- Volume 52, Issue 6, 2002
Volume 52, Issue 6, 2002
- Articles
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Pseudomonas chloritidismutans sp. nov., a non-denitrifying, chlorate-reducing bacterium.
More LessA Gram-negative, facultatively anaerobic, rod-shaped, dissimilatory chlorate-reducing bacterium, strain AW-1(T), was isolated from biomass of an anaerobic chlorate-reducing bioreactor. Phylogenetic analysis of the 16S rDNA sequence showed 100% sequence similarity to Pseudomonas stutzeri DSM 50227 and 98.6% sequence similarity to the type strain of P. stutzeri (DSM 5190(T)). The species P. stutzeri possesses a high degree of genotypic and phenotypic heterogeneity. Therefore, eight genomic groups, termed genomovars, have been proposed based upon deltaTm values, which were used to evaluate the quality of the pairing within heteroduplexes formed by DNA-DNA hybridization. In this study, DNA-DNA hybridization between strain AW-1(T) and P. stutzeri strains DSM 50227 and DSM 5190(T) revealed respectively 80.5 and 56.5% similarity. DNA-DNA hybridization between P. stutzeri strains DSM 50227 and DSM 5190(T) revealed 48.4% similarity. DNA-DNA hybridization indicated that strain AW-1(T) is not related at the species level to the type strain of P. stutzeri. However, strain AW-1(T) and P. stutzeri DSM 50227 are related at the species level. The physiological and biochemical properties of strain AW-1(T) and the two P. stutzeri strains were compared. A common characteristic of P. stutzeri strains is the ability to denitrify. However, in growth experiments, strain AW-1(T) could use only chlorate or oxygen as an electron acceptor and not nitrate, perchlorate or bromate. Strain AW-1(T) is the first chlorate-reducing bacterium described that does not possess another oxyanion-reduction pathway. Cell extracts of strain AW-1(T) showed chlorate and bromate reductase activities but not nitrate reductase activity. P. stutzeri strains DSM 50227 and DSM 5190(T) could use nitrate or oxygen as an electron acceptor, but not chlorate. Chlorate reductase activity, in addition to nitrate reductase activity, was detected in cell extracts of both P. stutzeri strains. Chlorite dismutase activity was absent in extracts of both P. stutzeri strains but was present in extracts of strain AW-1(T). Based on the hybridization experiments and the physiological and biochemical data, it is proposed that strain AW-1(T) be classified as a novel species of Pseudomonas, Pseudomonas chloritidismutans sp. nov. The type strain is strain AW-1(T) (= DSM 13592(T) = ATCC BAA-443(T)).
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Phylogeny of Maricaulis Abraham et al. 1999 and proposal of Maricaulis virginensis sp. nov., M. parjimensis sp. nov., M. washingtonensis sp. nov. and M. salignorans sp. nov.
Thirteen marine bacteria isolated from different locations, belonging to the genus Maricaulis, were characterized by 16S rRNA gene sequencing, DNA-DNA hybridizations and analysis of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from total lipids, mass spectrometry of polar lipids and determination of temperature and NaCl tolerances. The data obtained led to the identification of five new sulfoquinovosyl diacylglycerols, using tandem mass spectrometry, and the fragmentation patterns of the individual compounds. Four novel species were identified and described as Maricaulis virginensis sp. nov. (type strain VKM B-1 5139T)), Maricaulis parjimensis sp. nov. (type strain MCS 25(T)), Maricaulis washingtonensis sp. nov. (type strain MCS 6(T)) and Maricaulis salignorans sp. nov. (type strain MCS 18(T)). They differ in their temperature and salt tolerances and can be differentiated by their polar lipids and fatty acid patterns, as well as their ITS1 and 16S rRNA gene sequences.
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Pseudomonas thermotolerans sp. nov., a thermotolerant species of the genus Pseudomonas sensu stricto.
