- Volume 56, Issue 6, 2006

During the course of a phylogenetic evaluation of Saccharothrix strains held in the ARS Culture Collection, it was discovered that Saccharothrix coeruleoviolacea NRRL B-24058T is unrelated to other species within this genus, and a polyphasic study was undertaken to clarify its taxonomic position. Strain NRRL B-24058T is observed to be phylogenetically separate from the genus Saccharothrix and is most closely related to the genus Actinoalloteichus. The strain exhibits chemotaxonomic properties that distinguish it from members of Actinoalloteichus, including a whole-cell sugar pattern consisting of galactose and ribose as diagnostic sugars, phosphatidylethanolamine, phosphatidylethanolamine containing 2-OH fatty acids and diphosphatidylglycerol as the predominant polar lipids and MK-9(H4) and MK-10(H4) as the only menaquinones observed. Strain NRRL B-24058T is distinct from other taxa within the suborder Pseudonocardineae and a new genus to be named Goodfellowia gen. nov. is proposed. The type species of this new genus is Goodfellowia coeruleoviolacea gen. nov., comb. nov., and the type strain is NRRL B-24058T (=DSM 43935T=INA 3564T=JCM 9110T=NBRC 14988T=VKM Ac-1083T).

Strain DSM 17733T, isolated from the shore of Lake Abjata in Ethiopia, is a heterotrophic, alkaliphilic, moderately halophilic, Gram-positive, strictly aerobic, non-motile,non-endospore-forming bacterium. The organism grows optimally at 30–37 °C, pH 9 and 3 % (w/v) NaCl. Analysis of the cell wall showed the presence of murein of the type l-lys–gly–l-Glu, variation A4α. The G+C content of the genomic DNA was 69.0 mol%. Sequence analysis of 16S rRNA gene sequence of strain DSM 17733T placed the isolate in the genus Nesterenkonia. DNA–DNA hybridization of DSM 17733T with those organisms with the closest phylogenetic affiliation, i.e. Nesterenkonia halobia, Nesterenkonia lacusekhoensis and Nesterenkonia xinjiangensis, gave relatedness values of 48.5 %, 63.7 % (repetition, 57.2 %) and 35.7 % (repetition, 29.3 %), respectively. On the basis of both phenotypic and phylogenetic criteria and the low levels of DNA–DNA relatedness with the phylogenetically closest species N. xinjiangensis and N. halobia, it is proposed that the isolate be classified in a novel species, Nesterenkonia aethiopica sp. nov. The type strain is DSM 17733T (=CCUG 48939T).

The taxonomic status of an actinobacterial strain isolated from Mariana Trench sediment was determined using a polyphasic taxonomic approach. The strain, isolate MT1.1T, formed a distinct clade in the Micrococcineae 16S rRNA gene tree together with Dermacoccus nishinomiyaensis DSM 20448T. The organism had chemical and phenotypic properties consistent with its classification in the genus Dermacoccus and could be distinguished from D. nishinomiyaensis DSM 20448T using DNA–DNA relatedness and phenotypic data. The G+C content of the DNA of isolate MT1.1T was 65.2 mol%. It is evident that the organism merits recognition as a novel species in the genus Dermacoccus. The name proposed for this taxon is Dermacoccus abyssi sp. nov.; the type strain is MT1.1T (=DSM 17573T=NCIMB 14084T). The organism grows well at 40 MPa and hence is piezotolerant.

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the Streptacidiphilus 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus Streptacidiphilus. The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus Streptacidiphilus. The name proposed for this new taxon is Streptacidiphilus oryzae sp. nov.; the type strain is strain TH49T (=CGMCC 4.2012T=JCM 13271T).

A novel marine actinomycete, designated strain KST3-3T, which was isolated from a sediment sample of the coast of Jeju, Korea, was subjected to a polyphasic taxonomic characterization. The organism was characterized morphologically by the formation of motile, coccoid cells. A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the organism was related to the genera Kineosporia and Kineococcus, and members of the suborder Frankineae, and occupied the deepest branch outside a taxon encompassing members of the genus Kineococcus. The organism showed relatively low levels of 16S rRNA gene sequence similarity to members of the genera Kineococcus (93.0–93.4 %) and Kineosporia (93.1–93.8 %). The morphological and chemotaxonomic characteristics, albeit with a slightly higher level of sequence similarity to members of the genus Kineosporia, supported its classification within the genus Kineococcus. On the basis of the polyphasic data presented, it was evident that the organism should be assigned to a novel species of the genus Kineococcus, for which the name Kineococcus marinus sp. nov. is proposed. The type strain is strain KST3-3T (=KCCM 42250T=NRRL B-24439T).

Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic features of Arthrobacter duodecadis Lochhead 1958 indicated that the bacterium belonged within the genus Tetrasphaera. A. duodecadis IAM 14868T could be distinguished from other species by the presence of 3-hydroxy meso-diaminopimelic acid in the peptidoglycan and a series of 10-methyl fatty acids. In addition, DNA–DNA relatedness studies indicated that the strain belonged to a genomic species that could be readily distinguished from its nearest neighbours, the type strains of Tetrasphaera elongata, Tetrasphaera japonica and Tetrasphaera australiensis. These features support our proposal to reclassify A. duodecadis in the genus Tetrasphaera, as Tetrasphaera duodecadis comb. nov. The type strain is IAM 14868T (=NBRC 12959T=ATCC 13347T=NCIMB 9222T). An emended description of the genus Tetrasphaera is given.

Symbiotic interactions with bacteria are essential for the survival and reproduction of many insects. The European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae) engages in a highly specific association with bacteria of the genus Streptomyces that appears to protect beewolf offspring against infection by pathogens. Using transmission and scanning electron microscopy, the bacteria were located in the antennal glands of female wasps, where they form dense cell clusters. Using genetic methods, closely related streptomycetes were found in the antennae of 27 Philanthus species (including two subspecies of P. triangulum from distant localities). In contrast, no endosymbionts could be detected in the antennae of other genera within the subfamily Philanthinae (Aphilanthops, Clypeadon and Cerceris). On the basis of morphological, genetic and ecological data, ‘Candidatus Streptomyces philanthi’ is proposed. 16S rRNA gene sequence data are provided for 28 ecotypes of ‘Candidatus Streptomyces philanthi’ that reside in different host species and subspecies of the genus Philanthus. Primers for the selective amplification of ‘Candidatus Streptomyces philanthi’ and an oligonucleotide probe for specific detection by fluorescence in situ hybridization (FISH) are described.

Several halophilic archaea belonging to the genus Halococcus were isolated from stromatolites from Hamelin Pool, Shark Bay, Western Australia, collected during field trips in 1996 and 2002. This is the first incidence of halophilic archaea being isolated from this environment. Stromatolites are biosedimentary structures that have been formed throughout the earth's evolutionary history and have been preserved in the geological record for over 3 billion years. The stromatolites from Hamelin Pool, Western Australia, are the only known example of extant stromatolites forming in hypersaline coastal environments. Based on their 16S rRNA gene sequences and morphology, the isolates belong to the genus Halococcus. Strain 100NA1, isolated from stromatolites collected in 2002, was closely related to strain 100A6T that was isolated from the stromatolites collected in 1996, with a DNA–DNA hybridization value of 94±8 %. DNA–DNA hybridization values of strain 100A6T with Halococcus morrhuae NRC 16008 and Halococcus saccharolyticus ATCC 49257T were 17±6 and 11±7 %, respectively. The DNA G+C content of strain 100A6T was 60.5 mol% (T m). The main polar lipid was S-DGA-1, a sulphated glycolipid that has been detected in all strains of the genus Halococcus. Whole-cell protein profiles, enzyme composition and utilization of various carbon sources were distinct from those of all previously characterized Halococcus species. The recognition of this strain as representing a novel species within the genus Halococcus is justified, and the name Halococcus hamelinensis sp. nov. is proposed. The type strain is 100A6T (=JCM 12892T=ACM 5227T).

A Gram-negative, almost straight, rod-shaped, non-motile bacterium, designated CL-GP79T, was isolated from a highly eutrophic pond located within the campus of Seoul National University, Korea. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain CL-GP79T belongs to the family Flexibacteraceae, with Flectobacillus major as its closest relative (similarity of 95.7 %). The cellular fatty acids consist mainly of C16 : 1 ω5c (mean±sd, 26.9±10.8 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (19.2±2.3 %) and iso-C15 : 0 (12.1±1.3 %). The DNA G+C content was found to be 38.3 mol%. Phenotypic, chemotaxonomic and phylogenetic analyses indicated that strain CL-GP79T could be assigned to the genus Flectobacillus, but could be distinguished from F. major. The strain CL-GP79T therefore represents a novel species, for which the name Flectobacillus lacus sp. nov. is proposed, with CL-GP79T (=KCCM 42271T=JCM 13398T) as the type strain.

