Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 2007"
TL;DR: It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available and reveal extensive gene diversity within the current concept of "species".
Abstract: DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.
3,471 citations
TL;DR: A database containing 16S rRNA gene sequences of all prokaryotic type strains was generated and a web-based tool, named EzTaxon, was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods.
Abstract: 16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates. The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/
2,051 citations
TL;DR: A Gram-positive, motile, short-rod-shaped strain, isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach represents a novel species of the genus Georgenia, for which the nameGeorgenia ruanii sp.
Abstract: A Gram-positive, motile, short-rod-shaped strain, designated YIM 004T, was isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers that corresponded to those of its phylogenetic neighbour, Georgenia muralis, i.e. it possessed peptidoglycan type A4α with lysine as the diagnostic cell-wall diamino acid, the predominant menaquinone was MK-8(H4) and the major fatty acid was ai-C15 : 0. The G+C content of the genomic DNA was 72.9 mol%. Strain YIM 004T exhibited a 16S rRNA gene sequence similarity of 97.3 % and a DNA–DNA relatedness value of 18 % with respect to G. muralis DSM 14418T. On the basis of the phenotypic and genotypic differences between the isolate and G. muralis, strain YIM 004T represents a novel species of the genus Georgenia, for which the name Georgenia ruanii sp. nov. is proposed. The type strain is YIM 004T (=CCTCC AB 204065T=DSM 17458T=KCTC 19029T). In addition, an emended description of the genus Georgenia is presented.
766 citations
TL;DR: Small Gram-negative cocco-bacilli resembling Brucella strains from marine mammals were distinguished from the six recognized species by their pattern of utilization of eleven substrates in oxidative metabolism tests and phage lysis.
Abstract: Small Gram-negative cocco-bacilli resembling Brucella strains have been reported from marine mammals since the mid-1990s. Their placement in the genus Brucella has been supported by the following characteristics: they are aerobic, non-motile and catalase-positive, do not produce acid from carbohydrates and have a DNA–DNA relatedness value of >77 % with the six established members of the genus. Twenty-eight European isolates of the genus Brucella from marine mammals were distinguished from the six recognized species by their pattern of utilization of eleven substrates in oxidative metabolism tests and phage lysis. The 28 strains could be further separated into two groups with cetaceans and seals as their respective preferred hosts on the basis of molecular methods and on differences in the metabolism of l-arabinose, d-galactose and d-xylose. The names Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. are proposed for the isolates from cetaceans and seals, respectively. The type strain of Brucella ceti sp. nov. is NCTC 12891T (=BCCN 94-74T) and the type strain of Brucella pinnipedialis sp. nov. is NCTC 12890T (=BCCN 94-73T).
407 citations
TL;DR: The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phy toplasma groups representing three recently described and seven novel putative 'Candidatus Phytoplasma' taxa.
Abstract: Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the CLUSTAL_X program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative 'Candidatus Phytoplasma' taxa.
329 citations
TL;DR: Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae, and the names Bellilinea caldifistulae and Longilinea arvoryzae are proposed.
Abstract: Thermophilic (strain GOMI-1T) and mesophilic (strain KOME-1T) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil, respectively. The two strains were non-spore-forming, non-motile and Gram-negative. Both strains were obligately anaerobic micro-organisms, showing multicellular filamentous morphotypes more than 100 μm in length. The cell width for strain GOMI-1T was 0.2–0.4 μm and that of strain KOME-1T was 0.4–0.6 μm. Strain GOMI-1T could grow at 45–65 °C with a pH range of 6.0–7.5 (optimum growth at 55 °C, pH 7.0). The temperature range for growth of strain KOME-1T was 30–40 °C and the pH range was pH 5.0–8.5 (optimum growth around 37 °C, pH 7.0). Yeast extract was required for growth of both strains. Strain GOMI-1T was able to grow with a number of carbohydrates in the presence of yeast extract. In yeast extract-containing medium, strain KOME-1T could utilize proteins and a limited range of sugars for growth. The G+C contents of the DNA of strains GOMI-1T and KOME-1T were respectively 54.7 and 57.6 mol%. Major fatty acids of strain GOMI-1T were C16 : 0, C14 : 0 and iso-C15 : 0, whereas those of strain KOME-1T were iso-C15 : 0, anteiso-C15 : 0 and C14 : 0. Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1T and KOME-1T, the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi. Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae. Hence, we propose the names Bellilinea caldifistulae gen. nov., sp. nov., and Longilinea arvoryzae gen. nov., sp. nov., for strains GOMI-1T and KOME-1T. The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1T (=JCM 13669T =DSM 17877T) and KOME-1T (=JCM 13670T =KTCC 5380T).
