Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558^T, was isolated from sediment sampled in the Mariana Trench. Strain 960558^T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558^T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558^T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558^T is Planktotalea lamellibrachiae JAM 119^T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C_16 : 0, 11-methyl C_18 : 1  ω7c and C_18 : 1  ω7c and/or C_18 : 1  ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558^T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558^T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558^T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558^T (=KCTC 82619^T=MCCC 1K04727^T).

Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments

A Gram-negative, non-motile bacterium КMM 3653^T was isolated from a sediment sample from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis the strain КMM 3653^T was positioned within the family Rhodobacteraceae (class Alphaproteobacteria) forming a distinct lineage with the highest gene sequence similarities to the members of the genera Pacificibacter (95.2-94.7%) and Nioella (95.1-94.5%), respectively. According to the phylogenomic tree based on 400 conserved protein sequences, strain КMM 3653^T was placed in the cluster comprising Vannielia litorea, Nioella nitratireducens, Litoreibacter albidus and Pseudoruegeria aquimaris as a separate lineage adjacent to V. litorea KCTC 32083^T. The average nucleotide identity values between strain КMM 3653^T and V. litorea KCTC 32083^T, N. nitratireducens KCTC 32417^T, L. albidus KMM 3851^T, and P. aquimaris CECT 7680^T were 71.1, 70.3, 69.6, and 71.0%, respectively. Strain КMM 3653^T contained Q-10 as the predominant ubiquinone and C_18:1ω7c as the major fatty acid followed by C_16:0. The polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified aminolipids, and five unidentified lipids. The DNA G+C content of 61.8% was calculated from the genome sequence. Based on the phylogenetic evidence and distinctive phenotypic characteristics, we proposed strain KMM 3653^T (= KCTC 82575^T) to be classified as a novel genus and species Harenicola maris gen. nov., sp. nov.

Thalassobius aquimarinus sp. nov., isolated from the Sea of Japan seashore

An aerobic, Gram-negative, non-pigmented non-motile bacterium designed КMM 8518^T was isolated from a seawater sampled from the Sea of Japan seashore. Strain КMM 8518^T grew at 7-42 °C and in the presence of 1-7% NaCl. The phylogenetic analyses based on 16S rRNA gene and whole-genome sequences placed the novel strain КMM 8518^T into the genus Thalassobius as a separate lineage. Strain КMM 8518^T shared the highest 16S rRNA gene sequence similarity of 98% to Thalassobius gelatinovorus KCTC 22092^T and similarity values of ≤ 97% to other recognized Thalassobius species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 8518^T and T. gelatinovorus KCTC 22092^T were 79.6% and 23.5%, respectively. The major respiratory quinone was ubiquinone-10. The major fatty acid was C_18:1ω7c followed by 11-methyl C_18:1ω7c. Polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid, and three unidentified lipids. The DNA G+C content of 62.7% was calculated from genome sequence analysis. Based on the phylogenetic analyses and distinctive phenotypic characteristics, the marine bacterium КMM 8518^T is concluded to represent a novel species of the genus Thalassobius for which the name Thalassobius aquimarinus sp. nov. is proposed. The type strain of the species is strain KMM 8518^T (= KCTC 82576^T).

Pacificibacter aestuarii sp. nov., isolated from a tidal flat

A Gram-stain-negative, strictly aerobic bacterium, designated KJ21T, was isolated from a tidal flat in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain KJ21T was observed at 10-35 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 7.0) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain KJ21T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, 10-methyl C19 : 0 and C10 : 0 3-OH as the major fatty acids and ubiquinone-10 as the major isoprenoid quinone. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. The G+C content of the genomic DNA was 53.9 mol%. Phylogenic analysis based on 16S rRNA gene sequences showed that strain KJ21T formed a tight phylogenetic lineage with the members of the genus Pacificibacter with a 100 % bootstrap value. Strain KJ21T was most closely related to Pacificibacter maritimus KMM 9031T (98.7 %) and Pacificibacter marinus HDW-9T (98.4 %), and the DNA-DNA relatedness values between strain KJ21T and the type strains of P. maritimus and P. marinus were 46.9±4.2 % and 39.8±5.7, respectively. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain KJ21T represents a novel species of the genus Pacificibacter, for which the name Pacificibacter aestuarii sp. nov. is proposed. The type strain is KJ21T (=KACC 19098T=JCM 31805T).

Ascidiaceihabitans donghaensis gen. nov., sp. nov., isolated from the golden sea squirt Halocynthia aurantium

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RSS1-M3T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS1-M3T grew optimally at 30 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Strain RSS1-M3T exhibited the highest 16S rRNA gene sequence similarity (96.55 %) to the type strain of Pelagicola litoralis . Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS1-M3T clustered with the type strains, or proposed type strains, of Planktotalea frisia , Pacificibacter maritimus , Roseovarius marinus and Halocynthiibacter namhaensis , showing sequence similarity of 94.88–96.32 %. Strain RSS1-M3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The polar lipid profile of strain RSS1-M3T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, could be distinguished from those of the phylogenetically related genera. The DNA G+C content of strain RSS1-M3T was 55.8 mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic properties, strain RSS1-M3T is considered to represent a novel species of a new genus within the class Alphaproteobacteria , for which the name Ascidiaceihabitans donghaensis gen. nov., sp. nov. is proposed. The type strain is RSS1-M3T ( = KCTC 42118T = CECT 8599T).

Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, designated strain 2-3T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. This strain grew well with starch. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Rhodobacteraceae and that the strain was related most closely to the genus Pacificibacter (94.0 % sequence similarity to the type strain). The DNA G+C content was 52.4 mol%. The major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The major isoprenoid quinone was Q-10. Strain 2-3T did not grow at 4 or 35 °C, while the type strain of the type species of the genus Pacificibacter grows at both temperatures. From the taxonomic data obtained in this study, it is proposed that strain 2-3T be placed into a novel genus and species named Amylibacter marinus gen. nov., sp. nov. in the family Rhodobacteraceae . The type strain of Amylibacter marinus is 2-3T ( = NBRC 110140T = LMG 28364T).

Litoreibacter ponti sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated GJSW-31T, was isolated from seawater from the South Sea, South Korea. The novel strain 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 GJSW-31T clustered with the type strains of species of the genus Litoreibacter . Strain GJSW-31T exhibited 16S rRNA gene sequence similarity values of 95.2–98.5 % to the type strains of species of the genus Litoreibacter and sequence similarities of less than 96.18 % to type strains of the other species with validly published names. Strain GJSW-31T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain GJSW-31T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain GJSW-31T was 62.5 mol% and its DNA–DNA relatedness values with the type strains of Litoreibacter albidus , Litoreibacter janthinus , Litoreibacter meonggei and Litoreibacter ascidiaceicola were 13–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GJSW-31T is separate from other species of the genus Litoreibacter . On the basis of the data presented, strain GJSW-31T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter ponti sp. nov. is proposed. The type strain is GJSW-31T ( = KCTC 42114T = NBRC 110379T).

Pseudopelagicola gijangensis gen. nov., sp. nov., isolated from the sea squirt Halocynthia roretzi

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated YSS-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea of South Korea. Strain YSS-7T grew optimally at 25 °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 YSS-7T clustered with the type strains of Pelagicola litoralis , Planktotalea frisia , Pacificibacter maritimus and Roseovarius marinus . Strain YSS-7T exhibited the highest 16S rRNA gene sequence similarity (97.7 %) to the type strain of Pelagicola litoralis and sequence similarity of more than 96.0 % to the type strains of some other species. Strain YSS-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain YSS-7T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The fatty acid and polar lipid profiles of strain YSS-7T were different from those of the type strains of phylogenetically related species. The DNA G+C content of strain YSS-7T was 55.5 mol%. Other phenotypic properties demonstrated that strain YSS-7T is distinguished from phylogenetically related species. On the basis of the data presented, strain YSS-7T is considered to represent a novel genus and species, for which the name Pseudopelagicola gijangensis gen. nov., sp. nov. is proposed. The type strain of Pseudopelagicola gijangensis is YSS-7T ( = KCTC 42049T = CECT 8540T).

Loktanella maritima sp. nov. isolated from shallow marine sediments

An aerobic, Gram-stain-negative, non-motile bacterium, KMM 9530T, was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis positioned novel strain KMM 9530T in the genus Loktanella as a separate line adjacent to Loktanella sediminilitoris KCTC 32383T, Loktanella tamlensis JCM 14020T and Loktanella maricola JCM 14564T with 98.5–98.2 % sequence similarity. Strain KMM 9530T was characterized by its weak hydrolytic capacity and inability to assimilate most organic substrates. The major isoprenoid quinone was Q-10, polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid, an unknown aminolipid and unknown lipids, and the major fatty acid was C18 : 1ω7c. On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotypic characterization, it can be concluded that the novel strain KMM 9530T represents a novel species in the genus Loktanella , for which the name Loktanella maritima sp. nov. is proposed. The type strain of the species is KMM 9530T ( = NRIC 0919T = JCM 19807T).

Litoreibacter ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthia aurantium

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RSS4-C1(T), was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. The novel strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-3.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS4-C1(T) fell within the clade comprising the type strains of species of the genus Litoreibacter . Strain RSS4-C1(T) exhibited the highest 16S rRNA gene sequence similarity (99.6%) to the type strain of Litoreibacter albidus and sequence similarities of 96.5-98.5% to type strains of other recognized species of the genus Litoreibacter. Strain RSS4-C1(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c and 11-methyl-C(18 : 1)ω7c as the major fatty acids. The major polar lipids of strain RSS4-C1(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain RSS4-C1(T) was 58.0 mol% and its DNA-DNA relatedness values with type strains of four species of the genus Litoreibacter were 21-34%. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain RSS4-C1(T) is distinct from other species of the genus Litoreibacter. On the basis of the data presented, strain RSS4-C1(T) is considered to represent a novel species of the genus Litoreibacter, for which the name Litoreibacter ascidiaceicola sp. nov. is proposed. The type strain is RSS4-C1(T) ( = KCTC 42050(T) = CECT 8539(T)).

Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments

Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.

Litoreibacter halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi

A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated P-MA1-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain P-MA1-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain P-MA1-7T fell within the cluster comprising the type strains of four species of the genus Litoreibacter , exhibiting 16S rRNA gene sequence similarity values of 97.0–98.5 % to these four type strains and less than 95.9 % sequence similarity to the strains of the other species examined. Strain P-MA1-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain P-MA1-7T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain P-MA1-7T was 58.3 mol% and DNA–DNA relatedness values of strain P-MA1-7T with the type strains of the four species of the genus Litoreibacter were in the range of 8–21 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain P-MA1-7T was separate from other species of the genus Litoreibacter . On the basis of these data, strain P-MA1-7T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter halocynthiae sp. nov. is proposed. The type strain is P-MA1-7T ( = KCTC 32213T = CCUG 63416T).