Alcaligenes faecalis subsp. parafaecalis subsp. nov., a bacterium accumulating poly-beta-hydroxybutyrate from acetone-butanol bioprocess residues

The authors have previously isolated a solvent tolerant bacterium, strain G(T), (T = type strain) capable to convert acetone-butanol bioprocess residues into poly-beta-hydroxybutyrate. Strain G(T) was initially identified as Alcaligenes spp by standard bacteriological tests. In this study the taxonomic position of the bacterium was investigated in detail. The 165 rDNA sequence analysis, the G + C content of DNA (56 mol%) and the presence of ubiquinone Q-8 confirmed strain G(T) as a representative of the genus Alcaligenes. In the polyamine pattern of the bacterium putrescine and cadaverine were detected, but only trace amounts of 2-hydroxyputrescine. The extremely low content of 2-hydroxyputrescine is remarkable, since this unique diamine is a common marker for beta-proteobacteria. Phylogenetic analyses of 16S rDNA demonstrated that Alcaligenes sp. G(T) is most closely related to the species Alcaligenes faecalis (99.6% sequence similarity to A. faecalis HR4 and 98.7% sequence similarity to A. faecalis [ATCC 8750T = DSM 30030T]. On the basis of DNA-DNA relatedness (56% similarity), the unique polyamine pattern, the physiological and biochemical differences strain G(T) could be distinguished from the species A. faecalis. Therefore, a new subspecies for the species Alcaligenes faecalis is proposed; Alcaligenes faecalis subsp. parafaecalis subsp. nov.     

Syntrophomonas wolfei subsp. methylbutyratica subsp. nov., and assignment of Syntrophomonas wolfei subsp. saponavida to Syntrophomonas saponavida sp. nov. comb. nov

A spore-forming bacterium strain 4J5(T) was isolated from rice field mud. When co-cultured with Methanobacterium formicicum DSM 1535(T), strain 4J5(T) could syntrophically degrade saturated fatty acids with 4-8 carbon atoms, including 2-methylbutyrate. Phylogenetic analysis based on 16S rRNA gene similarity showed that strain 4J5(T) was most closely related to Syntrophomonas wolfei subsp. wolfei DSM 2245(T) (98.9% sequence similarity); however, it differed from the latter in the substrates utilized and its genetic characteristics. Therefore, a new subspecies Syntrophomonas wolfei subsp. methylbutyratica is proposed. The type strain is 4J5(T) (=CGMCC 1.5051(T)=JCM 14075(T)). Furthermore, based on 16S rRNA sequence divergence and substrate utilization, we propose the assignment of Syntrophomonas wolfei subsp. saponavida DSM 4212(T) to Syntrophomonas saponavida sp. nov. comb. nov.     

Two new subspecies of Photorhabdus luminescens, isolated from Heterorhabditis bacteriophora (Nematoda: Heterorhabditidae): Photorhabdus luminescens subsp. kayaii subsp. nov. and Photorhabdus luminescens subsp. thracensis subsp. nov

Bacterial isolates from nematodes from Turkish soil samples were initially characterized by molecular methods and seven members of the genus Photorhabdus identified to the species level, using riboprint analyses and metabolic properties. Strain 07-5 (DSM 15195) was highly related to the type strain of Photorhabdus luminescens subsp. laumondii DSM 15139T, and was regarded a strain of this subspecies. Strains 1121T (DSM 15194T), 68-3 (DSM 15198) and 47-10 (DSM 15197) formed one, strain 39-8T (DSM 15199T), 39-7 (DSM 15196) and 01-12 (DSM 15193) formed a second cluster that branched intermediate the three subspecies of Photorhabdus luminescens. Based upon moderate 16S rRNA gene sequence similarities and differences in metabolic properties among themselves and with type strains of the three subspecies we consider the two clusters to represent two new subspecies of Photorhabdus luminescens for which the names Photorhabdus luminescens subsp. kayaii, type strain 1121T (DSM 15194T, NCIMB 13951T), and Photorhabdus luminescens subsp. thracensis subsp. nov., type strain 39-8T (DSM 15199T, NCIMB 13952T) are proposed.     

