- Volume 54, Issue 3, 2004

A bacterium (named OT-1T) that showed algicidal activity was isolated from sea water of Masan Bay, Korea, during an outbreak of red tide. Phylogenetic analysis based on 16S rDNA sequences showed that the isolate formed a distinct phyletic lineage within the family Flavobacteriaceae of the Cytophaga–Flavobacterium–Bacteroides group. No species with a validly published name showed ⩾93 % 16S rRNA gene sequence similarity to strain OT-1T. The isolate had major amounts of iso-branched and 3-hydroxy iso-branched fatty acids and menaquinone 6 and a DNA G+C content of 34 mol%; these chemotaxonomic characters also supported the placement of the organism in the family Flavobacteriaceae. The strain was Gram-negative, yellow-pigmented, non-motile, non-gliding, flexirubin-negative, strictly aerobic, catalase-negative, oxidase-positive and halophilic. Na+, Ca2+ and Mg2+ ions were obligately required for growth. The strain utilized various sugars as sole carbon sources and degraded gelatin, skimmed milk and starch. Several phenotypic characters can be used to differentiate the test strain from phylogenetically related marine bacterial genera. On the basis of polyphasic evidence, it is proposed that strain OT-1T should be assigned to the family Flavobacteriaceae as Kordia algicida gen. nov., sp. nov. The type strain is OT-1T (=KCTC 8814PT=NBRC 1000336T).

Arcicella aquatica NO-502T, obtained from a neuston film on a freshwater lake and belonging to the phylum Bacteroidetes, is characterized by ring-forming cells. The bacterium is a strict aerobe, with optimal growth between 28 and 30 °C. Carbohydrates, but no organic acids or amino acids, are used as substrates. The G+C content of strain NO-502T is 34·5 mol%; its genome size is 2·9×109 Da. The genus Arcicella and its type species Arcicella aquatica (type strain NO-502T=LMG 21963T=CIP 107990T) are proposed, and descriptions of this genus and species are given.

Four light-yellow-pigmented, Gram-negative, short-rod-shaped, non-motile isolates were obtained from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The isolates studied were chemo-organotrophic, alkalitolerant and mesophilic. Polar lipids were analysed and phosphatidylethanolamine was the only phospholipid identified. The predominant cellular fatty acids were 15 : 0, i15 : 0, ai15 : 0, i15 : 1 and 15 : 1(n-6). The DNA G+C contents of the four strains were 34·0–34·4 mol%. The level of DNA relatedness of the four isolates was conspecific (88–98 %), indicating that they belong to the same species. The 16S rDNA sequence of strain KMM 3553T was determined. Phylogenetic analysis revealed that KMM 3553T formed a distinct phyletic line in the phylum Bacteroidetes, class Flavobacteria in the family Flavobacteriaceae and that, phylogenetically, this strain could be placed almost equidistant from the genera Gelidibacter and Psychroserpens (16S rRNA gene sequence similarities of 94 %). On the basis of significant differences in phenotypic and chemotaxonomic characteristics, it is suggested that the isolates represent a novel species in a new genus; the name Formosa algae gen. nov., sp. nov. is proposed. The type strain is KMM 3553T (=CIP 107684T).

Two bacterial strains, EHS11T and EPSA11T, which were isolated from the human oral cavity, were characterized in terms of phenotypic and biochemical characteristics, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates belonged to a novel species of the genus Prevotella. Strain EHS11T was related to Prevotella loescheii (about 95 % similarity), whereas strain EPSA11T was related to Prevotella oris (about 94 % similarity). Both strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid composition of strain EPSA11T was very similar to that of P. oris JCM 8540T. On the other hand, the cellular fatty acid composition of strain EHS11T was significantly different from those of other Prevotella species. The predominant fatty acids in strain EHS11T are C18 : 1 ω9c, C16 : 0 and C16 : 0 3-OH, whereas other Prevotella species, except for P. loescheii JCM 8530T, possess anteiso-C15 : 0, iso-C17 : 0 3-OH and C18 : 1 ω9c. The predominant fatty acids in P. loescheii JCM 8530T are anteiso-C15 : 0, C16 : 0 and C18 : 1 ω9c. DNA–DNA hybridization experiments revealed a genomic distinction of strains EHS11T and EPSA11T from P. loescheii JCM 8530T and P. oris JCM 8540T. On the basis of these data, two novel Prevotella species are proposed: Prevotella shahii sp. nov. and Prevotella salivae sp. nov. The type strains of P. shahii and P. salivae are EHS11T (=JCM 12083T=DSM 15611T) and EPSA11T (=JCM 12084T=DSM 15606T), respectively.

