- Volume 67, Issue 3, 2017

An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain HMF2268T, was isolated from a lagoon in the Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strain HMF2268T belonged to the genus Polaribacter and was most closely related to Polaribacter huanghezhanensis SM1202T (96.8 % similarity). Cellular fatty acids were dominated by iso-C15 : 0, iso-C15 : 0 3-OH, anteiso-C15 : 0 and iso-C15 : 1 G. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 34.3 mol%. Based on the polyphasic taxonomic analyses, it is concluded that strain HMF2268T represents a novel species of the genus Polaribacter , for which the name Polaribacter lacunae sp. nov. is proposed. The type strain is HMF2268T (=KCTC 42191T=CECT 8862T).

Strain KT0803T 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 KT0803T 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 19838T, 98.3 % with Gramella gaetbulicola DSM 23082T, 98.1 % with Gramella aestuariivivens BG-MY13T and Gramella aquimixticola HJM-19T, 98.0 % with Gramella lutea YJ019T, 97.9 % with Gramella portivictoriae DSM 23547T and 96.9 % with Gramella marina KMM 6048T. The DNA–DNA relatedness values were <35 % between strain KT0803T and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803T has been assigned to the genus Gramella , as Gramella forsetii sp. nov. The type strain is KT0803T (=DSM 17595T=CGMCC 1.15422T). An emended description of Gramella gaetbulicola Cho et al. 2011 is also proposed.

A novel indole-3-acetic acid-producing bacterium, designated TEGT-2T, was isolated from the roots of Sinopodophyllum hexandrum collected from the Qinling Mountains in shaanxi province, northwestern China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain TEGT-2T were Gram-stain-positive, strictly aerobic, endospore-forming rods and motile by means of peritrichous flagella. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TEGT-2T was a member of the genus Paenibacillus , exhibiting the highest sequence similarity to Paenibacillus pectinilyticus KCTC 13222T (97.9 %), Paenibacillus frigoriresistens CCTCC AB 2011150T (97.3 %), Paenibacillus ferrarius CCTCC AB 2013369T (96.9 %) and Paenibacillus alginolyticus NBRC 15375T (96.5 %). The only menaquinone detected was MK-7, and the major fatty acid was anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids, an unidentified aminolipid and two unidentified lipids. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 46.6 mol%. DNA–DNA relatedness values for strain TEGT-2T with respect to its closest phylogenetic relatives Paenibacillus pectinilyticus KCTC 13222T and Paenibacillus . frigoriresistens CCTCC AB 2011150T were lower than 40 %. Based on the phenotypic, phylogenetic and genotypic data, strain TEGT-2T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus qinlingensis sp. nov. is proposed. The type strain is TEGT-2T (=CCTCC AB 2015258T=KCTC 33806T).

Gram-stain-positive cocci were isolated from miscellaneous sites of the skin of healthy dogs as well as from infection sites in dogs. The closest relative by sequencing of the 16S rRNA gene was Macrococcus caseolyticus with 99.7 % sequence identity, but compared with M. caseolyticus , the novel strains shared only 90.8 to 93.5 % DNA sequence identity with cpn60, dnaJ, rpoB and sodA partial genes, respectively. The novel strains also exhibited differential phenotypic characteristics from M. caseolyticus , and the majority displayed a visible haemolysis on sheep blood agar, while M. caseolyticus did not have any haemolytic activity. They generated different matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS spectral profiles compared with the other species of the genus Macrococcus . Furthermore, strain KM 45013T shared only 53.7 % DNA–DNA relatedness with the type strain of M. caseolyticus , confirming that they do not belong to the same species. The DNA G+C content of strain KM 45013T was 36.9 mol%. The most abundant fatty acids were C14 : 0, C18 : 3ω6c (6, 9, 12) and C16 : 0 n alcohol. MK-6 was the menaquinone type of KM 45013T. Cell-wall structure analysis revealed that the peptidoglycan type was A3α l-Lys–Gly2–l-Ser. Based on genotypic and chemotaxonomic characteristics, we propose to classify these strains within a novel species of the genus Macrococcus for which the name Macrococcus canis sp. nov. is proposed. The type strain is KM 45013T (=DSM 101690T=CCOS 969T=CCUG 68920T).

