bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes
Authors: Pascual Javier , Macián M. Carmen , Arahal David R. , Garay Esperanza , Pujalte María J.
Published: November 2009

The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibrio core-group strains. Subsequent analysis allowed us to recognize toxR and rpoD as the most resolving individual genes and showed that concatenated sequences of rpoD, rctB and toxR were more useful than concatenated sequences of all seven genes. To validate our conclusions, MLSA similarities have been correlated with DNA–DNA relatedness values obtained in this study and values taken from the literature. Although the seven concatenated genes gave the best correlation, the concatenated sequences of rpoD, rctB and toxR have the practical advantage of showing a considerable gap between the maximal interspecies similarity and the minimal intraspecies similarity recorded, meaning that they can be used quite conveniently for species identification of vibrios.
Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil
Authors: Bala Kiran , Sharma Pooja , Lal Rup
Published: November 2009

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25T, was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006T (97.7 %). The 16S rRNA gene sequence similarity between strain P25T and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA–DNA relatedness between strain P25T and Sphingobium amiense IAM 15006T and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25T was 65 mol%. The polyamine profile showed the presence of spermidine. The predominant cellular fatty acids were summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25T also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain P25T from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25T (=MTCC 9472T =CCM 7543T).
Corynebacterium mustelae sp. nov., isolated from a ferret with lethal sepsis
Authors: Funke Guido , Frodl Reinhard , Bernard Kathryn A.
Published: November 2009

A non-lipophilic coryneform bacterium, strain 3105T, was isolated from various tissues of a ferret with lethal sepsis. The strain was characterized by phenotypic and chemotaxonomic methods, which suggested an assignment of the isolate to the genusCorynebacterium. Strain 3105Texhibited the following peculiar features that made it possible to differentiate it phenotypically from all other corynebacteria: its distinctive ‘humid cellar’-like odour, strong adherence to agar and a greenish-beige pigment. Strain 3105Texhibited more than 2.8 % 16S rRNA gene sequence divergence from its closest phylogenetic neighbour,CorynebacteriumpseudotuberculosisNCTC 3450T(97.12 % sequence similarity). Analysis of the highly variable region within therpoBgene sequence showed that strain 3105Texhibited more than 14 % divergence from its closest phylogenetic relative, againC. pseudotuberculosis. Based on the data presented, it is proposed that the ferret isolate should be classified within a novel species,Corynebacterium mustelaesp. nov. (type strain 3105T=CCUG 57279T=DSM 45274T).
Gaetbulicola byunsanensis gen. nov., sp. nov., isolated from tidal flat sediment
Authors: Yoon Jung-Hoon , Kang So-Jung , Jung Yong-Taek , Oh Tae-Kwang
Published: November 2009

A Gram-negative, non-motile and pleomorphic bacterial strain, SMK-114T, which belongs to the class Alphaproteobacteria, was isolated from a tidal flat sample collected in Byunsan, Korea. Strain SMK-114T grew optimally at pH 7.0–8.0 and 25–30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SMK-114T formed a cluster with Octadecabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 95.2–95.4 %. This cluster was part of the clade comprising Thalassobius species with a bootstrap resampling value of 76.3 %. Strain SMK-114T exhibited 16S rRNA gene sequence similarity values of 95.1–96.3 % to members of the genus Thalassobius. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. The DNA G+C content was 60.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-114T is considered to represent a novel species in a new genus for which the name Gaetbulicola byunsanensis gen. nov., sp. nov. is proposed. The type strain of Gaetbulicola byunsanensis is SMK-114T (=KCTC 22632T =CCUG 57612T).
Mucilaginibacter rigui sp. nov., isolated from wetland freshwater, and emended description of the genus Mucilaginibacter
Authors: Baik Keun Sik , Park Seong Chan , Kim Eun Mi , Lim Chae Hong , Seong Chi Nam
Published: November 2009

A non-motile, rod-shaped bacterium, designated strain WPCB133T, was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The strain contained MK-7 as the major isoprenoid quinone. The DNA G+C content was 47 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB133T forms an independent lineage within the genus Mucilaginibacter. Strain WPCB133T was distantly related to Mucilaginibacter kameinonensis SCKT (94.7 % sequence similarity), Mucilaginibacter paludis TPT56T (94.5 %) and Mucilaginibacter gracilis TPT18T (94.4 %). Phenotypic characteristics distinguished strain WPCB133T from members of the genus Mucilaginibacter. On the basis of evidence presented in this study, strain WPCB133T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter rigui sp. nov. is proposed. The type strain is WPCB133T (=KCTC 12534T =NBRC 101115T). An emended description of the genus Mucilaginibacter is also proposed.
Brucella inopinata sp. nov., isolated from a breast implant infection
Authors: Scholz Holger C. , Nöckler Karsten , Göllner Cornelia , Bahn Peter , Vergnaud Gilles , Tomaso Herbert , Al Dahouk Sascha , Kämpfer Peter , Cloeckaert Axel , Maquart Marianne , Zygmunt Michel S. , Whatmore Adrian M. , Pfeffer Martin , Huber Birgit , Busse Hans-Jürgen , De Barun Kumar
Published: November 2009