A Gram-negative bacterium designated LA1T was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7·5–10 % (w/v) NaCl. The major fatty acids in LA1T grown at 15 and 30 °C were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. The nucleotide sequence of the 16S rRNA gene showed that LA1T belonged in the Cytophaga–Flavobacterium–Bacteroides (CFB) group in the domain Bacteria. The closest described neighbour in terms of 16S rRNA gene sequence identity was Psychroflexus torquis ACAM 623T (94·4 % over 1423 bases), an obligate psychrophile from Antarctic sea-ice. The G+C content of 35·0 mol% was consistent with this affiliation. Phenotypic and genotypic analyses, including DNA hybridization, indicated that LA1T could be assigned to the genus Psychroflexus but, based on significant differences, including growth at 43 °C, it constitutes a novel species, Psychroflexus tropicus sp. nov., for which LA1T (=ATCC BAA-734T=DSM 15496T) is the type strain.

A Gram-negative, spore-forming anaerobe, KST, was isolated from an enrichment culture that was set up for anaerobic degradation of the aliphatic polyester poly(propylene adipate). The strain had the cellular organization of Sporomusa, vibrio-shaped cells and terminal round spores, and fermented sugars and sugar alcohols to propionic and acetic acid. Based on the morphological and physiological features as well as on a 16S rRNA gene similarity of 98 %, it was grouped with Propionispora vibrioides. A relatively low DNA–DNA hybridization value with the type strain of this species (47 %), and differences in substrate utilization and spore morphology, suggested that the strain should be classified in a separate species, Propionispora hippei sp. nov., with KST as the type strain (=DSM 15287T=ATCC BAA-665T).

Previously, analysis of 16S rDNA sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the ‘Bacteroidetes’. This symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several Encarsia parasitoid wasps (Hymenoptera: Aphelinidae). In this study, electron microscopy and phylogenetic analysis of the 16S rRNA and gyrB genes of symbionts from Encarsia hispida and Encarsia pergandiella are used to describe and further characterize these bacteria. Phylogenetic analyses based on these two genes showed that the Encarsia symbionts are allied with the Cytophaga aurantiaca lineage within the ‘Bacteroidetes’, with their closest described relative being the acanthamoeba symbiont ‘Candidatus Amoebophilus asiaticus’. The Encarsia symbionts share 97 % 16S rDNA sequence similarity with Brevipalpus mite and Ixodes tick symbionts and 88 % sequence similarity with ‘Candidatus A. asiaticus’. Electron microscopy revealed that many of the bacteria found in the ovaries of the two Encarsia species contained a regular, brush-like array of microfilament-like structures that appear to be characteristic of the symbiont. Finally, the role of this bacterium in parthenogenesis induction in E. hispida was confirmed. Based on phylogenetic analyses and electron microscopy, classification of the symbionts from Encarsia as ‘Candidatus Cardinium hertigii’ is proposed.

A novel Gram-negative, aerobic and moderately thermophilic bacterium, strain 4BONT, was isolated from a non-water-flooded Australian terrestrial oil reservoir. Cells were non-spore-forming straight rods, which were motile by means of a polar flagellum. The optimum growth conditions were 55 °C, pH 6·9 and 0·5 % NaCl. Strain 4BONT was oxidase- and catalase-positive; it grew on fumarate, pyruvate, succinate, formate, ethanol and yeast extract in the presence of oxygen or nitrate as terminal electron acceptor. Nitrate was reduced to nitrous oxide. The DNA G+C content of the strain was 58·6 mol%. The closest phylogenetic relative of strain 4BONT was Hydrogenophilus thermoluteolus (similarity of 91·8 %), of the β-Proteobacteria. As strain 4BONT is physiologically and phylogenetically different from H. thermoluteolus, it is proposed that it be assigned to a novel species of a novel genus, Petrobacter succinatimandens gen. nov., sp. nov. The type strain is 4BONT (=DSM 15512T=CIP 107790T).