Two psychrophilic flavobacteria, designated AT1042T and AT1048T, were isolated from terrestrial samples from the Antarctic. Results of 16S rRNA gene sequence analyses indicated a close relationship of these isolates to Flavobacterium flevense (96.9 % similarity for strain AT1042T) and Flavobacterium psychrolimnae (97.0 % for strain AT1048T). Cells were non-motile and non-gliding. Flexirubin-type pigments were absent. Both isolates were psychrophilic, with an optimum and maximum growth temperature of about 15 and 20 °C, respectively. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C contents (35–37 mol%) were consistent with the placement of the Antarctic isolates in the genus Flavobacterium. Phylogeny based on 16S rRNA gene sequences and several phenotypic characteristics could be used to differentiate these isolates from recognized Flavobacterium species. Despite high 16S rRNA gene sequence similarity (98.9 %) between strains AT1042T and AT1048T, they represented two distinct species as demonstrated by low genomic relatedness (34 %) and a number of differential phenotypic characters. The polyphasic data presented in this study indicated that the new isolates should be classified within two novel species in the genus Flavobacterium. The names Flavobacterium weaverense sp. nov. (type strain AT1042T=IMSNU 14048T=KCTC 12223T=JCM 12384T) and Flavobacterium segetis sp. nov. (type strain AT1048T=IMSNU 14050T=KCTC 12224T=JCM 12385T) are proposed for these Antarctic isolates.

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

A Gram-negative, non-motile, rod-shaped bacterial strain, designated DS-27T, was isolated from a soil sample, and its taxonomic position was investigated by using a polyphasic approach. The organism grew optimally at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Strain DS-27T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-27T is most closely related to the genus Pedobacter of the family Sphingobacteriaceae. Similarity values between the 16S rRNA gene sequences of strain DS-27T and the type strains of recognized Pedobacter species ranged from 90.6 to 95.5 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to categorize strain DS-27T as representing a species that is separate from recognized Pedobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-27T (=KCTC 12559T=CIP 108922T) was classified in the genus Pedobacter as a member of a novel species, for which the name Pedobacter sandarakinus sp. nov. is proposed.

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella–Chryseobacterium–Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G+C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4×105 cells ml−1, and untreated wastewater from a second plant yielded an estimated count of 1.4×104 cells ml−1. Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1T (=CCUG 46293T=CIP 108613T=ATCC BAA-825T=DSM 15886T).

Four isolates from freshly caught fish samples obtained from the South Atlantic Ocean off the South African coastline were shown to represent a novel species in the genus Chryseobacterium by means of a polyphasic taxonomic study. The four isolates had virtually identical whole-cell protein profiles, fatty acid profiles and biochemical properties. Analysis of the 16S rRNA sequence of strain LMG 23089T revealed 99.3 and 98.9 % similarity to the 16S rRNA sequences of the type strains of Chryseobacterium balustinum and Chryseobacterium scophthalmum, respectively. Strain LMG 23089T and the C. balustinum and C. scophthalmum type strains formed a stable lineage supported by a bootstrap value of 100 %. The levels of DNA–DNA hybridization towards these nearest phylogenetic neighbours were below 57 %. The absence of growth on MacConkey agar or at 37 °C (on nutrient agar), the capacity to grow in the presence of 5 % NaCl and the production of urease activity differentiate this novel taxon from C. balustinum and C. scophthalmum. The four isolates are formally classified as Chryseobacterium piscium sp. nov., with strain LMG 23089T (=CCUG 51923T) as the type strain. Its DNA G+C content is 33.6 mol%.

A marine bacterium, strain KOPRI 13342T, was isolated from a mature marine biofilm, including various marine algae, covering a rock-bed of the East Sea, Korea (also known as the Sea of Japan). Colonies of the isolate were orange-coloured on marine agar 2216. The isolate showed relatively high 16S rRNA gene sequence similarities to members of the genera Maribacter (91.2–92.4 % similarity), Zobellia (90.7–91.5 %) and Muricauda (90.7–91.4 %). Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that the isolate formed a phyletic lineage with members of the genus Muricauda. Cells were aerobic, motile, Gram-negative rods and they produced non-diffusible carotenoid pigments. Optimal growth was observed at pH 7.5–8.0 and 26–32 °C and required the presence of 3 % (w/v) sea salt. The strain required Ca2+ and K+ ions in addition to NaCl for growth. The dominant fatty acids were i-15 : 0, i-15 : 1ω10, 15 : 0 and 16 : 1ω9. The major respiratory quinone was MK-6. The DNA G+C content was 35.8 mol%. On the basis of this polyphasic taxonomic evidence, strain KOPRI 13342T should be classified as a representative of a novel species in a new genus in the family Flavobacteriaceae; the name Costertonia aggregata gen. nov., sp. nov. is proposed. The type strain of Costertonia aggregata is KOPRI 13342T (=KCCM 42265T=JCM 13411T).

