Christiangramia sediminicola sp. nov., a DNA-hydrolysing bacterium isolated from intertidal sediment

A Gram-stain-negative, yellow-pigmented, non-flagellated, motile by gliding, aerobic and rod-shaped bacterial strain, designated SM2212T, was isolated from intertidal sediment of Aoshan Bay in Qingdao, China. The strain grew at 5-35 °C and with 0.5-5.5% NaCl (w/v). It was able to reduce nitrate to nitrite and hydrolyse starch, gelatin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy genes showed that strain SM2212T belonged to the genus Christiangramia within the family Flavobacteriaceae, sharing the highest 16S rRNA gene sequence similarity with the type strain of Christiangramia echinicola (97.1%) and 96.2-97.0% 16S rRNA gene sequence similarity with those of other known species in the genus. The major cellular fatty acids were summed feature 3 (C16:1 ω7с and/or C16:1 ω6с), iso-C15:0, iso-C17: 03-OH, summed feature 9 (iso-C17:1  ω9c and/or 10-methyl C16:0) and C16:0. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The genomic DNA G+C content of strain SM2212T was 37.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain SM2212T and type strains of closely related known Christiangramia species were below 22.2 and 79.7%, respectively. Based on the polyphasic taxonomic analysis in this study, strain SM2212T is considered to represent a novel species in the genus Christiangramia, for which the name Christiangramia sediminicola is proposed. The type strain is SM2212T (=KCTC 92980T=MCCC 1K07684T).

Gramella oceanisediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean

A taxonomic study was carried out on strain GC03-9^T, which was isolated from deep-sea sediment of the Indian Ocean. The bacterium was Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped and gliding motile. Growth was observed at salinities of 0-9 % and at temperatures of 10-42 °C. The isolate could degrade gelatin and aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GC03-9^T belonged to the genus Gramella, with the highest sequence similarity to Gramella bathymodioli JCM 33424^T (97.9 %), followed by Gramella jeungdoensis KCTC 23123^T (97.2 %) and other species of the genus Gramella (93.4-96.3 %). The average nucleotide identity and the digital DNA-DNA hybridization estimate values between strain GC03-9^T and G. bathymodioli JCM 33424^T and G. jeungdoensis KCTC 23123^T were 25.1 and 18.7 % and 82.47 and 75.69 %, respectively. The principal fatty acids were iso-C_15 : 0 (28.0 %), iso-C_17 : 0 3OH (13.4 %), summed feature 9 (iso-C_17 : 1  ω9c and/or 10-methyl C_16 : 0; 13.3 %) and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c; 11.0 %). The G+C content of the chromosomal DNA was 41.17 mol%. The respiratory quinone was determined to be menaquinone-6 (100 %). Phosphatidylethanolamine, one unknown phospholipid, three unknown aminolipids and two unknown polar lipids were present. The combined genotypic and phenotypic data showed that strain GC03-9^T represents a novel species within the genus Gramella, for which the name Gramella oceanisediminis sp. nov. is proposed, with the type strain GC03-9^T (=MCCC M25440^T=KCTC 92235^T).

Gramella sediminis sp. nov., isolated from a tidal flat of the Yellow Sea

A novel species of the genus Gramella , designated ASW11-100T, was isolated from a tidal flat sediment in the Yellow Sea, PR China. Phylogenetic analysis based on 16S rRNA gene sequences and single-copy orthologous clusters revealed that strain ASW11-100T belonged to the genus Gramella , and exhibited 16S rRNA gene sequence similarities of 98.9, 98.8 and 98.7 % to Gramella sabulilitoris HSMS-1T, Gramella sediminilitoris GHTF-27T and Gramella forsetii KT0803T, respectively. The genome of strain ASW11-100T harbours 2950 protein-coding genes and 105 carbohydrate-active enzymes including 38 glycoside hydrolases. Seventeen of the glycoside hydrolases are organized in five distinct polysaccharide utilization loci, which are predicted to involve in the degradation of starch, glucans, arabinoxylans, arabinomannan, arabinans and arabinogalactans. The genomic DNA G+C content was 37.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain ASW11-100T and its closely related relatives were in ranges of 19.8–23.9% and 76.6–80.9 %, respectively. Cells of the isolate were Gram-negative, aerobic, non-flagellated and short rod-shaped. Carotenoid pigments were produced, but flexirubin-type pigments were absent. The major fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The sole respiratory quinone was menaquinone-6 and the major polar lipid was phosphatidylethanolamine. Based on the above polyphasic evidence, strain ASW11-100T should be considered to represent a novel Gramella species, for which the name Gramella sediminis sp. nov. is proposed. The type strain is ASW11-100T (=KCTC 82502T=MCCC 1K05580T).