A Gram-negative, non-motile, non-spore-forming coccoid bacterium (strain BO1T) was isolated recently from a breast implant infection of a 71-year-old female patient with clinical signs of brucellosis. Affiliation of strain BO1T to the genus Brucella was confirmed by means of polyamine pattern, polar lipid profile, fatty acid profile, quinone system, DNA–DNA hybridization studies and by insertion sequence 711 (IS711)-specific PCR. Strain BO1T harboured four to five copies of the Brucella-specific insertion element IS711, displaying a unique banding pattern, and exhibited a unique 16S rRNA gene sequence and also grouped separately in multilocus sequence typing analysis. Strain BO1T reacted with Brucella M-monospecific antiserum. Incomplete lysis was detected with bacteriophages Tb (Tbilisi), F1 and F25. Biochemical profiling revealed a high degree of enzymic activity and metabolic capabilities. In multilocus VNTR (variable-number tandem-repeat) analysis, strain BO1T showed a very distinctive profile and clustered with the other ‘exotic’ Brucella strains, including strains isolated from marine mammals, and Brucella microti, Brucella suis biovar 5 and Brucella neotomae. Comparative omp2a and omp2b gene sequence analysis revealed the most divergent omp2 sequences identified to date for a Brucella strain. The recA gene sequence of strain BO1T differed in seven nucleotides from the Brucella recA consensus sequence. Using the Brucella species-specific multiplex PCR assay, strain BO1T displayed a unique banding pattern not observed in other Brucella species. From the phenotypic and molecular analysis it became evident that strain BO1T was clearly different from all other Brucella species, and therefore represents a novel species within the genus Brucella. Because of its unexpected isolation, the name Brucella inopinata with the type strain BO1T (=BCCN 09-01T=CPAM 6436T) is proposed.
Actinopolymorpha cephalotaxi sp. nov., a novel actinomycete isolated from rhizosphere soil of the plant Cephalotaxus fortunei
Authors: Yuan Li-Jie , Zhang Yu-Qin , Yu Li-Yan , Sun Cheng-Hang , Wei Yu-Zhen , Liu Hong-Yu , Li Wen-Jun , Zhang Yue-Qin
Published: November 2009

An actinomycete, strain I06-2230T, was isolated from rhizosphere soil of the plant Cephalotaxus fortunei, collected from Yunnan province, south China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Actinopolymorpha. Cells grew on agar surfaces, with no penetration even after prolonged cultivation. Aerial hyphae were absent. Cells were irregularly shaped and remained attached as chains or aggregates. Chemotaxonomic data, which showed ll-diaminopimelic acid in the cell wall, glucose as the whole-cell sugar, type PI phospholipids and MK-9(H4) as the predominant menaquinone, supported the affiliation of strain I06-2230T to the genus Actinopolymorpha. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C16 : 1 H. The genomic DNA G+C content was 69.3 mol%. DNA–DNA hybridization data, in combination with chemotaxonomic, physiological and biochemical data, demonstrated that strain I06-2230T should be classified as representing a novel species of the genus Actinopolymorpha. The name Actinopolymorpha cephalotaxi sp. nov. is proposed, with strain I06-2230T (=DSM 45117T=CCM 7466T=KCTC 19293T) as the type strain.
Methanobacterium veterum sp. nov., from ancient Siberian permafrost
Authors: Krivushin Kirill V. , Shcherbakova Viktoria A. , Petrovskaya Lada E. , Rivkina Elizaveta M.
Published: November 2009

A methanogenic archaeon, strain MK4T, was isolated from ancient permafrost after long-term selective anaerobic cultivation. The cells were rods, 2.0–8.0 μm long and 0.40–0.45 μm wide, and stained Gram-negative. Optimal growth was observed at 28 °C and pH 7.0–7.2 and in 0.05 M NaCl. The isolate used H2plus CO2, methylamine plus H2and methanol plus H2as sources for growth and methanogenesis. Phylogenetic analysis of the 16S rRNA gene sequence of the strain showed close affinity withMethanobacterium bryantii(similarity >99 % to the type strain). On the basis of the level of DNA–DNA hybridization (62 %) between strain MK4TandMethanobacterium bryantiiVKM B-1629Tand phenotypic and phylogenetic differences, strain MK4Twas assigned to a novel species of the genusMethanobacterium,Methanobacterium veterumsp. nov., with the type strain MK4T(=DSM 19849T=VKM B-2440T).
Sphingomonas changbaiensis sp. nov., isolated from forest soil
Authors: Zhang Jia-Yue , Liu Xing-Yu , Liu Shuang-Jiang
Published: November 2009

