- Volume 60, Issue 11, 2010

A culture (designated strain HHS02T) was isolated from Chinese prawn (Penaeus chinensis, O'sbeck) and determined to be a member of the genus Vibrio. Strain HHS02T comprised slightly curved, rod-shaped, non-endospore-forming, Gram-negative, catalase-negative, oxidase-positive, O/129-sensitive and facultatively anaerobic cells that were motile by means of a single polar flagellum. Growth of strain HHS02T occurred in 0.5–7 % (w/v) NaCl [optimally in 1–3 % (w/v) NaCl] and between pH 7.0 and 10.0 (optimally at pH 8.0–9.0). The strain showed growth between 16 and 30 °C (optimum 20 °C). Analysis using the 16S rRNA, gapA, gyrB, mreB, pyrH, recA and topA gene sequences of the novel isolate revealed that the organism belonged to the genus Vibrio, with ∼98, 98, 90, 88, 92, 89 and 83 % sequence similarity, respectively, with representatives of the genus Vibrio. DNA–DNA hybridization experiments indicated that the novel strain was distinct from recognized species of the genus Vibrio. The major fatty acid components were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 38.7 %), C16 : 0 (22.9 %) and C18 : 1 ω7c (12.5 %). The G+C content of the genomic DNA was 44.4 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, it is concluded that strain HHS02T should be classified as a novel species of the genus Vibrio, for which the name Vibrio atypicus sp. nov. is proposed. The type strain is HHS02T (=CGMCC 1.8461T=LMG 24781T).

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

Legionella-like isolates, strains W03-356T, W03-357 and W03-359, from three independent water samples from the river Elbe, Germany, were analysed by using a polyphasic approach. Morphological and biochemical characterization revealed that they were Gram-negative, aerobic, non-spore-forming bacilli with a cut glass colony appearance that grew only on l-cysteine-supplemented buffered charcoal yeast extract agar. Phylogenetic analysis based on sequence comparisons of the 16S rRNA, macrophage infectivity potentiator (mip), gyrase subunit A (gyrA), ribosomal polymerase B (rpoB) and RNase P (rnpB) genes confirmed that the three isolates were distinct from recognized species of the genus Legionella. Phenotypic characterization of strain W03-356T based on fatty acid profiles confirmed that it was closely related to Legionella rubrilucens ATCC 35304T and Legionella pneumophila ATCC 33152T, but distinct from other species of the genus Legionella. Serotyping of the isolates showed that they were distinct from all recognized species of the genus Legionella. Strains W03-356T, W03-357 and W03-359 are thus considered to represent a novel species of the genus Legionella, for which the name Legionella dresdenensis sp. nov. is proposed. The type strain is W03-356T (=DSM 19488T=NCTC 13409T).

Three Gram-negative, aerobic, halophilic, non-motile, yellowish-pigmented bacteria, designated KMM 3896, KMM 3897 and KMM 3899T, were isolated from coastal seawater and sediment samples of the Sea of Japan, Russia. The isolates were shown to belong to the same species on the basis of 16S rRNA gene sequence similarities (99.6–99.9 %) and DNA–DNA relatedness (73–98 %). Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the isolates formed a subcluster within the genus Kangiella in the class Gammaproteobacteria. 16S rRNA gene sequence similarities between strain KMM 3899T and its closest phylogenetic neighbours, Kangiella koreensis SW-125T and Kangiella aquimarina SW-154T, were 96.6 and 95.5 %, respectively. On the basis of phenotypic differences and phylogenetic distances, it is proposed that strains KMM 3896, KMM 3897 and KMM 3899T are assigned to a novel species of the genus Kangiella, Kangiella japonica sp. nov. The type strain is KMM 3899T (=NRIC 0764T =JCM 16211T).

A Gram-negative, motile, non-spore-forming and lipolytic bacterial strain, designated Gung47T, was isolated from a tidal flat on the west coast of Korea. Strain Gung47T grew optimally at 30 °C and with 2−5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Gung47T belonged to the genus Photobacterium. Strain Gung47T exhibited 98.1 % 16S rRNA gene sequence similarity with Photobacterium rosenbergii LMG 22223T and 94.3–96.3 % similarity with other type strains of species of the genus Photobacterium. Strain Gung47T exhibited 47 % DNA–DNA relatedness to P. rosenbergii LMG 22223T. Strain Gung47T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids. In this study, two closely related type strains, P. rosenbergii LMG 22223T and Photobacterium halotolerans LMG 22194T, were also found to have Q-8 as the predominant ubiquinone. The DNA G+C content of strain Gung47T was 50.6 mol%. The differential phenotypic properties together with the phylogenetic and genetic distinctiveness of strain Gung47T demonstrated that this strain is distinguishable from recognized Photobacterium species. Therefore, strain Gung47T is considered to represent a novel species of the genus Photobacterium, for which the name Photobacterium gaetbulicola sp. nov. is proposed. The type strain is Gung47T (=KCTC 22804T =CCUG 58399T).

