Chae Hong Lim

Mucilaginibacter rigui sp. nov., isolated from wetland freshwater, and emended description of the genus Mucilaginibacter.

A non-motile, rod-shaped bacterium, designated strain WPCB133(T), was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The strain contained MK-7 as the major isoprenoid quinone. The DNA G+C content was 47 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB133(T) forms an independent lineage within the genus Mucilaginibacter. Strain WPCB133(T) was distantly related to Mucilaginibacter kameinonensis SCK(T) (94.7 % sequence similarity), Mucilaginibacter paludis TPT56(T) (94.5 %) and Mucilaginibacter gracilis TPT18(T) (94.4 %). Phenotypic characteristics distinguished strain WPCB133(T) from members of the genus Mucilaginibacter. On the basis of evidence presented in this study, strain WPCB133(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter rigui sp. nov. is proposed. The type strain is WPCB133(T) (=KCTC 12534(T) =NBRC 101115(T)). An emended description of the genus Mucilaginibacter is also proposed.

Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater

Two non-motile, orange- or yellow-pigmented bacteria, designated strains KYW48(T) and KYW147(T), were isolated from seawater collected from the South Sea, Republic of Korea. Cells of both strains were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids of strain KYW48(T) were C(18 : 1)ω7c (35.3 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) (22.7 %), C(17 : 1)ω6c (19.8 %), C(14 : 0) 2-OH (7.4 %) and C(16 : 0) (5.9 %), and those of strain KYW147(T) were C(18 : 1)ω7c (36.0 %), summed feature 3 (18.3 %), C(16 : 0) (14.7 %), 11-methyl C(18 : 1)ω7c (10.7 %), C(16 : 0) 2-OH (9.1 %) and C(18 : 1)ω9c (8.0 %). The predominant isoprenoid quinone of both strains was ubiquinone 10 (Q-10). The DNA G+C contents of strains KYW48(T) and KYW147(T) were 63.8 and 67.2 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strains KYW48(T) and KYW147(T) were grouped with the members of the family Erythrobacteraceae and formed a distinct clade with the members of the genus Altererythrobacter (<95.7 % sequence similarity). On the basis of the evidence presented in this study, the novel species Altererythrobacter namhicola sp. nov. (type strain KYW48(T)  = KCTC 22736(T)  = JCM 16345(T)) and Altererythrobacter aestuarii sp. nov. (type strain KYW147(T)  = KCTC 22735(T)  = JCM 16339(T)) are proposed.

Paenibacillus rigui sp. nov., isolated from a freshwater wetland.

A rod-shaped, endospore-forming, Gram-reaction-variable bacterial strain, designated WPCB173(T), was isolated from freshwater collected from the Woopo wetland, Republic of Korea. Based on its phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analysis, the isolate was identified as being a member of the genus Paenibacillus. Major polar lipids present in strain WPCB173(T) included phosphatidylethanolamine and several unidentified phospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C₁₅:₀ (65.2  %). The DNA G+C content was 48.3 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB173(T) clustered with species of the genus Paenibacillus, its closest neighbours being Paenibacillus chinjuensis WN9(T) (96.7  %) and Paenibacillus soli DCY03(T) (96.4  %). DNA-DNA hybridization of strain WPCB173(T) with P. soli DCY03(T) and P. chinjuensis WN9(T) showed relatedness values of only 10 and 19  %, respectively. On the basis of the phenotypic and phylogenetic evidence, strain WPCB173(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rigui sp. nov. is proposed. The type strain of the novel species is WPCB173(T) (=KCTC 13282(T) =JCM 16352(T)).

Bacillus rigui sp. nov., isolated from wetland fresh water.

Two Gram-stain-positive strains, WPCB074(T) and WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074(T) and WPCB165 belonged to the genus Bacillus and that strain WPCB074(T) was most closely related to Bacillus solisalsi YC1(T) (98.4 % sequence similarity), B. barbaricus V2-BIII-A2(T) (97.7 %), B. macauensis ZFHKF-1(T) (96.9 %), B. arsenicus Con a/3(T) (96.4 %) and B. gelatini LMG 21880(T) (95.1 %). The 16S rRNA gene sequences of strains WPCB074(T) and WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA-DNA relatedness between strain WPCB074(T) and the type strains of B. solisalsi, B. barbaricus, B. macauensis, B. arsenicus and B. gelatini were 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074(T) was characterized by having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and anteiso-C(15 : 0) as the major fatty acids. The DNA G+C content of strain WPCB074(T) was 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074(T) represents a novel species of the genus Bacillus for which the name Bacillus rigui sp. nov. is proposed. The type strain is WPCB074(T) (=KCTC 13278(T) =JCM 16348(T)).

Screening and characterization of a cellulase gene from the gut microflora of abalone using metagenomic library

A metagenomic fosmid library was constructed using genomic DNA isolated from abalone intestine. Screening of a library of 3,840 clones revealed a 36 kb insert of a cellulase positive clone (pAMHElO). A shotgun clone library was constructed using the positive clone (pAMHElO) and further screening of 3,840 shotgun clones with an approximately 5 kb insert size using a Congo red overlay revealed only one cellulase positive clone (pAMHL9). The pAMHL9 consisted of a 5,293-bp DNA sequence and three open reading frames (ORFs). Among the three ORFs, cellulase activity was only shown in the recombinant protein (CelAMll) coded by ORF3, which showed 100% identity with outer membrane protein A from Vibrio alginolyticus 12G01, but no significant sequence homology to known cellulases. The expressed protein (CelAMll) has a molecular weight of approximately 37 kDa and the highest CMC hydrolysis activity was observed at pH 7.0 and 37°C. The carboxymethyl cellulase activity was determined by zymogram active staining and different degraded product profiles for CelAMll were obtained when cellotetraose and cellopentaose were used as the substrates, while no substrate hydrolysis was observed on oligosaccharides such as cellobiose and cellotriose.

Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater

A non-motile, rod-shaped and aerobic marine bacterium, designated strain KYW314(T), was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative, catalase- and oxidase-positive and had proteolytic activity. The major fatty acids were iso-C(15 : 0) (17.2 %), C(16 : 0) (11.1 %), iso-C(17 : 0) (10.5 %) and C(18 : 1)ω 7c (10.0 %). The DNA G+C content was 56.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW314(T) formed a lineage within the genus Pseudidiomarina (95.4-97.3 % sequence similarity) and a distinct branch within the clade containing Pseudidiomarina taiwanensis PIT1(T) and Pseudidiomarina sediminum c121(T). Phenotypic characteristics could distinguish strain KYW314(T) from members of the genus Pseudidiomarina. On the basis of the data presented, strain KYW314(T) represents a novel species, for which the name Pseudidiomarina aestuarii sp. nov. is proposed. The type strain is KYW314(T) (=KCTC 22740(T) =JCM 16344(T)).

Shewanella fodinae sp. nov., isolated from a coal mine and from a marine lagoon

Strains JC15(T) and JC19 were isolated from samples collected from different locations in India, including a coal mine and a marine lagoon. Both strains were Gram-stain-negative rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, and hydrolysed casein, produced H(2)S and showed beta-haemolysis. Strain JC15(T) grew optimally at pH 6 (range pH 5-8) while strain JC19 grew optimally at pH 7 (range pH 6-9) and both had a growth temperature optimum of 30-37 degrees C (range 22-40 degrees C). Both strains could grow chemo-organoheterotrophically and chemolithoautotrophically. Neither strain required NaCl for growth and both could tolerate up to 9 % (w/v) NaCl, with optimum growth at 5 % NaCl. Vitamin B(12) was required as a growth factor by both strains. The major fatty acids were iso-C(15 : 0), C(17 : 1)omega8c and iso-C(13 : 0) 3-OH. The DNA G+C contents of strains JC15(T) and JC19 were 53.6 and 54.3 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strains JC15(T) and JC19 were most closely related to Shewanella haliotis DW01(T) (approximately 94 % sequence similarity) and to other members of the genus Shewanella. Genomic relatedness (DNA-DNA hybridization) between strains JC15(T) and JC19 is 88 %. On the basis of phenotypic and molecular genetic evidence, strain JC15(T) represents a novel species of the genus Shewanella, for which the name Shewanella fodinae sp. nov. is proposed. The type strain is JC15(T) (=CCUG 57102(T) =NBRC 105216(T) =KCTC 22506(T)).

Zhihengliuella aestuarii sp. nov., isolated from tidal flat sediment.

A Gram-stain-positive, ovoid to short rod-shaped, yellow-pigmented bacterium, designated strain DY66(T), was isolated from tidal-flat sediment collected from Deukryang Bay (Republic of Korea), and its taxonomic position was investigated by using a polyphasic approach. Strain DY66(T) grew optimally at 30 °C and pH 8-9 and in 2 % (w/v) NaCl. The peptidoglycan type was A4α, L-Lys-L-Ala-D-Glu, and tyvelose and glucose were the major cell-wall sugars. The predominant menaquinones were MK-10 and MK-9. Major cellular fatty acids (>10 % of total) were anteiso-C(15 : 0) and iso-C(15 : 0). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unknown aminophospholipid and three unknown aminolipids. The DNA G+C content was 59.1 mol%. This chemotaxonomic profile supported the assignment of strain DY66(T) to the genus Zhihengliuella. Phylogenetic analysis based on 16S rRNA gene sequences also indicated that strain DY66(T) belonged to the family Micrococcaceae and was related to the genus Zhihengliuella. On the basis of the evidence presented in this study, strain DY66(T) represents a novel species of the genus Zhihengliuella, for which the name Zhihengliuella aestuarii sp. nov. is proposed. The type strain is strain DY66(T) ( = KCTC 19557(T)  = JCM 16364(T)).

Psychrobacter aestuarii sp. nov., isolated from a tidal flat sediment

A Gram-negative-staining, non-motile, non-spore-forming and strictly aerobic bacterial strain, SC35(T), was isolated from tidal flat sediment collected from the South Sea, Korea, and subjected to a taxonomic study using a polyphasic approach. The organism grew optimally at 20-30 degrees C and with 1-2 % (w/v) NaCl. Strain SC35(T) contained ubiquinone-8 as the predominant respiratory lipoquinone and C(18 : 1)omega9c as the major fatty acid. The DNA G+C content was 48.5 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SC35(T) formed a lineage within the genus Psychrobacter (94.3-96.5 % sequence similarity), forming a distinct branch in a clade also containing Psychrobacter pacificensis NIBH P2K6(T) and Psychrobacter celer SW-238(T). On the basis of phenotypic and phylogenetic data, strain SC35(T) (=KCTC 22503(T)=JCM 16343(T)) was placed in the genus Psychrobacter as the type strain of a novel species, for which the name Psychrobacter aestuarii sp. nov. is proposed.