Geobacillus thermoleovorans subsp. stromboliensis subsp. nov., isolated from the geothermal volcanic environment

A novel thermophilic, aerobic, endospore-forming bacterium, designated strain PizzoT, was isolated from geothermal volcanic environment. Samples were collected from the Pizzo sopra la Fossa site at Stromboli Island (Eolian Islands, south of Italy) at the high altitude of 918 m. Cells of strain PizzoT were rod-shaped and stained Gram-positive. Growth was observed between 50 and 75 degrees C (optimum 70 degrees C) and at pH 5.0-8.0 (optimum pH 7.0). NaCl (0.4%, w/v) supported growth and among the hydrocarbons tested none induced growth. The G+C content of the DNA was 54.1 mol% and the sequence analysis of the 16S rRNA gene showed that the new isolate was phylogenetically closely related to the members of the Bacillus rRNA Group 5. DNA-DNA hybridization studies revealed a borderline similarity between the new isolate and Geobacillus thermoleovorans DSM 5366T (69.8%) and Geobacillus kaustophilus DSM 7263T (63.4%). On the basis of phylogenetic analysis and physiological traits of the isolate, it should be described as a new member of the Geobacillus thermoleovorans species and it is proposed that strain PizzoT can be classified as Geobacillus thermoleovorans subsp. stromboliensis, subsp. nov. (ATCC BAA-979T; DSM 15393T).     

Geobacillus toebii subsp. decanicus subsp. nov., a hydrocarbon-degrading, heavy metal resistant bacterium from hot compost

A thermophilic, spore-forming bacterial strain L1(T) was isolated from hot compost "Pomigliano Environment" s.p.a., Pomigliano, Naples, Italy. The strain was identified by using a polyphasic taxonomic approach. L1(T) resulted in an aerobic, gram-positive, rod-shaped, thermophilic with an optimum growth temperature of 68 degrees C chemorganotrophic bacterium which grew on hydrocarbons as unique carbon and energy sources and was resistant to heavy metals. The G+C DNA content was 43.5 mol%. Phylogenetic analysis of 16S rRNA gene sequence and Random Amplified Polymorphic DNA-PCR (RAPD-PCR) analysis of L1(T) and related strains showed that it forms within Geobacillus toebii, a separate cluster in the Geobacillus genus. The composition of cellular fatty acids analyses by Gas-Mass Spectroscopy differed from that typical for the genus Geobacillus in that it is lacking in iso-C15 fatty acid, while iso-C16 and iso-C17 were predominant. Isolates grew on a rich complex medium at temperatures between 55-75 degrees C and presented a doubling time (t(d)) of 2 h and 6 h using complex media and hydrocarbon media, respectively. Among hydrocarbons tested, n-decane (2%) was the more effective to support the growth (1 g/L of wet cells). The microorganism showed resistance to heavy metal tested during the growth. Furthermore, intracellular alpha-galactosidase and alpha-glucosidase enzymatic activities were detectable in the L1(T) strain. Based on phenotypic, phylogenetic, fatty acid analysis and results from DNA-DNA hybridization, we propose assigning a novel subspecies of Geobacillus toebii, to be named Geobacillus toebii subsp. decanicus subsp. nov., with the type strain L1(T) (=DSM 17041=ATCC BAA 1004).     

Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources

The aerobic degradation of phenol, chlorobenzene and dichlorobenzene as a sole carbon source has been observed in bacterial Gram-positive strain G2P^T isolated from a wastewater bioprocessor. Cells display branching mycelia fragmenting into rod and coccoid elements when grown on TSA. Aerial hyphae formation occurs when grown on phenol and chlorinated aromatics as the sole carbon source. Growth was observed at up to 0.75% phenol as a sole carbon source, indicating a strong tolerance for the compound. The 16S rRNA gene sequence shares the greatest similarity with members of the Rhodococcus genus, with the closest shared nucleotide identity of 98% with the aromatic toxin degrading bacteria Rhodococcus zopfii DSM 44108^T. Neighbor-joining and parsimony analysis of Corynebacterineae 16S rRNA gene sequences consistently places strain G2P^T in a clade shared with R. zopfii within the Rhodococcus rhodochrous subclade. Based on a unique polyphasic profile involving phenotypic, ribosomal DNA sequence analysis, DNA–DNA hybridization, mol% DNA G+C content and fatty acid composition, G2P^T is proposed to represent a previously uncharacterized, novel species in the genus Rhodococcus. The name Rhodococcus phenolicus is proposed for the isolate with the type strain G2P^T (=DSM 44812) (=NRL B-24343).     

Staphylococcus schleiferi subsp. coagulans subsp. nov., isolated from the external auditory meatus of dogs with external ear otitis

A new subspecies, Staphylococcus schleiferi subsp. coagulans, was isolated from the external auditory meatus of dogs suffering from external ear otitis and is described on the basis of studies of 21 strains. Phenotypic studies showed that these strains are more closely related to Staphylococcus intermedius than to other staphylococci, but DNA hybridization studies indicated that they are closely related to Staphylococcus schleiferi N850274T. On the basis of biochemical distinctiveness (positive test tube coagulase test and different carbohydrate reactions) and the etiological importance (frequent isolation from otitis specimens from dogs) of these strains, we propose to classify them as a subspecies of S. schleiferi. The strains of this new subspecies are coagulase tube test, beta-hemolysin, and heat-stable nuclease positive but clumping factor negative. A simple scheme for the differentiation of S. schleiferi subsp. coagulans from the other coagulase-positive staphylococci is presented. The type strain is GA211 (= JCM 7470).     

Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese

A new subspecies of the species Staphylococcus succinus, isolated from a Swiss surface ripened cheese, is described. This subspecies is differentiated from the species Staphylococcus succinus ATCC 700337T on the basis of DNA-DNA hybridisation, cell wall composition and phenotypic characteristics. Staphylococcus succinus subsp. casei could be distinguished among other things by its ability to reduce nitrate, form acid from D-mannose and D-melezitose, ferment adenosine, inosine, D-sorbitol, and 2,3-butanediol, but not D-alanine. The type strain of Staphylococcus succinus subsp. casei is DSM 15096 (CIP no. pending). The GenBank accession numbers for the reference sequences of the 16S rDNA and the hsp60 gene used in this study are AJ320272 and AF527482, respectively.     

Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay

Strain 28bB2T^T is a sulfate-reducing bacterium isolated in a previous study, obtained from a p-xylene-degrading enrichment culture. Physiological, phylogenetic and genomic characterizations of strain 28bB2T^T were performed to establish the taxonomic status of the strain. Cells of strain 28bB2T^T were short oval-shaped (0.8–1.2 × 1.2–2.7 μm), motile, and Gram-negative. For growth, the optimum pH was pH 6.5–7.0 and the optimum temperature was 28–32 °C. Strain 28bB2T^T oxidized toluene but could not utilize p-xylene. Sulfate and thiosulfate were used as electron acceptors. The G + C content of the genomic DNA was 53.8 mol%. The genome consisted of an approximately 8.3 Mb of chromosome and two extrachromosomal elements. On the basis of 16S rRNA gene analysis, strain 28bB2T^T was revealed to belong to the genus Desulfosarcina, with high sequence identities to Desulfosarcina ovata oXyS1^T (99.5%) and Desulfosarcina cetonica DSM 7267^T (98.7%). Results of Average Nucleotide Identity (ANI) calculation and digital DNA–DNA hybridization (dDDH) analysis showed that the strain 28bB2T^T should be classified as a subspecies under D. ovata. Based on physiological and phylogenetic data, strain 28bB2T^T (=NBRC 106234 =DSM 23484) is proposed as the type strain of a novel species in genus Desulfosarcina, Desulfosarcina ovata subsp. sediminis subsp. nov.     

