 was isolated from rhizosphere soil of a mangrove forest sample at Qingmei Gang, Sanya. The complete genome sequence of the strain HSG2 was obtained using PacBio Sequel HGAP.4 and comprised of 5,282,528 base pairs with a 71.9 mol% G + C content, 4504 protein-coding genes, and 71 RNAs. An in-silico analysis confirmed that genes associated with polysaccharide hydrolyzation, hydrocarbon degradation, and aerobic denitrification were presented in the genome. We also identified 24 natural product biosynthetic gene clusters for secondary metabolites, including those for streptobactin and nystatin A1. The complete genome sequence indicated that Streptomyces sp. HSG2 will provide insight into the biosynthesis and regulatory mechanisms for its secondary metabolites, and propose a potential use in biotechnological and novel bioactive natural product biosynthetic applications.

Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment.

Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.