One thermophilic (strain IMO-1T) and two mesophilic (strains KIBI-1T and YMTK-2T) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class ‘Anaerolineae’ of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 μm and the width was 0.3–0.4 μm for strain IMO-1T, 0.4–0.5 μm for strain KIBI-1T and thinner than 0.2 μm for strain YMTK-2T. Strain IMO-1T could grow at pH 6.0–7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1T was around 50 °C (growth occurred between 42 and 55 °C). Growth of the mesophilic strains KIBI-1T and YMTK-2T occurred at pH 6.0–7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25–50 °C with optimal growth at around 37 °C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G+C contents of the DNA of strains IMO-1T, KIBI-1T and YMTK-2T were respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1T were anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and anteiso-C15 : 0, whereas those for mesophilic strains KIBI-1T and YMTK-2T were branched C14 : 0, iso-C15 : 0, C16 : 0 and branched C17 : 0, and branched C17 : 0, C16 : 0, C14 : 0 and C17 : 0, respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon ‘Anaerolineae’ of the bacterial phylum Chloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylum Chloroflexi. Here, Anaerolinea thermolimosa sp. nov. (type strain IMO-1T=JCM 12577T=DSM 16554T), Levilinea saccharolytica gen. nov., sp. nov. (type strain KIBI-1T=JCM 12578T=DSM 16555T) and Leptolinea tardivitalis gen. nov., sp. nov. (type strain YMTK-2T=JCM 12579T=DSM 16556T) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon ‘Anaerolineae’ into Anaerolineae classis nov. and Caldilineae classis nov. We also propose the subordinate taxa Anaerolineales ord. nov., Caldilineales ord. nov., Anaerolineaceae fam. nov. and Caldilineaceae fam. nov.

The taxonomic positions of ‘Renobacter vacuolatum’ DSM 1277 and ‘Ancylobacter polymorphus’ DSM 2457 were investigated in this study. 16S rRNA gene sequence analysis indicated that both strains belonged to the genus Ancylobacter. DNA–DNA hybridization showed that they differed from Ancylobacter aquaticus DSM 101T and Ancylobacter rudongensis AS 1.1761T. According to molecular and phenotypic characteristics, strain DSM 1277T (=AS 1.2807T) is proposed as the type strain of Ancylobacter vacuolatus sp. nov. At the same time, valid publication of the name Ancylobacter polymorphus sp. nov. is proposed, with the type strain DSM 2457T (=AS 1.2800T=NCIMB 10516T).

Two denitrifying strains of heterotrophic, facultatively anaerobic bacteria, designated ZD1T and ZT1T, were isolated from sediment samples collected from mangrove ecosystems in Taiwan. The isolates were Gram-negative. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The isolates grew optimally in 1–3 % NaCl, but NaCl was not an absolute requirement for growth; only strain ZT1T grew in 13–14 % NaCl. Both isolates grew between 10 and 45 °C, with optimum growth at 30–35 °C. They were capable of anaerobic growth by denitrifying metabolism using nitrate or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, sucrose or mannitol as substrates. C18 : 1 ω7c was the most abundant fatty acid (32.6–35.7 %). The other major fatty acids included C16 : 1 ω7c (27.5–29.4 %) and C16 : 0 (20.1–22.0 %). The two isolates had 16S rRNA gene sequence similarity of 96.8 % and shared 94.1–96.8 % sequence similarity with the most closely related species, Oceanimonas doudoroffii, Oceanimonas baumannii, Oceanimonas smirnovii and Oceanisphaera litoralis. They could be distinguished from these species in that they were capable of fermentative metabolism, had relatively high DNA G+C contents (62.0–64.0 mol%) and contained C18 : 1 ω7c instead of C16 : 1 ω7c as the most abundant fatty acid. Characterization data accumulated in this study revealed that the two denitrifying isolates could be classified as representatives of two novel species in a new genus, Zobellella gen. nov., with Zobellella denitrificans sp. nov. (type strain ZD1T=BCRC 17493T=JCM 13380T) as the type species and Zobellella taiwanensis sp. nov. (type strain ZT1T=BCRC 17494T=JCM 13381T) as a second species.

A marine agarolytic bacterium, designated strain TMA1T, was isolated from a seawater sample collected in a shallow-water region of An-Ping Harbour, Taiwan. It was non-fermentative and Gram-negative. Cells grown in broth cultures were straight or curved rods, non-motile and non-flagellated. The isolate required NaCl for growth and exhibited optimal growth at 25 °C and 3 % NaCl. It grew aerobically and was incapable of anaerobic growth by fermenting glucose or other carbohydrates. Predominant cellular fatty acids were C16 : 0 (17.5 %), C17 : 1 ω8c (12.8 %), C17 : 0 (11.1 %), C15 : 0 iso 2-OH/C16 : 1 ω7c (8.6 %) and C13 : 0 (7.3 %). The DNA G+C content was 41.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Thalassomonas in the family Colwelliaceae. The name Thalassomonas agarivorans sp. nov. is proposed for the novel species, with TMA1T (=BCRC 17492T=JCM 13379T) as the type strain.