The unusually shaped bacteria of the genera Stella, Labrys and Angulomicrobium have been described based on their cell morphology and biochemistry. However, their phylogenetic relationships remain unresolved. An earlier study that was based on 5S rRNA gene sequences placed the genus Stella within the ‘Alphaproteobacteria’. In the present report, polar lipids and 16S rRNA genes of the type strains of the two species in the genus Stella, Stella humosa DSM 5900T and Stella vacuolata DSM 5901T, are studied, as well as the type strains of the monospecific genera Labrys (Labrys monachus VKM B-1479T) and Angulomicrobium (Angulomicrobium tetraedrale DSM 5895T). It was found that the genus Stella belongs to the order Rhodospirillales in the family Rhodospirillaceae, and not to the Acetobacteraceae. Whilst the position of the genus Angulomicrobium in the family Hyphomicrobiaceae was confirmed, the genus Labrys could not be placed into any known family, but was adjacent to the family ‘Beijerinckiaceae’. In addition, data were obtained for strain VKM B-1336, which was shown not to belong to the genus Angulomicrobium, and strain NCIMB 1785T (=DSM 15561T), for which the name Angulomicrobium amanitiforme sp. nov. is proposed.

A Gram-negative, oxidase- and catalase-positive, rod-shaped bacterium, designated strain KMM 3655T, was isolated from a coastal marine sediment sample. The novel bacterium required sodium ions for growth and grew between 0·5 and 5 % NaCl and at 4–37 °C, but not at 40 °C. It reduced nitrate, formed acids from glucose under aerobic and anaerobic conditions, utilized a limited spectrum of organic substrates and did not produce gelatinase, caseinase, amylase or chitinase. The major isoprenoid quinone was Q8. Polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. Fatty acid analysis of strain KMM 3655T revealed C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c as predominant components. The G+C content of the DNA was 51·1 mol%. Phylogenetic analysis of the 16S rDNA sequence placed the new isolate within the γ-Proteobacteria as a separate deep branch, with about 90 % sequence similarity to representatives of the genus Oceanospirillum and other remotely related genera. Combined phylogenetic and physiological data show that the new marine sediment isolate, KMM 3655T, represents a novel genus and species, for which the name Reinekea marinisedimentorum gen. nov., sp. nov. is proposed. The type strain is KMM 3655T (=DSM 15388T).

Phenotypic and genotypic studies revealed new tools for differentiating Burkholderia cepacia genomovar VI from Burkholderia multivorans and other B. cepacia-complex species. Hence, the name Burkholderia dolosa sp. nov. is proposed, with LMG 18943T (=CCUG 47727T) as the type strain. B. dolosa can be differentiated from other B. cepacia-complex bacteria by its inability to assimilate tryptamine, azelaic acid and salicin and by its failure to grow on the B. cepacia-selective medium PCAT. Both 16S rDNA and recA RFLP analysis revealed unique B. dolosa restriction patterns. In addition, new 16S rDNA- and recA-based PCR assays allowed its specific identification.

Six bacterial strains were isolated from healthy marine organisms that were collected from the coast of the Kanto area in Japan. Phylogenetic analysis based on 16S rDNA sequence similarity showed that the six isolates formed a separate cluster in the γ-Proteobacteria and were related to the genera Alteromonas and Glaciecola (<91·6 % similarity). The isolates were related closely to each other (DNA–DNA reassociation values of 74–93 %). The isolates had a polar flagellum and were Gram-negative, mesophilic, strictly aerobic rods that required salt for growth. Distinct phenotypic features of this group included the ability to hydrolyse agar and white pigmentation of colonies. The DNA G+C content of the isolates was 48–50 mol%. The major quinone was Q-8. Phenotypic characteristics of the isolates differed from those of members of the genera Alteromonas and Glaciecola. The name Agarivorans albus gen. nov., sp. nov. is proposed for the six isolates; the type strain is MKT 106T (=IAM 14998T=LMG 21761T).

A Legionella-like amoebal pathogen (LLAP), formerly named LLAP12T, was characterized on the basis of microscopic appearance, staining characteristics, growth in Acanthamoeba polyphaga at different temperatures, DNA G+C content, serological cross-reactivity and 16S rRNA and macrophage infectivity potentiator (mip) gene sequence analysis. LLAP12T was found to be a motile, Gram-negative bacterium that grew within cytoplasmic vacuoles in infected amoebae. The infecting bacteria induced lysis of their amoebal hosts and time taken to do so was dependent on incubation temperature. Recovery of LLAP12T from amoebae onto axenic media could not be achieved. Phylogenetic analysis of LLAP12T, based on 16S rRNA and mip gene sequence analysis, indicated that it lay within the radiation of the Legionellaceae and that it clustered specifically with Legionella lytica and Legionella rowbothamii. The divergence observed between LLAP12T and these two species was of a degree equal to, or greater than, that observed between other members of the family. In support of this delineation, LLAP12T was found not to cross-react serologically with any other Legionella species. The mip and 16S rRNA gene sequence-based analyses also indicated that LLAP12T was related very closely to two other previously identified LLAP isolates, LLAP4 and LLAP11. Taken together, these results support the proposal of LLAP12T as the type strain of Legionella drancourtii sp. nov.