304 citations
TL;DR: It was shown that strain Pseudomonas sp.
Abstract: The taxonomic position of Pseudomonas sp. B13T, isolated as a 3-chlorobenzoate-degrading organism and used for several groundbreaking studies on the enzymology and genetics of the degradative pathway for haloaromatic compounds, was studied in detail. The previously performed physiological studies, the detection of ubiquinone Q-9, the polyamine pattern with putrescine and spermidine as major polyamines, a fatty acid profile with C18 : 1
ω7c, summed feature 3 and C16 : 0 as quantitatively the most important constituents and the 16S rRNA gene sequence demonstrated that Pseudomonas sp. B13T indeed belongs to the genus Pseudomonas. The sequence of the Pseudomonas sp. B13T 16S rRNA gene demonstrated a high degree of similarity with that of Pseudomonas citronellolis DSM 50332T (98.9 %), Pseudomonas nitroreducens DSM 14399T (98.7 %), Pseudomonas jinjuensis DSM 16612T (98.1 %) and Pseudomonas multiresinivorans DSM 17553T (98.7 %). Thus it was shown that strain Pseudomonas sp. B13T can be distinguished from related species by the ability/inability to assimilate N-acetylgalactosamine, d-galactose, putrescine, trans-aconitate and mesaconate and some differences in the fatty acid profile. The positioning of Pseudomonas sp. B13T as a separate taxon was finally verified by DNA hybridization, which demonstrated less than 45 % DNA–DNA similarity between strain Pseudomonas sp. B13T and the reference strains. On the basis of these results, Pseudomonas sp. B13T represents a novel species for which the name Pseudomonas knackmussii sp. nov. is proposed. The type strain is B13T (=DSM 6978T=LMG 23759T).
303 citations
TL;DR: The phylogenetic and phenotypic analyses and DNA-DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5-37.9 mol%, MK-7 as the predominant menaquinone system and iso-C(15 : 0) as a major cellular fatty acid.
Abstract: Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10a(T), 11c and 12B, can tolerate 5 % (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria-Bertani agar medium. The optimum temperature for growth was 37 degrees C (range 16-45 degrees C) and the optimum pH was 7.0-8.0 (range pH 5.5-9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related to Bacillus fusiformis DSM 2898(T) (97.2 % similarity) and Bacillus sphaericus DSM 28(T) (96.9 %). DNA-DNA relatedness was greater than 97 % among the isolated strains and 61.1 % with B. fusiformis DSM 2898(T) and 43.2 % with B. sphaericus IAM 13420(T). The phylogenetic and phenotypic analyses and DNA-DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5-37.9 mol%, MK-7 as the predominant menaquinone system and iso-C(15 : 0) (32 % of the total) as a major cellular fatty acid. In contrast to the type species of the genus Bacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the name Lysinibacillus boronitolerans gen. nov., sp. nov. is proposed. The type strain of Lysinibacillus boronitolerans is strain 10a(T) (=DSM 17140(T)=IAM 15262(T)=ATCC BAA-1146(T)). It is also proposed that Bacillus fusiformis and Bacillus sphaericus be transferred to this genus as Lysinibacillus fusiformis comb. nov. and Lysinibacillus sphaericus comb. nov., respectively.
296 citations
TL;DR: It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group and provide higher resolution than 16S rRNA gene sequences.
Abstract: The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.