Bacterial strain V2M44Twas isolated from forest soil from the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M44Twere Gram-negative, rod-shaped and 0.3–0.4 μm in diameter and 1.5–2.5 μm long. The cells were strictly aerobic and were motile by means of peritrichous flagella. Growth occurred at 20–33 °C (optimum, 29–31 °C), at pH 5–8 (optimum, pH 6.0–7.0) and in the presence of 0−0.1 % (w/v) NaCl (optimum, 0.05 %). Strain V2M44Tcontained C17 : 1ω6c(38.9 %) and summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9tand/or C18 : 1ω12t, 31.5 %) as the major cellular fatty acids and Q-10 as the major respiratory quinone. The major polar lipids were sphingoglycolipid, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol along with two unidentified phospholipids and four unidentified glycolipids. The major component in the polyamine pattern wassym-homospermidine. The DNA G+C content was 65.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain V2M44Twas phylogenetically related to members of the genusSphingomonas, with sequence similarities ranging from 92.0–95.8 %. Based on these results, it is concluded that strain V2M44Trepresents a novel species of the genusSphingomonas, for which the nameSphingomonas changbaiensissp. nov. is proposed. The type strain is V2M44T(=CGMCC 1.7057T=NBRC 104936T).
Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland
Authors: Bae Jee-Yeon , Kim Ki-Yeon , Kim Ju-Hyoung , Lee Kangseok , Cho Jang-Cheon , Cha Chang-Jun
Published: November 2009

A novel bacterial strain designated CJ25T was isolated from the estuarine wetland of the Han river in Korea. Identification of this strain was carried out on the basis of polyphasic taxonomy. The isolate was Gram-staining-positive, rod-shaped, non-pigmented and motile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus chondroitinus DSM 5051T with 96.1 % similarity. The predominant fatty acids were anteiso-C15 : 0 (50.25 %), iso-C16 : 0 (18.54 %) and iso-C15 : 0 (10.00 %). The major isoprenoid quinone was MK-7. The G+C content of genomic DNA was 50 mol%. According to physiological data and 16S rRNA gene sequence analysis, the isolate was discriminated from related members of the genus Paenibacillus. Therefore, strain CJ25T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus aestuarii sp. nov. is proposed. The type strain is CJ25T (=KACC 13125T =JCM 15521T).
Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil
Authors: Reddy G. S. N. , Pradhan Suman , Manorama Ruth , Shivaji S.
Published: November 2009

Strain RuGl7Twas isolated from a soil sample collected at the periphery of the glacial Lake Roopkund in the Himalayan mountain range, India. Cells of RuGl7Twere Gram-positive, aerobic, rod-shaped, motile and grew optimally between 15 and 18 °C. Cells of RuGl7Tcontained 2,4-diaminobutyric acid in the cell-wall peptidoglycan and the major menaquinones were MK-10, MK-11 and MK-12. The polar lipids present were diphosphatidylglycerol and phosphatidylglycerol and an unknown lipid and the major fatty acid was anteiso-C15 : 0. Based on the above characteristics, strain RuGl7Twas assigned to the genusCryobacterium. Strain RuGl7Tshared a 16S rRNA gene sequence similarity of 97.0 and 99.0 % withCryobacterium psychrotoleransJCM 13925TandCryobacterium psychrophilumJCM 1463T, respectively. However, DNA–DNA relatedness values between strain RuGl7TandC. psychrotoleransandC. psychrophilumwere 28 and 23 %, respectively. Furthermore, strain RuGl7Texhibited several phenotypic and genotypic differences when compared withC. psychrotolerans,C. psychrophilumandCryobacterium mesophilum. Based on these differentiating characteristics, strain RuGl7Twas identified as a novel species of the genusCryobacteriumfor which the nameCryobacterium roopkundensesp. nov. is proposed. The type strain is RuGl7T(=DSM 21065T=JCM 15131T).
Corynebacterium pyruviciproducens sp. nov., a pyruvic acid producer
Authors: Tong Jia , Liu Chengxu , Summanen Paula H. , Xu Huaxi , Finegold Sydney M.
Published: November 2009

