Paenimyroides aestuarii gen. nov. sp. nov., a novel bacterium isolated from sediment in the Pearl River Estuary and reclassification of five Flavobacterium and four Myroides species.

An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and round bacterium, designated strain SCSIO 72103T, was isolated from sediment collected in the Pearl River Estuary, Guangdong Province, PR China and subjected to a polyphasic taxonomic study. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6-8 (optimum, pH 7) and with 1-5.5% NaCl (optimum, 1-3 %). Comparative 16S rRNA gene analysis indicated that strain SCSIO 72103T had the highest similarities to Flavobacterium baculatum SNL9T (94.7 %) and Myroides aquimaris SW105T (94.2 %). Phylogenetic analysis based 16S rRNA gene sequences showed that strain SCSIO 72103T formed a single clade with M. aquimaris SW105T. Strain SCSIO 72103T contained iso-C15 : 0 as the major fatty acid and the predominant respiratory quinone was menaquinone MK-6. These characteristics are consistent with those of F. baculatum SNL9T and M. aquimaris SW105T. Phosphatidylethanolamine, most notably, unidentified aminolipid and unidentified aminophospholipid were major polar lipids. Strain SCSIO 72103T had a single circular chromosome of 2.96 Mb with a DNA G+C content of 35.1 mol%. The average nucleotide identity, average amino acid identity (AAI) and digital DNA-DNA hybridization values showed that the pairwise similarities between SCSIO 72103T and the type strains of F. baculatum SNL9T and M. aquimaris SW105T were 78.5-80.5 %, 79.0-81.4 % and 22.7-22.8 %, respectively. The AAI values between species in this clade and the type species of Flavobacterium and Myroides were below the 65 % threshold, indicating that these species belong to a novel genus. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain SCSIO 72103T represents a new species of a novel genus, for which the name Paenimyroides aestuarii gen. nov. sp. nov. is proposed. The type strain is SCSIO 72103T (=KCTC 92043T=MCCC 1K06659T). It is also proposed that nine known species in the genera Flavobacterium and Myroides are reclassified as Paenimyroides species.

Streptomyces marincola sp. nov., a Novel Marine Actinomycete, and Its Biosynthetic Potential of Bioactive Natural Products.

Marine actinomycetes are an important source of antibiotics, but many of them are yet to be explored in terms of taxonomy, ecology, and functional activity. In this study, two marine actinobacterial strains, designated SCSIO 64649T and SCSIO 03032, were isolated, and the potential for bioactive natural product discovery was evaluated based on genome mining, compound detection, and antimicrobial activity. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 64649T formed a single clade with SCSIO 03032 (similarity 99.5%) and sister clades with the species Streptomyces specialis DSM 41924T (97.1%) and Streptomyces manganisoli MK44T (96.8%). The whole genome size of strain SCSIO 64649T was 6.63 Mbp with a 73.6% G + C content. The average nucleotide identity and digital DNA-DNA hybridization between strain SCSIO 64649T and its closest related species were well below the thresholds recommended for species delineation. Therefore, according to the results of polyphasic taxonomy analysis, the strains SCSIO 64649T and SCSIO 03032 are proposed to represent a novel species named Streptomyces marincola sp. nov. Furthermore, strains SCSIO 64649T and 03032 encode 37 putative biosynthetic gene clusters, and in silico analysis revealed that this new species has a high potential to produce unique natural products, such as a novel polyene polyketide compounds, two mayamycin analogs, and a series of post-translationally modified peptides. In addition, other important bioactive natural products, such as heronamide F, piericidin A1, and spiroindimicin A, were also detected in strain SCSIO 64649T. Finally, this new species' metabolic crude extract showed a strong antimicrobial activity. Thanks to the integration of all these analyses, this study demonstrates that the novel species Streptomyces marincola has a unique and novel secondary metabolite biosynthetic potential that not only is beneficial to possible marine hosts but that could also be exploited for industrial applications.

Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea.

A Gram-stain-positive, aerobic, non-pigmented and non-motile actinobacterium, designated strain SCSIO 67246T, was isolated from a stony coral sample collected from the Sanya sea area, Hainan province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SCSIO 67246T shared the highest similarities with Nocardioides rotundus MCCC 1A10561T (96.5 %) and Nocardioides sonneratiae KCTC 39565T (96.1%). The novel strain grew at 15-37 °C, at pH 5.0-10.0 and in the presence of 0-10 % (w/v) NaCl. The genome length of strain SCSIO 67246T was 3.52 Mbp with a DNA G+C content of 72.0 mol% and 3397 protein-coding genes. The novel strain showed an average nucleotide identity value of 76.5 % and a digital DNA-DNA hybridization value of 20.1 % with N. rotundus MCCC 1A10561T. Strain SCSIO 67246T contained MK-8(H4) as the major menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and five phospholipids. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω8c and summed feature 9 (iso-C17 : 1 ω9c/10-methyl C16 : 0). ll-2,6-Diaminopimelic acid was the diagnostic diamino acid. The whole-cell sugars were galactose, glucose and ribose. Based on this polyphasic taxonomic study, strain SCSIO 67246T represents a novel species of the genus Nocardioides, for which the name Nocardioides coralli sp. nov. is proposed. The type strain is SCSIO 67246T (=MCCC 1K06251T=KCTC 49719T).

