Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea

A Gram-stain-negative, non-spore-forming, motile, aerobic bacterium (strain C21T) was isolated from coral and identified using polyphasic identification approach. Global alignment of 16S rRNA gene sequences indicated that strain C21T shares 95.7 % sequence identity to its closest neighbour, Marinibactrum halimedae NBRC 110095T, followed by other type strains with identities of lower than 95 %. The average nucleotide identity and average amino acid identity values between strain C21T and M. halimedae NBRC 110095T were 69.6 and 64.8 %, respectively, indicating that strain C21T may represent a new species in a new genus. Phylogenetic analysis based on 16S rRNA gene and phylogenomic results indicated that strain C21T forms a distinct branch in the family Cellvibrionaceae. Cellular fatty acids and polar lipids could also readily distinguish strain C21T from closely related type strains. Therefore, strain C21T is suggested to represent a new species in a new genus, for which the name Sessilibacter corallicola gen. nov., sp. nov. is proposed. The type strain is C21T (=MCCC 1K03260T=KCTC 62317T).

Shewanella algae and Microbulbifer elongatus from marine macro-algae - isolation and characterization of agar-hydrolysing bacteria

Macro-algae are a good source of agar oligosaccharides, which can be obtained through bacterial enzymatic hydrolysis. The agarase enzyme secreted by the micro-organisms cleaves the cell wall of the algae and releases agar oligosaccharides as degradation products with various applications. Agarolytic bacteria were isolated from the marine algae Kappaphycus sp., and Sargassum sp., and studied for their agar-degrading properties. Among the 70 isolates, 2 isolates (A13 and Sg8) showed agarase activity in in vitro assays. The maximum agarolytic index was recorded in the isolate Sg8 (3.75 mm and 4.29 µg ml-1 agarase activity), followed by the isolate A13 (2.53 mm and 2.6 µg ml-1 agarase activity). Optimum agarase production of isolate Sg8 was observed at pH7 and at a temperature of 25 °C in 24-48 h, whereas for isolate A13 the optimum production was at pH7 and at a temperature of 37 °C in 48 h. The identities of the agarolytic isolates (Sg8 and A13) were confirmed based on microscopy, morphological, biochemical and molecular analysis as Shewanella algae [National Center for Biotechnology Information (NCBI) GenBank accession number MK121204.1] and Microbulbifer elongatus [NCBI GenBank accession number MK825484.1], respectively.

High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2T

Natrinema altunense strain AJ2T, a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembled the entire genome sequence of AJ2T (=CGMCC 1.3731T=JCM 12890T). We assembled 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC content (64.6%). Subsequently we predicted the gene content and generated genome annotation to identify the relationship between the epigenetic characteristics and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical proteins in nr database. This Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained its relationship to other strains in the Natrinema and Haloterrigena genera. We also confirmed the ANI value between every two species of Natrinema and Haloterrigena genera. In conclusion, our analysis furthered our understanding of the extreme-environment adapted strain AJ2T by characterizing its genome structure, gene content and phylogenetic placement. Our detailed case study will contribute to our overall understanding of why Natrinema strains can survive in such a high-altitude salt lake.

Marinibactrum halimedae gen. nov., sp. nov., a gammaproteobacterium isolated from a marine macroalga

Phylogenetic and taxonomic characterization was performed for a bacterium, designated strain Q-192T, isolated from the surface of the green macroalga Halimeda sp., collected from the subtropical Ishigaki Island, Japan. The isolate was a polysaccharide-producing, Gram-stain-negative, aerobic, rod-shaped, motile bacterium with a polar flagellum. The isolate was slightly halophilic, required Na+, Mg2+ and Ca2+ ions for growth, but did not require growth factors. The only isoprenoid quinone was ubiquinone-8.The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0. The main hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 45.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the isolate in the class Gammaproteobacteria. The phylogenetically closest relatives with validly published names were Pseudomaricurvus alkylphenolicus KU41GT, Teredinibacter turnerae T7902T, Pseudoteredinibacter isoporae SW-11T and Simiduia agarivorans SA1T with sequence similarities of 94.5, 94.1, 93.7 and 93.6 %, respectively. The isolate was distinguished from members of these genera by a combination of DNA G+C content, chemotaxonomic characteristics (respiratory quinone system, fatty acid profile and polar lipid composition) and other phenotypic features. Based on phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics, strain Q-192T is considered to represent a novel species of a new genus, for which the name Marinibactrum halimedae gen. nov., sp. nov. is proposed. The type strain of Marinibactrum halimedae is Q-192T ( = NBRC 110095T = NCIMB 14932T).

Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds

A new bacterial strain capable of reducing thalli of various seaweeds (red, green, and brown algae) was isolated from marine sediments of Uozu in Toyama Prefecture, Japan. We designated the strain Simiduia sp. TM-2 based on analyses of the 16S rRNA gene and gyrB gene sequences and its biochemical and morphological characteristics. Zymography methods revealed numerous active bands of alginate lyases, cellulases, and agarases in the cells and culture supernatants of TM-2, showing that the strain possessed multiple polysaccharide lyases. A novel agarase gene (agaTM2) was cloned from TM-2 and expressed in Escherichia coli. The resulting DNA sequence contained an open reading frame of 1764 bp that encoded a protein of 587 amino acids with an estimated molecular mass of 64 kDa and pI of 4.62. The deduced amino acid sequence, AgaTM2, had a typical signal peptide followed by a glycoside hydrolase family 16 catalytic domain and two carbohydrate-binding modules 6. A BLAST search indicated that AgaTM2 shared 75.5 % amino acid sequence identity with agarase from Simiduia agarivorans SA1. The cloned and purified AgaTM2 protein showed optimal activity at 35 °C and pH 8.0, and its thermostability increased in the presence of calcium ions. AgaTM2 degraded agarose to tetraose and hexaose.

Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

A taxonomic study was carried out on strain YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.

Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated DMCK3-4(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain DMCK3-4(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain DMCK3-4(T) clustered with the strains of three members of the genus Simiduia, with which it exhibited 97.0-99.0% sequence similarity. Sequence similarities to the type strains of the other species with validly published names were less than 92.2%. Strain DMCK3-4(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(17:1)ω8c, C(16:0), C(17:0) and C(18:1)ω7c as the major fatty acids. The major polar lipids of strain DMCK3-4(T) were phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain DMCK3-4(T) was 51.8 mol% and its mean DNA-DNA relatedness values with Simiduia agarivorans KCTC 23176(T), Simiduia areninigrae KCTC 23293(T) and Simiduia litorea NRIC 0917(T) were 23-34%, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain DMCK3-4(T) is distinct from other species of the genus Simiduia. On the basis of the data presented, strain DMCK3-4(T) is considered to represent a novel species of the genus Simiduia, for which the name Simiduia curdlanivorans sp. nov. is proposed. The type strain is DMCK3-4(T) ( = KCTC 42075(T) =CECT 8570(T)). An emended description of the genus Simiduia is also proposed.

Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan

An aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504T, was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504T belonged to the genus Simiduia as it was most closely related to Simiduia areninigrae KCTC 23293T (97.3 % sequence similarity). Strain KMM 9504T was characterized by the major ubiquinone Q-8, and by the predominance of C16 : 1ω7c, C17 : 1ω8c, followed by C16 : 0, C15 : 0, C17 : 0 and C12 : 1 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strain KMM 9504T represents a novel species of the genus Simiduia , for which the name Simiduia litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504T ( = NRIC 0917T = JCM 19759T).

A high-throughput solid phase screening method for identification of lignocellulose-degrading bacteria from environmental isolates

The development of cost-effective biofuels will require improvements in the efficiency of biomass deconstruction, a process typically carried out by lignocellulose-degrading enzymes. Environmental microbes represent an abundant and diverse source of lignocelluloses-degrading enzymes for use in biotechnology. However, identification of microorganisms that possess these enzymes has been slowed by a lack of rapid screening methodologies, particularly those that utilize native lignocellulosic substrates. In this report, we describe a new, solid-phase screening system for the identification of microbes capable of lignocellulose degradation. The critical component of this screening system is the use of acrylamide, instead of agar, as the solidifying agent. Our results show that this screening method allows for the identification of Gram-positive and Gram-negative bacteria that possess cellulose and hemicellulose degrading activities from environmental isolates.