A coryneform strain, 06-1773OT (=WAL 19168T), derived from a groin abscess sample was characterized using phenotypic and molecular taxonomic methods. Comparative analyses revealed more than 3 % divergence of the 16S rRNA gene sequence and about 10 % divergence of the partial rpoB gene sequence from the type strain of Corynebacterium glucuronolyticum. The strain could also be differentiated from C. glucuronolyticum by a set of phenotypic properties. A DNA–DNA relatedness study between strain WAL 19168T and C. glucuronolyticum CCUG 35055T showed a relatedness value of 13.3 % (13.7 % on repeat analysis). The genotypic and phenotypic data show that the strain merits classification within a novel species of Corynebacterium. We propose the name Corynebacterium pyruviciproducens sp. nov. for the novel species. The type strain is 06-1773OT (=WAL 19168T =CCUG 57046T =ATCC BAA-1742T).
Basfia succiniciproducens gen. nov., sp. nov., a new member of the family Pasteurellaceae isolated from bovine rumen
Authors: Kuhnert Peter , Scholten Edzard , Haefner Stefan , Mayor Désirée , Frey Joachim
Published: November 2009

Gram-negative, coccoid, non-motile bacteria that are catalase-, urease- and indole-negative, facultatively anaerobic and oxidase-positive were isolated from the bovine rumen using an improved selective medium for members of the Pasteurellaceae. All strains produced significant amounts of succinic acid under anaerobic conditions with glucose as substrate. Phenotypic characterization and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, infB and recN genes were performed on seven independent isolates. All four genes showed high sequence similarity to their counterparts in the genome sequence of the patent strain MBEL55E, but less than 95 % 16S rRNA gene sequence similarity to any other species of the Pasteurellaceae. Genetically these strains form a very homogeneous group in individual as well as combined phylogenetic trees, clearly separated from other genera of the family from which they can also be separated based on phenotypic markers. Genome relatedness as deduced from the recN gene showed high interspecies similarities, but again low similarity to any of the established genera of the family. No toxicity towards bovine, human or fish cells was observed and no RTX toxin genes were detected in members of the new taxon. Based on phylogenetic clustering in the MLSA analysis, the low genetic similarity to other genera and the phenotypic distinction, we suggest to classify these bovine rumen isolates as Basfia succiniciproducens gen. nov., sp. nov. The type strain is JF4016T (=DSM 22022T =CCUG 57335T).
Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus)
Authors: Balcázar José Luis , Pintado José , Planas Miquel
Published: November 2009

A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1
ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).
Kaistia terrae sp. nov., isolated from a wetland in Korea
Authors: Kim Soo-Jin , Weon Hang-Yeon , Kim Yi-Seul , Anandham Rangasamy , Yoo Seung-Hee , Park In-Cheol , Kwon Soon-Wo
Published: November 2009

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1
ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).
Oceanibaculum pacificum sp. nov., isolated from hydrothermal field sediment of the south-west Pacific Ocean
Authors: Dong Chunming , Lai Qiliang , Chen Liang , Sun Fengqin , Shao Zongze , Yu Ziniu
Published: November 2009

A taxonomic study was carried out on strain LMC2up-L3T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched with a sediment sample collected from a hydrothermal field of the south-west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LMC2up-L3T belonged to the genus Oceanibaculum, with the highest sequence similarity of 98.4 % to Oceanibaculum indicum P24T; similarity to other strains was below 93.1 %. DNA–DNA hybridization between strain LMC2up-L3T and O. indicum P24T was 31 %. rep-PCR fingerprints also differentiated strain LMC2up-L3T from O. indicum P24T. The G+C content of the chromosomal DNA was 67.7 mol%. The principal fatty acids were C16 : 1 (17.8 %), C16 : 0 (21.2 %), C18 : 1
ω7c (23.6 %), C18 : 0 (4.1 %), C18 : 1 2-OH (4.5 %) and C19 : 0 cyclo ω8c (17.4 %). The combined genotypic and phenotypic data show that strain LMC2up-L3T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculum pacificum sp. nov. is proposed, with the type strain LMC2up-L3T (=CCTCC AB 209059T =LMG 24859T =MCCC 1A02656T). An emended description of the genus Oceanibaculum is also provided.
Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest
Authors: Zhang Nan Nan , Qu Jian Hang , Yuan Hong Li , Sun Yan Mei , Yang Jin Shui
Published: November 2009

A yellow-coloured bacterium, T41T, was isolated from a soil sample of a subtropical rainforest in Nepal. Cells were Gram-reaction-positive, aerobic, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a cluster with Terrimonas ferruginea, Terrimonas lutea, Niabella soli, Flavisolibacter ginsengiterrae, Flavisolibacter ginsengisoli, Niastella yeongjuensis and Niastella koreensis in the phylum Bacteroidetes. The strain showed the highest sequence similarity to the type strain of Terrimonas lutea (93.2 %). The major isoprenoid quinone was MK-7 and the predominant cellular fatty acids (>10 %) were iso-15 : 0 (33.8 %), iso-15 : 1 G (13.3 %) and iso-17 : 0 3-OH (12.9 %). The DNA G+C content was 48.1 mol%. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strain T41T represents a novel species in a new genus in the phylum Bacteroidetes, for which the name Flavihumibacter petaseus gen. nov., sp. nov. is proposed. The type strain of Flavihumibacter petaseus is strain T41T (=CGMCC 1.7723T =NBRC 106054T).
Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum
Authors: Beneduzi Anelise , Costa Pedro B. , Parma Márcia , Melo Itamar S. , Bodanese-Zanettini Maria Helena , Passaglia Luciane M. P.
Published: November 2009