More LessA bacterium, strain CM3(T), which has an optimal growth temperature of approximately 47 degrees C and a maximal growth temperature of 55 degrees C, was isolated from a hexadecane enrichment culture, obtained from a sample of the industrial cooking water of a cork-processing plant. 16S rRNA gene sequence analysis demonstrated that this Gram-negative, aerobic, rod-shaped bacterium is related to species of the genus Pseudomonas. Phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of this isolate and the total fatty acid methyl ester profile revealed predominantly C16:1 and C18:1 at a growth temperature of 25 degrees C, whereas, at a growth temperature of 50 degrees C, C16:0 was the dominant fatty acid. This is the first report of a species of Pseudomonas sensu stricto that may be considered to be truly thermotolerant. Isolate CM3(T) (= DSM 14292(T) = LMG 21284(T)) represents the type strain of a novel species of the genus Pseudomonas, named Pseudomonas thermotolerans sp. nov.
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Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea.
More LessThree strains of denitrifying estuarine bacteria, OS217(T), 05220 and OS226, were characterized for their physiological and biochemical features, fatty acid profiles and their phylogenetic position based on 16S rDNA sequences. The strains were isolated from the oxic-anoxic interface of an anoxic basin of the central Baltic Sea. Phylogenetic analyses of the 16S rDNA sequences revealed a clear affiliation with members of the genus Shewanella of the gamma-Proteobacteria. The closest sequence similarity was seen with Shewanella baltica, Shewanella putrefaciens and Shewanella frigidimarina (95-96%). The dominant fatty acids were 16:1omega7c, 15:0 iso, 16:0 and 13:0 iso. The G+C content of the DNA ranged from 46.8 to 48.1 mol%. The strains were unpigmented, polarly flagellated, mesophilic, facultatively anaerobic and able to use nitrate, nitrite and sulphite as electron acceptors. Growth was observed at salinities from 0 to 6%, with an optimum between 1 and 3%. According to their morphology, physiology, fatty acid composition and 16S rRNA sequences, the described bacteria fitted well into the genus Shewanella, but could be easily distinguished from the Shewanella species described to date. Because of their capacity for vigorous denitrification, the name Shewanella denitrificans sp. nov. is suggested for the Baltic isolates, for which the type strain is OS217(T) (= DSM 15013(T) = LMG 21692(T)).
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Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov.
More LessLegume species belonging to the genus Lespedeza are annual or perennial herb or shrub plants that grow in the northern hemisphere. They are known for the formation of root nodules, but little information is available about their microsymbionts. In this study, 58 root-nodule isolates from Lespedeza spp., obtained from China and the USA, were characterized using numerical taxonomic analysis of phenotypic features, SDS-PAGE analysis of whole-cell proteins, DNA-DNA hybridization, 16S rRNA gene sequence analysis and cross-nodulation with selected legume species. From the results generated using these approaches, it was concluded that Lespedeza spp. were promiscuous hosts for rhizobia. Four main clusters of bacteria, which included 35 of the strains isolated from Lespedeza spp., were defined upon numerical taxonomic analysis; these groups corresponded to those determined from analyses of protein electrophoretic and DNA-DNA hybridization data. The four clusters were found to define strains belonging to one of four species, Sinorhizobium saheli, Bradyrhizobium japonicum, Bradyrhizobium elkanii or a novel species of the genus Bradyrhizobium. The strains of B. japonicum and B. elkanii were all from the USA soil samples, and their representative strains could not nodulate soybean. The seven strains found to represent the novel Bradyrhizobium sp. were from China. These were differentiated from recognized species of the genus Bradyrhizobium by all of the taxonomic methods used here; hence, it is proposed that the novel strains isolated from Lespedeza spp. represent a novel species of the genus Bradyrhizobium, Bradyrhizobium yuanmingense. The type strain of the novel species, CCBAU 10071(T) (= CFNEB 101(T)), formed ineffective nodules on Medicago sativa and Melilotus albus but did not nodulate soybean. The other 23 bacterial strains isolated from Lespedeza spp. were found to form single branches or small groups (two to three strains) that were related to Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium spp. on the basis of numerical taxonomic analysis, indicating the possibility that other rhizobial species are also associated with Lespedeza spp.
