Reclassification of Koreibacter algae as a later heterotypic synonym of Paraoerskovia marina and emended descriptions of the genus Paraoerskovia Khan et al. 2009 and of Paraoerskovia marina Khan et al. 2009.

16S rRNA gene sequences deposited for the type strains of Paraoerskovia marina (CTT-37(T); GenBank accession no. AB445007) and Koreibacter algae (DSW-2(T); FM995611) show a similarity of 100 %. Consequently, the type strains were subjected to a polyphasic recharacterization under direct comparison in order to clarify their taxonomic position. PvuII RiboPrint patterns and quantitative ratios of cellular fatty acids revealed strain-specific differences between P. marina DSM 21750(T) ( = CTT-37(T)) and K. algae DSM 22126(T) ( = DSW-2(T)). The percentage of DNA-DNA binding of 94 % indicated that the two type strains belong to the same genomospecies. Agreement in the peptidoglycan structure and polar lipid pattern, highly similar fatty acid profiles and MALDI-TOF mass spectra, the ability to produce acid from the same carbon sources, corresponding enzymic activities and DNA G+C contents of 70.8 ± 0.3 mol%, in addition to the consistent characteristics reported in the original descriptions, support the view that the two strains should be affiliated to the same species. According to Rules 38 and 42 of the Bacteriological Code, Koreibacter algae should be reclassified as later heterotypic synonym of Paraoerskovia marina, and the descriptions of the genus Paraoerskovia Khan et al. 2009 and of Paraoerskovia marina Khan et al. 2009 are emended accordingly.

Aeromonas aquariorum sp. nov., isolated from aquaria of ornamental fish.

During a survey to determine the prevalence of Aeromonas strains in water and skin of imported ornamental fish, 48 strains presumptively identified as Aeromonas were isolated but they could not be identified as members of any previously described Aeromonas species. These strains were subjected to a polyphasic approach including phylogenetic analysis derived from gyrB, rpoD and 16S rRNA gene sequencing, DNA-DNA hybridization, MALDI-TOF MS analysis, genotyping by RAPD and extensive biochemical and antibiotic susceptibility tests in order to determine their taxonomic position. Based on the results of the phylogenetic analyses and DNA-DNA hybridization data, we describe a novel species of the genus Aeromonas, for which the name Aeromonas aquariorum sp. nov. is proposed, with strain MDC47T (=DSM 18362T =CECT 7289T) as the type strain. This is the first Aeromonas species description based on isolations from ornamental fish.

Mycobacterium fluoranthenivorans sp. nov., a fluoranthene and aflatoxin B1 degrading bacterium from contaminated soil of a former coal gas plant.

Mycobacterium strain FA4T was isolated with fluoranthene as the single carbon source from soil of a former coal gas plant, polluted with polycyclic aromatic hydrocarbons. The physiological properties, fatty acid pattern, and the 16S ribosomal RNA gene sequence indicated membership to the genus Mycobacterium, but were different from all type strains of Mycobacterium species. Based on comparative 16S rRNA gene sequence analyses strain FA4T could be assigned to the Mycobacterium neoaurum taxon showing 98% sequence similarity to M. diernhoferi as its closest neighbour. The occurrence of epoxymycolate in the cell wall differentiates FA4 from all members of this taxon which synthesize wax-ester mycolates in addition to alpha-mycolates. Strain FA4T is able to degrade aflatoxin B1. This biological attribute might be useful in biological detoxification processes of foods and feeds. From the investigated characteristics it is concluded that strain FA4T represents a new species, for which we propose the name Mycobacterium fluoranthenivorans sp. nov. The type strain of Mycobacterium fluoranthenivorans is FA4T (DSM 44556T = CIP 108203T).

Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge.

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55-80 degrees C, with an optimum at 70 degrees C. The NaCl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). The pH range for growth was 6-6.7, with an optimum at approximately pH 6.25. H2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812T were similar to those of Thermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesulfobacteriaceae (similarity values of less than 90%). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812T could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T (46.0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812T represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812T (=DSM 15286T=JCM 11887T).

Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments.