A bacterial strain designated SBR5Twas isolated from the rhizosphere ofTriticum aestivum. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genusPaenibacillus, being most closely related toPaenibacillus graminisRSA19T(98.1 % similarity). The isolate was a Gram-reaction-variable, motile, facultatively anaerobic bacterium, with spores in a terminal position in cells. Starch was utilized and dihydroxyacetone and catalase were produced. Strain SBR5Tdisplayed plant-growth-promoting rhizobacteria characteristics: the ability to fix nitrogen and to produce siderophores and indole-3-acetic acid. The DNA G+C content was 55.1 mol%. Chemotaxonomic analysis of the isolated strain revealed that MK-7 was the predominant menaquinone, while the major fatty acid was anteiso-C15 : 0. DNA–DNA hybridization values between strain SBR5TandP. graminisRSA19T,Paenibacillus odoriferTOD45TandPaenibacillus borealisKK19Twere 43, 35 and 28 %, respectively. These DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain SBR5Tshould be considered as the nitrogen-fixing type strain of a novel species of the genusPaenibacillus, for which the namePaenibacillus riograndensissp. nov. is proposed. The type strain is SBR5T(=CCGB 1313T=CECT 7330T).
Niastella populi sp. nov., isolated from soil of Euphrates poplar (Populus euphratica) forest, and emended description of the genus Niastella
Authors: Zhang Kundi , Wang Yang , Tang Yali , Dai Jun , Zhang Lei , An Hongli , Luo Guangchao , Rahman Erkin , Fang Chengxiang
Published: November 2009

A novel bacterial strain, designated THYL-44T, was isolated from the soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, non-flagellated, non-motile and filamentous. Growth occurred at 17–37 °C (optimum 30 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (w/v; optimum 0 %). Flexirubin pigments were not produced. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain THYL-44T was closely related to Niastella koreensis KACC 11465T (95.5 % sequence similarity). The major respiratory quinone was MK-7 and the predominant cellular fatty acids were iso-C15 : 0 (28.6 %), iso-C17 : 0 3-OH (23.9 %) and iso-C15 : 1 G (17.4 %). The DNA G+C content was 45.2 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain THYL-44T represents a novel species of the genus Niastella, for which the name Niastella populi sp. nov. is proposed. The type strain is THYL-44T (=CCTCC AB 208238T=KCTC 22560T). On the basis of new data, an emended description of the genus Niastella is also proposed.
Two new marine ciliates, Euplotes sinicus sp. nov. and Euplotes parabalteatus sp. nov., and a new small subunit rRNA gene sequence of Euplotes rariseta (Ciliophora, Spirotrichea, Euplotida)
Authors: Jiang Jiamei , Zhang Qianqian , Hu Xiaozhong , Shao Chen , Al-Rasheid Khaled A. S. , Song Weibo
Published: November 2009

The morphology, infraciliature and silverline system of two marine Euplotes, Euplotes sinicus sp. nov. and Euplotes parabalteatus sp. nov., isolated from seawater near Qingdao, China, were investigated. E. sinicus is characterized by having conspicuous dorsal ridges, a single marginal cirrus and a silverline system of the double-patella-I type. E. parabalteatus is an extremely small form (only about 35 μm long) with 6–7 dorsal kineties and a silverline system of the double-eurystomus type. Small subunit (SSU) rRNA-based phylogenetic trees were constructed with three different methods and these firmly demonstrated that the novel species represent two distinct phylogenetic lineages within the genus Euplotes, branching as a sister group to all other sequenced congeners. In addition, the SSU rRNA gene of another rare, morphologically similar form, Euplotes rariseta, was sequenced. This revealed the phylogenetic position of E. rariseta to be basal to one of the major groups of Euplotes rather than close to Euplotes nobilii.
Paenibacillus hunanensis sp. nov., isolated from rice seeds
Authors: Liu Yang , Liu Lin , Qiu Fubin , Schumann Peter , Shi Yu , Zou Yuanyuan , Zhang Xiaoxia , Song Wei
Published: November 2009