Fifteen bacterial strains isolated from molasses grass (Melinis minutiflora Beauv.) were identified as nitrogen-fixers by using the acetylene-reduction assay and PCR amplification of nifH gene fragments. These strains were classified as a unique group by insertion sequence-PCR fingerprinting, SDS-PAGE protein patterns, DNA–DNA hybridization, 16S rRNA gene sequencing and morphological characterization. Phylogenetic analysis of the 16S rRNA gene indicated that these diazotrophic strains belonged to the genus Azospirillum and were closely related to Azospirillum lipoferum (with 97.5 % similarity). In all the analyses, including in addition phenotypic characterization using Biolog MicroPlates and comparison of cellular fatty acids, this novel group was found to be different from the most closely related species, Azospirillum lipoferum. Based on these data, a novel species, Azospirillum melinis sp. nov., is proposed for these endophytic diazotrophs of M. minutiflora, with TMCY 0552T (=CCBAU 5106001T=LMG 23364T=CGMCC 1.5340T) as the type strain.

Three Gram-negative, non-motile, non-pigmented, oxidase-positive coccobacilli capable of growth at temperatures from −10 to 30 °C and salinities of 0 to 1.7 M NaCl were isolated from Siberian permafrost and characterized. Both 16S rRNA and gyrB gene sequencing studies placed the isolates in the Gammaproteobacteria within the genus Psychrobacter. However, with higher bootstrap values and reproducible tree topologies, gyrB represented a more reliable phylogenetic marker for the taxonomy of Psychrobacter species. DNA–DNA hybridization data supported gyrB tree topologies and established two relatedness groups within the three isolates; neither of these groups was related at the species level to any previously described Psychrobacter species. The two groups of isolates could be differentiated phenotypically from 13 previously described Psychrobacter species using API strips. These results support the existence of two novel species of Psychrobacter, for which we propose the names Psychrobacter cryohalolentis sp. nov. (type strain K5T=DSM 17306T=VKM B-2378T) and Psychrobacter arcticus sp. nov. (type strain 273-4T=DSM 17307T=VKM B-2377T).

A heterotrophic, antibiotic-producing bacterium, strain T5T, was isolated from the German Wadden Sea, located in the southern region of the North Sea. Sequence analysis of the 16S rRNA gene of this strain demonstrated close affiliation with Roseobacter gallaeciensis BS107T (99 % similarity), but the results of genotypic (DNA–DNA hybridization and DNA G+C content) and phenotypic characterization revealed that strain T5T represents a novel species. The novel organism is strictly aerobic, Gram-negative, rod-shaped, motile and forms brown-pigmented colonies. Strain T5T produces the antibiotic tropodithietic acid throughout the exponential phase which inhibits the growth of bacteria from different taxa, as well as marine algae. Strain T5T requires sodium ions and utilizes a wide range of substrates, including oligosaccharides, sugar alcohols, organic acids and amino acids. The DNA G+C content is 55.7 mol%. Comparative 16S rRNA gene sequence analysis revealed that strains T5T and Roseobacter gallaeciensis BS107T group with Leisingera methylohalidivorans as their closest described relative within the Roseobacter clade (97.9 and 97.6 % sequence similarity, respectively) and with Ruegeria algicola (96.6 and 96.5 % similarity, respectively) of the Alphaproteobacteria. Comparison of strains T5T and Roseobacter gallaeciensis BS107T with Roseobacter denitrificans and Roseobacter litoralis showed striking differences in 16S rRNA gene sequence similarities, chemical composition, pigmentation, presence of bacteriochlorophyll a and antibiotic production. On the basis of these results, it is proposed that Roseobacter gallaeciensis is reclassified as the type species of a new genus, Phaeobacter, as Phaeobacter gallaeciensis comb. nov. (type strain BS107T=CIP 105210T=ATCC 700781T=NBRC 16654T=DSM 17395T). Strain T5T (=LMG 22475T=DSM 16374T) is proposed as the type strain of a novel species of this genus, Phaeobacter inhibens sp. nov. At the same time, emended descriptions are provided of the genera Roseobacter, Ruegeria and Leisingera, as well as reclassifying Ruegeria algicola as the type species of a new genus, Marinovum, with the name Marinovum algicola comb. nov.

