Streptocinnamides A and B, Depsipeptides from Streptomyces sp. KMM 9044.

The bacterium Streptomyces sp. KMM 9044 from a sample of marine sediment collected in the northwestern part of the Sea of Japan produces highly chlorinated depsiheptapeptides streptocinnamides A (1) and B (2), representatives of a new structural group of antibiotics. The structures of 1 and 2 were determined using nuclear magnetic resonance and mass spectrometry studies and confirmed by a series of chemical transformations. Streptocinnamide A potently inhibits Micrococcus sp. KMM 1467, Arthrobacter sp. ATCC 21022, and Mycobacterium smegmatis MC2 155.

Antibacterial low-molecular-weight compounds produced by the marine bacterium Rheinheimera japonica KMM 9513T.

Strain KMM 9513T was isolated from a sediment sample collected from the Sea of Japan seashore and selected due to its ability to inhibit indicator bacterial growth. The strain KMM 9513T has been recently described as a novel species Rheinheimera japonica. This study was undertaken to determine which substances produced by strain KMM 9513T could be responsible for its antimicrobial activity. Eight compounds were obtained from an ethyl acetate extract of R. japonica KMM 9513T. The structures of five diketopiperazines (4-8) and diisobutyl-, dibutyl- and bis(2-ethylhexyl) phthalates (1-3) were established on the basis of detailed interpretation of NMR data, by Marfey method and optical rotation data. The structures of diketopiperazines were determined as cyclo-(L-valyl-L-proline), cyclo-(L-valyl-D-proline), cyclo-(L-phenylalanyl-L-proline), cyclo-(L-leucyl-L-proline), and cyclo-(L-phenylalanyl-D-proline). Compounds 1-3, 5 and 8 revealed antimicrobial activities against Bacillus subtilis and/or Enterococcus faecium and Staphylococcus aureus. In this paper, we describe the isolation and structural elucidation of the isolated compounds 1-8. This is the first report of the characterisation of low molecular weight antibacterial metabolites produced by a member of the genus Rheinheimera.

Loktanella maritima sp. nov. isolated from shallow marine sediments.

An aerobic, Gram-stain-negative, non-motile bacterium, KMM 9530(T), was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis positioned novel strain KMM 9530(T) in the genus Loktanella as a separate line adjacent to Loktanella sediminilitoris KCTC 32383(T), Loktanella tamlensis JCM 14020(T) and Loktanella maricola JCM 14564(T) with 98.5-98.2% sequence similarity. Strain KMM 9530(T) was characterized by its weak hydrolytic capacity and inability to assimilate most organic substrates. The major isoprenoid quinone was Q-10, polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid, an unknown aminolipid and unknown lipids, and the major fatty acid was C18 : 1ω7c. On the basis of phylogenetic analysis, DNA-DNA hybridization and phenotypic characterization, it can be concluded that the novel strain KMM 9530(T) represents a novel species in the genus Loktanella, for which the name Loktanella maritima sp. nov. is proposed. The type strain of the species is KMM 9530(T) ( = NRIC 0919(T) = JCM 19807(T)).

Antimicrobial potential of deep surface sediment associated bacteria from the Sea of Japan.

The aim of this study was to survey microorganisms from the deep surface sediment samples collected from the Sea of Japan and to screen them for antimicrobial and antagonistic effects. Phylogenetic analysis revealed most isolates sharing 98-100 % sequence similarity to recognized species, including those recovered previously from marine or saline environments. Alteromonas, Halomonas, Marinobacter, Pseudoalteromonas, Salinicola, within the class Gammaproteobacteria, Sulfitobacter (Alphaproteobacteria), Bacillus, Paenibacillus and Paenisporosarcina (Firmicutes), Nocardiopsis and Streptomyces (Actinobacteria) occurred abundantly in all sediment samples. Antimicrobial screening revealed twenty three strains (13 %) capable to inhibit growth of one to eight test cultures and deep sediment isolates. Based on phylogenetic analysis mostly active strains belonged to the genera Bacillus, Brevibacillus, Nocardiopsis, Paenibacillus and Streptomyces. Antimicrobial substances (1-3) were isolated from strain Paenibacillus sp. Sl 79w showing a high inhibitory activity. On the basis of combined spectral analyses (IR, UV, (1)H and (13)C NMR) the compounds 1, 2 and 3 with [M + H](+) at 409.1 and 409.2 m/z, and with [M + Na](+) at 822.5 m/z were found to have a carbon skeleton of isocoumarin and peptide antibiotics, respectively. Our findings demonstrated that the deep surface sediments of the Sea of Japan represent an untapped source of diverse microorganisms capable of antimicrobial metabolite production.

Paenibacillus profundus sp. nov., a deep sediment bacterium that produces isocoumarin and peptide antibiotics.