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Rhizobium indigoferae sp. nov. and Sinorhizobium kummerowiae sp. nov., respectively isolated from Indigofera spp. and Kummerowia stipulacea.
More LessForty-eight rhizobial isolates from root nodules of Indigofera and Kummerowia, two genera of annual or perennial wild legumes growing in the Loess Plateau in north-western China, were characterized by a polyphasic approach. Two main groups, cluster 1 and cluster 2, were defined based upon the results of numerical taxonomy, SDS-PAGE of whole-cell proteins and DNA relatedness. All the isolates within cluster 1 were isolated from Indigofera and they were identified as Rhizobium strains by 16S rRNA gene analysis. DNA relatedness of 29.5-48.9% was obtained among the cluster 1 isolates and the reference strains for defined Rhizobium species. Cluster 2 consisted of isolates from Kummerowia stipulacea and was identified as belonging to Sinorhizobium by 16S rRNA gene analyses. DNA relatedness varied from 5.2 to 41.7% among the isolates of cluster 2 and reference strains for Sinorhizobium species. Considering the existence of distinctive features among these two groups and related species within the genera Rhizobium and Sinorhizobium, we propose two novel species, Rhizobium indigoferae sp. nov. for cluster 1, with isolate CCBAU 71714(T) (= AS 1.3046(T)) as the type strain, and Sinorhizobium kummerowiae sp. nov. for cluster 2, with isolate CCBAU 71042(T) (= AS 1.3045(T)) as the type strain.
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Paenibacillus turicensis sp. nov., a novel bacterium harbouring heterogeneities between 16S rRNA genes.
More LessA Gram-positive, facultatively anaerobic, rod-shaped, endospore-forming bacterium (strain MOL722(T)) was characterized using phenotypic and molecular methods. Fatty acid analysis and biochemical examination indicated that the isolate belongs to the Gram-positive bacteria with low DNA G+C content, probably to the genus Paenibacillus. Direct sequencing of the 16S rRNA gene showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded seven different sequences varying at 15 positions, with one being an insertion. The isolate shares 98.5% sequence similarity with Paenibacillus sp. P15-9, but less than 94% similarity with other paenibacilli and bacilli. Phylogenetic analysis with different treeing methods revealed that strain MOL722(T), together with Paenibacillus sp. P15-9, forms a novel monophyletic clade within the genus Paenibacillus. Based on phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium is classified as the novel species Paenibacillus turicensis sp. nov., the type strain of which is strain MOL722(T) (= DSM 14349(T) = NCCB 100011(T)).
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Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost.
A thermophilic, spore-forming rod isolated from hay compost in Korea was subjected to a taxonomic study. The micro-organism, designated strain SK-1(T), was identified as being aerobic, Gram-positive, motile and rod-shaped. Growth of the isolate was observed at 45-70 degrees C (optimum 60 degrees C) and pH 6.0-9.0 (optimum pH 7.5). The G+C content of the genomic DNA was 43.9 mol%. Chemotaxonomic characteristics of the isolate included the presence of mesodiaminopimelic acid in the cell wall and iso-C15:0 and iso-C17:0 as the major cellular fatty acids. The predominant isoprenoid quinone was MK-7. The chemotaxonomic characteristics of strain SK-1(T) were the same as those of the genus Geobacillus. Phylogenetic analysis based on 16S rDNA sequences showed that strain SK-1(T) is most closely related to Geobacillus thermoglucosidasius. However, the phenotypic properties of strain SK-1(T) were clearly different from those of G. thermoglucosidasius. The level of DNA-DNA relatedness between strain SK-1(T) and the type strain of G. thermoglucosidasius was 27%. On the basis of the phenotypic traits and molecular systematic data, strain SK-1(T) represents a novel species within the genus Geobacillus, for which the name Geobacillus toebii sp. nov. is proposed. The type strain is strain SK-1(T) (= KCTC 0306BP(T) - DSM 14590(T)).