The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri.

The taxonomic position of the nitrogen-fixing rice isolate A15, previously classified as Alcaligenes faecalis, was reinvestigated. On the basis of its small subunit ribosomal RNA (16S rRNA) sequence this strain identifies as Pseudomonas stutzeri. Phenotyping and fatty acid profiling confirm this result. DNA:DNA hybridisations, using the optical renaturation rate method, between strain A15 and Pseudomonas stutzeri LMG 11199T revealed a mean DNA-binding of 77%. The identification was further corroborated by comparative sequence analysis of the oprF gene, which encodes the major outer membrane protein of rRNA homology group I pseudomonads. Furthermore we determined the nifH sequence of this strain and of two putative diazotrophic Pseudomonas spp. and made a comparative analysis with sequences of other diazotrophs. These Pseudomonas NifH sequences cluster with NifH sequences isolated from the rice rhizosphere by PCR and of proteobacteria from the beta and gamma subclasses.     

Xylella fastidiosa subspecies: X. fastidiosa subsp. [correction] fastidiosa [correction] subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov

Xylella fastidiosa, a fastidious bacterium causing disease in over 100 plant species, is classified as a single species, although genetic studies support multiple taxons. To determine the taxonomic relatedness among strains of X. fastidiosa, we conducted DNA-DNA relatedness assays and sequenced the 16S-23S intergenic spacer (ITS) region using 26 strains from 10 hosts. Under stringent conditions (Tm -15 degrees C), the DNA relatedness for most X. fastidiosa strains was *70%. However, at high stringency (Tm -8 degrees C), three distinct genotypes (A, B, and C) were revealed. Taxon A included strains from cultivated grape, alfalfa, almond (two), and maple, interrelated by 85% (mean); taxon B included strains from peach, elm, plum, pigeon grape, sycamore, and almond (one), interrelated by 84%; and taxon C included only strains from citrus, interrelated by 87%. The mean reciprocal relatedness between taxons A and B, A and C, and B and C, were 58, 41, and 45%, respectively. ITS results also indicated the same grouping; taxons A and B, A and C, and B and C had identities of 98.7, 97.9, and 99.2%, respectively. Previous and present phenotypic data supports the molecular data. Taxon A strains grow faster on Pierce's disease agar medium whereas B and C strains grow more slowly. Taxon B and C strains are susceptible to penicillin and resistant to carbenicillin whereas A strains are opposite. Each taxon can be differentiated serologically as well as by structural proteins. We propose taxons A, B, and C be named X. fastidiosa subsp. fastidiosa [correction] subsp. nov, subsp. multiplex, subsp. nov., and subsp. pauca, subsp. nov., respectively. The type strains of the subspecies are subsp. fastidiosa [correction] ICPB 50025 (= ATTC 35879T and ICMP 15197), subsp. multiplex ICPB 50039 (= ATTC 35871 and ICMP 15199), and subsp. pauca ICPB 50031 (= ICMP 15198).     

<Emphasis Type="Italic">Photorhabdus luminescens</Emphasis> subsp. <Emphasis Type="Italic">kleinii</Emphasis> subsp. nov. (Enterobacteriales: Enterobacteriaceae)

Association between bacteria Photorhabdus and their nematode hosts Heterorhabditis represents one of the emerging models in symbiosis studies. In this study, we isolated the bacterial symbionts of the nematode Heterorhabditis georgiana. Using gyrB sequences for phylogenetic analysis, these strains were shown to be part of the species of Photorhbdus luminescens but with clear separation from currently recognized subspecies. Physiological properties and DNA–DNA hybridization profiles also supported the phylogenetic relationship of these strains. Therefore, a new subspecies, Photorhabdus luminescens subsp. kleinii subsp. nov., is proposed with the type strain KMD37^T (=DSM 23513 =ATCC =NRRL B-59419).     