Brevibacillus marinus sp. nov., a thermophilic bacterium isolated from deep sea sediment in the South China Sea.

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).

Diversity and Distribution of Uncultured and Cultured Gaiellales and Rubrobacterales in South China Sea Sediments.

Actinobacteria are ubiquitous in marine ecosystems, and they are regarded as an important, underexplored, potential pharmaceutical resource. The orders Gaiellales and Rubrobacterales are deep taxonomic lineages of the phylum Actinobacteria, both are represented by a single genus and contain only a few species. Although they have been detected frequently by high-throughput sequencing, their functions and characteristics in marine habitats remain unknown due to the lack of indigenous phenotypes. Here, we investigated the status of the orders in South China Sea (SCS) sediments using culture-independent and culture-dependent methods. Gaiellales is the second-most abundant order of Actinobacteria and was widely distributed in SCS sediments at water depths of 42-4,280 m, and four novel marine representatives in this group were successfully cultured. Rubrobacterales was present at low abundance in energy-limited marine habitats. An isolation strategy for Rubrobacterales from marine samples was proposed, and a total of 138 mesophilic Rubrobacterales strains were isolated under conditions of light and culture time combined with high-salinity or low-nutrient media. Marine representatives recovered in this study formed branches with a complex evolutionary history in the phylogenetic tree. Overall, the data indicate that both Gaiellales and Rubrobacterales can adapt to and survive in extreme deep-sea environments. This study lays the groundwork for further analysis of the distribution and diversity of the orders Gaiellales and Rubrobacterales in the ocean and provides a specific culture strategy for each group. The results open a window for further research on the ecological roles of the two orders in marine ecosystems.

Miltoncostaea marina gen. nov. sp. nov., and Miltoncostaea oceani sp. nov., a novel deep branching phylogenetic lineage within the class Thermoleophilia isolated from marine environments, and proposal of Miltoncostaeaceae fam. nov. and Miltoncostaeales ord. nov.

Two novel marine actinobacteria, designated as SCSIO 60955T and SCSIO 61214T, were isolated from deep-sea sediment samples collected from the South China Sea. The cells of these organisms stained Gram-negative and were rod shaped. These strains were aerobic, and catalase- and oxidase-positive. Optimal growth occurred at 28 °C and pH 7 over 14 days of cultivation. Both strains possessed phospholipids and phosphoglycolipids. The main menaquinone was MK-7. The major fatty acid was C16:0. The peptidoglycan structure was type A1γ' (meso-Dpm). Analysis of genome sequences revealed that the genome size of SCSIO 60955T was 3.37 Mbp with G + C content of 76.1%, while the genome size of SCSIO 61214T was 3.67 Mbp with a G + C content of 74.8%. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains were 73.4% and 97.7% and that with other recognized Thermoleophilia species were less than 69.1% and 87.8%, respectively. Phylogenetic analysis of the 16S rRNA gene sequences showed that strains SCSIO 60955T and SCSIO 61214T were separately clustered together and formed a well-separated phylogenetic branch distinct from their most related neighbor Gaiella occulta. Based on the data presented here, these two strains are proposed to represent two novel species of a novel genus, for which the name Miltoncostaea marina gen. nov., sp. nov., with the type strain SCSIO 60955T (=DSM 110281T =CGMCC 1.18757T), and Miltoncostaea oceani sp. nov., with the type strain SCSIO 61214T (=KCTC 49527T =CGMCC 1.18758T) are proposed. We also propose that these organisms represent a novel family named Miltoncostaeaceae fam. nov. of a novel order Miltoncostaeales ord. nov.

Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea.

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909T and SCSIO 52915T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909T and SCSIO 52915T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909T (=KCTC 49412T=CGMCC 1.13853T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915T (=KCTC 49411T=CGMCC 1.13852T), are proposed.

Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments.

A novel marine actinobacterium, strain SCSIO 58843T, was isolated from the sediment sample collected from the South China Sea. Strain SCSIO 58843T was Gram-stain-positive, aerobic and rod shaped. The whole-cell hydrolysis of amino acids contained dd-DAP, alanine, glutamic acid, glycine and aspartic acid. The main menaquinone was MK-9(H8). The major fatty acids were C17 : 1 ω8c and C17 : 0. The major phospholipids were diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phospatidylcholine (PC) and phosphatidylinositolmannoside (PIM). The G+C content of the genomic DNA was 72.5 %. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 58843T formed a new lineage in the family Iamiaceae and had the highest similarity of 93.8 % with Iamia majanohamensis DSM 19957T. Strain SCSIO 58843T can be distinguished from these known genera in the family Iamiaceae by polyphasic data analyses, and represents a novel genus and novel species, for which Actinomarinicola tropica gen. nov., sp. nov is proposed with the type strain SCSIO 58843T(=KCTC 49408T=CGMCC 1.17503T).