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Rothia amarae sp. nov., from sludge of a foul water sewer.
A Gram-positive bacterium, strain J18(T), isolated from sludge of a foul water sewer, was subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacterium based on its 16S rDNA sequence showed that it belongs to the genus Rothia and forms a distinct phyletic clade with the type strain of Rothia nasimurium. Morphological, physiological and chemotaxonomic characteristics supported the assignment of this organism to the genus Rothia and distinguished it from the type strains of all validly described Rothia species. Therefore, it is proposed that this bacterium be classified in the genus Rothia as Rothia amarae sp. nov. The type strain is strain J18(T) (= AS 4.1721(T) = JCM 11375(T)).
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Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic gamma-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae).
More LessA cellulolytic, dinitrogen-fixing bacterium isolated from the gill tissue of a wood-boring mollusc (shipworm) Lyrodus pedicellatus of the bivalve family Teredinidae and 58 additional strains with similar properties, isolated from gills of 24 bivalve species representing 9 of 14 genera of Teredinidae, are described. The cells are Gram-negative, rigid, rods (0.4-0.6 x 3-6 microm) that bear a single polar flagellum. All isolates are capable of chemoheterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Xylan, pectin, carboxymethylcellulose, cellobiose and a variety of sugars and organic acids also support growth. Growth requires addition of combined nitrogen when cultures are vigorously aerated, but all isolates fix dinitrogen under microaerobic conditions. The pH, temperature and salinity optima for growth were determined for six isolates and are approximately 8.5, 30-35 degrees C and 0.3 M NaCl respectively. The isolates are marine. In addition to NaCl, growth requires elevated concentrations of Ca2+ and Mg2+ that reflect the chemistry of seawater. The DNA G+C content ranged from 49 to 51 mol%. Four isolates were identical with respect to small-subunit rRNA sequence over 891 positions compared and fall within a unique clade in the gamma-subclass of the Proteobacteria. Based on morphological, physiological and phylogenetic characteristics and specific symbiotic association with teredinid bivalves, a new genus and species, Teredinibacter turnerae gen. nov., sp. nov., is proposed. The type strain is T7902(T) (= ATCC 39867(T) = DSM 15152(T)).
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Characterization of a novel halophilic archaeon, Halobiforma haloterrestris gen. nov., sp. nov., and transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov.
More LessStrain 135(T), a novel red-pigmented, aerobic, extremely halophilic member of the Archaea showing rod, coccus and slightly pleomorphic morphology, was isolated from hypersaline soil close to Aswan (Egypt). This organism is neutrophilic, motile and requires at least 2.2 M NaCl, but no MgCl2, for growth and exhibits optimal growth at 42 degrees C. Polar lipid analysis revealed the presence of sulfated triglycosyl diether and triglycosyl diether as the sole glycolipids as well as the absence of the glycerol diether analogue of phosphatidyl glycerosulfate. C20:C20 and C20:C25 core lipids are present in almost equal proportions. The G+C content of the DNA is 66.9 mol%. 16S rDNA analysis revealed that strain 135(T) was a member of the phyletic group defined by the family Halobacteriaceae, but there was a low degree of similarity to other members of this family. Highest similarity values of 96.4 and 93.8-94.3% were obtained to the 16S rDNA of Natronobacterium nitratireducens and Natronobacterium gregoryi, Natronococcus occultus and Natronococcus amylolyticus. Strain 135(T) is able to accumulate polyhydroxybutyrate as intracellular reserve material. On the basis of the data presented, strain 135(T) should be placed in a new genus, Halobiforma gen. nov. as Halobiforma haloterrestris sp. nov. The type strain is strain 135(T) (= DSM 13078(T) = JCM 11627(T)). Moreover, the transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov. is proposed.