275 citations
TL;DR: The pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.
Abstract: The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.
265 citations
TL;DR: Results indicate that the four species of the V. fischeri group represent a lineage within the Vibrionaceae that is distinct from other genera, and propose their reclassification in a new genus, Aliivibrio gen. nov.
Abstract: Four closely related species, Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis, form a clade within the family Vibrionaceae; the taxonomic status and phylogenetic position of this clade have remained ambiguous for many years. To resolve this ambiguity, we tested these species against other species of the Vibrionaceae for phylogenetic and phenotypic differences. Sequence identities for the 16S rRNA gene were > or =97.4 % among members of the V. fischeri group, but were < or =95.5 % for members of this group in comparison with type species of other genera of the Vibrionaceae (i.e. Photobacterium and Vibrio, with which they overlap in G+C content, and Enterovibrio, Grimontia and Salinivibrio, with which they do not overlap in G+C content). Combined analysis of the recA, rpoA, pyrH, gyrB and 16S rRNA gene sequences revealed that the species of the V. fischeri group form a tightly clustered clade, distinct from these other genera. Furthermore, phenotypic traits differentiated the V. fischeri group from other genera of the Vibrionaceae, and a panel of 13 biochemical tests discriminated members of the V. fischeri group from type strains of Photobacterium and Vibrio. These results indicate that the four species of the V. fischeri group represent a lineage within the Vibrionaceae that is distinct from other genera. We therefore propose their reclassification in a new genus, Aliivibrio gen. nov. Aliivibrio is composed of four species: Aliivibrio fischeri comb. nov. (the type species) (type strain ATCC 7744(T) =CAIM 329(T) =CCUG 13450(T) =CIP 103206(T) =DSM 507(T) =LMG 4414(T) =NCIMB 1281(T)), Aliivibrio logei comb. nov. (type strain ATCC 29985(T) =CCUG 20283(T) =CIP 104991(T) =NCIMB 2252(T)), Aliivibrio salmonicida comb. nov. (type strain ATCC 43839(T) =CIP 103166(T) =LMG 14010(T) =NCIMB 2262(T)) and Aliivibrio wodanis comb. nov. (type strain ATCC BAA-104(T) =NCIMB 13582(T) =LMG 24053(T)).
TL;DR: Data obtained and new data indicate that Ensifer adhaerens and 'Sinorhizobium morelense' are not heterotypic synonyms, but represent separate species, which supports the proposal to unite Ensifer and SinorhIZobium in a single genus.
Abstract: Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107-2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and 'Sinorhizobium morelense' are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.
TL;DR: The phylogenetic relationships among phy toplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works, however, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups.
Abstract: Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.
TL;DR: On the basis of physiological characteristics and DNA-DNA hybridization data, it is suggested that strain MLHE-1(T) represents a novel species within the genus Alkalilimnicola for which the name Alkalspirillum mobile ehrlichii is proposed.
Abstract: A facultative chemoautotrophic bacterium, strain MLHE-1(T), was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1(T) were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1(T) could oxidize but not grow on CO, while CH(4) neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1(T) assimilated inorganic carbon via the Calvin-Benson-Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1(T) grew over broad ranges of pH (7.3-10.0; optimum, 9.3), salinity (15-190 g l(-1); optimum 30 g l(-1)) and temperature (13-40 degrees C; optimum, 30 degrees C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1(T) in the class Gammaproteobacteria (family Ectothiorhodospiraceae) and most closely related to Alkalispirillum mobile (98.5 %) and Alkalilimnicola halodurans (98.6 %), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1(T) was able to oxidize As(III). On the basis of physiological characteristics and DNA-DNA hybridization data, it is suggested that strain MLHE-1(T) represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1(T) (=DSM 17681(T)=ATCC BAA-1101(T)). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology.
TL;DR: It is proposed that all the intracellular symbionts known to cluster closely with the type strain of W. pipientis, including those in the currently recognized supergroups (A-H), are officially given this name.