A polyphasic taxonomic study was performed to characterize a new bacterial isolate, designated KMM 3654(T), from a marine bottom sand sample. The strain was Gram-negative, encapsulated, aerobic, moderately halophilic and grew between 0.5 and 10 % NaCl and at 4-42 degrees C. Its DNA G+C content was 56.4 mol%. Isolate KMM 3654(T) was phylogenetically closely related to members of the genus Oceanimonas, showing 96.7 and 95.6 % 16S rRNA gene sequence similarity to Oceanimonas doudoroffii DSM 7028(T) and Oceanimonas baumannii ATCC 700832(T), respectively. Strain KMM 3654(T) shared some physiological and chemotaxonomic properties with these two Oceanimonas species, but differed from them in morphology, growth at 4 degrees C, urease activity, weak phenol degradation and utilization of phenylacetate. On the basis of phenotypic and phylogenetic evidence, Oceanisphaera litoralis gen. nov., sp. nov. is proposed, with the type strain KMM 3654(T) (=DSM 15406(T)).

Petrotoga olearia sp. nov. and Petrotoga sibirica sp. nov., two thermophilic bacteria isolated from a continental petroleum reservoir in Western Siberia.

Strictly anaerobic, thermophilic bacteria (strains SL24T, SL25T, SL27, SL29 and SL32) were isolated from a deep, continental oil reservoir in Western Siberia (Russia). These motile, rod-shaped organisms were surrounded by a sheath-like structure, a feature characteristic of the Thermotogales. On the basis of partial 16S rDNA sequences (500 nucleotides), strains SL25T, SL27, SL29 and SL32 were identical. Therefore, only strains SL24T and SL25T were studied in detail. The optimum temperature for growth of both strains was 55 degrees C. Their optimum pH for growth was 7.5 and their optimum NaCl concentration was between 20 and 30 g l(-1). The novel isolates reduced elemental sulfur and cystine, but not thiosulfate or sulfate, to hydrogen sulfide. The G+C contents of the genomic DNA of strains SL24T and SL25T were respectively 35 and 33 mol%. Phylogenetically, both strains are most closely related to Petrotoga miotherma, there being 98.9-99.4% similarity between their 16S rDNA sequences. Phenotypic properties and DNA-DNA hybridization experiments indicate that the strains belong to two novel species, for which the names Petrotoga olearia (type strain SL24T = DSM 13574T = JCM 11234T) and Petrotoga sibirica (type strain SL25T= DSM 13575T = JCM 11235T) are proposed.

Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species.

A polycyclic aromatic hydrocarbon-degrading bacterium isolated from coal tar-contaminated soil in Denmark was characterized by a polyphasic approach. Phylogenetically and chemotaxonomically, it was related to members of the genus Mycobacterium. The isolate contains chemotaxonomic markers that are diagnostic for the genus Mycobacterium; i.e. the meso isomer of 2,6-diaminopimelic acid, arabinose and galactose as diagnostic whole-cell sugars, MK-9(H2) as the principal isoprenoid quinone, a mycolic acid pattern of alpha-mycolates, ketomycolates and wax-ester mycolates, unbranched saturated and unsaturated fatty acids plus a small amount of tuberculostearic acid and a significant amount of a C18:0 secondary alcohol. Based on the unique combination of chemical markers among mycobacteria, it is proposed that the isolate should be assigned to a new species, Mycobacterium frederiksbergense sp. nov. This novel species is phylogenetically closely related to Mycobacterium diernhoferi, Mycobacterium neoaurum and Mycobacterium hodleri. The type strain of M. frederiksbergense is strain FAn9T (= DSM 44346T = NRRL B-24126T).

Thermosipho geolei sp. nov., a thermophilic bacterium isolated from a continental petroleum reservoir in Western Siberia.