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Characterization of Serratia isolates from soil, ecological implications and transfer of Serratia proteamaculans subsp. quinovora Grimont et al. 1983 to Serratia quinivorans corrig., sp. nov.
More LessEleven strains of Serratia were isolated from different soils and the guts of invertebrates and characterized by their sensitivity to eight indigenous bacteriophages. They were also classified according to bacteriocin production and sensitivity, BiOLOG plate and API 20E strip profiles and 16S rRNA sequence information. One strain was thus identified as Serratia plymuthica, another as Serratia fonticola. The remaining strains were shown to be closely related to Serratia proteamaculans subsp. quinovora Grimont et al. 1983 after DNA-DNA cross-hybridization demonstrated relatedness greater than 70% with the type strain of this subspecies. From an ecological perspective, our results illustrated the wide variation in sensitivity that closely related Serratia strains have towards various indigenous soil phages and that these phages have broad host ranges within the genus. Furthermore, the phage and bacteriocin interactions within the Serratia strains examined were intricate and did not reflect phylogenetic relationships. These results together imply that complex interactions will occur in soil within the natural community of Serratia strains and their bacteriophages. DNA-DNA cross-hybridization and phenotypic characterization showed that S. proteamaculans subsp. quinovora strains formed a cohesive group at the species level. It is therefore concluded that these strains should be designated as Serratia quinivorans corrig., sp. nov.
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Nocardiopsis metallicus sp. nov., a metal-leaching actinomycete isolated from an alkaline slag dump.
A taxonomic study was carried out on a metal-mobilizing, alkaliphilic bacterium from an alkaline slag dump, strain KBS6(T). The strain produced substrate and aerial mycelia. Growth occurred in the pH range 7.0-10.5, with an optimum at pH 8.5. A salt concentration of up to 10% was tolerated, and various organic substrates were used for growth. The results of a 16S rDNA sequence comparison revealed that strain KBS6(T) belongs to the genus Nocardiopsis. DNA-DNA hybridization with the two closest relatives, Nocardiopsis exhalans and Nocardiopsis prasina, gave similarity values of 18.2 and 44.1%, respectively, which indicated that strain KBS6(T) represents a novel species of the genus Nocardiopsis. This is consistent with the morphological, physiological and chemotaxonomic data. Because of the ability of this micro-organism to solubilize metals, the name Nocardiopsis metallicus sp. nov. is proposed for strain KBS6(T) (= DSM 44598(T) = NRRL B-24159(T)), this being the type strain.
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Phylogenetic relationships amongst tetrahymenine ciliates inferred by a comparison of telomerase RNAs.
More LessThe phylogenetic relationships between ciliate species in the suborder Tetrahymenina, order Hymenostomata, was investigated by comparing their telomerase RNA (TER) sequences. This relatively small RNA is an integral part of telomerase, the ribonucleoprotein enzyme that catalyses the synthesis of telomeric DNA. Despite a relatively rapid rate of primary sequence divergence, conserved functional and structural elements within TERs facilitate the accurate alignment of truly homologous nucleotides. The tetrahymenine phylogeny derived from distance analysis of TER sequences is largely consistent with those based on rRNA and histone sequences.
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Cryptococcus statzelliae sp. nov. and three novel strains of Cryptococcus victoriae, yeasts isolated from Antarctic soils.
