- Volume 58, Issue 9, 2008

A rod-shaped marine bacterium, designated CL-Z59T, was isolated from seawater enriched with zooplankton. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CL-Z59T belongs to the genus Nocardioides, the highest level of sequence similarity (99.2 %) being found with respect to Nocardioides marinisabuli KCCM 42681T. However, DNA–DNA hybridization experiments between strain CL-Z59T and N. marinisabuli KCCM 42681T revealed a mean relatedness value of 33 %. Cells were Gram-positive, strictly aerobic and non-motile. Strain CL-Z59T grew optimally at pH 6–7 and 25–30 °C and at a NaCl concentration of 3 %. The isolate was characterized chemotaxonomically as having ll-diaminopimelic acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the predominant cellular fatty acid was iso-C16 : 0. The DNA G+C content was 73.3 mol%. On the basis of phylogenetic, genotypic and phenotypic data, strain CL-Z59T represents a novel species of the genus Nocardioides, for which the name Nocardioides salarius sp. nov. is proposed. The type strain is CL-Z59T (=KCCM 42320T=DSM 18239T).

A novel halophilic, filamentous, actinomycete strain, designated YIM 90648T, was isolated from a salt lake in Xinjiang Province, north-west China, and subjected to a polyphasic taxonomic study. Optimal growth occurred at 37 °C, pH 7.0–8.0 and 15 % (w/v) NaCl. The aerial mycelium of strain YIM 90648T formed long chains of spores at maturity and the spores were cylindrical with smooth surfaces. Spore chains with pseudosporangia at the end were borne on the substrate mycelium and most spores had wrinkled surfaces. Strain YIM 90648T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and ribose as the major whole-cell components. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol mannoside. MK-10(H8), MK-11(H4), MK-11(H6) and MK-11(H8) were the predominant menaquinones. The major fatty acids were i-C16 : 0 and ai-C17 : 0. The DNA G+C content was 68 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 90648T formed a distinct lineage within the family Nocardiopsaceae and showed 16S rRNA gene sequence similarity of 93.3–95.0 % with members of the family Nocardiopsaceae. On the basis of the polyphasic evidence, a novel genus and species, Haloactinospora alba gen. nov., sp. nov., is proposed to accommodate this isolate. The type strain of Haloactinospora alba is YIM 90648T (=DSM 45015T =CCTCC AA 206008T).

A Gram-positive, aerobic actinomycete, designated strain YIM 45505T, was isolated from a soil sample collected from Yunnan province, south-west China. Cells exhibited cream–white aerial mycelium and orange–yellow to yellow–brown substrate mycelium. The substrate mycelium fragmented into rod-shaped elements, and the aerial mycelium formed long chains of spores. 16S rRNA gene sequence analysis revealed that strain YIM 45505T was related most closely to Pseudonocardia oroxyli DSM 44984T (98.5 % similarity) and Pseudonocardia halophobica IMSNU 21327T (97.5 %). The G+C content of the DNA of strain YIM 45505T was 74.1 mol%. Combined with results of DNA–DNA hybridization and phenotypic tests, these data revealed that strain YIM 45505T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia ailaonensis sp. nov. is proposed. The type strain is YIM 45505T (=KCTC 19315T =DSM 44979T).