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

The genus Herbaspirillum of the Betaproteobacteria mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. The plant-associated bacterial isolates N3T, N5 and N9 were derived from surface-sterilized wheat roots. After phylogenetic analysis of 16S rRNA gene sequence data the isolates could be allocated to the genus Herbaspirillum, and 99.9 % similarity to the sequence of Herbaspirillum lusitanum P6-12T was found. A set of 16S rRNA gene-targeted oligonucleotide probes was developed for the identification of the three novel isolates and H. lusitanum (Hhilu446), and for the specific detection of several other Herbaspirillum species described recently. For higher phylogenetic resolution, the 23S rRNA gene sequences of all members of the genus was sequenced and used to construct a phylogenetic tree. Isolates N3T, N5 and N9 formed a group that was distinct from all other Herbaspirillum species. In addition, isolate N3T and H. lusitanum P6-12T exhibited a DNA–DNA hybridization value of only 25 %. The value for DNA–DNA hybridization between N3T and other members of the genus Herbaspirillum was between 14 and 32 %; DNA–DNA hybridization between strain N3T and isolates N5 and N9 produced values above 95 %. This places the three isolates as representatives of a novel species within the genus Herbaspirillum. A Biolog GN2 assay supported this conclusion. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c, and the DNA G+C content ranged from 60.9 to 61.5 mol%. Therefore these three isolates should be classified within a novel species, for which the name Herbaspirillum hiltneri sp. nov. is proposed. The type strain is N3T (=DSM 17495T=LMG 23131T).

Six red-pigmented strains of the Alphaproteobacteria with optimal growth between 45 and 54 °C were previously isolated from coloured biofilms in two fine-paper machines and one pulp dryer. The strains were found to be resistant to 15 p.p.m. 2,2-dibromo-3-nitrilopropionamide, a common industrial biocide. 16S RNA gene sequence similarity of the isolates was 99.7–100 %. Ribotyping using the restriction enzymes PvuII and EcoRI showed that four of the isolates (C-lvk-R2A-1, C-lvk-R2A-2T, C-R2A-52d and C-R2A-5d) belong to a single species. 16S rRNA gene-based phylogenetic analysis revealed that, together with Rhodobacter blasticus ATCC 33485T, the isolates form a deep line of descent (94.7–94.9 % sequence similarity) within the family Rhodobacteraceae loosely affiliated with the Rhodobacter/Paracoccus clade. The isolates were strictly aerobic and oxidase-positive (catalase was weakly positive) and utilized a wide range of substrates including pentoses, hexoses, oligosaccharides and sugar alcohols. The predominant constituents in their cellular fatty acid profiles were C19 : 0 cyclo ω8c (39–44 %), C18 : 0 (21–24 %) and C16 : 0 (21–23 %). Fatty acids present in smaller amounts included C18 : 1 ω7c, C10 : 0 3-OH, C18 : 1 ω7c 11-methyl, C20 : 2 ω6,9c and C17 : 0 cyclo, amongst others. Polar lipids included diphosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid, but not phosphatidylethanolamine. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. The polyamine patterns consisted of the major compounds putrescine, spermidine and sym-homospermidine. The major respiratory lipoquinone was ubiquinone Q-10. The DNA G+C content was 69.4–70.2 mol%. On the basis of the phylogenetic and phenotypic evidence, the biofilm isolates were classified in a new genus, Rubellimicrobium gen. nov.; four of the isolates are assigned to the type species, Rubellimicrobium thermophilum gen. nov., sp. nov. Strain C-lvk-R2A-2T (=CCUG 51817T=DSM 16684T=HAMBI 2421T) is the type strain of Rubellimicrobium thermophilum.

A Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16T, was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16T grew optimally at pH 6.0–7.0 and 30 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16T joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16T and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16T, demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16T (=KCTC 12543T=CIP 108839T) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.

An isolate of purple non-sulfur bacteria was obtained from an acidic Sphagnum peat bog and designated strain RST. The colour of cell suspensions of this bacterium growing in the light under anaerobic conditions is purplish red. Cells of strain RST are rod-shaped, 0.8–1.0 μm wide and 2.0–6.0 μm long, motile by means of polar flagella, reproduce by budding and have a tendency to form rosette-like clusters in older cultures. The cells contain lamellar intracytoplasmic membranes underlying, and parallel to, the cytoplasmic membrane. The photosynthetic pigments are bacteriochlorophyll a and carotenoids; the absorption spectrum of living cells shows maxima at 377, 463, 492, 527, 592, 806 and 867 nm. The cells grow photoheterotrophically under anaerobic or microaerobic conditions with various organic carbon sources or grow photolithoautotrophically with H2 and CO2. Strain RST is a moderately acidophilic organism exhibiting growth at pH values between 4.8 and 7.0 (with an optimum at pH 5.2–5.5). The major fatty acids are 16 : 1ω7c and 18 : 1ω7c; the major quinones are Q-10 and Q-9. The DNA G+C content of strain RST is 62.6 mol%. Analysis of the 16S rRNA gene sequence revealed that the novel isolate is most closely related (97.3 % sequence similarity) to the type strain ATCC 25092T of the moderately acidophilic purple non-sulfur bacterium Rhodoblastus acidophilus, formerly named Rhodopseudomonas acidophila. However, in contrast to Rbl. acidophilus, strain RST is not capable of aerobic growth in the dark, has no spirilloxanthin among the carotenoids and differs in the pattern of substrate utilization. The value for DNA–DNA hybridization between strain RST and Rbl. acidophilus ATCC 25092T is only 22 %. Thus, strain RST represents a novel species of the genus Rhodoblastus, for which the name Rhodoblastus sphagnicola sp. nov. is proposed. Strain RST (=DSM 16996T=VKM B-2361T) is the type strain.

