Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.

Leucobacter allii sp. nov. and Leucobacter rhizosphaerae sp. nov., isolated from rhizospheres of onion and garlic, respectively

Three bacterial strains, H21R-40^T and H21R-36 from garlic (Allium sativum) and H25R-14^T from onion (Allium cepa), were isolated from plant rhizospheres sampled in the Republic of Korea. Results of 16S rRNA gene sequence analysis revealed the highest sequence similarity of strain H21R-40^T to Leucobacter celer subsp. astrifaciens CBX151^T (97.3 %) and Leucobacter triazinivorans JW-1^T (97.2 %), and strain H25R-14^T to Leucobacter insecticola HDW9B^T (98.8 %) and Leucobacter humi Re6^T (98.4 %), while the sequence similarity between strains H21R-40^T and H21R-36 was 99.8 %. According to the phylogenomic tree, strains H21R-40^T with H21R-36 formed an independent clade separable from other Leucobacter species within the genus Leucobacter and strain H25R-14^T clustered with Leucobacter insecticola HDW9B^T, Leucobacter coleopterorum HDW9A^T and Leucobacter viscericola HDW9C^T. Strains H21R-40^T and H21R-36 had orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values (98.1 % and 86.9 %, respectively) higher than the threshold ranges for species delineation (95-96 % and 70 %, respectively). The OrthoANI and dDDH values between two strains (H21R-40^T and H25R-14^T) and the type strains of species of the genus Leucobacter were lower than 81 and 24 %, respectively. The peptidoglycan type of three strains was type B1. The major menaquinones and major polar lipids of the strains were MK-11 and MK-10, and diphosphatidylglycerol, phatidylglycerol and an unidentified glycolipid, respectively. The major fatty acids (more than 10 % of the total fatty acids) of strains H21R-40^T and H21R-36 were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0, and those of strain H25R-14^T were anteiso-C_15 : 0 and iso-C_16 : 0. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Leucobacter, named Leucobacter allii sp. nov. (H21R-40^T and H21R-36) and Leucobacter rhizosphaerae sp. nov. (H25R-14^T). The respective type strains are H21R-40^T (=DSM 114348^T=JCM 35241^T=KACC 21839^T=NBRC 115481^T) and H25R-14^T (=DSM 114346^T=JCM 35239^T=KACC 21837^T=NBRC 115479^T).

Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis

A Gram-stain-positive, strictly aerobic, polar flagellated, short rod-shaped bacterium, designated DFW100M-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis collected from Wanju-gun, South Korea. The growth range of NaCl concentration was 0–3 % (w/v) (optimally 0 % (w/v)), the temperature range for growth was 10–40 °C (optimally 28–30 °C), and the pH range for growth was pH 6.0–9.0 (optimally pH 7.0–8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DFW100M-13T had a high sequence similarity to members of the genus Microbacterium , having the highest similarity with Microbacterium luticocti DSM 19459T (97.7 %), Microbacterium rhizosphaerae CHO1T (97.1 %), and Microbacterium immunditiarum SK 18T (97.0 %), and formed a distinct lineage with Microbacterium luticocti DSM 19459T within the genus Microbacterium . A phylogenetic tree based on house-keeping genes also showed the result similar to the 16S rRNA gene-based tree. The main respiratory quinone (>10 %) was MK-11, MK-12 and MK-10, and the predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, an inidentified glycolipid and an unidnetified lipid. The peptidoglycan type was supposed to be the B2ß with amino acids d-alanine, d-glutamic acid, glycine, l-homoserine and d-ornithine. The genomic DNA G+C content was 68.0 mol%. Based on the polyphasic taxonomic data, strain DFW100M-13T is considered to represent a novel species, for which the name Microbacterium protaetiae sp. nov. is proposed. The type strain is DFW100M-13T (=KACC 19323T=NBRC 113120T).

Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas

A bacterium that was Gram-staining-positive, facultatively anaerobic, non-motile, rod- or filamentous-shaped, designated as strain 2JSPR-7T, was isolated from a gut of larvae of Allomyrina dichotoma which were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. 2JSPR-7T had the highest 16S rRNA gene sequence similarity to Xylanibacterium ulmi XIL08T (98.1 %), Xylanimicrobium pachnodae NBRC 107786T (97.8 %) and Xylanimonas cellulosilytica DSM 15894T (97.5 %). Optimum growth conditions were at 28–30 °C, pH 7–8 and 0 % salt concentration. The cellular fatty acids mainly consisted of anteiso-C15 : 0, C14 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, four unidentified phospholipids and two unidentified glycophospholipids. The major menaquinones were MK-8(H4) and MK-9(H4). The peptidoglycan structure was suggested to be the type A3α (A11.14) l-Lys–l-Ser with the presence of d-Ala, l-Ala, d-Glu, l-Ser and l-Lys. Whole cell sugars were rhamnose, ribose and glucose. The DNA G+C content was 72.7 mol%. We encountered difficulty in selecting a suitable genus to accommodate strain 2JSPR-7T from any of the genera Xylanimonas , Xylanimicrobium and Xylanibacterium based on the polyphasic approach including phylogenetic and phenotypic characterization. Therefore, it is proposed to combine the genera Xylanimicrobium and Xylanibacterium with the genus Xylanimonas considering the priority of publication and to classify strain 2JSPR-7T in the genus as Xylanimonas allomyrinae sp. nov. The type strain of the novel species is 2JSPR-7T (=KACC 19330T=NBRC 113052T). In addition, the description of the genus Xylanimonas is emended, and Xylanibacterium ulmi and Xylanimicrobium pachnodae are reclassified as Xylanimonas ulmi comb. nov. and Xylanimonas pachnodae comb. nov., respectively.

Algoriphagus kandeliae sp. nov., isolated from mangrove rhizosphere soil

Strain XY-J91^T, a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15-50 °C (optimum 40 °C), at pH 5.5-9.5 (optimum 7.0-8.0) and with 0-8 % (w/v) NaCl (optimum 1-2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91^T was 40.4 mol%. Strain XY-J91^T exhibited highest 16S rRNA gene sequence similarities to the type strains of Algoriphagus marincola SW-2^T (96.66 %), Algoriphagus taiwanensis CC-PR-82^T (96.21%), Algoriphagus ornithinivorans JC2052^T (96.16%), Algoriphagus confluentis HJM-2^T (95.73%) and Algoriphagus zhangzhouensis 12C11^T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91^T represents a novel species of the genus Algoriphagus, for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91^T (=MCCC 1K03612^T=KCTC 72216^T).

Gryllotalpicola protaetiae sp. nov., isolated from insect Protaetia brevitarsis seulensis, and emended descriptions of the genus Gryllotalpicola and the species Gryllotalpicola soli

A bacterial strain, designated 2DFW10M-5^T, was isolated from gut of the larva of Protaetia brevitarsis seulensis collected in the Republic of Korea. Cells of the strain were Gram-stain-positive, non-motile and rod-shaped. The strain grew at the range of 10-37 °C (optimum, 28-30 °C) and pH 4.0-8.0 (optimum, pH 7.0) and tolerated up to 1 % NaCl (w/v; optimum, 0 %) on Reasoner's 2A medium. It was catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain 2DFW10M-5^T showed the highest similarity to Gryllotalpicola daejeonensis RU-04^T (98.4 %), Gryllotalpicola soli KIS12-7^T (98.2 %), Gryllotalpicola kribbensis PU-02^T (97.5 %), Gryllotalpicola koreensis RU-16^T (97.4 %) and Gryllotalpicola reticulitermitis TS-56^T (97.2 %). The phylogenetic tree based on the 16S rRNA gene sequence revealed that strain 2DFW10M-5^T fell into the radius of the genus Gryllotalpicola. The predominant fatty acid was ω-cyclohexyl-C_17:0. The polar lipids of strain 2DFW10M-5^T were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and two unidentified lipids. The detected isoprenoid quinones were MK-11 (61.0 %), MK-10 (33.7 %) and MK-12 (5.3 %). The peptidoglycan contained d- and l-alanine, d-glutamic acid, glycine, l-serine and d-lysine with l-lysine as the diamino acid. The DNA G+C content calculated from the genome sequence of strain 2DFW10M-5^T was 69.2 mol%. On the basis of its genomic, phylogenetic and phenotypic properties and distinctiveness, strain 2DFW10M-5^T represents a novel species of the genus Gryllotalpicola, for which the name Gryllotalpicola protaetiae sp. nov. is proposed. The type strain is 2DFW10M-5^T (=KACC 19316^T=NBRC 113049^T).

Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil

Strain KUDC5002^T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25-37°C and pH 5.0-12.0, and showed optimal growth at 30 °C and pH 7.0-8.0. Strain KUDC5002^T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002^T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C_18 : 1 ω9c (17.3 %), iso-C_16 : 0 (16.0 %) and iso-C_17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002^T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24^T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002^T should be considered a novel species in the genus Nocardioides, for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002^T (=KCTC 39855^T=DSM 106604^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Demequina litorisediminis sp. nov., isolated from a tidal flat, and emended description of the genus Demequina

A Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, GHD-1T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. It grew optimally at 30 °C, at pH 6.5-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain GHD-1T fell within the cluster comprising the type strains of species of the genus Demequina. Strain GHD-1T exhibited 16S rRNA gene sequence similarity values of 97.0-98.8 % to the type strains of Demequinaglobuliformis, D. salsinemoris, D. flava, D. sediminicola and D. activiva, and of 95.5-96.9 % to the type strains of the other species of the genus Demequina. The peptidoglycan type of strain GHD-1T is A4β based on l-Orn-l-Ser-l-Asp. It contained DMK-9(H4) and DMK-8(H4) as the major menaquinones and anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified glycolipid. The DNA G+C content of strain GHD-1T was 68.7 mol%, and its DNA-DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 13-29 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GHD-1T is separated from other recognized species of the genus Demequina. On the basis of the data presented, strain GHD-1T is considered to represent a novel species of the genus Demequina, for which the name Demequina litorisediminis sp. nov. is proposed. The type strain is GHD-1T (=KCTC 52260T=NBRC 112299T).

Proposal of nine novel species of the genus Lysinimicrobium and emended description of the genus Lysinimicrobium

Thirteen novel Gram-stain-positive bacteria were isolated from various samples collected from mangrove forests in Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence comparisons showed that the 13 isolates formed a single clade with Lysinimicrobium mangrovi HI08-69T, with a similarity range of 97.6-99.5 %. The peptidoglycan of the isolates was of the A4α type with an interpeptide bridge comprising Ser-Glu and an l-Ser residue at position 1 of the peptide subunit. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. These chemotaxonomic characteristics corresponded to those of the genus Lysinimicrobium. On the basis of the phenotypic and phylogenetic data, along with average nucleotide identity values among the isolates, we concluded that the 13 isolates should be assigned to the following nine novel species of the genus Lysinimicrobium: Lysinimicrobium aestuarii sp. nov. (type strain HI12-104T = NBRC 109392T = DSM 28144T), Lysinimicrobium flavum sp. nov. (type strain HI12-45T = NBRC 109391T = DSM 28150T), Lysinimicrobium gelatinilyticum sp. nov. (type strain HI12-44T = NBRC 109390T = DSM 28149T), Lysinimicrobium iriomotense sp. nov. (type strain HI12-143T = NBRC 109399T = DSM 28146T), Lysinimicrobium luteum sp. nov. (type strain HI12-123T = NBRC 109395T = DSM 28147T), Lysinimicrobium pelophilum sp. nov. (type strain HI12-111T = NBRC 109393T = DSM 28148T), Lysinimicrobium rhizosphaerae sp. nov. (type strain HI12-135T = NBRC 109397T = DSM 28152T), Lysinimicrobium soli sp. nov. (type strain HI12-122T = NBRC 109394T = DSM 28151T) and Lysinimicrobium subtropicum sp. nov. (type strain HI12-128T = NBRC 109396T = DSM 28145T). In addition, an emended description of the genus Lysinimicrobium is proposed.

Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil

A bacterial strain, PSGM2-16(T), was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16(T) revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4%), Fodinibacter luteus YIM C003(T) (97.2%) and Lapillicoccus jejuensis R-Ac013(T) (97.0%), and the phylogenetic tree showed that strain PSGM2-16(T) formed a subgroup with Ornithinibacter aureus HB09001(T) and F. luteus YIM C003(T) within the family Intrasporangiaceae. The major fatty acids (>10% of the total fatty acids) of strain PSGM2-16(T) were iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with meso-diaminopimelic acid as the diagnostic diamino acid. DNA-DNA hybridization values between strain PSGM2-16(T) and closely related taxa were much less than 70%. The genomic DNA G+C content of strain PSGM2-16(T) was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16(T) represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16(T) ( = KACC 17299(T)= DSM 27137(T)= NBRC 109598(T)).

Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity

Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.

Jatrophihabitans soli sp. nov., isolated from soil

One bacterial strain, designated KIS75-12T, isolated from a soil sample collected from Wonsando island located in Boryeong city, Republic of Korea, was characterized as aerobic, Gram-stain-positive, non-flagellated and a short rod. It grew between temperatures of 15–37 °C, pH 4–9 and 0–3.0 % (w/v) NaCl. The 16S rRNA gene analysis showed the strain was moderately related to Jatrophihabitans endophyticus S9-650T (97.7 %) and revealed low sequence similarity (≤94.7 %) with all the other species with validly published names. Its major fatty acid was iso-C16 : 0. The predominant menaquinone of strain KIS75-12T was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol and several small amounts of phosphatidylinositol, aminolipids and glycolipid. The peptidoglycan contained meso-A2pm as diagnostic diamino acid and the peptidoglycan type is A4γ. The genomic DNA G+C content of the type strain was 72.1 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain KIS75-12T could be clearly distinguished from the only member of the genus Jatrophihabitans , J. endophyticus . Therefore, the results of this study indicate the existence of a representative of a novel species of the genus Jatrophihabitans , for which we propose the name Jatrophihabitans soli sp. nov., with strain KIS75-12T ( = KACC 17298T = DSM 45908T  =  NBRC 109658T) as the type strain. An emended description of the genus Jatrophihabitans is also given.

Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola

Two strains of species of the genus Marmoricola , designated KIS18-7T and JOS5-1T, were isolated from soil samples in Korea. The 16S rRNA gene sequence of strain KIS18-7T showed highest similarities with Marmoricola scoriae Sco-D01T (97.8 %), Marmoricola aequoreus SST-45T (97.6 %) and Marmoricola aurantiacus BC 361T (97.3 %), and strain JOS5-1T had highest sequence similarities with M. aequoreus SST-45T (97.5 %) and Marmoricola bigeumensis MSL-05T (97.3 %). The sequence similarity between KIS18-7T and JOS5-1T was 98.1 %. Phylogenetic analysis showed that these strains grouped with species of the genus Marmoricola . The major fatty acids of strain KIS18-7T were iso-C16 : 0 and C17 : 1ω8c, and C17 : 1ω8c, C18 : 0 10-methyl (TBSA), C18 : 1ω9c, C17 : 0 10-methyl and C16 : 0 2-OH for strain JOS5-1T. Strain KIS18-7T contained the polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine, while strain JOS5-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown aminolipid and two unknown phospholipids. The peptidoglycan of both strains contained ll-diaminopimelic acid as the diagnostic diamino acid and a single glycine residue as the interpeptide bridge (type A3γ). The major menaquinone of both strains was MK-8(H4). The G+C contents of the DNA of strains KIS18-7T and JOS5-1T were 68.0 mol% and 62.9 mol%, respectively. These data demonstrate that strains KIS18-7T and JOS5-1T are representatives of two novel species of the genus Marmoricola , for which the names Marmoricola solisilvae sp. nov. (type strain KIS18-7T = KACC 17307T = DSM 27140T = NBRC 109601T) and Marmoricola terrae sp. nov. (type strain JOS5-1T = KACC 17308T = DSM 27141T = NBRC 109602T) are proposed.

