- Volume 52, Issue 6, 2002

Five isolates of a previously undescribed species of purple non-sulfur phototrophic bacteria were characterized. They were Gram-negative, had mobile, budding vibrioid cells and contained lamellar intracytoplasmic membranes. Cultures produced red pigments in the light. Live cells of photosynthetic cultures exhibited absorption maxima at 382, 460-464, 494-496, 534-538, 596, 804-806 and 870-874 nm, indicating the presence of bacteriochlorophyll a and carotenoids belonging to the spirilloxanthin series in cells. The new isolates grew anaerobically or microaerobically in the light, but not aerobically in the dark. Optimal growth occurred at 35-40 degrees C and at pH 6.5-8.5. Various organic compounds were used as photosynthetic electron donors and carbon sources. Sulfate was used as sulfur source for growth. Ubiquinone 10 was synthesized as the major quinone. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain gc(T), a representative of the new isolates, was closest to Rhodopseudomonas palustris, with a similarity of 97.5%. DNA-DNA hybridization further distinguished strain gc(T) from Rhodopseudomonas palustris at the species level. Therefore, the name Rhodopseudomonas faecalis sp. nov. was proposed for the new isolates. The type strain is gc(T) ( = AS1.2176(T) = JCM 11668(T)).

A Gram-negative bacterium, designated NS12(T), was previously isolated from duplicate treatments of surface-sterilized Zea mays stems. The plants were grown in synthetic soil under greenhouse conditions and watered with fertilizer containing no nitrogen. Strain NS12(T) was not isolated from plants watered with the standard level or 20% (w/v) of the standard level of nitrogen. Cells were bent rods that formed chains of irregular shapes in R2A broth. Unlike its closest described relative Runella slithyformis, strain NS12(T) fermented glucose and sucrose. The G+C content was 49 mol%. Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the domain Bacteria and is most closely related to R. slithyformis, a member of the Flexibacter group within the Cytophaga-Flexibacter-Bacteroides phylum. Phenotypic and genotypic analyses indicated that strain NS12(T) could not be assigned to any recognized species; therefore a new species designated Runella zeae sp. nov. is proposed, for which NS12(T) ( = ATCC BAA-293(T) = LMG 21438(T)) is the type strain.

A total of 26 strains, including 15 strains isolated from garlic plants with the typical symptoms of 'Café au lait' disease and 11 strains isolated from diseased or healthy rice seeds and sheaths infested by Pseudomonas fuscovaginae, were compared with 70 type or reference strains of oxidase-positive pathogenic or non-pathogenic fluorescent pseudomonads. The strains were characterized by using a polyphasic taxonomic approach. Numerical taxonomy of phenotypic characteristics showed that the garlic and rice strains were related to each other. However, they clustered into separate phenons, distinct from those of the other strains tested, and were different in several nutritional tests. On the basis of DNA-DNA hybridization, the garlic and rice strains constituted two distinct DNA hybridization groups, indicating that they belonged to separate species. The two groups of strains were also well differentiated by siderotyping. Garlic strains were pathogenic to garlic plants and either weakly pathogenic or non-pathogenic on rice; rice strains were either weakly pathogenic or non-pathogenic on rice and non-pathogenic on garlic. A phylogenetic analysis of 16S rRNA gene sequences confirmed that the two groups of strains belonged to the y-Proteobacteria and to the genus Pseudomonas. The names Pseudomonas salomonii sp. nov. and Pseudomonas palleroniana sp. nov. are respectively proposed for the garlic strains and the rice strains. The type strains are P. salomonii CFBP 2022(T) ( = ICMP 14252(T) = NCPPB 4277(T)) and P. palleroniana CFBP 4389(T) (= ICMP 14253(T) = NCPPB 4278(T)).

A variety of genes and analytical methods have been applied to the study of phylogenetic relationships within the genus Bartonella, but so far the results have been inconsistent. While previous studies analysed single protein-encoding genes, we have analysed an alignment containing the sequences of three important phylogenetic markers, RNase P RNA, 16S rRNA and 23S rRNA, merged by catenation, to determine the phylogenetic relationships within the genus Bartonella. The dataset described here comprises 13 different Bartonella strains, including the seven strains that are known to be human pathogens. A variety of algorithms have been used to construct phylogenetic trees based on the combined alignment and, for comparison purposes, each individual gene. Trees generated from the catenated alignment are more consistent (independent of algorithm) and robust (higher bootstrap support). It is suggested that a phylogenetic analysis incorporating the RNase P RNA, 16S rRNA and 23S rRNA be used to study the phylogenetic relationships within the genus Bartonella.