Two novel anaerobic, mesophilic, biohydrogen-producing bacteria, designated strains ZGM211T and G1T, were isolated from lake sediment. 16S rRNA and ATP synthase beta subunit (atp D) gene sequences and phylogenetic analysis of strains ZGM211T and G1T revealed an affiliation to the genus Clostridium sensu stricto (cluster I of the clostridia), with Clostridium acetobutylicum as the closest characterized species, showing the same sequence similarity of 96.4 % to the type strain (98.9 % between the two isolates). Cells of the two strains were rod shaped. Growth occurred at 20–45 °C, pH 4.0–8.0 and NaCl concentrations up to 2 % (w/v). Grown on glucose, the main fermentation products were H2, CO2, acetate and butyrate. The major fatty acids were C14 : 0 and C16 : 0. The DNA G+C contents of strains ZGM211T and G1T were 40.7 and 41.5 mol%, respectively. Based on phenotypic, chemotaxonomic and phylogenetic differences, strains ZGM211T (=CICC 24070T=BCRC 80950T) and G1T (=CICC 24069T=BCRC 80949T) are proposed as the type strains of novel species of the genus Clostridium with the names Clostridium guangxiense sp. nov. and Clostridium neuense sp. nov., respectively.

A unicellular cyanobacterium, strain Alchichica-D10, was isolated from microbialites of the alkaline Lake Alchichica, Mexico. The cells were short rods (3.9±0.6 µm in length and 1.1±0.1 µm in width) forming biofilms of intense emerald green colour. They exhibited red autofluorescence under UV light excitation. UV-visible absorption spectra revealed that they contain chlorophyll a and phycocyanin, and electron microscopy showed the presence of thylakoids. The strain grew within a temperature range of 15–30 °C. Genomic DNA G+C content was 52.2 mol%. The most remarkable feature of this species was its granular cytoplasm, due to the presence of numerous intracellular spherical granules (16–26 per cell) with an average diameter of 270 nm. These granules, easily visible under scanning electron microscopy, were composed of amorphous carbonate containing Ca, Mg, Ba and Sr. A multi-gene phylogeny based on the analysis of 59 conserved protein markers supported robustly that this strain occupies a deep position in the cyanobacterial tree. Based on its phenotypic characters and phylogenetic position, strain Alchichica-D10 is considered to represent a new genus and novel species of cyanobacteria for which the name Gloeomargarita lithophora gen. nov., sp. nov. is proposed. The type strain is Alchichica-D10 (Culture Collection of Algae and Protozoa CCAP strain 1437/1; Collections de Cyanobactéries et Microalgues Vivantes of the Museum National d’Histoire Naturelle in Paris strain PMC 919.15). Furthermore, a new family, Gloeomargaritaceae, and a new order, Gloeoemargaritales, are proposed to accommodate this species under the International Code of Nomenclature for algae, fungi and plants.

A novel Gram-stain-negative, rod-shaped, non-motile strain, designated GKXT, was isolated from deep seawater. Strain GKXT was able to grow at 20–35 °C (optimum, 25 °C), pH 5.5–9.5 (optimum, 7.5) and 0–4.0 % (w/v) NaCl (optimum, 1.0 %). The major fatty acids were C16 : 1ω9c (15.4 %), C16 : 0 (18.4 %), C14 : 0 (12.0 %), iso-C14 : 0 (30.1 %) and anteiso-C15 : 0 (5.7 %). Strain GKXT contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as the main polar lipids. The only isoprenoid quinone was menaquinone-9. The diagnostic amino acids of the cell-wall peptidoglycan contained meso-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GKXT belonged to the genus Luteolibacter in the family Verrucomicrobiaceae . The 16S rRNA gene sequence of this strain showed 98.0, 93.5 and 93.3 % sequence similarity, respectively, with those of Luteolibacter arcticus MC 3726T, L.uteolibacter pohnpeiensisA4T-83T and L.uteolibacter cuticulihirudinis E100T. DNA–DNA hybridization value of strain GKXT with L. arcticus MC 3726T was 33.1 %. The G+C content of the genomic DNA was 59.5 mol%. On the basis of the genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics, strain GKXT was proposed to represent a novel species of the genus Luteolibacter , named Luteolibacter flavescens sp. nov. (type strain GKXT=MCCC 1K03193T=KCTC 52361T).

A novel Gram-stain-negative bacterium, designated strain PC-2T, was isolated from penicillin fermentation fungi residue with pig manure co-compost in China. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that strain PC-2T should be assigned to the genus Chelatococcus and that it had 98.9 % similarity with Chelatococcus daeguensis , 98.8 % with Chelatococcus sambhunathii , 98.4 %, with Chelatococcus caeni and 96.0 % with Chelatococcus asaccharovorans . The G+C content of genomic DNA was 70.9 mol%. On the basis of the phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data, strain PC-2 T represents a novel species of the genus Chelatococcus , for which the name Chelatococcus composti sp. nov. is proposed. The type strain is PC-2T (=DSM 101465T=CGMCC 1.15283T).

A novel facultatively methanol-utilizing bacterial strain, SM30T, was isolated from rice rhizosphere. Strain SM30T was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30T showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30T is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18 : 1ω7c and 18 : 1ω6c) and cyclo 19 : 0ω8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30T represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30T (=NBRC 111955T=DSM 102969T).

