RESULTS:

Two novel strains designated YLB-02T and YLB-04T were isolated from the deep-sea sediments of Yap Trench located in the Pacific Ocean. Cells of the strains were Gram-stain-positive oxidase- and catalase-positive and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YLB-02T belonged to the genus Oceanobacillus and strain YLB-04T belonged to the genus Bacillus . Strain YLB-02T showed similarities of 96.9 % with Ornithinibacillus contaminans CCUG 53201T 96.3 % with Oceanobacillus profundus CL-MP28T 96.1 % with Oceanobacillus halophilus J8BT and 95.7 % with Oceanobacillus bengalensis Ma-21T. Strain YLB-04T showed the highest sequence similarity of 97.4 % with Bacillus notoginsengisoli SYP-B691T. The average nucleotide identity (ANI) and the DNA–DNA hybridisation (DDH) estimate values for strain YLB-02T and YLB-04T with their related type strains were below the respective threshold for species differentiation. The G+C contents of strains YLB-02T and YLB-04T were 37.3 and 45.4 mol%. The predominant (>10 %) cellular fatty acids of strain YLB-02T were iso-C14 : 0 iso-C15 : 0 iso-C16 : 0 and C16 : 1ω7c alcohol and those of strain YLB-04T were C16 : 0 iso-C15 : 0 anteiso-C15 : 0 and C18 : 0. Their predominant ubiquinone was MK-7. The cell-wall peptidoglycan of strain YLB-02T contained glutamic acid alanine aspartic acid lysine and ornithine but no meso-diaminopimelic acid while strain YLB-04T contained meso-diaminopimelic acid glutamic acid alanine aspartic acid lysine and ornithine. In addition to diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG) the polar lipids of strain YLB-02T also consisted of an unidentified glycolipid (GL) two unidentified polar lipids (L1 and L2) and two unidentified phospholipids (PL1 and PL2) and those of strain YLB-04T also consisted of phosphatidylethanolamine (PE) and an unidentified phospholipid (PL). Based on phenotypic genotypic and chemotaxonomic characteristics two novel species are proposed Oceanobacillus piezotolerans sp. nov. with YLB-02T (=MCCC 1A12699T=JCM 32870T) and Bacillus piezotolerans sp. nov. with YLB-04T (=MCCC 1A12711T=JCM 32872T) as the type strains.

A taxonomic study was carried out on strain MT13131T which was isolated from deep-sea sediment of the Indian Ocean during the screening of oil-degrading bacteria. The chain length range of n-alkanes (C8 to C32) oxidized by strain MT13131T was determined in this study. The bacterium was Gram-negative oxidase- and catalase-positive single rod shaped and motile by peritrichous flagella. Growth was observed at salinities of 1–12 % and at temperatures of 10–42 °C. The isolate was capable of Tween 20 40 and 80 hydrolysis but incapable of gelatin cellulose or starch hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT13131T belonged to the genus Alcanivorax with highest sequence similarity to Alcanivorax marinus R8-12T (96.92 %) other species of genus Alcanivorax shared 92.96–96.69 % sequence similarity. The principal fatty acids were summed feature 3 (C16 : 1ω6c/ω7c) summed feature 8 (C18 : 1ω7c/ω6c) C16 : 0 and C12 : 0 3OH. The G+C content of the chromosomal DNA was 64.2 mol%. Phosphatidylglycerol phosphatidylethanolamine three aminolipids and three phospholipids were present. The combined genotypic and phenotypic data showed that strain MT13131T represents a novel species within the genus Alcanivorax for which the name Alcanivorax mobilis sp. nov. is proposed with the type strain MT13131T (=MCCC 1A11581T=KCTC 52985T).