A polyphasic taxonomic study was performed on the phytopathogenic bacterial strains DAPP-PG 224(T) and DAPP-PG 228, which cause brown spot on yellow Spanish melon (Cucumis melo var. inodorus) fruits. Based on the presence of glucuronosyl ceramide (SGL-1) in cellular lipids, the results of fatty acid analysis and 16S rDNA sequence comparison, the strains had been identified as belonging to the genus Sphingomonas and as phylogenetically related to Sphingomonas mali, Sphingomonas pruni and Sphingomonas asaccharolytica. The levels of 16S rDNA sequence similarity of these three species to strain DAPP-PG 224(T) were respectively 98.0, 98.0 and 97.4%. DNA-DNA hybridization experiments between strains pathogenic on melon fruit and S. mali, S. pruni and S. asaccharolytica revealed < or = 16% relatedness. Based on these results, the two isolates studied are regarded as independent from the type strains of the three species mentioned above. Sphingomonas strains from melon fruits are recognized as forming a genetically and phenotypically discrete species and to be differentiated by phenotypic characteristics from all 29 named species of the genus. Thus, the name Sphingomonas melonis sp. nov. is proposed for the isolates from diseased melon fruits. The type strain is DAPP-PG 224(T) (= LMG 19484(T) = DSM 14444(T)). The G+C content of DNA of the type strain is 65.0 mol%.

Bdellovibrio-and-like organisms (BALO) are Gram-negative, predatory bacteria that inhabit terrestrial, freshwater and salt-water environments. Historically, these organisms have been classified together despite documented genetic differences between isolates. The genetic diversity of these microbes was assessed by sequencing the 16S rRNA gene. Primers that selectively amplify predator 16S rDNA, and not contaminating prey DNA, were utilized to study 17 freshwater and terrestrial and nine salt-water BALO isolates. When the 16S rDNA sequences were compared with representatives of other bacterial classes, 25 of the 26 BALO isolates clustered into two groups. One group, supported 100% by bootstrap analysis, included all of the Bdellovibrio bacteriovorus isolates. Each member of this group was isolated from either a freshwater or terrestrial source. The genetic distance between these isolates was less than 12%. The other group, supported 94% by bootstrap analysis, includes Bacteriovorax starrii, Bacteriovorax stolpii and the salt-water isolates. The salt-water isolates form a subgroup (83% by bootstrap) and differ within the subgroup by less than 110%. This observation implies that the salt-water isolates arose from Bacteriovorax progenitors. The difference between isolates in different clades is over 17%, a quantity similar to differences between bacterial species in different classes. However, both the Bdellovibrio and Bacteriovorax clades were closest to other representatives of the delta-Proteobacteria using maximum-likelihood. One freshwater isolate, James Island, was distinct from all other BALO (> 19%), but differed from Pseudomonas putida, a member of the gamma-Proteobacteria, by only 3%. Thus, by 16S rDNA sequence analysis, the BALO appear to have multiple origins, contrary to the unified taxonomic grouping based on morphology and natural history. These observations are consistent with the need to review and revise the taxonomy of these organisms.

A Gram-positive, aerobic, spherical actinobacterium, designated strain 4-0(T), was isolated from a medieval wall painting and characterized to determine its taxonomic position. The peptidoglycan of strain 4-0(T) was of type A4alpha, with lysine as the diagnostic cell wall diamino acid and an interpeptide bridge of Lys-Gly-Glu. Its quinone system contained predominantly MK-9(H2) (64%) and its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, four unknown glycolipids, two unknown phospholipids and an unknown lipid. The fatty acid profile of strain 4-0(T) was represented by significant amounts of ai-C15:0 and moderate amounts of ai-C17:0, i-C16:0 and i-C15:0 fatty acids. Spermidine was predominant in the polyamine pattern. The G+C content of the genomic DNA was 68 mol%. Comparative 16S rDNA sequence studies revealed the highest similarity values (95.4-96.1%) between strain 4-0(T) and species of the genus Micrococcus and certain species of the genus Arthrobacter, including Arthrobacter pascens DSM 20545(T), Arthrobacter ramosus DSM 20546(T), Arthrobacterprotophormiae DSM 20168(T), Arthrobacternicotianae DSM 20123(T) and Arthrobacter globiformis DSM 20124(T). Phylogenetic analyses demonstrated that strain 4-0(T) branches deeply on the Micrococcus lineage. Because it is almost equidistant phylogenetically from the genera Micrococcus and Arthrobacter and possesses significant differences in chemotaxonomic characteristics from members of these genera, it is suggested that strain 4-0(T) be classified as a novel species in a new genus; the name Citricoccus muralis gen. nov., sp. nov. is proposed. The type strain is strain 4-0(T) (= DSM 11442(T) CCM 4981(T)).