Abstract: Wolbachia pipientis is a maternally inherited, intracellular bacterium found in more than 20 % of all insects, as well as numerous other arthropods and filarial nematodes. It has been the subject of a growing number of studies in recent decades, because of the remarkable effects it has on its arthropod hosts, its potential as a tool for biological control of arthropods of agricultural and medical importance and its use as a target for treatment of filariasis. W. pipientis was originally discovered in cells of the mosquito Culex pipiens and is the only formally described member of the genus. Molecular sequence-based studies have revealed a number of phylogenetically diverse strains of W. pipientis. Owing to uncertainty about whether W. pipientis comprises more than one species, researchers in the field now commonly refer to W. pipientis simply as Wolbachia. In this note, we briefly review higher-level phylogenetic and recombination studies of W. pipientis and propose that all the intracellular symbionts known to cluster closely with the type strain of W. pipientis, including those in the currently recognized supergroups (A-H), are officially given this name.
TL;DR: Two facultatively aerobic, heterotrophic bacteria capable of degrading pectin, xylan, laminarin and some other polysaccharides were obtained from the acidic Sphagnum peat bog Bakchar, in western Siberia, Russia, and were designated strains TPT18(T) and TPT56(T).
Abstract: Two facultatively aerobic, heterotrophic bacteria capable of degrading pectin, xylan, laminarin and some other polysaccharides were obtained from the acidic Sphagnum peat bog Bakchar, in western Siberia, Russia, and were designated strains TPT18T and TPT56T. Cells of these isolates are Gram-negative, non-motile, long rods that are covered by large capsules. On ageing, they transform into spherical L-forms. Strains TPT18T and TPT56T are acido- and psychrotolerant organisms capable of growth at pH 4.2–8.2 (with an optimum at pH 6.0–6.5) and at 2–33 °C (with an optimum at 20 °C). The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c); the quinones are MK-7 and MK-6. Comparative 16S rRNA gene sequence analysis revealed that the novel strains share 97 % sequence similarity and belong to the family Sphingobacteriaceae; however, they are related only distantly to members of the genera Pedobacter (91.8–93.3 % similarity) and Sphingobacterium (89.6–91.2 % similarity). The DNA G+C content of strains TPT18T and TPT56T is 42.4 and 46.1 mol%, respectively. The low DNA–DNA hybridization value (42 %) and a number of phenotypic differences between strains TPT18T and TPT56T indicated that they represent two separate species. Since the two isolates are clearly distinct from all currently described members of the family Sphingobacteriaceae, we propose a novel genus, Mucilaginibacter gen. nov., containing two novel species, Mucilaginibacter gracilis sp. nov. and Mucilaginibacter paludis sp. nov. The type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis are respectively TPT18T (=ATCC BAA-1391T =VKM B-2447T) and TPT56T (=ATCC BAA-1394T =VKM B-2446T).
TL;DR: The phenotypic characterization and phylogenetic data support the placement of isolates C23T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which the name Haloquadratum walsbyi is proposed.
Abstract: Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA–DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S-layer compared with that of isolate C23T. The phenotypic characterization and phylogenetic data support the placement of isolates C23T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which we propose the name Haloquadratum walsbyi gen. nov., sp. nov. The type strain of Haloquadratum walsbyi is C23T (=JCM 12705T=DSM 16854T).
TL;DR: The phylogenetic studies based on 16S rRNA gene sequence data, together with conclusive DNA-DNA reassociation experiments, strongly support the proposal that these strains represent two novel species within the genus Burkholderia.