Gramella crocea sp. nov., isolated from activated sludge of a seafood processing plant

A novel aerobic Gram-negative strain, designated as YB25^T, was isolated from an activated sludge sample collected from a seafood processing plant in Zhoushan, Zhejiang Province, China, and characterized by using a polyphasic taxonomic approach in this study. Strain YB25^T was motile by gliding, and short-rod-shaped. The isolate grew at 4-37 °C (optimum 28 °C), pH 6.0-9.0 (optimum pH 7.0) and 0.0-10.0% NaCl (optimum 2.0%, w/v). Phylogenetic analysis based on 16S rRNA gene indicated that strain YB25^T belonged to the genus Gramella, and showed the highest sequence similarity of 97.59% to Gramella lutea YJ019^T. The DNA G + C content was 39.5%. In silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain YB25^T with most closely strains were below the threshold, which is considered to the phylogenetic definition of a novel species. Chemotaxonomic analysis indicated that the only respiratory quinone was menaquinone-6 and the major fatty acids were iso-C_15:0, anteiso-C_15:0, iso-C_17:0 3-OH, and summed feature 9 (iso-C_17:1ω9c and C_16:0 10 methyl). The polar lipid profile was composed of phosphatidylethanolamine, an unidentified phospholipid, two unidentified amino lipids, three unidentified glycolipids, and four unidentified lipids. Compared with the reference strains, strain YB25^T contained higher abundance of genes for carbohydrates metabolism,nitrogen metabolism, sulfur metabolism and respiration based on its genomic metabolic pathways and had been found a certain potential in the degradation of pectin. On the basis of the taxonomic evidence, strain YB25^T represents a novel species of the genus Gramella, for which the name Gramella crocea sp. nov. is proposed. The type strain is YB25^T (= KCTC 82680 ^T = MCCC 1K05761^T).

Gramella sabulilitoris sp. nov., isolated from a marine sand

A Gram-stain-negative, aerobic, non-spore-forming, motile by gliding and rod-shaped bacterial strain, designated HSMS-1^T, was isolated from a marine sand collected from the Yellow Sea, Republic of Korea, and identified by a polyphasic taxonomic approach. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that HSMS-1^T fell within the clade comprising the type strains of species of the genus Gramella. HSMS-1^T exhibited 16S rRNA gene sequence similarity values of 99.0 and 98.7 % to the type strains of Gramella echinicola and Gramella sediminilitoris and of 93.3-98.5 % to the type strains of the other species of the genus Gramella. The ANI and dDDH values between HSMS-1^T and the type strains of G. echinicola, Gramella gaetbulicola, Gramella forsetii, Gramella salexigens, Gramella portivictoriae and Gramella flava were 72.6-79.3 % and 17.4-22.2 %, respectively. Mean DNA-DNA relatedness value between HSMS-1^T and the type strain of G. sediminilitoris was 18 %. HSMS-1^T contained MK-6 as the predominant menaquinone and iso-C_15 : 0, anteiso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_16 : 0 as the major fatty acids. The major polar lipid of HSMS-1^T was phosphatidylethanolamine. The DNA G+C content of HSMS-1^T from genomic sequence data was 39.2 %. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that HSMS-1^T is separated from recognized species of the genus Gramella. On the basis of the data presented, strain HSMS-1^T is considered to represent a novel species of the genus Gramella, for which the name Gramella sabulilitoris sp. nov. is proposed. The type strain is HSMS-1^T(=KACC 19899^T=NBRC 113648^T).