A Gram-stain-negative, non-spore-forming, rod-shaped bacterium, B555-2T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. According to phylogenetic analysis with 16S rRNA gene sequences, the novel strain was most closely related to Polymorphobacter fuscus D40PT and Polymorphobacter multimanifer 262-7T with 98.4 and 96.9 % similarity, respectively. It grew optimally at pH 7 and 15 °C with 0.6 % NaCl (m/v). Carotenoid was detected from the cells. Major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, phophatidylmonomethy lethanolamine, phophatidylcholine. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (42.8 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (28.8 %), C14 : 0 2-OH (10.1 %) and C16 : 0 (8.2 %). The predominant ubiquinone was Q-10. The DNA G+C content was 62.1 mol%. In DNA–DNA hybridization tests, strain B555-2T shared 21.9 and 18.6 % DNA–DNA relatedness with P . fuscus D40PT and P . multimanifer 262-7T, respectively. Accordingly, strain B555-2T represents a novel species in the genus Polymorphobacter , for which the name Polymorphobacter glacialis sp. nov. is proposed. The type strain is B555-2T (=CGMCC 1.15519T=KCTC 52396T).

A new betaproteobacterium, CGII-59m2T, was isolated from an activated sludge bioreactor which treated landfill leachate. The 16S rRNA gene sequence analysis revealed that strain CGII-59m2T belonged to the family Alcaligenaceae and shared the highest pairwise similarity values with Parapusillimonas granuli LMG 24012T (97.7 %), various species of the genus Bordetella (97.3–97.0 %) and Candidimonas nitroreducens LMG 24812T (97.0 %). Cells of strain CGII-59m2T were rod-shaped, non-motile, and oxidase- and catalase-positive. The predominant fatty acids were C16 : 1ω7c, C16 : 0, cyclo C17 : 0 and C18 : 1ω7c, the major respiratory quinone was Q-8, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid. The G+C content of the genomic DNA of strain CGII-59m2T was 62.3 mol%. The new bacterium can be distinguished from the closely related type strains based on its non-motile cells and its high C16 : 1ω7c fatty acid content. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGII-59m2T is considered to represent a novel species of a new genus, for which the name Caenimicrobium hargitense gen. nov., sp. nov. is proposed. The type strain is CGII-59m2T (=DSM 29806T=NCAIM B.02615T).

A group of seven Chilean isolates presumptively belonging to Vibrio tapetis was isolated from diseased fine flounders (Paralichthys adspersus) and red conger eel (Genypterus chilensis) experimentally reared in Quintay (Chile). All isolates were confirmed as members of V. tapetis on the basis of matrix-assisted laser desorption ionization time-of-flight MS, 16S rRNA gene sequencing, DNA–DNA hybridization values and G+C content. The ERIC-PCR and REP-PCR patterns were homogeneous among those isolates recovered from the same host (red conger or fine flounders), but distinct from the type strains V. tapetis subsp. tapetis CECT 4600T and V. tapetis subsp. britannicus CECT 8161T. On the basis of atpA, rpoA, rpoD, recA and pyrH gene sequence similarities (99.7–100 %) and clustering in the phylogenetic trees, the red conger isolates (Q20, Q047, Q48 and Q50) were confirmed as representing V. tapetis subsp. tapetis . However, they differed from V. tapetis subsp. tapetis CECT 4600T in their lipase, alpha quimiotripsin and non-acid phosphatase production. On the other hand, the fine flounder isolates (QL-9T, QL-35 and QL-41) showed rpoD, recA and pyrH gene sequence similarities ranging from 91.6 to 97.7 % with the type strains of the two V. tapetis subspecies (CECT 4600T and CECT 8161T) and consistently clustered together as an independent phylogenetic line within V. tapetis . Moreover, they could be differentiated phenotypically from strains CECT 4600T and CECT 8161T by nine and three different biochemical tests, respectively. In conclusion, the presence of V. tapetis in diseased red conger eel and fine flounder was demonstrated, extending the known host range and geographical location for this pathogen. Furthermore, this study demonstrates that the three isolates from fine flounder represent a novel subdivision within V. tapetis , for which the name V. tapetis subsp. quintayensis subsp. nov. is proposed and with QL-9T (=CECT 8851T=LMG 28759T) as the type strain. Although QL-9T was isolated from kidney of diseased fine flounder specimens, the challenge assays showed that it was non-pathogenic for this species.