Several nocardioform actinomycetes were isolated from tufaceous surfaces with whitish-grey patinas in the catacombs of St Callistus in Rome, Italy. The morphology of the isolates and their chemotaxonomic characteristics such as ll-diaminopimelic acid in the cell-wall peptidoglycan, the major menaquinone of MK-9(H4), phosphatidylinositol, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids, as well as complex cellular fatty acid patterns with anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0 as predominating components, were in agreement with their classification as members of the genus Kribbella by 16S rRNA gene sequence analysis. The isolates fell into two clusters as revealed by their ribosomal intergenic spacer, RiboPrint and cellular fatty acid patterns and by their MALDI-TOF mass spectra. The two clusters were represented by the strains BC631T and BC633T which shared 97.9 % 16S rRNA gene sequence similarity. Strain BC631T represented a cluster of yellow pigmented strains and was a phylogenetic neighbour of Kribbella koreensis DSM 17837T (gene sequence similarity 98.0 %), while strain BC633T was related to Kribbella flavida DSM 17836T and Kribbella karoonensis DSM 17344T (gene sequence similarities of 98.8 % and 98.6 %, respectively). Strains BC631T and BC633T could be differentiated from each other and from their closest phylogenetic neighbours by phenotypic characteristics and DNA–DNA relatedness values far below 70 %. It is concluded that the two new strains represent two novel species, for which the names Kribbella catacumbae sp. nov. (type strain BC631T=DSM 19601T=JCM 14968T) and Kribbella sancticallisti sp. nov. (type strain BC633T=DSM 19602T=JCM 14969T) are proposed.

Five bacterial isolates were recovered from dermatitis or organ lesions of five agamid lizards. Three strains were recovered from Uromastyx species with dermatitis or septicaemia. All five isolates were Gram-positive small rods that could not be identified using conventional phenotypic systems. They grew on sheep blood agar as small haemolytic colonies after 24 h of incubation at temperatures between 25 and 42 °C under aerobic, microaerophilic or anaerobic conditions. They were catalase-positive and non-motile. Comparative analysis of 16S rRNA gene sequences revealed that the strains represent a new taxon within the class Actinobacteria. Their nearest phylogenetic neighbours were determined as Brachybacterium faecium LMG 19847T (95.9 % 16S rRNA gene sequence similarity) and Dermabacter hominis NCIMB 13131T (95.3 % similarity). The DNA G+C content of one of the novel isolates, strain IMP2T, was 61 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of coryneform bacteria, it is proposed that this novel taxon be classified as Devriesea agamarum gen. nov., sp. nov. The type strain is IMP2T (=LMG 24257T=CCUG 55056T).

A novel actinomycete strain, OFN S17T, was isolated from a sample collected from Altamira Cave, Cantabria, Spain. This strain was identified by using a polyphasic taxonomic approach. The 16S rRNA, hsp65 and sod gene sequences of the strain were determined and compared with those of representative Nocardia species. The results showed that strain OFN S17T should be assigned to the genus Nocardia. Phylogenetic analysis indicated that strain OFN S17T was most closely related to the type strain of Nocardia tenerifensis (98.6, 96.2 and 96 % similarity, respectively, for the 16S rRNA, hsp65 and sod gene sequences). The DNA G+C content was 64.4 mol%. DNA–DNA hybridization analyses revealed 29 % relative reassociation between the DNA of strain OFN S17T and N. tenerifensis DSM 44704T. The phenotypic and genotypic data show that strain OFN S17T merits recognition as a representative of a novel species of the genus Nocardia, for which the name Nocardia altamirensis sp. nov. is proposed. The type strain is OFN S17T (=CIP 109606T =DSM 44997T).

Strain PON10T is a yellow-pigmented, Gram-positive, aerobic, motile, rod-shaped bacterium isolated from the Pindari glacier of the Indian Himalayas. The cell-wall peptidoglycan contained dl-diaminobutyric acid as the diamino acid. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 and the major isoprenoid quinones were MK-10 and MK-11. Based on the above characteristics, strain PON10T was assigned to the genus Leifsonia. blast sequence similarity results indicated that Leifsonia ginsengi and Leifsonia poae were the nearest relatives, with 16S rRNA gene sequence similarity of 97.0 and 96.8 % to the respective type strains. A difference of 3 % in the 16S rRNA gene sequence indicated that PON10T represents a novel species of the genus Leifsonia, and therefore DNA–DNA hybridization was not done. In addition, PON10T showed a number of differences from Leifsonia ginsengi and Leifsonia poae with respect to phenotypic and chemotaxonomic characteristics. Thus, based on the differences it exhibited from Leifsonia ginsengi and Leifsonia poae, strain PON10T was identified as representing a novel species named Leifsonia pindariensis sp. nov. The type strain is PON10T (=LMG 24222T =MTCC9128T). An emended description of the genus Leifsonia is also presented.

A Gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain BG-1T, was isolated from a salt lake, Lake Bagaejinnor, in Inner Mongolia, China. Strain BG-1T was able to grow at 25–55 °C, required at least 2.5 M NaCl for growth (with an optimum at 3.4 M NaCl) and grew at pH 6.0–9.0 (with an optimum at pH 7.5). Hypotonic treatment with less than 2.0 M NaCl caused cell lysis. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence positioned the isolate within the genus Halorubrum in the family Halobacteriaceae. Strain BG-1T was most closely related to Halorubrum aidingense 31-hongT (98.8 % sequence similarity), Halorubrum saccharovorum NCIMB 2081T (98.6 %), Halorubrum lacusprofundi ACAM 34T (98.6 %) and Halorubrum lipolyticum 9-3T (98.4 %). However, values for DNA–DNA hybridization between strain BG-1T and the most closely related members of the genus Halorubrum were below 40 %. Analysis of the polar lipids of strain BG-1T revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid found in neutrophilic species of the genus Halorubrum. The G+C content of the genomic DNA was 69.4 mol% (T m). Comparison of the phenotypic characteristics of the strain with those of Halorubrum species supported the conclusion that BG-1T represents a novel species within this genus, for which the name Halorubrum kocurii sp. nov. is proposed. The type strain is BG-1T (=CECT 7322T =CGMCC 1.7018T =JCM 14978T).

A Gram-negative, motile, rod-shaped, extremely halophilic archaeon, designated strain HPC1-2T, was isolated from pla-ra, a salt-fermented fish product of Thailand. Strain HPC1-2T was able to grow at 20–60 °C (optimum at 37–40 °C), at 2.6–5.1 M NaCl (optimum at 3.4–4.3 M NaCl) and at pH 5.0–8.0 (optimum at pH 7.0–7.5). Hypotonic treatment with less than 1.7 M NaCl caused cell lysis. The major polar lipids of the isolate were C20C20 derivatives of phosphatidylglycerol, methylated phosphatidylglycerol phosphate, phosphatidylglycerol sulfate, triglycosyl diether, sulfated triglycosyl diether and sulfated tetraglycosyl diether. The G+C content of the DNA was 65.5 mol%. 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Halobacterium in the family Halobacteriaceae. Based on 16S rRNA gene sequence similarity, strain HPC1-2T was related most closely to Halobacterium salinarum DSM 3754T (99.2 %) and Halobacterium jilantaiense JCM 13558T (97.8 %). However, low levels of DNA–DNA relatedness suggested that strain HPC1-2T was genotypically different from these closely related type strains. Strain HPC1-2T could also be differentiated based on physiological and biochemical characteristics. Therefore, strain HPC1-2T is considered to represent a novel species of the genus Halobacterium, for which the name Halobacterium piscisalsi sp. nov. is proposed. The type strain is HPC1-2T (=BCC 24372T=JCM 14661T=PCU 302T).

An extracellular polysaccharide-producing bacterium, strain SCKT, was isolated from a soil sample taken from Kameino, Fujisawa, Japan. The isolate was Gram-negative and cells were non-motile, irregular-shaped rods that grew optimally at 25 °C and grew between pH 5 and 8. Strain SCKT contained MK-7 as the major isoprenoid quinone, iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids and sphingolipids, with d-17 : 0 as the main dihydrosphingosine. Flexirubin-type pigments were also present. The DNA G+C content was 43.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain SCKT was shown to belong to the genus Mucilaginibacter. The 16S rRNA gene sequence similarity between strain SCKT and the two type strains of Mucilaginibacter was 93 %. The results of physiological and biochemical tests allowed phenotypic differentiation of the strain from published Mucilaginibacter species. Therefore, strain SCKT represents a novel species, for which the name Mucilaginibacter kameinonensis sp. nov. is proposed. The type strain is SCKT (=NBRC 102645T =KCTC 22227T).