Abstract: Several strains of the fungus Rhizopus microsporus harbour endosymbiotic bacteria for the production of the causal agent of rice seedling blight, rhizoxin, and the toxic cyclopeptide rhizonin. R. microsporus and isolated endobacteria were selected for freeze-fracture electron microscopy, which allowed visualization of bacterial cells within the fungal cytosol by their two parallel-running envelope membranes and by the fine structure of the lipopolysaccharide layer of the outer membrane. Two representatives of bacterial endosymbionts were chosen for phylogenetic analyses on the basis of full 16S rRNA gene sequences, which revealed that the novel fungal endosymbionts formed a monophyletic group within the genus Burkholderia. Inter-sequence similarities ranged from 98.94 to 100%, and sequence similarities to members of the Burkholderia pseudomallei group, the closest neighbours, were 96.74-97.38%. In addition, the bacterial strains were distinguished from their phylogenetic neighbours by their fatty acid profiles and other biochemical characteristics. The phylogenetic studies based on 16S rRNA gene sequence data, together with conclusive DNA-DNA reassociation experiments, strongly support the proposal that these strains represent two novel species within the genus Burkholderia, for which the names Burkholderia rhizoxinica sp. nov. (type strain, HKI 454T=DSM 19002T=CIP 109453T) and Burkholderia endofungorum sp. nov. (type strain, HKI 456T=DSM 19003T=CIP 109454T) are proposed.
TL;DR: The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision).
Abstract: The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
TL;DR: Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OL-4(T) was most closely related to the fatty-acid-oxidizing, syntrophic bacterium Syntrophomonas sp.
Abstract: An anaerobic, mesophilic, syntrophic fatty-acid-oxidizing bacterium, designated strain OL-4T, was isolated as a co-culture with Methanobacterium formicicum DSM 1535NT from an anaerobic expanded granular sludge bed reactor used to treat an oleate-based effluent. Strain OL-4T degraded oleate, a mono-unsaturated fatty acid, and straight-chain fatty acids C4 : 0–C18 : 0 in syntrophic association with Methanobacterium formicicum DSM 1535NT. Even-numbered fatty acids were degraded to acetate and methane whereas odd-numbered fatty acids were degraded to acetate, propionate and methane. Branched-chain fatty acids were not degraded. The bacterium could not grow axenically with any other substrate tested and therefore is considered to be obligately syntrophic. Fumarate, sulfate, thiosulfate, sulfur and nitrate could not serve as electron acceptors for strain OL-4T to degrade oleate or butyrate. Cells of strain OL-4T were curved rods, formed spores and showed a variable response to Gram staining. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OL-4T was most closely related to the fatty-acid-oxidizing, syntrophic bacterium Syntrophomonas sp. TB-6 (95 % similarity), Syntrophomonas wolfei subsp. wolfei DSM 2245T (94 % similarity) and Syntrophomonas erecta DSM 16215T (93 % similarity). In addition to this moderate similarity, phenotypic and physiological characteristics, such as obligate syntrophy, spore formation and utilization of a broader substrate range, differentiated strain OL-4T from these Syntrophomonas species. Therefore strain OL-4T represents a novel species, for which the name Syntrophomonas zehnderi sp. nov. is proposed. The type strain is OL-4T (=DSM 17840T=JCM 13948T).
TL;DR: Revised standards for novel species of the class Mollicutes are proposed that reflect recent advances in molecular systematics and the species concept for prokaryotes.
Abstract: Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA–DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.
TL;DR: Three strains, Br3437(T), Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella and Mimosa bimucronata and are classified within a novel species, for which the name Burkholderia nodosa sp.
Abstract: Three strains, Br3437T, Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437T) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437T (=LMG 23741T=BCRC 17575T), was isolated from nodules of M. scabrella.
TL;DR: Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (n=21) were well-differentiated, indicating the utility of the method as an identification tool, and it is used for routine diagnosis of xanthomonad species.
