- Volume 63, Issue Pt_4, 2013

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia , showing 98.3 % sequence similarity to Stappia indica B106T and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621T . Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1–L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1T could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10T represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 T ( = CCUG 59208T = LMG 25538 T = CCM 7757T).

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585T, was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585T was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis . Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223T, Sphingopyxis marina DSM 22363T and Sphingopyxis litoris DSM 22379T. The polar lipids of strain G1A_585T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585T was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585T ( = DSM 25081T  = LMG 26646T). Because Sphingopyxis flavimaris DSM 16223T, Sphingopyxis marina DSM 22363T and Sphingopyxis litoris DSM 22379T form a phylogenetic group together with strain G1A_585T that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151T = DSM 16223T = KCTC 12232T), Sphingorhabdus marina comb. nov. (type strain FR1087T = DSM 22363T = IMSNU 14132T = KCTC 12763T = JCM 14161T) and Sphingorhabdus litoris comb. nov. (type strain FR1093T = DSM 22379T = IMSNU 14133T = KCTC 12764T = JCM 14162T).

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated SW024T, was isolated from surface seawater of the South Pacific Gyre (26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina muelleri KMM 6020T, Aquimarina macrocephali JAMB N27T, Aquimarina addita JC2680T, Aquimarina mytili PSC33T, Aquimarina intermedia KMM 6258T, Aquimarina latercula ATCC 23177T, Aquimarina spongiae A6T, Aquimarina agarilytica ZC1T and Aquimarina brevivitae SMK-19T (96.1, 95.5, 95.0, 94.4, 94.3, 94.0, 93.4, 93.3 and 93.2 % similarities, respectively), demonstrating that the novel strain belonged to the genus Aquimarina . The DNA G+C content of strain SW024T was 30.8 mol%. The major respiratory quinone of strain SW024T was MK-6. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, and iso-C15 : 0 3-OH. The polar lipids of strain SW024T were phosphatidylethanolamine, three unknown aminolipids and five unknown polar lipids. On the basis of combined phenotypic and phylogenetic analyses, strain SW024T represents a novel species of the genus Aquimarina , for which the name Aquimarina longa sp. nov. is proposed. The type strain is SW024T ( = CGMCC 1.11007T = JCM 17859T). An emended description of A. muelleri is also proposed.

Two red-pigmented isolates, designated RQ-33T and TU-13, were recovered from hot spring runoffs on the Island of São Miguel in the Azores, Portugal. These organisms have an optimum growth temperature of approximately 45 °C and an optimum pH for growth between 7.5 and 8.5. Based on 16S rRNA gene sequence analysis, the novel isolates were most closely related to the type strain of Cecembia lonarensis at 96.4 % pairwise similarity. Cells of the two isolates were non-motile, rod-shaped, Gram-stain-negative, strictly aerobic, and oxidase- and catalase-positive. The major fatty acids were iso-C15 : 0 and C15 : 0, phosphatidylethanolamine was the major polar lipid, and menaquinone 7 was the major respiratory quinone. Based on phylogenetic analyses, and physiological and biochemical characteristics, these isolates from the Azores represent a novel species of the genus Cecembia for which the name Cecembia calidifontis is proposed with strain RQ-33T ( = DSM 21411T = LMG 24596T) as the type strain. The description of the genus Cecembia is also emended.

A taxonomic study was carried out on a novel bacterium, designated strain ck-I2-15T, which was isolated from deep-sea sediment collected from the South-west Indian Ocean Ridge. Cells of strain ck-I2-15T were Gram-reaction-negative, rod-shaped, non-motile, moderately halophilic and capable of denitrification. Growth was observed with 0–9 % (w/v) NaCl and at temperatures of 10–37 °C. The novel strain was unable to degrade gelatin. The dominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major respiratory quinone was MK6 and the polar lipid profile comprised phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, one unidentified glycolipid and four other unidentified lipids. The G+C content of the genomic DNA was 38 mol%. 16S rRNA gene sequence comparison indicated that strain ck-I2-15T was most closely related to Galbibacter mesophilus Mok-17T (92.9 % sequence similarity), followed by ‘Joostella atrarenae’ M1-2 (92.8 %), Joostella marina En5T (92.7 %) and Zhouia amylolytica HN-171T (91.6 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ck-I2-15T formed a clade with the genus Galbibacter , within the family Flavobacteriaceae . Several phenotypic properties allowed strain ck-I2-15T to be distinguished from its closest phylogenetic relatives. On the basis of the phenotypic and phylogenetic data, strain ck-I2-15T represents a novel species of the genus Galbibacter , for which the name Galbibacter marinus is proposed. The type strain is ck-I2-15T ( = CCTCC AB 209062T = LMG 25228T = MCCC 1A03044T).