Three actinobacterial strains FXJ8.128 FXJ8.269T and FXJ8.309 were isolated from deep-sea sediments collected from the Carlsberg Ridge and Southwest Indian Ridge at depths of 3690 1800 and 2461 m respectively. The three strains had highly similar 16S rRNA gene sequences (99.8–99.9 % identities) and formed a monophyletic clade within the Brevibacterium 16S rRNA gene tree showing 98.2–98.9 % 16S rRNA gene sequence identities with type strains Brevibacterium epidermidis NCIMB 702286T Brevibacterium iodinum DSM 20626T Brevibacterium linens DSM 20425T Brevibacterium oceani BBH7T and Brevibacterium permense VKM Ac-2280T. All three isolates showed activity towards the breakdown of pectin and fluoranthene. They contained MK-8(H2) as the most predominant menaquinone diphosphatidylglycerol phosphatidylglycerol and a glycolipd as the main polar lipids and anteiso-C15 : 0 and anteiso-C17 : 0 as the major cellular fatty acids. Moreover the three isolates were distinguished readily from the phylogenetically related type strains by DNA–DNA hybridization values by random amplified polymorphic DNA fingerprint profiles and by a range of physiological and biochemical characteristics. On the basis of the above polyphasic taxonomic data strains FXJ8.128 FXJ8.269T and FXJ8.309 represent a novel species of the genus Brevibacterium for which the name Brevibacterium sediminis sp. nov. is proposed. The type strain is FXJ8.269T (=CGMCC 1.15472T=DSM 102229T).

A novel bacterium designated SCSIO 07575T was isolated from a deep-sea hydrothermal sediment sample collected from the western Pacific Ocean. Growth at 65 °C was observed but not at 70 °C or below 37 °C. The optimum conditions for growth were at 55–65 °C pH 7.0 and in the presence of 2 % (w/v) NaCl. Strain SCSIO 07575T showed filamentous growth. Unstable formation of white aerial mycelia was observed which disappeared after several times’ subculture. Abundant substrate mycelia were observed with grape-like spores. No soluble pigment was observed. Phylogenetic analysis of 16S rRNA gene sequences showed that SCSIO 07575T belonged to the family Thermoactinomycetaceae and formed a distinct clade in the phylogenetic tree. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose xylose glucose and galactose. The polar lipids were diphosphatidylglycerol phosphatidylglycerol phosphatidylethanolamine an unidentified aminophospholipid and two unidentified phospholipids. The predominant menaquinone was MK-7. Major fatty acids were iso-C_15 : 0 iso-C_17 : 0 and iso-C_16 : 0. Based on the whole genome sequence analysis the genome size was 2 751 094 bp with a DNA G+C value of 57.2 mol% including one circular chromosome and one plasmid. On the basis of polyphasic data strain SCSIO 07575T represented a novel species of a new genus within the family Thermoactinomycetaceae for which the name Staphylospora gen. nov. is proposed with the type species Staphylospora marina sp. nov. and the type strain SCSIO 07575T (=DSM 106793T=CGMCC 1.15879T).

A Gram-stain-negative short rod-shaped yellow bacterium (strain LMO-1T) was isolated from deep-sea sediment of the Mariana Trench Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1T belonged to genus Sphingomonas with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2T (96.3 %) followed by Sphingomonas prati W18RDT (96.1 %) Sphingomonas arantia 6PT (96.0 %) and Sphingomonas montana W16RDT (95.9 %). The predominant polar lipids were phosphatidylethanolamine sphingoglycolipid phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) C16 : 0 and C14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1T was 69.2 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LMO-1T and CC-Nfb-2T were 75.9 and 20.5 % respectively. Based on these data LMO-1T should be classified as representing a novel species of the genus Sphingomonas for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1T (=MCCC 1K04066T=JCM 33666T).

A novel thermophilic bacterium designated SCSIO 07484T was isolated from marine sediment sampled in the South China Sea. Growth occurred at 30–60 °C pH 6.0–8.0 and in the presence of 0–3 % (w/v) NaCl. Cells of strain SCSIO 07484T were rod-shaped and flagellum-forming. No soluble pigment was observed. The phylogenetic analysis of the 16S rRNA gene sequences indicated that SCSIO 07484T belonged to the family Paenibacillaceae and clustered with members of the genus Brevibacillus in the phylogenetic trees with less than 96.2 % similarities. The cell wall contained meso-diaminopimelic acid. Whole-cell hydrolysates contained arabinose glucose and ribose. The predominant menaquinone was MK-7. Major fatty acids were iso-C16 : 0 iso-C15 : 0 C16 : 0 and iso-C14 : 0. Diphosphatidylglycerol phosphatidylglycerol phosphatidylethanolamine and phosphatidylmonomethylethanolamine were its diagnostic polar lipids. The whole genome size of strain SCSIO 07484T was 4 079 826 bp with a DNA G+C content of 56.2 mol% including one circular chromosome of 3 978392 bp and one plasmid of 101434 bp. Based on the polyphasic analysis of strain SCSIO 07484T it is considered to represent a novel species of the genus Brevibacillus for which the name Brevibacillus marinus sp. nov. is proposed with the type strain SCSIO 07484T (=DSM 106769T=CGMCC 1.15814T).