Abstract: The genus Xanthomonas currently comprises 27 species with validly published names that are important crop and horticultural pathogens. We have constructed a phylogram from alignment of gyrase B (gyrB) sequences for all xanthomonad species, both to indicate inter-species relatedness and as an aid for rapid and accurate species-level identification. The phylogeny indicated a monophyletic group, with X. albilineans and X. sacchari as the most ancestral species. Three species, X. hyacinthi, X. translucens and X. theicola, formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised X. cucurbitae, X. cassavae and X. codiaei; group 2 comprised X. arboricola, X. campestris, X. populi, X. hortorum, X. gardneri and X. cynarae; group 3 contained the remaining species, within which two further clades, supported by a 100 % bootstrap value, were identified. Group 3A comprised X. axonopodis, X. euvesicatoria, X. perforans and X. melonis, together with X. alfalfae, X. citri and X. fuscans, whose names were recently validly published. Group 3B contained the monocot pathogens X. vasicola and X. oryzae. Two recently identified species, X. cynarae and X. gardneri, were poorly discriminated and were related closely to X. hortorum. Three species, X. perforans, X. euvesicatoria and X. alfalfae, had identical gyrB sequences. Partial sequencing of a further five genes from these species found only minor sequence differences that confirmed their close relatedness. Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (n=21) were well-differentiated, indicating the utility of the method as an identification tool, and we now use this method for routine diagnosis of xanthomonad species.
TL;DR: The minimal standards are considered as guidelines for authors to prepare descriptions of novel taxa and have been endorsed by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halomonadaceae.
Abstract: Following Recommendation 30b of the Bacteriological Code (1990 Revision), a proposal of minimal standards for describing new taxa within the family Halomonadaceae is presented. An effort has been made to evaluate as many different approaches as possible, not only the most conventional ones, to ensure that a rich polyphasic characterization is given. Comments are given on the advantages of each particular technique. The minimal standards are considered as guidelines for authors to prepare descriptions of novel taxa. The proposals presented here have been endorsed by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halomonadaceae.
TL;DR: The feasibility of using the mitochondrial cox1 gene as a taxonomic marker for 'barcoding' and identifying Tetrahymena species and some other ciliated protists is demonstrated.
Abstract: The mitochondrial cytochrome-c oxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of the cox1 gene in identifying ciliates, 75 isolates of the genus Tetrahymena and three non-Tetrahymena ciliates that are close relatives of Tetrahymena, Colpidium campylum, Colpidium colpoda and Glaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of the cox1 sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates of Tetrahymena borealis, Tetrahymena lwoffi, Tetrahymena patula and Tetrahymena thermophila could be identified by their cox1 sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on a cox1 neighbour-joining (NJ) tree. However, strains identified as Tetrahymena pyriformis and Tetrahymena tropicalis showed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on a cox1 NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence of Tetrahymena was about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates of T. pyriformis and Tetrahymena setosa on the one hand and some isolates of Tetrahymena furgasoni and T. lwoffi on the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrial cox1 gene as a taxonomic marker for ‘barcoding’ and identifying Tetrahymena species and some other ciliated protists.
TL;DR: Two novel species, Prevotella copri sp.
Abstract: Six strains (CB7(T), CB18, CB23, CB26, CB28 and CB35(T)) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7(T), CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35(T) were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7(T) and CB35(T) were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7(T) (=JCM 13464(T)=DSM 18205(T)) and CB35(T) (=JCM 13469(T)=DSM 18206(T)), respectively.
TL;DR: A novel species, Aspergillus brasiliensis sp.
Abstract: A novel species, Aspergillus brasiliensis sp. nov., is described within Aspergillus section Nigri. This species can be distinguished from other black aspergilli based on intergenic transcribed region, β-tubulin and calmodulin gene sequences, by amplified fragment length polymorphism analysis and by extrolite profiles. A. brasiliensis isolates produced naphtho-γ-pyrones, tensidol A and B and pyrophen in common with Aspergillus niger and Aspergillus tubingensis, but also several unique compounds, justifying their treatment as representing a separate species. None of the isolates were found to produce ochratoxin A, kotanins, funalenone or pyranonigrins. The novel species was most closely related to A. niger, and was isolated from soil from Brazil, Australia, USA and The Netherlands, and from grape berries from Portugal. The type strain of Aspergillus brasiliensis sp. nov. is CBS 101740T (=IMI 381727T=IBT 21946T).
TL;DR: Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus and were able to reduce nitrate and to hydrolyse aesculin.
