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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.

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).

Complete genome sequence of Pedobacter cryoconitis PAMC 27485, a CRISPR-Cas system-containing psychrophile isolated from Antarctica.

Pedobacter cryoconitis PAMC 27485, an aerobic, Gram-negative, facultatively psychrophilic bacterium, was isolated from Antarctic soil. Here we report the complete genome of P. cryoconitis PAMC 27485, which contains a type II CRISPR-Cas system and genes encoding useful enzymes (e.g. proteases). The genome sequence of P. cryoconitis PAMC 27485 could provide insights into its adaptive immune system against foreign genetic elements and biotechnological potential.

Sediminicola arcticus sp. nov., a psychrophilic bacterium isolated from deep-sea sediment, and emended description of the genus Sediminicola.

A Gram-stain-negative, rod-shaped and non-motile strain, designated PAMC 27266(T), was isolated from deep-sea sediment of the Arctic Ocean. Analysis of the 16S rRNA gene sequence of strain PAMC 27266(T) showed closest affiliation with the genus Sediminicola . Phylogenetic analyses revealed that strain PAMC 27266(T) formed a robust clade with Sediminicola luteus CNI-3(T), with which it shared 98.9% 16S rRNA gene sequence similarity. Genomic relatedness analyses based on the average nucleotide identity and genome-to-genome distance showed that strain PAMC 27266(T) is clearly distinguished from S. luteus . Cells of strain PAMC 27266(T) grew optimally at 15 °C and pH 6.5-7.5 in the presence of 3.5% (w/v) sea salts. The major polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids. The only respiratory quinone was menaquinone-6. The major cellular fatty acids (>10%) were C16 : 1ω6c and/or C16 : 1ω7c and C15 : 0. The genomic DNA G+C content was 37.9 mol%. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose strain PAMC 27266(T) ( =KCCM 43038(T) =JCM 19894(T)) as the type strain of a novel species, with the name Sediminicola arcticus sp. nov.

Complete genome sequence of Pseudomonas antarctica PAMC 27494, a bacteriocin-producing psychrophile isolated from Antarctica

Antimicrobial-producing, cold-adapted microorganisms have great potential for biotechnological applications in food, pharmaceutical, and cosmetic industries. Pseudomonas antarctica PAMC 27494, a psychrophile exhibiting antimicrobial activity, was isolated from an Antarctic freshwater sample. Here we report the complete genome of P. antarctica PAMC 27494. The strain contains a gene cluster encoding microcin B which inhibits DNA regulations by targeting the DNA gyrase. PAMC 27494 may produce R-type pyocins and also contains a complete set of proteins for the biosynthesis of adenosylcobalamin and possibly induces plant growth by supplying pyrroloquinoline quionone molecules.