Menaquinone Composition of Some Sporeforming Actinomycetes

Streptomyces koelreuteriae sp. nov., isolated from the rhizosphere soil of Koelreuteria paniculata and healthy leaves of Xanthium sibiricum

Two actinomycete strains, designated MG62T and CRLD-Y-1, were isolated from rhizosphere soil of Koelreuteria paniculata and healthy leaves of Xanthium sibiricum, respectively, in Hunan province, PR China. They could produce abundant aerial mycelia that generated rod-shaped spores with spiny surfaces. Morphological features of the two strains are typical of the genus Streptomyces. Strains MG62T and CRLD-Y-1 exhibited 99.93 % 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between them were 99.99 and 100 %, respectively, suggesting that they belonged to the same species. 16S rRNA gene sequences analysis revealed that the two strains belonged to the genus Streptomyces and showed highest similarities to Streptomyces violarus NBRC 13104T (99.07-99.29 %) and Streptomyces arenae ISP 5293T (99.21-99.35 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MG62T and CRLD-Y-1 were closely related to S. violarus NBRC 13104T and S. arenae ISP 5293T. However, the ANI, dDDH and multilocus sequence analysis evolutionary distance values between the two strains and their relatives provide a robust basis upon which to verify strains MG62T and CRLD-Y-1 as representing a novel species. Moreover, a comprehensive comparison of phenotypic and chemotaxonomic characteristics further confirmed that the two strains were distinct from their relatives. Based on all these data above, strains MG62T and CRLD-Y-1 should represent a novel Streptomyces species, for which the name Streptomyces koelreuteriae sp. nov. is proposed. The type strain is MG62T (=JCM 34747T=MCCC 1K06175T).

Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies

In the genus Streptomyces, several validly described species have been reduced to synonyms of earlier described species though additional synonyms remain to be detected given the previous dependence on traditional phenotypic methods. In this study, genome-based procedures, including DNA-DNA hybridization analyses, overall genome-related indices, such as ANI, dDDH and AAI, revealed that certain strains recorded genomic indices above the threshold values used to define species boundaries. The results of phylogenetic and phylogenomic trees based on concatenated and phylogenomic analyses showed that 33 out of 364 tested species could be assigned to 15 species groups and that 18 Streptomyces species names be reclassified as later heterotypic synonyms of earlier validly published species. Consequently, it is proposed that S. albaduncus is a later heterotypic synonym of S. griseoloalbus; S. bellus is a synonym of S. coeruleorubidus; S. gancidicus and S. rubiginosus are synonyms of S. pseudogriseolus; S. niveoruber is a synonym of S. griseoviridis; S. griseomycini is a synonym of S. griseostramineus; S. jietaisiensis is a synonym of S. griseoaurantiacus; S. pluricolorescens is a synonym of S. rubiginosohelvolus; S. nashvillensis is a synonym of S. tanashiensis; S. yerevanensis is a synonym of S. flaveus; S. durhamensis is a synonym of S. filipinensis; S. recifensis is a synonym of S. griseoluteus; S. canaries and S. olivaceoviridis are synonyms of S. corchorusii; S. melanosporofaciens is a synonym of S. antimycoticus; S. albulus is a synonym of S. noursei; and S. janthinus and S. violarus are synonyms of S. violaceus. Additionally, seven of these 18 Streptomyces species have been designated subspecies.

Nucisporomicrobium flavum gen. nov., sp. nov., a new member of the family Micromonosporaceae isolated from saline-alkali soil

A Gram-stain-positive, aerobic actinobacterium, designated strain NEAU-24T, was isolated from saline-alkali soil collected from Daqing City, Heilongjiang Province, PR China. Strain NEAU-24T was found to produce abundant substrate mycelia but no aerial hyphae. The substrate mycelia formed irregular pseudosporangia consisting of nuciform spores, and the surface of the spores was smooth. 16S rRNA gene sequence analysis showed that strain NEAU-24T clustered with Pseudosporangium ferrugineum 3-44-a(19)T, Couchioplanes caeruleus subsp. azureus DSM 44103T and C. caeruleus subsp. caeruleus DSM 43634T within the family Micromonosporaceae and was most closely related to P. ferrugineum 3-44-a(19)T (99.17 %). The strain contained meso-diaminopimelic acid as the cell-wall diamino acid and MK-9(H6) as the menaquinone. The whole cell sugar profile consisted of glucose, galactose, xylose and arabinose. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, phosphatidylinositol and an unidentified lipid. The major fatty acids were summarized as C16 : 0, C15 : 0, C17 : 0, iso-C16 : 0 and iso-C17 : 0. The low digital DNA–DNA hybridization and average nucleotide identity values could differentiate strain NEAU-24T from its related type strains. The phenotypic, genetic and chemotaxonomic data also indicated that strain NEAU-24T occupied a branch separated from those of known genera in the family Micromonosporaceae. In addition, genomic analysis confirmed that strain NEAU-24T had the potential to produce chitinase. Therefore, strain NEAU-24T represents a novel species of a new genus and species in the family Micromonosporaceae, for which the name Nucisporomicrobium flavum gen. nov., sp. nov. is proposed. The type strain of Nucisporomicrobium flavum is NEAU-24T (=CCTCC AA 2020016T=JCM 33973T).