Three strictly anaerobic, thermophilic bacteria (SL31T, SL30 and MLM39636) were isolated from a deep continental oil reservoir in Western Siberia (Russia). Following the mid-exponential phase of growth, the non-motile rod-shaped organisms were surrounded by a sheath-like structure. As DNA-DNA hybridizations showed that these strains were highly related genomically, only strain SL31T was studied in detail. The temperature range for growth of strain SL31T was between 45 and 75 degrees C, with optimum growth at 70 degrees C. Its optimum pH and NaCl concentration for growth were pH 7.5 and 20-30 g l(-1), respectively. The novel isolate reduced elemental sulfur and cystine, but not thiosulfate or sulfate, to hydrogen sulfide. The G+C content of the genomic DNA was 30.0 mol %. As determined by 16S rDNA sequence analysis, this organism belonged to the genus Thermosipho. DNA-DNA hybridization levels between strain SL31T and type strains of the previously described species of Thermosipho were less than 10%. On the basis of physiological and molecular properties, it is proposed that this organism should be placed in a new species, Thermosipho geolei sp. nov. The novel organism represents the first species of the genus Thermosipho that has been isolated from a petroleum reservoir. The type strain is SL31T ( = DSM 13256T = JCM 10986T).

Nonomuraea dietzii sp. nov..

The taxon 'Sebekia benihana', an actinomycete of industrial significance, has been subjected to a polyphasic taxonomic study. 16S rDNA sequence analyses of strain DSM 44320 (= NRRL 11111) revealed 100% similarity to the 16S rDNA sequence of Nonomuraea roseola DSM 43767T and high values (>98.5%) to some other species of this genus. DNA-DNA similarity values of less than 31% observed between strain DSM 44320 and N. roseola DSM 43767T, Nonomuraea recticatena DSM 43937T and Nonomuraea africana DSM 43748T indicate that this strain represents an individual genospecies. Differences between strain DSM 44320T and the 16 validly described Nonomuraea species occur in the primary structure of the 16S rDNA, the physiological test profile, the morphology of mycelium and the spore surface and the colour of substrate mycelium. The only strain of 'S. benihana', DSM 44320T (= NRRL 11111T), is proposed as the type strain of a new species of the genus Nonomuraea, Nonomuraea dietzii sp. nov..

Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil.

A total of 131 bacterial isolates related to Pseudomonas corrugata were obtained from an agricultural soil from northern Germany. Based on 16S rRNA gene sequences, PCR-based genome fingerprinting and multilocus enzyme electrophoresis, they formed two groups, A (119 strains) and B (12 strains). As members of each group were highly similar, a single strain of each group was subsequently characterized by a polyphasic taxonomic approach. The selected member of group A was identified as a strain of Pseudomonas brassicacearum, whereas the selected member of group B was distinct from other species of the genus Pseudomonas. Although DNA-DNA hybridization suggested a close affiliation of the group B strain with P. brassicacearum and Pseudomonas thivervalensis and ribotyping suggested a close affiliation with P. brassicacearum, RAPD data, 16S rRNA gene sequencing and phenotypic characterization indicated the presence of a distinct taxonomic entity. This strain differed from the type strains of P. thivervalensis and P. brassicacearum in 10 and 12 metabolic properties, respectively, whereas the two organisms differ from one another by only two properties. Strains of group B are therefore considered to be members of a new species, for which the name Pseudomonas kilonensis sp. nov. is proposed. The type strain is strain 520-20T (= DSM 13647T = CFBP 5372T).

Isolation and characterization of Thermococcus sibiricus sp. nov. from a Western Siberia high-temperature oil reservoir.

Anaerobic organotrophic hyperthermophilic Archaea were isolated from five of eight samples from oil wells of the Samotlor oil reservoir (depth, 1,799-2,287 m; temperature, 60 degrees-84 degrees C). Three strains were isolated in pure cultures and characterized phylogenetically on the basis of comparison of the 16S rRNA gene sequences. All strains belonged to a new species of the genus Thermococcus, with Thermococcus litoralis, Thermococcus aggregans, Thermococcus fumicolans, and Thermococcus alcaliphilus being the nearest relatives (range of sequence similarity, 97.2%-98.8%). Strain MM 739 was studied in detail. The new isolate grew on peptides but not on carbohydrates. Elemental sulfur had a stimulatory effect on growth. The temperature range for growth was between 40 degrees and 88 degrees C, with the optimum at 78 degrees C; the pH range was 5.8 to 9.0, with the optimum around 7.3; and the salinity range was 0.5% to 7.0%, with the optimum at 1.8%-2.0%. The doubling time at optimal growth conditions was about 43 min. The G+C content of the DNA was 38.4 mol%. The DNA-DNA relatedness between strain MM 739 and T. litoralis was 27%; between strain MM 739 and T. aggregans, it was 22%. Based on the phenotypic and genomic differences with known Thermococcus species, the new species Thermococcus sibiricus is proposed. The isolation of a hyperthermophilic archaeum from a deep subsurface environment, significantly remote from shallow or abyssal marine hot vents, indicates the existence of a subterranean biosphere inhabited by indigenous hyperthermophilic biota.

Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov.

A polyphasic taxonomic study was performed on the type strain of Bacillus thermosphaericus DSM 10633T and three related soil isolates. On the basis of phenotypic characteristics, chemotaxonomic profiles and phylogenetic data a new genus, Ureibacillus gen. nov., is proposed for the strains in the Bacillus thermosphaericus cluster. Strains of this cluster fall into two DNA-DNA similarity groups: while one group contains the type strain of Ureibacillus thermosphaericus comb. nov. and a single soil isolate, the other contains two soil isolates. The two groups differed in the composition of isoprenoid quinones and some phenotypic properties. These data support the description of a novel species of Ureibacillus for which the name Ureibacillus terrenus is proposed. The type strain of this new species is TH9AT (= DSM 12654T = LMG 19470T).

A polyphasic taxonomic study of thermophilic bacilli from shallow, marine vents.

Eighty-seven thermophilic, aerobic, spore-forming bacteria were isolated from shallow, marine, thermal vents of the Eolian Islands (Italy) and tested for a broad spectrum of phenotypic characteristics. A numerical taxonomy study was performed on these isolates and 8 thermophilic Bacillus and Geobacillus reference strains by 89 selected features. Results from cluster analysis showed the formation of nine clusters. Most of the isolates (83%) fell into several phenetically well distinguished clusters, loosely related to Geobacillus thermodenitrificans. The remaining isolates grouped together with different reference strains. Eighteen isolates, representative of the different clusters, were selected for subsequent genotypic characterisation, including partial 16S rDNA sequence analysis of 18 strains and almost complete 16S rDNA sequences of 9 strains. Subsequent DNA/DNA reassociation studies and determination of the base composition of DNA identified seven isolates as Geobacillus thermodenitrificans, two isolates as G. thermoleovorans and one isolate as Bacillus pallidus. Four isolates represented two novel species of Bacillus. The remaining four represented novel Geobacillus species, one of which has recently been described as Bacillus vulcani DSMZ 13174 T.

Reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus (Ahmad et al. 2000) comb. nov.

A polyphasic study was performed on five thermophilic strains belonging to the genus Bacillus, isolated from soil of different geographical areas. 16S rRNA gene sequence analysis placed these isolates in RNA group 5, with Saccharococcus caldoxylosilyticus and [Bacillus] thermoglucosidasius being the closest phylogenetic neighbours. The type species of Saccharococcus, Saccharococcus thermophilus, was only moderately related to these two species and the novel isolates. DNA-DNA hybridization studies and comparison of morphological, chemotaxonomic and phenotypic features supported the close relationship between the novel isolates and Saccharococcus caldoxylosilyticus. These data justify the reclassification of Saccharococcus caldoxylosilyticus. Following the transfer of the validly described Bacillus species of group 5 into the genus Geobacillus, the reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus comb. nov. is proposed. This species can be distinguished genomically from Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, Geobacillus thermodenitrificans and Saccharococcus thermophilus by a specific PCR-RFLP assay targeting the 16S rDNA.

Bacillus thermodenitrificans sp. nov., nom. rev.

