Yung Mi Lee

Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine Glacier Cryoconite

The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.

Cultured bacterial diversity and human impact on alpine glacier cryoconite.

The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

Diversity of Cold-Active Protease-Producing Bacteria from Arctic Terrestrial and Marine Environments Revealed by Enrichment Culture

A new approach for enrichment culture was applied to obtain cold-active protease-producing bacteria for marine and terrestrial samples from Svalbard, Norway. The method was developed for the enrichment of bacteria by long-term incubation at low temperatures in semi-solid agar medium containing meat pieces as the main source of carbon and energy. ZoBell and 0.1× nutrient broth were added for marine and terrestrial microorganisms, respectively, to supply basal elements for growth. One to three types of colonies were observed from each enrichment culture, indicating that specific bacterial species were enriched during the experimental conditions. Among 89 bacterial isolates, protease activity was observed from 48 isolates in the screening media containing skim milk. Good growth was observed at 4°C and 10°C while none of the isolates could grow at 37°C. At low temperatures, enzyme activity was equal to or higher than activity at higher temperatures. Bacterial isolates were included in the genera Pseudoalteromonas (33 isolates), Arthrobacter (24 isolates), Pseudomonas (16 isolates), Psychrobacter (6 isolates), Sphingobacterium (6 isolates), Flavobacterium (2 isolates), Sporosarcina (1 isolate), and Stenotrophomonas (1 isolate). Protease activity was observed from Pseudoalteromonas (33 isolates), Pseudomonas (10 isolates), Arthrobacter (4 isolates), and Flavobacterium (1 isolate).

Polar and Alpine Microbial Collection (PAMC): a culture collection dedicated to polar and alpine microorganisms

Microorganisms in polar areas may have important ecological roles in biogeochemical cycles and the food chain. They are adapted to polar environments by means of special physiological adaptation mechanisms that include cold-adapted enzymes and cryoprotectants such as exopolysaccharides. Culture collections for polar microorganisms can provide research resources for ecological and physiological studies. The Polar and Alpine Microbial Collection (PAMC) is a specialized culture collection for maintenance and distribution of polar and alpine microorganisms. A database system was developed to share important data fields with DarwinCore2 and Ocean Biogeographic Information System database schemas. Approximately 1,500 out of 5,500 strains maintained in PAMC have been identified and belonged primarily to the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Many of the microbial strains can grow at low temperature and produce proteases, lipases, and/or exopolysaccharides. PAMC provides search tools based on keywords such as taxonomy, geographical origin, habitat, and physiological characteristics. Biological materials and information provided by PAMC will be important resources for ecological and physiological studies on polar and alpine microorganisms.

Genome Sequence of a Novel Member of the Genus Psychrobacter Isolated from Antarctic Soil

Psychrobacter spp. have shown characteristics indicating remarkable capabilities at subzero temperatures that identify them as potential model organisms for the study of low-temperature adaptations. Here we present the draft genome sequence of Psychrobacter sp. PAMC 21119, which was isolated from permafrost soil of Antarctica; this information could provide insight into adaptation and evolution strategies under extreme environmental conditions.

Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater

A Gram-stain-positive, rod-shaped and non-motile strain, designated PAMC 27367(T), was isolated from rainwater collected on the Bering Sea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Rhodococcus. Phylogenetic analyses revealed that strain PAMC 27367(T) formed a robust clade with the type strains of Rhodococcus rhodnii, Rhodococcus aetherivorans and Rhodococcus ruber with 16S rRNA gene sequence similarities of 96.3 %, 95.8 % and 95.5 %, respectively. Cells of the strain grew optimally at 25 °C and at pH 6.5-7.0 in the presence of 0-2 % (w/v) sea salts. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and three unknown phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Cell wall analysis showed that strain PAMC 27367(T) contained meso-diaminopimelic acid. The genomic DNA G+C content was 77.1 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Rhodococcus aerolatus sp. nov., with PAMC 27367(T) ( = KCTC 29240(T) = JCM 19485(T)) as the type strain.

Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment.