Syntrophomonas erecta subsp. sporosyntropha subsp. nov., a spore-forming bacterium that degrades short chain fatty acids in co-culture with methanogens

Two obligate anaerobic bacterial strains (5-3-Z(T) and Y4-1) were isolated from river sediment and rice field mud, respectively. They degraded straight-chain fatty acids with 4-8 carbon atoms in syntrophic association with methanogens, however, neither tested branch-chain fatty acids nor could benzoate be degraded. The strains formed spores when cocultured with methanogens on butyrate, or when grew on butyrate plus dimethyl sulfoxide (DMSO) in pure culture. The cells were slightly curved rods with Gram-negative cell wall structure, and contained small amount of poly beta-hydroxyalkanoate. The strains could not degrade butyrate alone, nor could use fumarate, sulfate, thiosulfate, sulfur or nitrate as electron acceptors except DMSO for butyrate degradation. The generation time of strain 5-3-Z(T) was about 12h when growing on crotonate at 37 degrees C. The growth of the new strains occurred in the range of pH 5.5-8.4, and of temperature 20-48 degrees C, and at NaCl concentration of 0-700 mM. The G+C content of the genomic DNA of strain 5-3-Z(T) was 40.6mol%. Phylogenetic analysis based on 16S rRNA gene similarity showed the two strains to be a member of species Syntrophomonas erecta (98.4-98.9% sequence similarity), however they differed from the existing strains in both phenotypic and genetic characteristics. Therefore, a new subspecies of S. erecta, S. erecta subsp. sporosyntropha was proposed. The type strain was 5-3-Z(T) (=CGMCC1.5032(T)=JCM13344(T)).     

Corynebacterium aquatimens sp. nov., a lipophilic Corynebacterium isolated from blood cultures of a patient with bacteremia

An unknown lipophilic coryneform bacterium isolated from the blood cultures of a patient with bacteremia was characterized by phenotypic and molecular genetic methods. Chemical analysis revealed the presence of short chain mycolic acids consistent with the genus Corynebacterium. The DNA G+C content was 60.8mol%. Comparative 16S rRNA gene sequence analysis demonstrated that the isolate represents a new subline within the genus Corynebacterium. The closely phylogenetic relative of the unknown bacterium was found to be C. tuscaniense (97.8% sequence similarity). Partial rpoB gene sequence revealed that strain IMMIB L-2475(T) exhibited 13.5% sequence divergence with C. tuscaniense. The unknown bacterium was distinguished from C. tuscaniense by, DNA-DNA hybridization, cellular fatty acid profiles, MALDI-TOF analyses of cell extracts and biochemical tests. Based on the phylogenetic and phenotypic criteria, it is proposed that this bacterium be classified as new species, Corynebacterium aquatimens sp. nov., and is represented by strain IMMIB L-2475(T) (=DSM 45632(T)=CCUG 61574(T)).     

Ultrastructural alterations induced by Δ(24(25))-sterol methyltransferase inhibitors on Trichomonas vaginalis

In a search for thermophilic ethanol-tolerant bacteria, water-sediment samples collected at springs in Yunnan province of China were screened by ethanol enrichment. A novel thermophilic bacterium, strain E13(T) , was isolated. It exhibits a unique and remarkable ability to preferably grow in the presence of ethanol and is able to tolerate 13% (v/v) ethanol at 60 °C. The isolate is a facultative aerobic, Gram-positive, motile, spore-forming rod that is capable of utilizing a range of carbon sources, such as xylose, arabinose and cellobiose. Phylogenetic analysis based on 16S rRNA gene similarity showed the strain to be affiliated with the species Anoxybacillus flavithermus (99.2% sequence similarity). DNA-DNA hybridization comparisons demonstrated a 64.8% DNA-DNA relatedness between strain E13(T) and A. flavithermus DSM 2641(T) . On the basis of phenotypic characteristics, phylogenetic data and DNA-DNA hybridization data, it was concluded that the isolate merited classification as a novel subspecies of A. flavithermus, for which the name Anoxybacillus flavithermus ssp. yunnanensis ssp. nov. is proposed. The type strain of this subspecies is E13(T) (=CCTCC AB2010187(T) =KCTC 13759(T) ).     