In order to clarify the intraspecies taxonomic position of the non-photosynthetic algal species Prototheca zopfii, as well as the aetiology of bovine mammary protothecosis, a selection of P. zopfii strains isolated from clinical cases of protothecal mastitis and from various environmental habitats was characterized using a polyphasic molecular approach. Based on sequence analysis of the 18S rRNA gene, which showed distinct differences between the three currently known biotypes or ‘variants’, specific oligonucleotides were designed and used in biotype-specific PCRs. Furthermore, the pattern of cellular fatty acids was evaluated. Typing by means of these techniques revealed that the previously defined biotypes of P. zopfii were clearly different. Based on sequence analysis, the pattern of fatty acids and physiological characteristics, it is proposed that biotype 3 should be reclassified as representing a novel species, Prototheca blaschkeae sp. nov. (type strain, RZIII-3T=SAG 2064T). Furthermore, it is proposed that P. zopfii merits reclassification as a species comprising at least two genotypes that in future could probably be considered to represent two subspecies.

Penicillium jamesonlandense is a novel species from Greenland that grows exceptionally slowly at 25 °C and has an optimum temperature for growth of 17–18 °C. The novel species is more psychrotolerant than any other Penicillium species described to date. Isolates of this novel species produce a range of secondary metabolites with a high chemical diversity, represented by kojic acid, penicillic acid, griseofulvin, pseurotin, chrysogine, tryptoquivalins and cycloaspeptide. Penicillium ribium, another novel psychrotolerant species from the Rocky Mountains, Wyoming, USA, produces asperfuran, kojic acid and cycloaspeptide. Originally reported from an unidentified Aspergillus species isolated from Nepal, cycloaspeptide A is reported here for the first time from the two novel Penicillium species and two known psychrotolerant species with high chemical diversity, Penicillium soppii and Penicillium lanosum. All species, except P. ribium, produce a combination of cycloaspeptide and griseofulvin. However, P. ribium (3/5 strains) produced the precursor to griseofulvin, norlichexanthone. The type strain of Penicillium jamesonlandense sp. nov. is DAOM 234087T (=IBT 21984T=IBT 24411T=CBS 102888T) and the type strain of Penicillium ribium sp. nov. is DAOM 234091T (=IBT 16537T=IBT 24431T).

A Gram-positive, non-spore-forming isolate, designated YIM 70212T, was isolated from a hypersaline soil sample collected from Qinghai, north-west China. Cells of the isolate were orange-pigmented, motile cocci with multiple flagella. A polyphasic taxonomic investigation was carried out on the isolate. The organism grew at 10–45 °C and pH 7.5–11.0, with optimum growth at 28 °C and pH 8.0–9.5. Strain YIM 70212T grew optimally in the presence of 10 % NaCl, KCl or MgCl2.6H2O and growth was observed in 1–25 % NaCl, KCl or MgCl2.6H2O. The peptidoglycan type was A1γ. Ribose and minor amounts of galactose were detected as the whole-cell sugars. MK-5 was the only menaquinone. The major cellular fatty acids were ai-C15 : 0 (52.4 %) and ai-C17 : 0 (26.5 %). The DNA G+C content was 47.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 70212T formed a distinct lineage within the order Bacillales and was most closely related to members of the genus Marinococcus, showing 16S rRNA gene sequence similarity levels of 91.0–91.4 %. Based on the high 16S rRNA gene sequence divergence and differences in phenotypic characteristics, it is proposed that the unknown strain be classified in a novel genus and species with the name Sinococcus qinghaiensis gen. nov., sp. nov.; the type strain of Sinococcus qinghaiensis is YIM 70212T (=KCTC 3943T=DSM 17008T).

A thermophilic, alkaliphilic and catalase-positive bacterium, designated strain HA6T, was isolated from a hot spring in China. The strain was aerobic and chemo-organotrophic and grew optimally at 60 °C, pH 8.5 and 1.5 % (w/v) NaCl. The cells were Gram-positive rods, forming single terminal endospores. The predominant cellular fatty acids were iso-C15 : 0 and iso-C17 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C content was 45.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain HA6T formed a distinct lineage within the family Bacillaceae and was most closely related to Bacillus horti K13T and Bacillus smithii DSM 4216T, with sequence similarities of 91.8 and 93.1 %, respectively. On the basis of its physiological and molecular properties, strain HA6T should be placed in a novel genus and species, for which the name Caldalkalibacillus thermarum gen. nov., sp. nov. is proposed. The type strain of Caldalkalibacillus thermarum is strain HA6T (=CGMCC 1.4242T=JCM 13486T).