A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130(T), was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4-20 °C, pH 6.0-9.0 and 0.5-5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130(T) belonged to the genus Psychroserpens and was closely related to Psychroserpens mesophilus, Psychroserpens damuponensis and Psychroserpens burtonensis with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130(T) could be clearly distinguished from other species of the genus Psychroserpens . The genomic DNA G+C content was 32.7 mol%. The major fatty acids (>10 %) were C20 : 4ω6c (13.2 %), iso-C15 : 0 (12.3 %), iso-C15 : 1 G (11.7 %) and iso-C15 : 0 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130(T) represents a novel species of the genus Psychroserpens, for which the name Psychroserpens jangbogonensis sp. nov. is proposed. The type strain is PAMC 27130(T) ( = KCTC 42128(T) = JCM 30228(T)).

Algibacter psychrophilus sp. nov., a psychrophilic bacterium isolated from marine sediment.

A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-negative, rod-shaped, non-motile and psychrophilic bacterial strain, PAMC 27237T, was isolated from marine sediment of the Ross Sea, Antarctica. Strain PAMC 27237T grew at 0-20 °C (optimally at 17 °C), at pH 5.0-9.5 (optimally at pH 7.0) and in the presence of 0-3.5 % (w/v) NaCl (optimally at 1.5-2.5 %). The major fatty acids (≥5 %) were iso-C17 : 0 3-OH, C17 : 0 2-OH, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), iso-C15 : 0 3-OH, anteiso-C17 : 1ω9c, anteiso-C15 : 1 A, iso-C16 : 0 3-OH and iso-C15 : 1 G. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, four unidentified lipids and a glycolipid. The major respiratory quinone was MK-6. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27237T belongs to the genus Algibacter, showing high similarities with the type strains of Algibacter agarivorans (97.2 %), Algibacter agarilyticus (97.0 %) and Algibacter mikhailovii (96.4 %). Average nucleotide identity values between strain PAMC 27237T and the type strains of A. agarivorans and A. agarilyticuswere 83.1 and 84.2 %, respectively, and mean genome-to-genome distances were 22.4-24.2 %, indicating that strain PAMC 27237T is clearly distinguished from the most closely related species of the genus Algibacter. The genomic DNA G+C content calculated from genome sequences was 33.5 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain PAMC 27237T is considered to represent a novel species of the genus Algibacter, for which the name Algibacter psychrophilus sp. nov. is proposed. The type strain is PAMC 27237T ( = KCTC 42130T = JCM 30370T).

Characterization of Two Antimicrobial Peptides from Antarctic Fishes (Notothenia coriiceps and Parachaenichthys charcoti)

We identified two antimicrobial peptides (AMPs) with similarity to moronecidin in Antarctic fishes. The characteristics of both AMPs were determined using moronecidin as a control. Moronecidin, which was first isolated from hybrid striped bass, is highly salt-resistant, and possesses broad-spectrum activity against various microbes. The moronecidin-like peptide from Notothenia coriiceps exhibited a narrower spectrum of activity and a higher salt sensitivity than moronecidin. The AMP from Parachaenichthys charcoti exhibited similar antimicrobial activity to moronecidin, and similar salt sensitivity. In an experiment to identify toxic effects, both of the moronecidin-like peptides from the Antarctic fishes exhibited lower hemolytic activity than moronecidin. In spite of its low toxicity, the AMP from N. coriiceps is unlikely to be considered as a candidate for antibiotic development, owing to its narrow spectrum of activity and high salt sensitivity. In contrast, the high salt resistance and broad-spectrum activity of the AMP from P. charcoti could be more advantageous for clinical use than moronecidin, since it could kill bacteria under physiological conditions with low toxicity. A further comparison of these two AMPs from Antarctic fishes with other AMPs could help to reduce the toxicity of AMPs for clinical use.

Genome Sequence of a Salinibacterium sp. Isolated from Antarctic Soil

The draft genome of Salinibacterium sp. PAMC 21357, isolated from permafrost soil of Antarctica, was determined. Here we present a 3.1-Mb draft genome sequence of Salinibacterium sp. that could provide further insight into the genetic determination of its cold-adaptive properties.