A Gram-stain-negative, motile, non-spore-forming bacterium, designated strain Y4G10-17T, was isolated from the saline–alkali farmland top soil, Inner Mongolia, northern China. Strain Y4G10-17T could grow at 4–45 °C (with 30 °C as the optimal temperature), pH 6.0–12.0 (optimal at pH 9.0) and in the presence of 1.0–12.0 % (w/v) NaCl (optimal at 4.0–6.0 %). Phylogenetic analysis based on the eight different copies of the 16S rRNA gene sequences revealed that strain Y4G10-17T shared the highest sequence similarity with Aliidiomarina maris CF12-14T, 97.93–98.66 %, and lower than 97.0 % sequence similarity with all other type strains. Its major cellular fatty acids contained iso-C15 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 1 F, iso-C11 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Q-8 was the predominantubiquinone. The major polar lipids of strain Y4G10-17T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown lipids and one unknown aminolipid. The genomic DNA G+C content was 49.3 mol%. DNA–DNA hybridization revealed that strain Y4G10-17T showed 20.2±5 % genomic DNA relatedness with its close relative A. maris CF12-14T. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y4G10-17T represents a novel species within the genus Aliidiomarina , for which the name Aliidiomarina soli sp. nov. is proposed. The type strain is Y4G10-17T (=CGMCC 1.15759T=KCTC 52381T).

Bacterial strains 4M-Z03T, 4M-K16T and DHG59T were isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31′ E 23° 10′ N). The three strains grew well at 28 °C, pH 5.0–6.0 on R2A medium. On the basis of 16S rRNA gene sequence analysis, the three strains, together with Dyella humi DHG40T, formed a distinct phyletic clade within the genus Dyella , and the sequence similarities between any strains of the clade ranged from 97.8 to 98.5 %. Sequence analysis of concatenated partial gyr B, lep A and rec A gene sequences also strongly suggested that the three strains represented three novel species of the genus Dyella . The respiratory lipoquinone of the three strains was ubiquinone-8, and their DNA G+C content was 58.2–59.0 mol%. The fatty acid profiles differed substantially among these three strains, although they had two common major fatty acids, iso-C15 : 0 and iso-C17 : 1ω9c. The DNA–DNA relatedness among the three strains and the type strains of the closest species of the genus Dyella examined was lower than 50 %. The results of genotypic and phenotypic characterization presented above demonstrate that the three strains examined represent three novel species of the genus Dyella , for which the names Dyella acidisoli sp. nov. (type strain 4M-Z03T=NBRC 111980T=KCTC 52131T), Dyella flagellata sp. nov. (type strain 4M-K16T=NBRC 111981T=KCTC 52130T) and Dyella nitratireducens sp. nov. (type strain DHG59T=NBRC 111472T=LMG 29201T=CGMCC 1.15439T) are proposed.

The morphology and infraciliature of one freshwater ciliate, Cyclidium sinicum spec. nov., isolated from a farmland pond in Harbin, northeastern China, was investigated using living observation and silver staining methods. Cyclidium sinicum spec. nov. could be distinguished by the following features: body approximately 20–25×10–15 µm in vivo; buccal field about 45–50 % of body length; 11 somatic kineties; somatic kinety n terminating sub-caudally; two macronuclei and one micronucleus; M1 almost as long as M2; M2 triangle-shaped. The genus Cyclidium is re-defined as follows: body outline usually oval or elliptical, ventral side concave, dorsal side convex; single caudal cilium; contractile vacuole posterior terminal; adoral membranelles usually not separated; paroral membrane ‘L’-shaped, with anterior end terminating at the level of anterior end of M1; somatic kineties longitudinally arranged and continuous. Phylogenetic trees based on the SSU rDNA sequences showed that C. sinicum spec. nov. clusters with the type species, Cyclidium glaucoma, with full support. Cyclidium is not monophyletic with members of the clade of Cyclidium+Protocyclidium+Ancistrum+Boveria.

Strawberry plants showing symptoms of lethal redness disease were found in production fields located in Tucumán province, Argentina. The presence of phytoplasmas was confirmed by PCR of 16S rDNA gene using phytoplasma universal primers. According to the 16S rDNA gene sequence identity, the four isolates analysed are related to the X-disease group (16SrIII) (identity ~99 %). These results were confirmed by in silico RFLP, actual RFLP and also by phylogenetic analyses of the 16S rDNA gene. This new phytoplasma was named as Strawberry X-Redness (StrawXR). The results from virtual and actual RFLP analyses of 16S rDNA gene revealed the presence of subgroup 16SrIII-J and three new 16SrIII subgroups. This is the first record of phytoplasmas from X-disease group associated strawberry in Argentina. These results confirm the prevalence of X-disease group and also contribute to the knowledge of diversity of phytoplasmas in this region.

According to the current version of Rule 12c of the International Code of Nomenclature of Prokaryotes, one of the ways in which a specific epithet can be treated is as an adjective that must agree in gender with the generic name. I propose emending this part of Rule 12c to specify that such adjectives must be in the singular form in the nominative case.