Two polyunsaturated fatty acid (PUFA) producing strains (ACEM 6 and ACEM 9(T)) isolated from a temperate, humic-rich river estuary in Tasmania, Australia, were found to be members of the genus Shewanella. These strains were able to utilize humic compounds (tannic acid) and derivatives (2,6-anthraquinone disulfonate) as sole carbon sources and as electron acceptors for anaerobic respiration. The major fatty acids were typical of the genus Shewanella; however, PUFAs mostly made up of eicosapentaenoic acid were produced at high levels (10.2-23.6% of total fatty acids) and at relatively high incubation temperatures (10.2% at 24 degrees C). Sequence analysis indicated that ACEM 6 and ACEM 9(T) had identical 16S rDNA sequences and were most closely related to Shewanella japonica (sequence similarity 97.1%). DNA hybridization and phenotypic characteristics confirmed that the isolates constituted a novel species of the genus Shewanella, which is designated Shewanella olleyana sp. nov. (type strain ACEM 9(T) = ACAM 644(T) = LMG 21437(T)).

The taxonomy of soil isolates AP-20(T) and AP-37 was examined. These alkaliphilic organisms grew over a wide pH range (pH 7.0-13.0). The growth rate was higher at pH 8.0-12.0 than at pH 7.0. The G+C composition of these strains averaged 53 mol%. These strains contained MK-7 as the main respiratory quinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The major cellular fatty acid of the isolates was 12-methyltetradecanoic acid. Levels of 16S rDNA similarity between strain AP-20(T), AP-37 and other Paenibacillus species were 94.2-90.2%. Phylogenetic analysis based on 16S rDNA sequence revealed that strains AP-20(T) and AP-37 formed an evolutionary lineage distinct from other Paenibacillus species. Based on the evaluation of morphological, physiological and chemotaxonomic characteristics, and on 16S rDNA sequence comparison, the new species Paenibacillus daejeonensis sp. nov. is proposed; the type strain is AP-20(T) ( = KCTC 3745(T) = JCM 11236(T)).

On the basis of phenotypic and genotypic characteristics and 16S rDNA sequence analysis, a novel species belonging to the genus Pseudomonas sensu stricto was identified. The saprophytic, fluorescent bacterium, designated KMM 3447(T), was isolated from a drinking water reservoir near Vladivostok City, Russia. The novel organism was a Gram-negative, aerobic, rod-shaped bacterium that produced a cyclic depsipeptide with surface-active properties. It degraded casein, but did not degrade gelatin, starch, agar or Tween 80. The bacterium was also haemolytic. Growth of the novel bacterium occurred between 4 and 35 degrees C. The predominant cellular fatty acids of the novel pseudomonad were C16:0, C16:1(n-7), C18:1(n-7) and C17.0 cyclo; branched fatty acids were only found in trace amounts. The G+C content of the novel bacterium was 61.0 mol%. 16S rDNA sequence analysis indicated that the novel bacterium had a clear affiliation with Pseudomonas fluorescens and species closely related to this recognized pseudomonad. DNA-DNA hybridization experiments showed that the novel bacterium bound at low levels (27-53%) with the DNA of the type strains of its nearest phylogenetic relatives, namely Pseudomonas tolaasii, Pseudomonas veronii, Pseudomonas orientalis and Pseudomonas rhodesiae, indicating that the novel bacterium represented a novel species within the genus Pseudomonas, for which the name Pseudomonas extremorientalis is proposed; the type strain is KMM 3447(T) (= LMG 19695(T)).

A polyphasic study was undertaken to establish the taxonomic position of a soil isolate that had provisionally been assigned to the genus Rhodococcus. The organism showed a combination of phenotypic properties typical of rhodococci and formed a distinct phyletic line within the Rhodococcus erythropolis 165 rDNA subclade. The organism was readily distinguished from representatives of validly described species classified in this subclade on the basis of DNA-DNA relatedness and phenotypic data. Consequently, it is proposed that the organism be recognized as a novel species of Rhodococcus, Rhodococcus maanshanensis sp. nov. The type strain is strain M712(T) (= AS 4.1720(T) = JCM 11374(T)).