A Gram-negative, non-spore-forming, non-flagellated, motile-by-gliding rod, designated SSK2-3T, was isolated from the junction between seawater and a freshwater spring at Jeju island, South Korea. Strain SSK2-3T grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SSK2-3T clustered with type strains of species of the genus Mariniflexile , with which it exhibited 97.2–97.8 % 16S rRNA gene sequence similarity. Sequence similarity between the isolate and the other strains used in the phylogenetic analysis was <95.6 %. Strain SSK2-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and C15 : 0 as the major fatty acids. The major polar lipids of strain SSK2-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-3T was 32.4 mol%. DNA–DNA relatedness between the isolate and Mariniflexile gromovii KCTC 12570T, Mariniflexile fucanivorans DSM 18792T and Mariniflexile aquimaris HWR-17T was 19, 15 and 20 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK2-3T is separate from other members of the genus Mariniflexile . On the basis of the data presented, strain SSK2-3T is considered to represent a novel species of the genus Mariniflexile , for which the name Mariniflexile jejuense sp. nov. is proposed. The type strain is SSK2-3T ( = KCTC 23958T  = CCUG 62414T). An emended description of the genus Mariniflexile is given.

Two orange, rod-shaped, Gram-reaction-negative, aerobic bacterial strains devoid of flagella and gliding motility, designated strains KYW371T and KS18 were isolated from a seawater sample and a shellfish Ruditapes philippinarum, respectively, collected from Gwangyang Bay, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the family Flavobacteriaceae ; and that strain KYW371T was most closely related to Algibacter mikhailovii LMG 23988T (96.7 % sequence similarity), Pontirhabdus pectinivorans JC2675T (96.3 %), Postechiella marina M091T (95.6 %) and Hyunsoonleella jejuensis CNU004T (95.3 %). The 16S rRNA gene sequence similarity (98.8 %) and DNA–DNA relatedness (78.1 %) between strains KYW371T and KS18 indicated that these two strains represented a single species. The predominant cellular fatty acids of strain KYW371T were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. Flexirubin-type pigments were absent. MK-6 was the only isoprenoid quinone and the DNA G+C content was 34.8–36.6 mol%. Data from this taxonomic study employing a polyphasic approach suggested that the isolates represent a novel species in a new genus in the family Flavobacteriaceae , for which the name Marinivirga aestuarii gen. nov., sp. nov. is proposed. The type strain is KYW371T ( = KCTC 23449T = JCM 17452T), and an additional strain of the species is KS18 ( = KCTC 23128 = JCM 16845). Emended descriptions of the genera Hyunsoonleella , Jejuia and Pontirhabdus and the species Hyunsoonleella jejuensis , Jejuia pallidilutea and Pontirhabdus pectinivorans are also proposed.

Bacterial strains CNX-216T and CNU-914T were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were Gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216T were short, non-motile rods, whereas cells of strain CNU-914T were short, curved rods with gliding motility. The DNA G+C contents of CNX-216T and CNU-914T were respectively 57.7 and 44.4 mol%. Strains CNX-216T and CNU-914T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes . Strain CNX-216T exhibited low 16S rRNA gene sequence identity (87.1 %) to the nearest type strain, Cesiribacter roseus 311T, and formed a well-supported lineage that is outside all currently described families in the order Cytophagales . Strain CNU-914T shared 97.6 % 16S rRNA gene sequence identity with ‘Porifericola rhodea’ N5EA6-3A2B and, together with ‘Tunicatimonas pelagia’ N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales . Based on our polyphasic taxonomic characterization, we propose that strains CNX-216T and CNU-914T represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216T  = DSM 25187T  = KCCM 90102T) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914T  = DSM 25186T  = KCCM 90101T) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov.

A Gram-negative, rod-shaped, pale-orange-pigmented bacterial strain with xylan-degrading activity designated YC7004T was isolated from a rotten-wood sample collected at Jinju, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally on R2A medium at 30 °C and at pH 6. The major isoprenoid quinone was MK7 and major fatty acids were summed feature 3, iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and C16 : 1ω5c. The G+C content of the genomic DNA was 40.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the strain belongs to the genus Mucilaginibacter in the family Sphingobacteriaceae . The most closely related species were Mucilaginibacter daejeonensis (95.5 %), Mucilaginibacter frigoritolerans (94.6 %) and Mucilaginibacter mallensis (94.0 %). Based on the phylogenetic and chemotaxonomic data analyses, strain YC7004T represents a novel species of the genus Mucilaginibacter with the proposed name of Mucilaginibacter jinjuensis sp. nov. The type strain is YC7004T ( = KACC 16571T = NBRC 108856T).