A Gram-negative bacterium, designated strain CW 186T, was isolated from forest soil in Anhui province, China. Cells of strain CW 186T were strictly aerobic, non-motile and rod-shaped. The strain grew optimally at 25–30 °C and pH 6.0–8.0. The major cellular fatty acids of strain CW 186T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (9.8 %) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 33.7 %). The predominant isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 36.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain CW 186T formed a monophyletic cluster with Sphingobacterium daejeonense LMG 23402T, Sphingobacterium composti LMG 23401T, Sphingobacterium composti DSM 18850T, Sphingobacterium mizutaii ATCC 33299T and Sphingobacterium spiritivorum ATCC 33861T. Sequence similarities were less than 94 % (the maximal similarity was about 93.9 % to S. composti LMG 23401T) to Sphingobacterium species with validly published names. A polyphasic taxonomic study including chemotaxonomic and phylogenetic analyses demonstrated that strain CW 186T should be classified as representing a novel species of the genus Sphingobacterium, for which the name Sphingobacterium anhuiense sp. nov. is proposed. The type strain is CW 186T (=KCTC 22209T=CCTCC AB 207197T).

A rod-shaped, Gram-negative, chemo-organotrophic, heterotrophic, strictly aerobic, gliding bacterial strain, SW5T, capable of degrading sulphated fucans from brown algae was isolated from a water-treatment facility that recycles the effluent of an alginate-extraction plant in Landerneau (Brittany, France). Its taxonomic position was investigated by a polyphasic approach. Strain SW5T formed dark-yellow colonies, was oxidase-negative and catalase-positive and grew optimally at 25 °C and pH 7.5 and in the presence of 2.5 % (w/v) NaCl. The DNA G+C content was 34.5 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene allocated strain SW5T to the genus Mariniflexile in the family Flavobacteriaceae, with a similarity of 98.4 % to the type strain of Mariniflexile gromovii, the only recognized Mariniflexile species. Its low level of DNA–DNA relatedness (<25 %) with the type strain of this species and differentiating phenotypic characteristics demonstrated that strain SW5T constitutes a novel Mariniflexile species, for which the name Mariniflexile fucanivorans sp. nov. is proposed. Strain SW5T (=CIP 109502T =DSM 18792T) is the type strain.

A Gram-negative, non-motile, pleomorphic bacterial strain, designated SMK-142T, was isolated from a tidal flat of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain SMK-142T grew optimally at pH 7.0–8.0, 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SMK-142T clustered with Lutibacter litoralis with which it exhibited a 16S rRNA gene sequence similarity value of 91.2 %. This cluster joined the clade comprising the genera Tenacibaculum and Polaribacter at a high bootstrap resampling value. Strain SMK-142T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 37.2 mol%. Strain SMK-142T was differentiated from three phylogenetically related genera, Lutibacter, Tenacibaculum and Polaribacter, on the basis of low 16S rRNA gene sequence similarity values and differences in fatty acid profiles and in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-142T represents a novel genus and species for which the name Aestuariicola saemankumensis gen. nov., sp. nov. is proposed (phylum Bacteroidetes, family Flavobacteriaceae). The type strain of the type species, Aestuariicola saemankumensis sp. nov., is SMK-142T (=KCTC 22171T=CCUG 55329T).

A Gram-negative, rod-shaped, yellow pigmented bacterium, strain NJ-26T, was isolated from sediment of the eutrophicated Guanting Reservoir in Beijing, China. A phylogenetic analysis based on 16S rRNA gene sequences placed strain NJ-26T within the genus Flavobacterium in the family Flavobacteriaceae. The highest sequence similarity was found with Flavobacterium cucumis R2A45-3T (97.7 %). The major fatty acids (>5 %) of the isolate were iso-C15 : 0, iso-C17 : 1 ω9c, C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. The G+C content of the genomic DNA was 40.6 mol%. The DNA–DNA relatedness value with F. cucumis R2A45-3T was 5.4 %. Molecular and phenotypic data suggest that strain NJ-26T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium cheniae sp. nov. is proposed. The type strain is NJ-26T (=CGMCC 1.6844T =NBRC 103934T).

