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 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 salexigens sp. nov., isolated from seawater

A Gram-stain-negative, rod-shaped, aerobic bacterial strain, designated LPB0144^T was isolated from the seawater of South Sea, Korea. The 16S rRNA gene sequence was found to share the highest sequence similarity to Gramella sediminilitoris GHTF-27^T (97.7 %) and the strain branched within the radiation of the genus Gramella in phylogenetic trees. Thus, the taxonomic position of the novel isolate was investigated using a polyphasic approach and complete genome sequencing. Strain LPB0144^T has a circular chromosome of 2.98 Mb with DNA G+C content of 38.2 mol%. The genome includes 2604 protein-coding genes and three copies of rRNA operons. The detected respiratory quinone (MK-6) and the major polar lipid (phosphatidylethanolamine) resemble the chemotaxonomic profile of other Gramella species. The major cellular fatty acid profile (iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0) is also within the range of Gramella, but detailed composition and amounts were found to be different from those of closely related neighbours. Many biochemical and physiological characteristics also distinguished the isolate from other species within the genus Gramella. On the basis of polyphasic taxonomic data obtained here, we propose strain LPB0144^T as a novel Gramella species, for which the name Gramella salexigens sp. nov. is proposed. The type strain is LPB0144^T (=KACC 18894^T=JCM 31560^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).

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

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated BG-MY13T, was isolated from a tidal flat sediment on the South Sea, South Korea. Strain BG-MY13T grew optimally at 30–35 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BG-MY13T falls within the cluster comprising the type strains of species of the genus Gramella . Strain BG-MY13T exhibited 16S rRNA gene sequ4ence similarity values of 96.9–97.8 % to the type strains of Gramella echinicola , Gramella gaetbulicola , Gramella portivictoriae and Gramella marina and of 94.6–96.5 % to the type strains of other species of the genus Gramella with validly published names. Strain BG-MY13T 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 were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain BG-MY13T was 38.9 mol% and DNA–DNA relatedness values with the type strains of G. echinicola , G. gaetbulicola , G. portivictoriae and G. marina were 12–23 %. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain BG-MY13T is separated from other species of the genus Gramella . On the basis of the data presented, strain BG-MY13T is considered to represent a novel species of the genus Gramella , for which the name Gramella aestuariivivens sp. nov. is proposed. The type strain is BG-MY13T ( = KCTC 42285T = NBRC 110677T).

Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment

A Gram-staining-negative, yellow-pigmented, strictly aerobic, zeaxanthin-producing, rod-shaped, non-endospore-forming, appendaged bacterial strain that exhibits gliding motility, designated CC-AMSZ-TT, was isolated from marine sediment off coastal Kending, Taiwan. Strain CC-AMSZ-TT shared 94.9 % and 96.7–94.1 % 16S rRNA gene sequence similarities with Gramella echinicola KMM 6050T and other species of the genus Gramella , respectively, and formed a distinct phyletic lineage in phylogenetic trees. The major (≥5 % of the total) fatty acids were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c and iso-C17 : 1ω9c and/or C16 : 0 10-methyl. Phosphatidylethanolamine, six unidentified lipids and three unidentified aminolipids were the polar lipid components. The DNA G+C content was 38.6 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMSZ-TT represents a novel species of the genus Gramella , for which the name Gramella oceani sp. nov. is proposed. The type strain is CC-AMSZ-TT ( = JCM 18809T = BCRC 80547T).

Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola

A Gram-stain negative, strictly aerobic, zeaxanthin-producing, rod-shaped, non-spore-forming bacterial strain which is motile by gliding, designated CC-AMWZ-3(T), was isolated from surface seawater off coastal Kending, Taiwan. Strain CC-AMWZ-3(T) was found to share 93.3 % and 96.0-92.4 % pairwise 16S rRNA gene sequence similarity to Gramella echinicola KMM 6050(T) and other Gramella species, respectively, and formed distinct phyletic lineage during phylogenetic analysis. The major fatty acids were identified as C16:0, iso-C15:0, anteiso-C15:0, C16:1 ω6c and/or C16:1 ω7c and iso-C17:1 ω9c and/or C16:0 10-methyl. Polar lipids were found to include phosphatidylethanolamine, six unidentified lipids and three unidentified aminolipids. The DNA G+C content was determined to be 40.6 mol%. Menaquinone-6 was the sole respiratory quinone identified and triamine-sym-homospermidine was the predominant polyamine. Based on the polyphasic characteristics that are in line with those of Gramella species, in addition to distinguishing phylogenetic and phenotypic features, strain CC-AMWZ-3(T) appears to represent a novel species of the genus Gramella, for which the name Gramella planctonica sp. nov. (type strain CC-AMWZ-3(T) = JCM 18807(T) = BCRC 80553(T)) is proposed. In addition, emended descriptions of the species Gramella aestuarii and Gramella echinicola are also proposed.

Gramella flava sp. nov., a member of the family Flavobacteriaceae isolated from seawater

A novel Gram-negative, yellow-pigmented, aerobic, motile by gliding, rod-shaped marine bacterium (JLT2011T) was isolated from surface seawater. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2011T could be assigned to the genus Gramella and was most closely related to Gramella gaetbulicola , with 96.2 % similarity. The genomic DNA G+C content was 42.1 %. The predominant fatty acids were C16 : 0, iso-C15 : 0, C18 : 0 and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). The major menaquinone was MK-6. The major components of the polar lipid profile were phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. On the basis of phenotypic, genotypic and taxonomic data presented, strain JLT2011T is considered to represent a novel species of the genus Gramella , for which the name Gramella flava sp. nov. is proposed; the type strain is JLT2011T ( = CGMCC 1.12375T = LMG 27360T).

Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterial strain motile by gliding, designated BS12T, was isolated from a tidal flat at Boseong, Korea. Cells were moderately halotolerant, catalase- and oxidase-positive rods. Growth was observed at 5–40 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 7.0–7.5) and in the presence of 1–11 % (w/v) NaCl (optimum, 2–4 %). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The polar lipid pattern comprised phosphatidylethanolamine, four unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 42.3 mol% and the only respiratory quinone was menaquinone 6. Phylogenetic inference based on 16S rRNA gene sequences showed that strain BS12T formed a tight phyletic lineage with members of the genus Gramella . Strain BS12T was most closely related to ‘ Gramella jeungdoensis’ HMD3159 with sequence similarity of 97.5 %, but the DNA–DNA relatedness value between the two strains was only 22.1±2.2 %. On the basis of phenotypic and molecular features, strain BS12T was shown to represent a novel species of the genus Gramella , for which the name Gramella aestuarii sp. nov. is proposed. The type strain is BS12T ( = KACC 16188T = JCM 17790T). An emended description of Gramella echinicola is also proposed.