A novel bacterial strain designated SW136T was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative aerobic catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136T represented a novel member of the genus Aurantimonas forming a distinct cluster with ‘ Aurantimonas litoralis ’ Aurantimonas coralicida and Aurantimonas manganoxydans (98.2 98.1 and 97.9% sequence similarity respectively). The predominant cellular fatty acid of strain SW136T was C18 : 1  ω7c. Strain SW136T contained ubiquinone-10 as the dominant respiratory quinone and diphosphatidylglycerol phosphatidylcholine phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA–DNA hybridization values of strain SW136T with A. coralicida CGMCC 1.12222T and A. manganoxydans CGMCC 1.12225T were 78.8 and 78.6 % and 21.5 and 25.5 % respectively. On the basis of phylogenetic inference and phenotypic characteristics we propose that strain SW136T represents a novel species of the genus Aurantimonas with the name Aurantimonas marina sp. nov. The type strain is SW136T (=CGMCC 1.17725T=KCTC 82366T).

A novel Gram-stain-negative aerobic gliding rod-shaped and carotenoid-pigmented bacterium designated A20-9T was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 % at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T followed by similarities of 90.4 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T respectively. Its complete genome size was 4 035 598 bp the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity 62.7 % average amino acid identity value 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol phosphatidylglycerol phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %) iso-C16 : 0 3-OH (12.4 %) and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c 11.6 %). Combining the genotypic and phenotypic data A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus for which the name Croceimicrobium hydrocarbonivorans gen. nov. sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).

A taxonomic study was carried out on strain PA15-N-34T which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0–15.0% NaCl and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %) followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %–97.0 %). The average nucleotide identity and DNA–DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46–81.78% and 18.7–25.2 % respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c; 31.2 %) C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine phosphatidylglycerol diphosphatidylglycerol four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax for which the name Alcanivorax sediminis sp. nov. is proposed with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).

Two novel Gram-stain-negative aerobic rod-shaped carotenoid-pigmented and non-flagellated bacteria designated BC31-1-A7T and BC31-3-A3T were isolated from polyethylene-terephthalate-degrading bacterial consortia enriched from deep-sea sediment collected in the Pacific Ocean. Optimal growth of both strains was observed at 28–32 °C at pH 7.5 and in the presence of 3–4% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strains BC31-1-A7T and BC31-3-A3T were closely related to Muricauda aquimarina JCM 11811T Muricauda lutimaris KCTC 22173T Muricauda ruestringensis DSM 13258T Muricauda zhangzhouensis DSM 25030T Muricauda oceani JCM 33902T and Muricauda oceanensis KCTC 72200T with 96.8–98.9% sequence similarity. The 16S rRNA gene sequence similarity between strains BC31-1-A7T and BC31-3-A3T was 97.5%. The genomic G+C contents of strains BC31-1-A7T and BC31-3-A3T were 42.1 and 41.6 mol% respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain BC31-3-A3T strain BC31-1-A7T and their six closely related type strains were 77.6–84.3% and 20.5–27.9% respectively. Menaquinone-6 was detected as the major isoprenoid quinone in all strains. Their major fatty acids were iso-C15:0 iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids of strains BC31-1-A7T and BC31-3-A3T were identified as one phosphatidylethanolamine some unidentified polar lipids and one aminolipid. Based on their distinct taxonomic characteristics strains BC31-1-A7T and BC31-3-A3T represent two novel species in the genus Muricauda . The names proposed to accommodate these two strains are Muricauda aurea sp. nov. and Muricauda profundi sp. nov. and the type strains are BC31-1-A7T (=MCCC M23246T=KCTC 82569T) and BC31-3-A3T (=MCCC M23216T=KCTC 82302T) respectively.