A Gram-stain-negative, oxidase- and catalase-positive bacterial strain that was motile by gliding and produced a pink pigment, designated DCY49T, was isolated from soil of a ginseng field in a mountainous region of Chungbuk province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY49T belonged to the genus Pedobacter (93.0–96.3 % similarity). Strain DCY49T contained MK-7 as the predominant menaquinone. The major fatty acids were summed feature 3 (containing C16 : 1ω7c, C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0, and the main polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA of strain DCY49T was 40.5 mol%. Strain DCY49T differed from related Pedobacter species by a number of phenotypic characteristics. On the basis of data from the present polyphasic study, strain DCY49T is described as representing a novel species of the genus Pedobacter , for which the name Pedobacter ginsengiterrae sp. nov. is proposed. The type strain is DCY49T ( = KCTC 23317T = JCM 17338T).

Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4T and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15–37 °C and at pH 6.5–7.0. The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were phosphatidyl-N-methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4T and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4T and B4a-b5 were affiliated with Pedobacter species in the family Sphingobacteriaceae . Strains N7d-4T and B4a-b5 shared 99.9 % sequence similarity, and the most closely related Pedobacter type strains were Pedobacter composti TR6-06T (96.5 and 96.7 % sequence similarity, respectively), P. oryzae N7T (95.4 and 95.6 %) and P. caeni LMG 22862T (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other Pedobacter species. Based on these data, the isolates are considered to represent a novel species of the genus Pedobacter , for which the name Pedobacter luteus sp. nov. is proposed. The type strain is N7d-4T ( = KCTC 22699T  = DSM 22385T).

Five strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae , and the most closely related species was Prevotella tannerae . P. tannerae and the novel taxon are deeply branched from the genus Prevotella , with sequence identities to the type strain of the type species of Prevotella , Prevotella melaninogenica , of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12T ( = DSM 22548T  = CCUG 58091T) and the type strain of Alloprevotella tannerae is ATCC 51259T  = CCUG 34292T  = CIP 104476T  = NCTC 13073T. Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.

Two strictly anaerobic bacterial strains, designated IP3-3T and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3T and SBP-1 were characterized using a polyphasic approach. Both IP3-3T and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4–1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3T and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum Chloroflexi most closely related to but distinct from the species Dehalogenimonas lykanthroporepellens (96.2 % pairwise similarity) and Dehalococcoides mccartyi (90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus Dehalogenimonas for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3T ( = JCM 17062T = NRRL B-59545T).

Two Gram-stain-negative, non-motile, non-pigmented cocci, designated IMCC11369T and IMCC11389, were isolated from surface seawater of the East Sea of Korea by high-throughput cultivation based on dilution to extinction. Strains IMCC11369T and IMCC11389 shared 99.9 % 16S rRNA gene sequence similarity and >86.3 % DNA–DNA relatedness, which suggested that they belong to the same genomic species. The isolates were most closely related to Lentisphaera araneosa HTCC2155T (99.0 % 16S rRNA gene sequence similarity). Phylogenetic analysis revealed that the isolates formed a robust cluster with L. araneosa HTCC2155T. DNA–DNA relatedness values, however, showed that the isolates were distantly related to L. araneosa HTCC2155T (2.0–18.6 %), which suggested that they represent a separate genomic species in the genus Lentisphaera . The two isolates were phenotypically differentiated from their closest relative by several characteristics, including degradation of macromolecules and carbon source utilization. The DNA G+C content was 44.5–45.2 mol% and the predominant cellular fatty acids were C14 : 0, C16 : 1ω9c and C16 : 0. Strain IMCC11369T contained MK-7 as the respiratory quinone and phosphatidylethanolamine and an unknown lipid as the major polar lipids. On the basis of data obtained in this study, a novel species is proposed to accommodate the isolates, Lentisphaera marina sp. nov. The type strain is IMCC11369T ( = KCTC 23780T = NBRC 108776T).

Yellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for ‘Candidatus Phytoplasma ’ species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3–1F7/7R2, 4Fwd/3Rev–4Fwd/5Rev and P1/P7–R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A blast search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of ‘Candidatus Phytoplasma oryzae ’ and 97.8 % identity with that of ‘Candidatus Phytoplasma cynodontis ’. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a ‘Candidatus Phytoplasma oryzae ’-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI.

Strain DMKU-RK359T, representing a novel yeast species, was isolated from the external surface of a sugar-cane leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 region of the large-subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, strain DMKU-RK359T was assigned to a novel Wickerhamomyces species. The novel species was closest to Wickerhamomyces ciferrii, but differed from it by 0.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6 % nucleotide substitutions in the ITS region. The name Wickerhamomyces siamensis sp. nov. is proposed (type strain DMKU-RK359T  = BCC 50732T  = NBRC 108900T  = CBS 12570T).