Strain NJ-44T, isolated from sediment of the eutrophic Guanting Reservoir in Beijing (China), was subjected to a taxonomic study using a polyphasic approach. The strain was aerobic, with salmon-pink-pigmented colonies on R2A agar. Cells were single, Gram-negative rods, motile by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NJ-44T belonged to the phylum Bacteroidetes, with Terrimonas ferruginea ATCC 13524T (90.8 % similarity), Terrimonas lutea DYT (90.5 %) and Niabella aurantiaca R2A15-11T (89.1 %) as its closest relatives. Strain NJ-44T was clearly differentiated from members of the genera Terrimonas and Niabella in its DNA G+C content (40.6 mol%) and its major fatty acids, iso-C15 : 1 G, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 1 A and iso-C15 : 0 3-OH. It is proposed that strain NJ-44T represents a novel genus and species, named Sediminibacterium salmoneum gen. nov., sp. nov. The type strain of Sediminibacterium salmoneum is strain NJ-44T (=CGMCC 1.6845T =NBRC 103935T).

A novel anaerobic, mesophilic, amino-acid-utilizing bacterium, strain 158T, was isolated from an anaerobic digester of a wastewater treatment plant. Cells of strain 158T were non-motile, rod-shaped (2.0–3.0 × 0.8–1.0 μm) and stained Gram-negative. Optimal growth occurred at 37 °C and pH 7.0 in an anaerobic basal medium containing 1 % Casamino acids. Strain 158T fermented arginine, histidine, lysine and serine and showed growth on yeast extract, brain-heart infusion (BHI) medium and tryptone, but not on carbohydrates, organic acids or alcohols. The end products of degradation were: acetate, butyrate, H2 and CO2 from arginine; acetate, propionate, butyrate, H2 and CO2 from lysine; and acetate, propionate, butyrate, valerate, H2 and CO2 from histidine, serine, BHI medium, Casamino acids and tryptone. The DNA G+C content was 55.8 mol%. The 16S rRNA gene sequence of strain 158T showed only 92.6 % sequence similarity with that of Synergistes jonesii, the only described species of the ‘Synergistes’ group. The major cellular fatty acids were iso-C15 : 0 (16.63 %), iso-C15 : 0 3-OH (12.41 %) and C17 : 1 ω6c (9.46 %) and the polar fatty acids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylamine; these fatty acid profiles did not resemble those of any recognized bacterial species. Due to the considerable differences in genotypic, phenotypic and phylogenetic characteristics between strain 158T and those of its nearest relative, it is proposed that strain 158T represents a novel species in a new genus, Cloacibacillus evryensis gen. nov., sp. nov., in the phylum ‘Synergistetes’. The type strain is 158T (=DSM 19522T=JCM 14828T).

A Gram-negative, pleomorphic, rod-shaped, non-spore-forming bacterium, designated strain NS05T, was isolated from soil after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS05T was shown to be phylogenetically related to the genera Ancylobacter, Starkeya and Angulomicrobium (96.3–98.1 % sequence similarity), class Alphaproteobacteria. Strain NS05T was most closely related to Ancylobacter rudongensis AS 1.1761T (98.1 % sequence similarity). The whole-cell fatty acid pattern of strain NS05T was typical of those found in members of the genus Ancylobacter. Its main components were C18 : 1 ω7c (60.4 %), C19 : 0 ω8c cyclo (28.3 %) and C16 : 0 (7.4 %) and hydroxylated compounds were absent. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS05T with respect to the four Ancylobacter species with validly published names. Therefore, it is concluded that NS05T represents a novel species of the genus Ancylobacter, for which the name Ancylobacter oerskovii sp. nov. is proposed. The type strain is NS05T (=DSM 18746T =CCM 7435T). Two other oxalate-utilizing strains, NS03 and NS04, isolated from paper-mill effluents, were shown by 16S rRNA gene sequence analysis to be affiliated to the species Ancylobacter polymorphus. The study of their physiological properties extends the knowledge of the physiological variability within this species.