Four Gram-stain-positive, aerobic or facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated strains FeL05T, FeL11, Fek19 and Fek21, were isolated from seeds of hybrid rice (Oryza sativa L. Jinyou 611), and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains were members of the genus Paenibacillus. They showed 95.4 % sequence similarity or less with strains of other Paenibacillus species. The G+C content of strain FeL05T was found to be 53.3 mol%. Its predominant respiratory quinone was MK-7. The predominant cellular fatty acids were anteiso-C15 : 0 (61.7 %), C16 : 0 (10.9 %), iso-C16 : 0 (7.0 %), anteiso-C17 : 0 (6.7 %) and iso-C15 : 0 (5.2 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain FeL05T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hunanensis sp. nov. is proposed. The type strain is strain FeL05T (=ACCC 10718T =CGMCC 1.8907T =DSM 22170T).
Actinomadura sputi sp. nov., isolated from the sputum of a patient with pulmonary infection
Authors: Yassin A. F. , Spröer C. , Siering C. , Klenk H.-P.
Published: November 2009

The taxonomic position of an actinomycete, strain IMMIB L-889T, isolated from the sputum of a 64-year-old man, was determined using a polyphasic taxonomic approach. The strain had chemical and morphological properties that were consistent with its classification in the genus Actinomadura. It formed a distinct phyletic line in the 16S rRNA gene tree of Actinomadura and was most closely related to the type strain of Actinomadura hallensis (98.4 % sequence similarity), but could be readily distinguished from the latter species using DNA–DNA relatedness and phenotypic data. The combined genotypic and phenotypic data indicate that strain IMMIB L-889T represents a novel species of the genus Actinomadura, for which the name Actinomadura sputi sp. nov. is proposed. The type strain is IMMIB L-889T (=DSM 45233T=CCUG 56587T).
Dietzia timorensis sp. nov., isolated from soil
Authors: Yamamura Hideki , Lisdiyanti Puspita , Ridwan Roni , Ratnakomala Shanti , Sarawati Rasti , Lestari Yulin , Triana Evi , Kartina Gina , Widyastuti Yantyati , Ando Katsuhiko
Published: November 2009

An actinomycete strain, ID05-A0528T, was isolated using the SDS-yeast extract pre-treatment method from soil under mahogany (Swietenia mahogani) trees in West Timor, Indonesia, and was examined by using a polyphasic taxonomic approach. Chemotaxonomic and phylogenetic characterizations demonstrated that the novel strain belongs to the genus Dietzia. 16S rRNA gene sequencing studies showed that the strain was related to Dietzia cinnamea (97.2 %). Results of phenotypic and phylogenetic analyses determined that strain ID05-A0528T is different from the known species of the genus Dietzia. It is proposed that the isolate should be classified as a representative of a novel species of the genus Dietzia, with the name Dietzia timorensis sp. nov. The type strain is ID05-A0528T (=BTCC B-560T =NBRC 104184T).
Actinoallomurus acaciae sp. nov., an endophytic actinomycete isolated from Acacia auriculiformis A. Cunn. ex Benth.
Authors: Thamchaipenet Arinthip , Indananda Chantra , Bunyoo Chakrit , Duangmal Kannika , Matsumoto Atsuko , Takahashi Yoko
Published: November 2009

A novel endophytic actinomycete, strain GMKU 931T, was isolated from the root of a wattle tree, Acacia auriculiformis A. Cunn. ex Benth., collected at Kasetsart University, Bangkok, Thailand. Strain GMKU 931T produced short spiral chains of smooth-surfaced spores on the aerial mycelium. Lysine and meso-diaminopimelic acid were present in the cell-wall peptidoglycan. Whole-cell hydrolysates contained galactose, madurose and mannose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 and iso-C16 : 1. The major phospholipids were phosphatidylinositol and phosphatidylglycerol. A phylogenetic analysis based on 16S rRNA gene sequences suggested that strain GMKU 931T forms a distinct phyletic line within the recently proposed genus Actinoallomurus. The significant differences in phenotypic and genotypic data indicate that strain GMKU 931T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus acaciae sp. nov. is proposed. The type strain is GMKU 931T (=BCC 28622T =NBRC 104354T =NRRL B-24610T).
Maribacter stanieri sp. nov., a marine bacterium of the family Flavobacteriaceae
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Mikhailov Valery V.
Published: November 2009

The taxonomic status of two novel heterotrophic, Gram-negative, gliding and yellow pigmented bacterial strains was established in this study. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strains formed a distinct lineage within the genus Maribacter, a member of the family Flavobacteriaceae, with sequence similarities of 96.3–98.5 % to recognized species of the genus Maribacter. The maximum growth temperature of the strains was 35 °C and they required NaCl or seawater for growth. They hydrolysed aesculin and gelatin, reduced nitrates to nitrites and produced acid from carbohydrates. The DNA G+C contents of strains KMM 6025 and KMM 6046T were 36–37 mol%. On the basis of phenotypic, genotypic and phylogenetic characteristics, it is suggested that the new isolates represent a novel species of the genus Maribacter, for which the name Maribacter stanieri sp. nov. is proposed. The type strain is KMM 6046T (=KCTC 22023T=LMG 22581T).
Agromyces atrinae sp. nov., isolated from fermented seafood
Authors: Park Eun-Jin , Kim Min-Soo , Jung Mi-Ja , Roh Seong Woon , Chang Ho-Won , Shin Kee-Sun , Bae Jin-Woo
Published: November 2009