Two bacterial strains, 5420S-12T and 5420S-16T, isolated from air samples, were characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 5420S-12T was related phylogenetically to Microvirga subterranea FaiI4T (97.4 % sequence similarity) and Microvirga guangxiensis 25BT (97.1 %) and that strain 5420S-16T was closely related to Balneimonas flocculans TFBT (98.0 %) and Microvirga guangxiensis 25BT (97.2 %). The G+C content of the genomic DNA was 62.2 mol% for strain 5420S-12T and 61.5 mol% for strain 5420S-16T. The major fatty acid was C18 : 1 ω7c. The results of DNA–DNA hybridization and the phenotypic data showed that strains 5420S-12T and 5420S-16T could be distinguished from phylogenetically related species and represent two novel species within the genus Microvirga, for which the names Microvirga aerophila sp. nov. (type strain 5420S-12T =KACC 12743T =NBRC 106136T) and Microvirga aerilata sp. nov. (type strain 5420S-16T =KACC 12744T =NBRC 106137T) are proposed. Furthermore, the reclassification of Balneimonas flocculans as Microvirga flocculans comb. nov. (type strain TFBT =JCM 11936T =KCTC 12101T =IAM 15034T =ATCC BAA-817T) is proposed and an emended description of the genus Microvirga is provided.

A novel gammaproteobacterium, strain CN3T, was isolated from the faeces of wild boar. Strain CN3T was facultatively anaerobic and appeared coccoid or rod-shaped. The partial 16S rRNA gene sequence determined for strain CN3T suggested a distant relationship with members of the orders ‘Enterobacteriales’ and Pasteurellales. The gene sequence showed highest similarity (90.3 %) with Obesumbacterium proteus DSM 2777T, a member of the family Enterobacteriaceae. The closest relatives outside the order ‘Enterobacteriales’ according to 16S rRNA gene sequence analysis were members of the order Pasteurellales with 88.7 % similarity (Mannheimia haemolytica NCTC 9380T and Actinobacillus lignieresii NCTC 4189T). In contrast to most members of the order ‘Enterobacteriales’, strain CN3T was oxidase-positive. The pattern of fatty acids, in particular the high relative abundance of C18 : 1 ω7c (38.5 %), was clearly distinct from the conserved pattern found for members of the order Pasteurellales. EcoRI ribotyping of strain CN3T yielded no significant similarity to existing database entries. The major ubiquinone of strain CN3T was Q-8. The DNA G+C content was 36.4 mol%. Strain CN3T hosted a phage and secreted considerable amounts of three proteins into the culture supernatant. A spontaneous mutant of strain CN3T was isolated which formed long filaments. Microscopic studies revealed the presence of a capsule that the mutant strain was unable to partition after cell division. Strain CN3T thus represents a novel species within a new genus, for which the name Orbus hercynius gen. nov., sp. nov. is proposed. The type strain of the type species is CN3T (=DSM 22228T=CCUG 57622T). Classification of the novel species to the family and order level will require further investigations.

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6T, the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6T did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5–4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA–DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6T and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6T was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6T (=CCUG 55948T=CCM-A-29:1289T) as the type strain.

Strain BZ30T was isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic bacterium was psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) (37.4 %), C18 : 1 ω7c (19.6 %), C16 : 0 (8.2 %), C14 : 0 2-OH (8.0 %) and C16 : 0 2-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30T belonged to the family Sphingomonadaceae of the α-4 group of the phylum Proteobacteria, and was related to the members of the genus Sphingopyxis, sharing the highest sequence similarities with the type strains of Sphingopyxis chilensis (98.3 %), S. witflariensis (98.2 %), S. taejonensis (97.4 %) and S. ginsengisoli (97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30T represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis bauzanensis is proposed. The type strain is BZ30T (=DSM 22271T =CGMCC 1.8959T =CIP 110136T).

Novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains ShipT and MimT, with the ribulose monophosphate pathway of C1 assimilation are described. Cells were strictly aerobic, Gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. The predominant cellular fatty acids were C16 : 0 and C16 : 1. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol; diphosphatidylglycerol was absent. The two strains lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains ShipT and MimT were 50.7 and 54.5 mol% (T m), respectively. The level of 16S rRNA gene sequence similarity between these strains was very high (99.8 %) but they shared a low level of DNA–DNA relatedness (44 %). Based on 16S rRNA gene sequence analysis and low levels of DNA–DNA relatedness with the type strains of recognized species of the genus Methylophilus (31–36 %), strains ShipT and MimT are considered to represent novel species of the genus Methylophilus, for which the names Methylophilus flavus sp. nov. (type strain ShipT =DSM 23073T =VKM B-2547T =CCUG 58411T) and Methylophilus luteus sp. nov. (type strain MimT =DSM 22949T =VKM B-2548T =CCUG 58412T) are proposed.