Eleven psychrotolerant Bacillus strains with ornithine as diamino acid in position 3 of the peptide side chain of the cell wall and a G+C range of 35.7-38.4 mol% were characterized taxonomically. DNA-DNA hybridization studies confirmed previously physiologically established groups. High DNA-binding values (> 70%) were found within groups I A (consisting of the type strain of Bacillus insolitus DSM 5(T) and Bacillus insolitus DSM 2272), I B (consisting of isolates 3H1(T0, 71H1, 84E1, 87H2 and 4H2) and I C (consisting of isolates 68E39T), 61E1, 4E3 and 67E1). Low DNA-binding values (< 60%) were revealed between the three groups. Consequently, strains of groups I B and I C were considered as being representatives of new psychrotolerant species. For group I B strains the name Bacillus psychrotolerans sp. nov. is proposed with the type strain 3H1(T) (= DSM 11706(T) = NCIMB 13838(T)) and for group I C strains the name Bacillus psychrodurans sp. nov. is proposed with the type strain 68E3(T) (= DSM 11713(T) = NCIMB 13837(T)).

A strain of a novel non-chromogenic mycobacterium was isolated from synovial tissue from a 68-year-old female with bursitis of her right elbow. The slowly growing strain had a unique PCR-restriction enzyme analysis (PRA) profile of the hsp65 gene and 16S rRNA gene sequence in comparison with other mycobacterium species. The most closely related species, as determined by 16S rRNA gene sequence analysis, are Mycobacterium malmoense, Mycobacterium marinum, Mycobacterium ulcerans and members of the Mycobacterium tuberculosis complex. The HPLC and biochemical profiles resembled those of Mycobacterium gastri, although differences were noted in the peak-height ratio of the HPLC pattern and the nitrate and pyrazinamidase tests. On the basis of PRA, HPLC, biochemical and 16S rRNA gene sequence analyses, the name Mycobacterium lacus sp. nov. is proposed for this potential pathogen. The type strain is strain NRCM 00-255(T) (= ATCC BAA-323(T) = DSM 44577(T)).

Two newly isolated strains of obligately anaerobic bacteria from human faeces are shown here to be related to Fusobacterium prausnitzii, which is regarded as one of the most abundant colonizers of the human colon. These strains, along with Fusobacterium prausnitzii ATCC 27768(T) and 27766, are non-motile and produce butyrate, formate and lactate, but not hydrogen as fermentation products. A new finding is that all four strains produce D-lactate, but not L-lactate. The strains have a requirement for acetate in the growth medium and this may account for the previously reported requirement for rumen fluid. The DNA G+C content of the four strains is 47-57 mol%. Together with phylogenetic analysis based on 16S rRNA sequencing, this establishes that Fusobacterium prausnitzii strains are only distantly related to Fusobacterium sensu stricto and are more closely related to members of Clostridium cluster IV (the Clostridium leptum group). It is proposed that a new genus, Faecalibacterium gen. nov. be created; this genus should include Faecalibacterium prausnitzii gen. nov., comb. nov. ATCC 27768(T) (= NCIMB 13872(T)) (formerly Fusobacterium prausnitzii) as the type species together with ATCC 27766 and the newly isolated strains A2-165 and L2-6.

Sixteen nitrogen-fixing strains isolated from the rhizosphere of maize planted in Cerrado soil, Brazil, which showed morphological and biochemical characteristics similar to the gas-forming Paenibacillus spp., were phenotypically and genetically characterized. Their identification as members of the genus Paenibacillus was confirmed by using specific primers based on the 16S rRNA gene. SDS-PAGE of whole-cell proteins, API 50CH, morphological and biochemical tests, amplified rDNA-restriction analysis (ARDRA), DNA-relatedness analyses, denaturing-gradient gel electrophoresis (DGGE) and 16S rRNA gene sequence determinations were performed to characterize the novel isolates and to compare them to strains of other nitrogen-fixing Paenibacillus spp. Phenotypic analyses showed that the 16 strains were very homogeneous and shared a high level of relatedness with Paenibacillus polymyxa and Paenibacillus peoriae. However, none of the novel isolates was able to ferment glycerol (positive test for P. polymyxa), L-arabinose or D-xylose (positive tests for P. polymyxa and P. peoriae) or utilize succinate (positive test for P. peoriae). Genetic approaches also indicated a high level of similarity among the novel isolates and P. polymyxa and P. peoriae, but the novel strains clearly could not be assigned to either of these two recognized species. On the basis of the features presented in this study, the 16 novel isolates were considered to represent members of a novel species within the genus Paenibacillus, for which the name Paenibacillus brasilensis is proposed. The type strain is PB1 72(T) (= ATCC BAA-413(T) = DSM 14914(T)).