A Gram-staining-positive, aerobic, non-motile and rod-shaped bacterium, designated P27T, was isolated from a traditional fermented seafood. The isolate grew optimally with 0–2.0 % (w/v) NaCl and at pH 6–7 and 30 °C. The predominant menaquinones were MK-12 and MK-11. The major cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major cell-wall sugars were galactose, mannose and rhamnose. The peptidoglycan amino acids of strain P27T were 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content of strain P27T was 69.0 mol%. Based on its 16S rRNA gene sequence, strain P27T showed highest pairwise similarity with Agromyces cerinus subsp. cerinus JCM 9083T (97.0 % similarity). Based on phenotypic, genotypic and phylogenetic studies, strain P27T represents a novel species in the genus Agromyces, for which the name Agromyces atrinae sp. nov. is proposed. The type strain is P27T (=KCTC 19593T =JCM 15913T).
Brevibacillus fluminis sp. nov., isolated from sediment of estuarine wetland
Authors: Choi Mi-Jin , Bae Jee-Yeon , Kim Ki-Yeon , Kang Hojeong , Cha Chang-Jun
Published: November 2009

Identification of a bacterial strain, designated CJ71T, was carried out using a polyphasic taxonomic approach. Strain CJ71T was isolated from sediment from the estuarine wetland of the Han River, South Korea, by enrichment culture using pyrene as the sole carbon and energy source. The isolate was white-pigmented, rod-shaped, Gram-positive, strictly aerobic and motile. 16S rRNA gene sequence analysis revealed that strain CJ71T had the highest sequence similarity (96.9 %) to Brevibacillus formosus DSM 9885T. The predominant cellular fatty acids in strain CJ71T were anteiso-C15 : 0 (49.5 %), iso-C15 : 0 (16.9 %), iso-C14 : 0 (16.9 %) and iso-C16 : 0 (4.9 %). The major isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 52.4 mol%. Results from the polyphasic taxonomic study suggest that strain CJ71T represents a novel species of the genus Brevibacillus for which the name Brevibacillus fluminis sp. nov. is proposed; the type strain is CJ71T (=KACC 13381T=JCM 15716T)
Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost
Authors: Denizci Aziz Akın , Kazan Dilek , Erarslan Altan
Published: November 2009

A Gram-stain-positive, obligately alkaliphilic bacterium designated strain GMBE 72T was isolated from mushroom compost from Yalova, located in the Marmara region of Turkey. Cells were aerobic, straight rods and they formed subterminal to terminal ellipsoidal endospores. The isolate was catalase-positive, oxidase-negative and motile and contained a type A1γ peptidoglycan based on meso-diaminopimelic acid. The strain grew at pH 8.0–12.5. The major cellular fatty acid was anteiso-C15 : 0. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain GMBE 72T belonged to the genus Bacillus and exhibited 98.2 % sequence similarity to Bacillus pseudofirmus DSM 8715T. DNA–DNA reassociation was 56 % between GMBE 72T and B. pseudofirmus DSM 8715T. According to our polyphasic characterization, strain GMBE 72T represents a novel species of the genus Bacillus, for which the name Bacillus marmarensis sp. nov. is proposed. The type strain is GMBE 72T (=DSM 21297T =JCM 15719T).
Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species
Authors: Rong Xiaoying , Huang Ying
Published: November 2009

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.
Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan
Authors: Tanaka Naoto , Romanenko Lyudmila A. , Frolova Galina M. , Mikhailov Valery V.
Published: November 2009

The phenotypic and phylogenetic characteristics of an aerobic, Gram-negative, motile, non-pigmented Alteromonas-like bacterium (designated strain KMM 3894T), isolated from a sandy sediment sample collected offshore of the Sea of Japan, were investigated. Comparative 16S rRNA gene sequence analysis revealed that strain KMM 3894T belonged to the genus Aestuariibacter and was most closely related to Aestuariibacter halophilus JC2043T (95.5 % sequence similarity). Fatty acid analysis showed C16 : 1
ω7c, C18 : 1
ω7c, and C16 : 0 as the dominant components. Strain KMM 3894T could be differentiated from recognized species of the genus Aestuariibacter by its ability to grow at 4 °C and at 30 °C, the optimum temperature for growth, and its inability to utilize most carbohydrates. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain KMM 3894T is considered to represent a novel species of the genus Aestuariibacter, for which the name Aestuariibacter litoralis sp. nov. is proposed. The type strain is KMM 3894T (=NRIC 0754T=JCM 15896T).
Demequina salsinemoris sp. nov., isolated on agar media supplemented with ascorbic acid or rutin
Authors: Matsumoto Atsuko , Nakai Kengo , Morisaki Kurimi , Ōmura Satoshi , Takahashi Yōko
Published: November 2009