苯酚高效降解菌的筛选和降解特性的研究

从天津市煤气厂的活性污泥中筛选、分离得到一株高效苯酚降解菌。经BIOLOG细菌自动鉴定系统及16SrDNA鉴定,该菌株为粪产碱杆菌(Alcaligenesfaecalis)。苯酚降解实验证实,该菌能在76h内完全降解1600mg·L-1的苯酚,并且随着苯酚浓度的增加,底物抑制作用增强,细胞得率下降。     

Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis.

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412(T), which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.     

Proposal of two subspecies of Fusobacterium necrophorum (Flügge) Moore and Holdeman: Fusobacterium necrophorum subsp. necrophorum subsp. nov., nom. rev. (ex Flügge 1886), and Fusobacterium necrophorum subsp. funduliforme subsp. nov., nom. rev. (ex Hallé 1898)

The biological and biochemical properties, DNA base compositions, and levels of DNA-DNA homology of two biovars of Fusobacterium necrophorum were examined. Some differences were found between the two biovars in biological and biochemical properties. The G + C contents of DNAs from biovar A strains VPI 2891T (T = type strain), NCTC 10576, N167, Fn47, and Fn43, were 32, 30, 29, 28, and 31 mol%, respectively. The G + C contents of DNAs from biovar B strains Fn524T, 606, Fn49, Fn45, and 1260 were 30, 31, 27, 31, and 30 mol%, respectively. Labeled DNA from biovar A strain VPI 2891T exhibited 100 to 80% relatedness to DNAs from biovar A strains and 59 to 51% relatedness to DNAs from biovar B strains. Labeled DNA from biovar B strain Fn524T exhibited 100 to 81% relatedness to DNAs from biovar B strains and 71 to 60% relatedness to DNAs from biovar A strains. Therefore, the names Fusobacterium necrophorum subsp. necrophorum subsp. nov., nom. rev. (ex Flügge 1886), and Fusobacterium necrophorum subsp. funduliforme subsp. nov., nom. rev. (ex Hallé 1898), are proposed for Fusobacterium necrophorum biovars A and B, respectively. The type strain of F. necrophorum subsp. necrophorum is strain VPI 2891 (= JCM 3718 = ATCC 25286), and the type strain of F. necrophorum subsp. funduliforme is strain Fn524 (= JCM 3724).     

Staphylococcus cohnii subspecies: Staphylococcus cohnii subsp. cohnii subsp. nov. and Staphylococcus cohnii subsp. urealyticum subsp. nov.

Two major subspecies of Staphylococcus cohnii, namely S. cohnii subsp. cohnii, from humans, and S. cohnii subsp. urealyticum, from humans and other primates, are described on the basis of a study of 14 to 25 strains and 18 to 33 strains, respectively. DNA-DNA hybridization studies conducted in our laboratory in 1983 (W. E. Kloos and J. F. Wolfshohl, Curr. Microbiol. 8:115-121, 1983) demonstrated that strains representing the different subspecies were significantly divergent. S. cohnii subsp. urealyticum can be distinguished from S. cohnii subsp. cohnii on the basis of its greater colony size; pigmentation; positive urease, beta-glucuronidase, and beta-galactosidase activities; delayed alkaline phosphatase activity; ability to produce acid aerobically from alpha-lactose; and fatty acid profile. The type strain of S. cohnii subsp. cohnii is ATCC 29974, the designated type strain of S. cohnii Schleifer and Kloos 1975b, 55. The type strain of S. cohnii subsp. urealyticum is ATCC 49330.