Two novel thermophilic bacterial strains, with an optimum growth temperature of between 50 and 60 degrees C, were isolated from the Chi-ban Hot Springs in eastern Taiwan. Strains CB-225 and CB-226(T) were aerobic, thermophilic, non-sporulating, yellow-pigmented heterotrophic organisms. These strains exhibited an unusual denitrification reaction, reducing nitrite, but not nitrate, with the production of N2O only. On the basis of a phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, morphological, physiological and biochemical characteristics, and fatty acid compositions, it was found that the novel strains belonged to the genus Pseudoxanthomonas and represented a novel species within this genus, for which the name Pseudoxanthomonas taiwanensis is proposed; the type strain is CB-226(T) (= ATCC BAA-404(T) = CCRC 17172(T)). P. taiwanensis differs from the only member of the genus Pseudoxanthomonas, the mesophilic species Pseudoxanthomonas broegbernensis, in that it exhibits a higher growth temperature and different morphological characteristics, such as the absence of polar flagella.

We propose the establishment of a new species, Streptomyces avermectinius, based on characterization of strain MA-4680(T) and morphological and phylogenetic comparisons with closely related members of the genus Streptomyces. The 16S rDNA sequence was obtained from this strain and used to place it among Streptomyces species using the variable alpha region and the nearly complete 16S rDNA sequence. Four Streptomyces species were selected as related species from phenotypic data, three species from phylogenetic databases on alpha region sequences and two species from phylogenetic data using nearly complete 16S rDNA sequences. Analysis of DNA-DNA hybridization tests distinguished strain MA-4680(T) from these eight Streptomyces species. The type strain is strain MA-4680(T) (= ATCC 31267(T) = NRRL 8165(T)).

Over the course of the past decade, actinomycetes have been isolated from the placentas of horses diagnosed with nocardioform placentitis. The incidence of this infection has generally been low, with typically no more than 30 animals affected in most years, but the incidence increased through 1999, with placentas from 144 mares found to be infected. Approximately half of the cases result in loss of the foal. A typical actinomycete with branching mycelium was isolated from placental lesions, and a comparison of the sequence of the 16S rDNA gene against the public databases indicated a relationship to members of the suborder Pseudonocardineae. Phylogenetic analysis of representative isolates revealed a close relationship to Crossiella cryophila, and subsequent polyphasic comparisons determined that these isolates represent a novel species of Crossiella, for which the name Crossiella equi sp. nov. is proposed, with strain LDDC 22291-98(T) (= NRRL B-24104(T) = DSM 44580(T)) as the type strain.

An anaerobic enrichment medium (pH 10) with thiosulfate as electron donor and nitrate as electron acceptor was inoculated with sediment from soda lake Fazda (Wadi Natrun, Egypt); a novel strain, ALEN 1(T), was isolated from the subsequent enrichment culture. Cells of strain ALEN 1(T) had a spiral morphology (0.3-0.45 x 1-4 microm), were motile and had a single polar flagellum. Sphaeroplasts were formed by the cells and were rapidly lysed during prolonged aerobic incubation of cultures. Cells of strain ALEN 1(T) contained a membrane-associated yellow pigment. The metabolism of this novel organism was obligately chemolithoautotrophic, and thiosulfate or sulfide were utilized as electron donors. Washed cells of strain ALEN 1(T) oxidized thiosulfate, sulfide, polysulfide and elemental sulfur to sulfate. Best growth was observed when the strain was grown under micro-oxic conditions (1-2% O2 in gas phase), whereas growth was inhibited under fully oxic conditions. Nitrate was reduced to nitrite without growth of the novel organism, but other nitrogen oxides were not utilized as electron acceptors. Strain ALEN 1(T) was alkaliphilic and moderately halophilic. It grew between pH 8 and 10.4 (optimum around pH 10) with a salt concentration of between 0.3 and 1.5 M Na+ (optimum 0-5 M). The maximum growth rate (0.08 h(-1)) of the organism was achieved in a thiosulfate-limited micro-oxic continuous culture (pH 10). Phylogenetic analyses of the 16S rDNA sequences of strain ALEN 1(T) and its closest relatives demonstrated that this strain formed a deep branch within the gamma-Proteobacteria, with no obvious association to any described cluster of species/genera. On the basis of its unique physiological properties and distinct phylogenetic position, it is proposed that strain ALEN 1(T) (= DSM 14786(T) = UNICEM 212(T)) represents a novel genus within the gamma-Proteobacteria, for which the name Thioalkalispira is proposed. It is also proposed that the type species of this novel genus be named Thioalkalispira microaerophila.