Gramella antarctica sp. nov., isolated from marine surface sediment

A Gram-stain-negative, aerobic, yellow-coloured, motile by gliding, rod-shaped bacterial strain, designated R17H11^T, was isolated from surface sediment collected from the Ross Sea, Antarctica. Growth optimally occurred at 25-30 °C, at pH 7.0-7.5 and in the presence of 3 % NaCl (w/v). Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R17H11^T clustered together with Gramella flava JLT2011^T and fell within the genus Gramella. Strain R17H11^T shared the highest 16S rRNA gene similarities (96.1 and 96.0 %) with the type strains of Gramella forsetii and G. flava, and 92.6-95.5 % similarities with those of other known Gramella species. Strain R17H11^T contained menaquinone-6 as the only isoprenoid quinone. The major fatty acids (>5 %) were summed feature 3 (17.5 %, comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 (14.0 %), summed feature 9 (11.8 %, comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C17 : 0 3-OH (11.8 %), iso-C16 : 0 (7.4 %), C17 : 1ω6c (6.9 %) and anteiso-C15 : 0 (5.1 %). The major polar lipids were phosphatidylethanolamine, four unidentified lipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified glycolipid. The DNA G+C content of strain R17H11^T was 38.6 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic characteristics, strain R17H11^T represents a novel species in the genus Gramella, for which the name Gramellaantarctica sp. nov. is proposed. The type strain of the novel species is R17H11^T (=GDMCC 1.1208^T=KCTC 52925^T).

Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011

Strain KT0803^T was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as 'Gramella forsetii' KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange-yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22-25 °C, at pH 7.5 and at a salinity between 2-3 %. Strain KT0803^T hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838^T, 98.3 % with Gramella gaetbulicola DSM 23082^T, 98.1 % with Gramella aestuariivivens BG-MY13^T and Gramella aquimixticola HJM-19^T, 98.0 % with Gramella lutea YJ019^T, 97.9 % with Gramella portivictoriae DSM 23547^T and 96.9 % with Gramella marina KMM 6048^T. The DNA-DNA relatedness values were <35 % between strain KT0803^T and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803^T has been assigned to the genus Gramella, as Gramella forsetii sp. nov. The type strain is KT0803^T (=DSM 17595^T=CGMCC 1.15422^T). An emended description of Gramella gaetbulicolaCho et al. 2011 is also proposed.

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.

Gramella sediminilitoris sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-spore-forming, motile by gliding and coccoid, ovoid or rod-shaped bacterial strain, designated GHTF-27^T, was isolated from a tidal flat at Goheung, South Korea, and subjected to a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-5.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GHTF-27^T belongs to the genus Gramella. It exhibited 16S rRNA gene sequence similarity values of 97.6-98.3 % to the type strains of Gramella aestuariivivens, Gramella echinicola, Gramella gaetbulicola, Gramella aquimixticola, Gramella aestuarii and Gramella portivictoriae, respectively, and of 93.8-96.7 % to the type strains of the other species of the genus Gramellawith validly published names. Strain GHTF-27^T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids of strain GHTF-27^T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain GHTF-27^T was 39.7 mol% and DNA-DNA relatedness values with the type strains of the six phylogenetically closely related species of the genus Gramellawere 12-28 %. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain GHTF-27^T is separated from other species of the genus Gramella. On the basis of the data presented, strain GHTF-27^T is considered to represent a novel species of the genus Gramella, for which the name Gramella sediminilitorissp. nov. is proposed. The type strain is GHTF-27^T (=KCTC 52208^T =NBRC 111992^T).

Gramella aquimixticola sp. nov., isolated from water of an estuary environment

A Gram-stain-negative, aerobic, non-spore-forming bacterial strain, motile by gliding and with rod-shaped or ovoid cells, was isolated from water of an estuary environment at Hwajinpo, South Korea. The strain was designated HJM-19T and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain HJM-19T belongs to the genus Gramella. It exhibited 16S rRNA gene sequence similarity values of 97.2-98.1 % to the type strains of Gramella portivictoriae, Gramella aestuariivivens, Gramella marina, Gramella echinicola and Gramella aestuarii, and of 93.9-96.5 % to the type strains of the other species of the genus Gramella with validly published names. Strain HJM-19T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c and C17 : 0 2-OH as the major fatty acids. The major polar lipids of strain HJM-19T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain HJM-19T was 48.0 mol%, and its DNA-DNA relatedness values with the type strains of the five phylogenetically closely related species of the genus Gramella were 11-23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HJM-19T is separated from other species of the genus Gramella. On the basis of the data presented, strain HJM-19T is considered to represent a novel species of the genus Gramella, for which the name Gramella aquimixticola sp. nov. is proposed. The type strain is HJM-19T ( = KCTC 42706T = NBRC 111224T).