Draft genome sequences of eight type strains of the genus demequina

Here, we report the draft genome sequences of the type strains of Demequina aestuarii, Demequina aurantiaca, Demequina flava, Demequina globuliformis, Demequina lutea, Demequina oxidasica, Demequina salsinemoris, and Demequina sediminicola. The genome sequences presented here will facilitate taxonomical, ecological, and functional studies of members of the genus Demequina.

Draft Genome Sequence of Lysinimicrobium mangrovi NBRC 105856T, Isolated from the Rhizosphere of a Mangrove

Here, we report the draft genome sequence of the only species of the genus Lysinimicrobium, Lysinimicrobium mangrovi NBRC 105856^T, isolated from the rhizosphere of a mangrove. The first genomic sequence of this genus and species presented here will facilitate taxonomical, ecological, and functional studies of this rare actinobacterial group.

Nocardioides daecheongensis sp. nov., isolated from soil

Strain KIS2-16(T) was isolated from a soil sample collected from Daecheong Island of Incheon region, South Korea. KIS2-16(T) was Gram-staining-positive, aerobic, non-spore-forming, non-motile, catalase-positive, oxidase-negative and mesophilic. On the basis of 16S rRNA gene sequence analysis, strain KIS2-16(T) represented a member of the genus Nocardioides, being most closely related to the type strains of species of the genus Nocardioides, Nocardioides maradonensis RP-B30(T) (97.8 % sequence similarity) and Nocardioides ultimimeridianus RP-B26(T) (97.0 %). The fatty acid profile of KIS2-16(T) was dominated by C18 : 1ω9c, C17 : 1ω8c, C16 : 0, C18 : 0 10-methyl (TBSA), C16 : 0 2-OH and C17 : 0 2-OH. The major isoprenoid quinone was MK-8(H4), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The peptidoglycan structure was A3γ-type with ll-diaminopimelic acid. The genomic DNA G+C content of KIS2-16(T) was 64.9 mol%. Strain KIS2-16(T) showed DNA-DNA hybridization values of less than 70 % with the closely related species of the genus Nocardioides. Based on phenotypic, genotypic and phylogenetic data, the isolate represents a novel species of the genus Nocardioides, for which the name Nocardioides daecheongensis sp. nov. (type strain KIS2-16(T) = DSM 27136(T) = KACC 17297(T) = NBRC 109597(T)) is proposed.

Gryllotalpicola soli sp. nov., isolated from soil

A novel Gram-stain-positive, short rod-shaped, non-flagellated and mesophilic strain, KIS12-7(T), isolated from a soil sample collected from Daecheong-Island in Ongjin County, Republic of Korea, was studied using a polyphasic approach. Phylogenetic trees based on the 16S rRNA gene sequence revealed that the novel strain was a member of the genus Gryllotalpicola, showing more than 97.0 % sequence similarity with Gryllotalpicola daejeonensis RU-04(T) (98.0 %), Gryllotalpicola koreensis RU-16(T) (97.7 %) and Gryllotalpicola kribbensis PU-02(T) (97.3 %). However, DNA-DNA relatedness values demonstrated that strain KIS12-7(T) could be clearly distinguished from closely related species of the genus Gryllotalpicola. The cell-wall peptidoglycan of strain KIS12-7(T) was of the type B2 and the acyl type was acetyl. The predominant menaquinones were MK-11 and MK-10. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The G+C content of the genomic DNA was 72.1 mol%. On the basis of the evidence presented, strain KIS12-7(T) is a representative of a novel species of the genus Gryllotalpicola, and the name Gryllotalpicola soli sp. nov. is proposed; the type strain is KIS12-7(T) ( = DSM 27182(T) = KACC 17302(T) = NBRC 109659(T)).

Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products

Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.

Oryzihumus terrae sp. nov., isolated from soil and emended description of the genus Oryzihumus

A Gram-stain-positive, aerobic, non-flagellated bacterium, designated KIS22-12(T), was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. Cells were non-spore-forming cocci showing catalase-positive and oxidase-negative reactions. Growth of strain KIS22-12(T) was observed between 10 and 35 °C (optimum, 28-30 °C), between pH 5.0 and 9.0 (optimum, pH 7.0) and with 0-3% (w/v) NaCl. Strain KIS22-12(T) contained MK-8(H4) as the predominant menaquinone, and C17 : 1ω8c, iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Strain KIS22-12(T) contained diphosphatidylglycerol, phosphatidylinositol, one unknown aminophospholipid, one unknown aminolipid, two unknown phospholipids and one unknown lipid. The peptidoglycan type was A1γ. The G+C content of the genomic DNA was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS22-12(T) formed a phyletic lineage with Oryzihumus leptocrescens KV-628(T). 16S rRNA gene sequence similarity between the two strains was 96.5%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain KIS22-12(T) represents a novel species within the genus Oryzihumus, for which the name Oryzihumus terrae sp. nov. is proposed. The type strain is KIS22-12(T) ( = KACC 16543(T) = DSM 27161(T) = NBRC 109596(T)). An emended description of the genus Oryzihumus is also provided.

Janibacter cremeus sp. nov., an actinobacterium isolated from sea sediment

A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus Janibacter , with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus Janibacter . Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus Janibacter . Therefore, strain HR08-44T represents a novel species of the genus Janibacter , for which the name Janibacter cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).

Zhihengliuella flava sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Zhihengliuella

A novel Gram-staining-positive actinobacterium, designated H85-3(T), was isolated from a sea sediment sample and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H85-3(T) was closely related to the members of the genus Zhihengliuella with pairwise sequence similarities of 97.4-98.6 %. The peptidoglycan of strain H85-3(T) was found to be of the A4α type with lysine as the diagnostic diamino acid. The menaquinones were MK-9, MK-10 and MK-8 (56 : 30 : 14) and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. These data supported the affiliation of strain H85-3(T) to the genus Zhihengliuella. Meanwhile, the results of DNA-DNA hybridization, along with the differences in some phenotypic characteristics, indicated that strain H85-3(T) should be distinguished from the recognized species of the genus Zhihengliuella. Therefore, strain H85-3(T) represents a novel species of the genus Zhihengliuella, for which the name Zhihengliuella flava sp. nov. is proposed; the type strain is H85-3(T) ( = NBRC 109021(T) = DSM 26152(T)). An emended description of the genus Zhihengliuella is also proposed.

Paraoerskovia sediminicola sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Paraoerskovia

A novel Gram-stain-positive actinobacterium, designated H25-14T, was isolated from a sea sediment sample, and its taxonomic position was investigated by a polyphasic approach. The peptidoglycan type of strain H25-14T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H25-14T was closely related to Paraoerskovia marina NBRC 104352T (98.3 %). However, DNA–DNA hybridization data and phenotypic characteristics revealed that strain H25-14T differed from P. marina NBRC 104352T. Therefore, strain H25-14T represents a novel species of the genus Paraoerskovia , for which the name Paraoerskovia sediminicola sp. nov. is proposed. The type strain is H25-14T ( = NBRC 108565T = DSM 25477T). An emended description of the genus Paraoerskovia is also proposed.

Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment

Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus Demequina formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized Demequina species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus Demequina , for which the names Demequina flava sp. nov. and Demequina sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.