An aerobic, methanotrophic bacterium, designated KYGT, was isolated from a forest soil in Germany. Cells of strain KYGT were Gram-negative, non-motile, slightly curved rods that multiplied by binary fission and produced yellow colonies. The cells contained intracellular granules of poly-β-hydroxybutyrate at each cell pole, a particulate methane monooxygenase (pMMO) and stacks of intracytoplasmic membranes (ICMs) packed in parallel along one side of the cell envelope. Strain KYGT grew at pH 5.2–7.2 and 2–33 °C and could fix atmospheric nitrogen under reduced oxygen tension. The major cellular fatty acid was C18 : 1 ω7c (81.5 %) and the DNA G+C content was 61.4 mol%. Strain KYGT belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the obligate methanotroph Methylocapsa acidiphila B2T (98.1 % 16S rRNA gene sequence similarity and 84.7 % pmoA sequence similarity). Unlike Methylocapsa acidiphila B2T, which grows only on methane and methanol, strain KYGT was able to grow facultatively on acetate. Facultative acetate utilization is a characteristic of the methanotrophs of the genus Methylocella, but the genus Methylocella does not produce pMMO or ICMs. Strain KYGT differed from Methylocapsa acidiphila B2T on the basis of substrate utilization pattern, pigmentation, pH range, cell ultrastructure and efficiency of dinitrogen fixation. Therefore, we propose a novel species, Methylocapsa aurea sp. nov., to accommodate this bacterium. The type strain is KYGT (=DSM 22158T =VKM B-2544T).

Three yeast strains, 1AD8T, 3AD15 and 3AD23, belonging to a previously unknown yeast species were isolated from two independent batches of the Spanish blue-veined Cabrales cheese, a traditional cheese manufactured without the addition of starter and mould cultures. Physiological characterization revealed that the unknown yeast is not fermentative and does not assimilate lactose; rather it assimilates dl-lactic acid and ethanol, major end products of lactic acid bacteria metabolism in cheese. The novel yeast is anamorphic. Phylogenetic tree reconstruction based on nucleotide sequence comparison of the D1/D2 region of the 26S rRNA gene showed that Pichia terricola and Pichia fermentans are the closest relatives of the unknown species. The name Candida cabralensis sp. nov. is proposed, and the isolate 1AD8T (=CECT 13027T =CBS 11679T) is the type strain of this novel taxon.

On the basis of the nucleotide divergence in the internal transcribed spacer (ITS) domain of the rRNA gene and the D1/D2 domain of the 26S rRNA gene, species of the genus Hyphopichia can be divided into different phylogenetic groups. In this study, three distinct phylogenetic clusters as well as a novel species, Hyphopichia pseudoburtonii sp. nov. with type strain CBS 2455T (=JCM 16346T), are introduced. Mating studies indicate that strains belonging to Hyphopichia pseudoburtonii are heterothallic.

Most eugregarine apicomplexans infecting the intestines of marine invertebrates have been described within the family Lecudinidae and the type genus Lecudina. The diversity of these parasites is vast and poorly understood and only a tiny number of species has been characterized at the molecular phylogenetic level. DNA sequences coupled with high-resolution micrographs of trophozoites provide an efficient and precise approach for delimiting gregarine lineages from one another and also facilitate our overall understanding of gregarine biodiversity. In this study, phylogenetic analyses of small subunit (SSU) rDNA sequences from five (uncultivated) gregarines isolated from polychaetes and nemerteans in the North-eastern Pacific Ocean are presented. Lecudina phyllochaetopteri sp. nov. was isolated from the intestines of the parchment tubeworm Phyllochaetopterus prolifica (Polychaeta). Lecudina longissima and Lecudina polymorpha were both isolated from the intestines of Lumbrineris japonica (Polychaeta). Difficilina tubulani sp. nov. was isolated from the nemertean Tubulanus polymorpha and Difficilina paranemertis sp. nov. was isolated from the nemertean Paranemertes peregrina. This is the first report of molecular sequence data from gregarines that infect nemerteans. The two novel species of the genus Difficilina described in this study formed a strongly supported clade in the phylogenetic analyses. This Difficilina clade formed the sister group to a robust subclade of lecudinids consisting of Lecudina longissima, Lecudina phyllochaetopteri sp. nov. (which lacked epicytic folds), Lecudina tuzetae, species of the genus Lankesteria and several sequences derived from previous environmental DNA surveys of marine biodiversity.