A polyphasic study was performed on 10 soil isolates of thermophilic denitrifying Bacillus strains from different geographical areas. The presence of two main characteristic bands following amplification of the internal transcribed spacer (ITS) region of rrn operons suggests a close relatedness to 'Bacillus thermodenitrificans'. The isolates cluster around two strains of 'B. thermodenitrificans' in riboprint and fatty acid analyses, though differences occur at the strain level. Subsequent DNA-DNA reassociation studies including the 10 isolates, 'B. thermodenitrificans' DSM 465T and DSM 466, and Bacillus stearothermophilus ATCC 12980T and Bacillus thermoleovorans ATCC 43513T revealed such a high level of genomic relatedness between the isolates and the DSM strains (> 73% similarity) that they must be considered strains of the same taxon. The degree of DNA-DNA similarity between the 12 strains of 'B. thermodenitrificans' and the type strains of the other two phylogenetically neighbouring Bacillus species was significantly lower (21-43% similarity). Based upon phylogenetic, chemotaxonomic and phenotypic evidence, the designation of B. thermodenitrificans sp. nov., nom. rev. is proposed. The type strain of B. thermodenitrificans is DSM 465T.

Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil.

Twelve bacterial strains isolated from tar-contaminated soil were subjected to a polyphasic taxonomic study. The strains possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, MK-9(H2) as the predominant menaquinone, long-chain mycolic acids of the Gordonia-type, straight-chain saturated and monounsaturated fatty acids, and considerable amounts of tuberculostearic acid. The G + C content of the DNA was 68 mol%. Chemotaxonomic and physiological properties and 16S rDNA sequence comparison results indicated that these strains represent a new species of the genus Gordonia. Because of the ability of these strains to use alkanes as a carbon source, the name Gordonia alkanivorans is proposed. The type strain of Gordonia alkanivorans sp. nov. is strain HKI 0136T (= DSM 44369T).

Desulfonispora thiosulfatigenes gen. nov., sp. nov., a taurine-fermenting, thiosulfate-producing anaerobic bacterium.

Strain GKNTAUT has been described as a bacterium able to ferment the organosulfonate taurine (2-aminoethanesulfonate) quantitatively to acetate, ammonia and thiosulfate, an unusual metabolic product. This novel fermentation has now also been observed in four independent isolates from two continents. All five organisms were strictly anaerobic, Gram-positive, motile, spore-forming bacteria. Enrichments with isethionate (2-hydroxyethanesulfonate) and cysteate (2-amino-3-sulfopropionate), in contrast, yielded bacteria that disproportionated the sulfonate to sulfate and sulfide. The phylogenetic location of the taurine fermenters was analysed on the basis of 16S rDNA sequences. Strain GKNTAUT (= DSM 11270T = ATCC 700533T) is described as the type strain of a new genus and species, for which the name Desulfonispora thiosulfatigenes gen. nov., sp. nov. is proposed.

The correlation between morphological and phylogenetic classification of myxobacteria.

In order to determine whether morphological criteria are suitable to affiliate myxobacterial strains to species, a phylogenetic analysis of 16S rDNAs was performed on 54 myxobacterial strains that represented morphologically 21 species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of 'Corallococcus', previously 'Chondrococcus', within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium ('Sorangium') cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria ('Polyangium thaxteri' Pl t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947T and Angiococcus disciformis An d1), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia.

Strain INSLUZT (= DSM 4273T) was isolated from a biogas-producing bioreactor treating wastewater of a palm oil mill on North-Sumatra (Indonesia). Cells of strain INSLUZT were highly irregularly coccoid, 1.25-2.0 microns in diameter, had a cell envelope consisting of the cytoplasmic membrane and an S-layer of hexagonally arranged glycoprotein subunits with an M(r) of 120,000, and were flagellated (motility was not observed). Cells were mesophilic and grew most rapidly at 40 degrees C on H2/CO2' formate, 2-propanol/CO2 2-butanol/CO2 and cyclopentanol/CO2 to give methane. Tungstate promoted growth on H2/CO2 with acetate as the solely required organic medium supplement. The G + C content of DNA was 59 mol% (Tm method) and 59.5 mol% (HPLC method). 16S rDNA analysis revealed a phylogenetic relationship to Methanoculleus species; the name Methanoculleus palmolei sp. nov. is therefore proposed for strain INSLUZT (= DSM 4273T).