Thirty-one bacteria that belonged to the genus Pseudomonas were isolated from cyanobacterial mat samples that were collected from various water bodies in Antarctica. All 31 isolates were psychrophilic; they could be divided into three groups, based on their protein profiles. Representative strains of each of the three groups, namely CMS 35T, CMS 38T and CMS 64T, were studied in detail. Based on 16S rRNA gene sequence analysis, it was established that the strains were related closely to the Pseudomonas fluorescens group. Phenotypic and chemotaxonomic characteristics further confirmed their affiliation to this group. The three strains could also be differentiated from each other and the closely related species Pseudomonas orientalis, Pseudomonas brenneri and Pseudomonas migulae, based on phenotypic and chemotaxonomic characteristics and the level of DNA–DNA hybridization. Therefore, it is proposed that strains CMS 35T (=MTCC 4992T=DSM 15318T), CMS 38T (=MTCC 4993T=DSM 15319T) and CMS 64T (=MTCC 4994T=DSM 15321T) should be assigned to novel species of the genus Pseudomonas as Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov., respectively.

Halomonas boliviensis sp. nov. is proposed for two moderately halophilic, psychrophilic, alkalitolerant bacteria, LC1T (=DSM 15516T=ATCC BAA-759T) and LC2 (=DSM 15517=ATCC BAA-760), both of which were isolated from a soil sample around the lake Laguna Colorada, located at 4300 m above sea level in the south-west region of Bolivia. The bacteria are aerobic, motile, Gram-negative rods that produce colonies with a cream pigment. Moreover, they are heterotrophs that are able to utilize various carbohydrates as carbon sources. The organisms reduce nitrate and show tryptophan deaminase activity. The genomic DNA G+C contents were 51·4 mol% for isolate LC1T and 52·6 mol% for isolate LC2. Based on 16S rDNA sequence analysis, isolates LC1T and LC2 were identified as members of the genus Halomonas and clustered closely with Halomonas variabilis DSM 3051T and Halomonas meridiana DSM 5425T. However, DNA–DNA relatedness between the new isolates and the closest related Halomonas species was low.

Halomonas ventosae sp, nov. includes three moderately halophilic, exopolysaccharide-producing strains isolated from saline soils in Jaén (south-eastern Spain). These strains can grow anaerobically using either nitrate or nitrite as terminal electron acceptor and hydrolyse both tyrosine and phenylalanine. Their G+C content varies between 72·6 and 74·3 mol%. The affiliation of the isolates with the genus Halomonas was confirmed by 16S rRNA gene sequence comparison. DNA–DNA hybridization shows 70·4–82·7 % relatedness among the three strains. Nevertheless, their relatedness is less than 43 % compared to related reference strains. The proposed type strain for Halomonas ventosae is strain Al12T (=CECT 5797T=DSM 15911T). It grows best at 8 % (w/v) sea salts and requires the presence of Na+. Its major fatty acids are 18 : 1 ω7c, 16 : 0, 16 : 1 ω7c, and 15 : 0 iso 2-OH. The predominant respiratory lipoquinone found in strain Al12T is ubiquinone with nine isoprene units (Q-9).

A total of 25 strains isolated from parrots, budgerigars, parakeets (Psittaciformes) and a chicken, mostly associated with respiratory disease or septicaemia, were classified as a new genus, Volucribacter gen. nov., within the family Pasteurellaceae, on the basis on unique phenotypic characteristics and clear monophyly as determined by 16S rRNA gene sequence comparison. Comparison of 16S rRNA gene sequences from six strains showed at least 98·8 % similarity and the closest similarity outside the genus was found to Bisgaard taxon 34 and to Pasteurella avium, at 94·6 and 94·5 %, respectively. Phenotypes that separate the new genus from other genera of the Pasteurellaceae included at least two characters. The genus includes two species, Volucribacter psittacicida sp. nov. and Volucribacter amazonae sp. nov., corresponding to the two biovars previously outlined, underlining that most isolates have been obtained from psittacine birds. The two species can be separated by fermentation of meso-inositol, (−)-l-fucose, maltose and dextrin and a positive ONPG test. The type strains for Volucribacter psittacicida and Volucribacter amazonae are respectively Gerl. 236/81T (=CCUG 47536T=DSM 15534T) and 146/S8/89T (=CCUG 47537T=DSM 15535T).