More LessA morphological and physiological characterization of yeast strains CBS 8908, CBS 8915, CBS 8920, CBS 8925(T) and CBS 8926, isolated from Antarctic soils, was performed. Phylogenetic analyses of the sequences of the D1/D2 regions and the adjacent internal transcribed spacer (ITS) regions of the large-subunit rDNA of these strains placed them into the Tremellales clade of the Hymenomycetes. The sequence data identified strains CBS 8908, CBS 8915 and CBS 8920 as belonging to the species Cryptococcus victoriae. Strains CBS 8925(T) and CBS 8926 were found to represent an unique clade within the Hymenomycetes, with Dioszegia crocea CBS 6714(T) being their closest phylogenetic relative. Fatty acid composition and proteome fingerprint data for these novel strains were also obtained. No sexual state was observed. A novel basidiomycetous species, Cryptococcus statzelliae, is proposed for strains CBS 8925(T) and CBS 8926.
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Reclassification of the Sporobolomyces roseus and Sporidiobolus pararoseus complexes, with the description of Sporobolomyces phaffii sp. nov.
More LessMore than 50 ballistoconidium-forming yeast strains, isolated from plant leaves collected in Yunnan, China, were identified as Sporobolomyces roseus Kluyver & van Niel by conventional methods. However, comparison of the internal transcribed spacer (ITS) region and 265 rDNA D1/D2 domain sequences indicated that these strains represented more than one species. Type or authentic strains of the synonyms of Sporobolomyces roseus and the closely related species Sporidiobolus pararoseus Fell & Tallman were employed in the rDNA sequence comparison. Sporobolomyces boleticola Ramírez, Sporobolomyces pollaccii Verona & Ciferri, Sporobolomyces roseus var. madurae Janke and Torulopsis somala Verona were confirmed to be conspecific with Sporobolomyces roseus. Another synonym of this species, Sporobolomyces salmoneus Derx, was located together with Sporobolomyces marcillae Santa Maria in a separate clade. Two synonyms of Sporidiobolus pararoseus, Sporobolomyces carnicolor Yamasaki & Fujii (nom. inval.) and Sporobolomyces japonicus Iizuka & Goto, were revealed to represent two distinct species. The name Sporobolomyces carnicolor is validated, with strain CBS 4215(T) as the type strain. A novel species represented by five of the selected Yunnan strains was confirmed, for which the name Sporobolomyces phaffii sp. nov. is proposed (type strain CH 2.052(T) = AS 2.2137(T) = JCM 11491(T) = CBS 9129(T)). This study also indicates that yeast species with similar ITS sequences may have quite different D1/D2 sequences.
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Citeromyces siamensis sp. nov., a novel halotolerant yeast isolated in Thailand.
More LessTwo halotolerant yeast strains, H130(T) and H149, were isolated from dry salted squid and fermented soybeans, respectively, in Thailand. Both isolates grew by multilateral budding, produced asci that had one roughened spherical ascospore and contained ubiquinone Q-8. These characteristics were shared by Citeromyces matritensis, the only species of the genus Citeromyces. Strains H130(T) and H149 were differentiated from C matritensis by their ability to assimilate L-sorbose and L-lysine and to grow at 37 degrees C. The novel isolates were more tolerant to higher concentrations of cations (3 M NaCl or 0.8 M LiCI) and to higher osmotic pressure (60% glucose) than C. matritensis. A phylogenetic analysis of 18S rRNA gene sequence data indicated that the two novel isolates represented a sister species to C. matritensis. Furthermore, DNA-DNA hybridization data indicated that the isolates were clearly distinct from the type strain of C. matritensis (IFO 0954(T). Based on the above characteristics, strains H130(T) and H149 are proposed to represent a novel species within the genus Citeromyces, Citeromyces siamensis; the type strain is H130(T) (= IFO 11052(T) = JCM 11522(T) = TISTR 5777(T) = CBS 9153(T)).
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Necessary corrections to the Approved Lists of Bacterial Names according to Rule 40d (formerly Rule 46). Request for an opinion.
More LessAccording to Rule 40d (formerly Rule 46), the authorship and dates of ten subspecies cited in the Approved Lists of Bacterial Names should be corrected. It is requested that such changes be approved by the Judicial Commission.
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Volumes and issues
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Volume 74 (2024)
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