A novel bacterial strain Sl 79(T) was isolated from a deep surface sediment sample obtained from the Sea of Japan and investigated by phenotypic and molecular methods. The bacterium Sl 79(T) was Gram-positive, facultatively anaerobic, spore-forming, motile and able to form two different types of colonies. It contained the major menaquinone MK-7 and anteiso-C(15:0) followed by iso-C(15:0) as predominant fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Sl 79(T) belonged to the genus Paenibacillus where it clustered to Paenibacillus apiarius NRRL NRS-1438(T) with a sequence similarity of 97.7 % and sharing sequence similarities below than 96.7 % to other validly named Paenibacillus species. Strain Sl 79(T) was found to possess a remarkable inhibitory activity against indicatory microorganisms. On the basis of combined spectral analyses, strain Paenibacillus sp. Sl 79(T) was established to produce isocoumarin and novel peptide antibiotics. On the basis of DNA-DNA relatedness, phenotypic and phylogenetic data obtained, it was concluded that strain Sl 79(T) represents a novel species, Paenibacillus profundus sp. nov. with the type strain Sl 79(T) = KMM 9420(T) = NRIC 0885(T).

Isolation, phylogenetic analysis and screening of marine mollusc-associated bacteria for antimicrobial, hemolytic and surface activities.

This study was undertaken to survey culturable heterotrophic bacteria associated with the marine ark shell Anadara broughtoni inhabiting in the Sea of Japan, and to test isolates for their antimicrobial, hemolytic and surface activities with an emphasis on low-molecular-weight metabolites search. A total of 149 strains were isolated and identified phenotypically. A total of 27 strains were selected to be investigated phylogenetically by 165 rRNA gene sequence analysis. The most bacteria were affiliated with members of the Gammaproteobacteria and Alphaproteobacteria, and Less with Firmicutes, Actinobacteria, and Cytophaga-Flavobacterium-Bacteroides (CFB) group. The isolates capable of hemolysis were numerically abundant in the genera Pseudoalteromonas, Aeromonas and Bacillus. The six Gram-positive isolates belonging to the genera Bacillus, Paenibacillus and Saccharothrix and two Gram-negative strains related to Pseudomonas and Sphingomonas, possessed antimicrobial activity against indicator strains and to each other. Antimicrobial, hemolytic and surface activities were revealed in butanot extracts of cells or cell-free supernatant of six active strains. This points to availability of active low-molecular-weight metabolites. Substances with hemolytic and surface activities were isolated from strain Bacillus pumilus An 112 and characterized as cyclic depsipeptides with molecular masses 1021, 1035, 1049, 1063 and 1077 Da. The recovery of strains producing antimicrobial and surface-active substances suggests that microorganisms associated with the marine bivalve are potential source of bioactive metabolites.

Diversity and antagonistic activity of sea ice bacteria isolated from the sea of Japan.

The aim of the study was to survey cultivable heterotrophic bacteria from sea ice samples collected from Peter the Great Bay of the Sea of Japan, and to test the isolates for antagonistic activity. A total of 195 strains were isolated and investigated by a phenotypic approach. The 16S rRNA gene sequence analysis of thirty eight strains revealed primarily representatives of the class Gammaproteobacteria, phylum Bacteroidetes, and phylum Actinobacteria. Members of the class Alphaproteobacteria were a minor component. Most strains shared 98-99% sequence similarity to recognized species, including those recovered previously from Antarctic or Arctic sea ice or polar environments, Shewanella frigidimarina, Psychrobacter urativorans, Psychrobacter glacincola, Psychrobacter fozii, Pseudomonas veronii, or Pseudomonas proteolytica. At least seven bacterial groups may represent novel species within known genera. Five isolates have been previously described as the novel species Marinomonas primoryensis and Psychrobacter maritimus. Antagonistic activity assays revealed a number of strains-antagonists of the Pseudomonas fluorescens group, Bacillus and Nocardioides displaying remarkable antifungal and antibacterial activities. For the first time our findings show that sea ice offshore in the Sea of Japan represents an untapped source of bacterial biodiversity and microorganisms capable of antibacterial and antifungal metabolite production.

Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.

An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5-96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C(16 : 0) and C(18 : 1) as predominant fatty acids and 2-OH C(14 : 0) as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA-DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).

Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina.

A heterotrophic, aerobic, Gram-negative, pigmented and gliding bacterium, strain KMM 6258(T), was isolated from the sea urchin Strongylocentrotus intermedius and investigated using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the closest relatives of the novel strain are Aquimarina muelleri, Stanierella latercula and Gaetbulimicrobium brevivitae, members of the family Flavobacteriaceae, with sequence similarities of 96.3, 96.4 and 96.2 %, respectively. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, assigned strain KMM 6258(T) to the genus Aquimarina as Aquimarina intermedia sp. nov. (type strain KMM 6258(T)=DSM 17527(T)=JCM 13506(T)=LMG 23204(T)). The reclassification of Stanierella latercula as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae as Aquimarina brevivitae comb. nov. is proposed.

Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius.

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44-45 mol%. The predominant fatty acids were C15 : 0 iso, C16:1omega5c, C17:1 iso omega9c, C17:0 iso 3-OH and summed feature 3 (C16:1omega7c and/or C15:0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).