Abstract: Two strains named ESC1(T) and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 999 % similarity to the respective type strains Despite this high similarity, the results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum The DNA-DNA hybridization values were respectively 70, 66 and 55 % with respect to O lupini LUP21(T), O anthropi DSM 6882(T) and Ochrobactrum tritici DSM 13340(T) The predominant fatty acids were C(18 : 1)omega7c and C(18 : 1) 2-OH Strains ESC1(T) and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin They produced beta-galactosidase and beta-glucosidase and did not produce urease after 48 h incubation The G+C content of strain ESC1(T) was 564 mol% Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp nov The type strain is ESC1(T) (=LMG 22713(T)=CECT 7172(T))
TL;DR: Based on phylogenetic analysis and physiological tests, strain R7(T) is proposed to represent a novel genus and species, Pelosinus fermentans gen. nov., in the Sporomusa-Pectinatus-Selenomonas group.
Abstract: The goal of this project was to isolate representative Fe(III)-reducing bacteria from kaolin clays that may influence iron mineralogy in kaolin. Two novel dissimilatory Fe(III)-reducing bacteria, strains G12T and G13T, were isolated from sedimentary kaolin strata in Georgia (USA). Cells of strains G12T and G13T were motile, non-spore-forming regular rods, 1–2 μm long and 0.6 μm in diameter. Cells had one lateral flagellum. Phylogenetic analyses using the 16S rRNA gene sequence of the novel strains demonstrated their affiliation to the genus Geobacter. Strain G12T was most closely related to Geobacter pelophilus (94.7 %) and Geobacter chapellei (94.1 %). Strain G13T was most closely related to Geobacter grbiciae (95.3 %) and Geobacter metallireducens (95.1 %). Based on phylogenetic analyses and phenotypic differences between the novel isolates and other closely related species of the genus Geobacter, the isolates are proposed as representing two novel species, Geobacter argillaceus sp. nov. (type strain G12T=ATCC BAA-1139T=JCM 12999T) and Geobacter pickeringii sp. nov. (type strain G13T=ATCC BAA-1140T=DSM 17153T=JCM 13000T). Another isolate, strain R7T, was derived from a primary kaolin deposit in Russia. The cells of strain R7T were motile, spore-forming, slightly curved rods, 0.6×2.0–6.0 μm in size and with up to six peritrichous flagella. Strain R7T was capable of reducing Fe(III) only in the presence of a fermentable substrate. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing less than 92 % similarity to bacteria of the Sporomusa–Pectinatus–Selenomomas phyletic group, including ‘Anaerospora hongkongensis’ (90.2 %), Acetonema longum (90.6 %), Dendrosporobacter quercicolus (90.9 %) and Anaerosinus glycerini (91.5 %). On the basis of phylogenetic analysis and physiological tests, strain R7T is proposed to represent a novel genus and species, Pelosinus fermentans gen. nov., sp. nov. (type strain R7T=DSM 17108T=ATCC BAA-1133T), in the Sporomusa–Pectinatus–Selenomonas group.
TL;DR: P phenotypic, genotypic and phylogenetic analyses revealed that strain PRAA4-1(T) and Chromobacterium violaceum form a monophyletic clade, with the closest ancestral taxon Vogesella indigofera within the Betaproteobacteria.
Abstract: Strain PRAA4-1(T), a motile, Gram-negative, violet-pigmented bacterium, was isolated from Maryland forest soil and found to be orally toxic to Colorado potato beetle larvae and other insects. Morphological, biological, biochemical and molecular characterization revealed that this strain was most similar to Chromobacterium violaceum, the type species and only currently recognized member of the genus Chromobacterium. DNA-DNA hybridization with C. violaceum ATCC 12472(T) was 27 %. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain PRAA4-1(T) and Chromobacterium violaceum form a monophyletic clade, with the closest ancestral taxon Vogesella indigofera within the Betaproteobacteria. On the basis of phenotypic, genotypic and phylogenetic analyses, strain PRAA4-1(T) (=NRRL B-30655(T)=DSM 17043(T)) is proposed as the type strain of a novel species of the genus Chromobacterium, Chromobacterium subtsugae sp. nov.