Three strains, KV-810T, KV-811 and KV-816, were isolated from mangrove soil from a southern island in Japan on media supplemented with ascorbic acid or rutin. These strains contained l-ornithine as the diagnostic diamino acid in the cell-wall peptidoglycan and DMK-9(H4) as the predominant menaquinone. The G+C content of the DNA was 70–72 mol%. These characteristics in combination with 16S rRNA gene sequence analysis revealed that the novel strains belonged to the genus Demequina. The DNA–DNA hybridization values showed that the three new strains belonged to the same species, a novel species of the genus Demequina. Therefore strains KV-810T, KV-811 and KV-816 are proposed as representing a novel species, Demequina salsinemoris sp. nov. The type strain is KV-810T (=DSM 22060T=NBRC 105323T).
Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment
Authors: Park Sooyeon , Kang So-Jung , Oh Ki-Hoon , Oh Tae-Kwang , Yoon Jung-Hoon
Published: November 2009

A Gram-negative, non-motile, non-spore-forming bacterial strain, S1-3T, was isolated from a tidal flat sediment on the west coast of Korea and its taxonomic position was investigated. Strain S1-3T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Strain S1-3T contained MK-7 as the predominant menaquinone and C16 : 1
ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids. The DNA G+C content was 41.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain S1-3T fell within the clade comprising Algoriphagus species, clustering with Algoriphagus halophilus IMSNU 14013T, with which it exhibited 99.6 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence similarity between strain S1-3T and the type strains of other Algoriphagus species was 94.0–97.1 %. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain S1-3T demonstrated that this strain is distinguishable from the other Algoriphagus species as well as A. halophilus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain S1-3T is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus lutimaris sp. nov. is proposed. The type strain is S1-3T (=KCTC 22630T =CCUG 57608T).
Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field
Authors: Cho Chun Hwi , Lee Jung-Sook , An Dong-Shan , Whon Tae Woong , Kim Song-Gun
Published: November 2009

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 346T) was isolated from the soil of a ginseng field in South Korea and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequences, strain Gsoil 346T was shown to belong to the genus Nocardioides in the family Nocardioidaceae, with the most closely related species being Nocardioides aquiterrae GW-9T (96.6 % 16S rRNA gene sequence similarity); however, the strain clustered in a distinct branch of the phylogenetic tree with Nocardioides kongjuensis A2-4T (96.2 %), Nocardioides aromaticivorans H-1T (96.1 %), Nocardioides nitrophenolicus NSP41T (96.1 %) and Nocardioides simplex ATCC 15799T (95.9 %). Strain Gsoil 346T was characterized chemotaxonomically and found to have ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, phosphatidylinositol and phosphatidylglycerol as the major polar lipids, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C18 : 1
ω9c and C17 : 1
ω8c as the major fatty acids. The G+C content of the genomic DNA of the novel strain was 73.0 mol%. These chemotaxonomic properties supported the placement of strain Gsoil 346T in the genus Nocardioides. The results of physiological and biochemical tests, along with the phylogenetic analysis, allowed strain Gsoil 346T to be differentiated genotypically and phenotypically from recognized species of the genus Nocardioides. Therefore, strain Gsoil 346T represents a novel species, for which the name Nocardioides panacisoli sp. nov. is proposed, with Gsoil 346T (=KCTC 19470T=DSM 21348T) as the type strain.
Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum
Authors: C. Garcia Lorena , Martínez-Molina Eustoquio , Trujillo Martha E.
Published: November 2009

A novel actinomycete, designated strain GUI 15T, isolated from the root nodules of a Pisum sativum plant was characterized taxonomically by using a polyphasic approach. The 16S rRNA gene sequence of strain GUI 15T showed highest similarity to Micromonospora pattaloongensis TJ2-2T (98.7 %) and Polymorphospora rubra TT 97-42T (98.5 %). Phylogenetic analysis based on the gyrase B gene also supported the close relationship of these three strains, but indicated that strain GUI 15T should be assigned to the genus Micromonospora. Chemotaxonomic results confirmed the position of the isolate in the genus Micromonospora, but revealed differences at the species level. The novel strain could be distinguished from recognized Micromonospora species by using a combination of physiological and biochemical tests. Based on these observations, strain GUI 15T is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora pisi sp. nov. is proposed. The type strain is GUI 15T (=DSM 45175T=LMG 24546T).