Six strains of lactic acid bacteria (LAB) were isolated from a ripe fig. These strains constituted a highly homogeneous, but distinct, cluster that was separate from other LAB species in a polyphasic approach including dot-blot DNA–DNA hybridization, SDS-PAGE whole-cell protein profiling, carbohydrate fermentation ability, growth characteristics, enzymic profiling, pulsed-field gel electrophoresis macrorestriction analysis and RFLPs. Phylogenetic analysis based on 16S rRNA gene sequencing positioned a representative strain, LC51T, in a distinct line of descent within the recently described clade comprising Leuconostoc ficulneum, Leuconostoc fructosum and Leuconostoc durionis; L. ficulneum was its closest neighbour (98 % sequence similarity). DNA–DNA hybridization values and chemotaxonomic and biochemical characteristics, including enzymic profiles detected with API ZYM microtubes, confirmed that this group of strains is distinct from L. ficulneum and represents a novel species within the genus Leuconostoc. Taking into account the common origin and phylogenetic proximity, the name Leuconostoc pseudoficulneum sp. nov. is proposed. Strain LC51T (=DSM 15468T=CECT 5759T) is the type strain; the DNA G+C content of this strain is 44.5 mol%.

A Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001T was most closely related to Virgibacillus species (95.3–96.1 %), Oceanobacillus species (95.6–95.7 %), Bacillus firmus IAM 12464T (95.5 %) and Bacillus niacini IFO 15566T (95.2 %). However, strain WSBC 24001T showed the highest level of sequence similarity to an unnamed strain, MB-9T (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G+C contents of strains WSBC 24001T and MB-9T were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4β (l-orn←d-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001T could be distinguished from strain MB-9T by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA–DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001T and MB-9T are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001T=DSM 15681T=CCM 7096T) and Ornithinibacillus californiensis sp. nov. (type strain MB-9T=DSM 16628T=CCM 7237T).

Although the type species of the genus Thermoanaerobium, Thermoanaerobium brockii, was transferred to Thermoanaerobacter, Thermoanaerobium acetigenum was not transferred. Therefore, Thermoanaerobium acetigenum should be reclassified. Based on 16S rRNA gene sequence analysis and re-examination of physiological properties of the type strain, X6BT (=DSM 7040T=ATCC BAA-1149T), we propose that Thermoanaerobium acetigenum should be reclassified as Caldicellulosiruptor acetigenus comb. nov. Strain X6BT contains two separate 16S rRNA genes bracketing another species in the phylogenetic 16S rRNA gene-based tree.

Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530T. Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097T (=ATCC BAA-1242T=DSM 44942T).

The evolutionary history and relationship between plastids of dinoflagellate algae and apicomplexan parasites have been controversial both because the organelles are unusual and because their genomes contain few comparable genes. However, most plastid proteins are encoded in the host nucleus and targeted to the organelle, and several of these genes have proved to have interesting and informative evolutionary histories. We have used expressed sequence tag (EST) sequencing to generate gene sequence data from the nuclear genome of the dinoflagellate Heterocapsa triquetra and inferred phylogenies for the complete set of identified plastid-targeted proteins. Overall, dinoflagellate plastid proteins are most consistently related to homologues from the red algal plastid lineage (not green) and, in many of the most robust cases, they branch with other chromalveolate algae. In resolved phylogenies where apicomplexan data are available, dinoflagellates and apicomplexans are related. We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria.

Recent molecular phylogenetic studies have led to the erection of the phylum Amoebozoa, uniting naked and testate lobose amoebae, the mycetozoan slime moulds and amitochondriate amoeboid protists (Archamoebae). Molecular data together with ultrastructural evidence have suggested a close relationship between Mycetozoa and Archamoebae, classified together in the Conosea, which was named after the cone of microtubules that, when present, is characteristic of their kinetids. However, the relationships of conoseans to other amoebozoans remain unclear. Here, we obtained the complete small-subunit (SSU) rRNA gene sequence (2746 bp) of the enigmatic, multiflagellated protist Multicilia marina, which has formerly been classified either in a distinct phylum, Multiflagellata, or among lobose amoebae. Our study clearly shows that Multicilia marina belongs to the Amoebozoa. Phylogenetic analyses including 60 amoebozoan SSU rRNA gene sequences revealed that Multicilia marina branches at the base of the Conosea, together with another flagellated amoebozoan, Phalansterium solitarium, as well as with Gephyramoeba sp., Filamoeba nolandi and two unidentified amoebae. This is the first report showing strong support for a clade containing all flagellated amoebozoans and we discuss the position of the root of the phylum Amoebozoa in the light of this result.