A rapid and efficient method for the extraction and identification of menaquinones from Actinomycetes in wet biomass

Background

Menaquinones are constituents of prokaryote cell membranes where they play important functions during electron transport. Menaquinone profiles are strongly recommended for species classification when proposing a new Actinomycetes taxon. Presently, the most widely used methods to determine menaquinones are based on freeze-dried cells. Taxonomic research in our lab has revealed that menaquinone concentrations are low for some species of the genus Microbacterium, leading to difficulties in identifying menaquinones.

Results

Menaquinones extracted using the novel lysozyme-chloroform-methanol (LCM) method were comparable in quality to those obtained using the Collins method, the most widely used method. All tested strains extracted via the LCM method showed higher concentrations of menaquinones than those extracted via the Collins method. For some Microbacterium strains, the LCM method exhibited higher sensitivity than the Collins method, and more trace menaquinones were detected with the LCM method than the Collins method. In addition, LCM method is faster than the Collins method because it uses wet cells.

Conclusion

The LCM method is a simple, rapid and efficient technique for the extraction and identification of menaquinones from Actinomycetes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02240-z.

Micromonospora terminaliae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of the medicinal plant Terminalia mucronata

An endophytic actinobacterium, strain TMS7T, was isolated from the stem of a Thai medicinal plant collected from the grounds of the Phujong-Nayoa National park, Ubon Ratchathani province, Thailand. As a result of a polyphasic taxonomy study, this strain was identified as a member of the genus Micromonospora. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelium with hyphae forming a single microspore was non-motile. Stran TMS7T was identified according to its 16S rRNA gene sequence as a new member of the genus Micromonospora. The closest phylogenetic members sharing a similarity were Micromonospora chersina DSM 44151T at 99.4 % and Micromonospora rosaria DSM 803T, Micromonospora tulbaghiae TVU1T, Micromonospora inositola DSM 43819T and Micromonospora endolithica DSM 44398T all at 99.2 %. Chemotaxonomic data including cell wall components, major menaquinones and major fatty acids confirmed the affiliation of strain TMS7T to the genus Micromonospora. The results of the phylogenetic analysis, addition to physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain TMS7T and the most closely related species with validly published names. The name proposed for the novel species is Micromonospora terminaliae sp. nov. The type strain is TMS7T (=DSM 101760T=NRRL B-65345T).

Planomonospora algeriensis sp. nov., an actinobacterium isolated from a Saharan soil of Algeria

A filamentous actinobacterium, designated strain PM3^T, was isolated from a Saharan soil sample collected from Béni-Abbès, Béchar (South-West Algeria). A polyphasic taxonomic study was carried out to establish the status of strain PM3^T. The isolate was found to have morphological and chemotaxonomical properties associated with members of the genus Planomonospora. The new isolated microorganism developed cylindrical sporangia arranged in double parallel rows on aerial mycelium, each one containing a motile single sporangiospore. The cell wall of the strain was found to contain meso-diaminopimelic acid. Whole-cell hydrolysates were found to contain madurose, glucose, mannose and ribose. The predominant menaquinone was identified as MK-9(H₂) (69.6%). The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, phosphatidylhydroxyethanolamine and glucosamine-containing lipids. The major fatty acids were found to be C_17:1ω9c (38.6%) and C_17:0 (24.2%). Results of 16S rRNA gene sequence comparison revealed that strain PM3^T shared a high degree of 16S rRNA gene sequence similarity with Planomonospora sphaerica DSM 44632^T (99.3%), Planomonospora parontospora subsp. parontospora DSM 43177^T (99.2%) and P. parontospora subsp. antibiotica DSM 43869^T (99.0%). DNA-DNA hybridization values between strain PM3^T and the type strains of the closely related species were between 58.4 and 70.1%. The combination of phylogenetic analysis, DNA-DNA relatedness data, phenotypic characteristics and chemotaxonomic data support the conclusion that strain PM3^T represents a novel species of the genus Planomonospora, for which the name Planomonospora algeriensis sp. nov. is proposed. The type strain is PM3^T (=DSM 46752^T = CECT 9047^T).

Microbacterium enclense sp. nov., isolated from sediment sample

A novel bacterium (strain NIO-1002(T)) belonging to the genus Microbacterium was isolated from a marine sediment sample in Chorao Island, Goa Province, India. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Cells of this strain were Gram-stain-positive, non-motile, non-spore-forming rods that formed yellow-pigmented colonies. It grew in 0-12% (w/v) NaCl and at 25-37 °C, with optimal growth at 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1002(T) is associated with members of the genus Microbacterium, with highest sequence similarity with Microbacterium hominis CIP 105731(T) (98.1%) and Microbacterium testaceum KCTC 9103(T) (98.0%). Within the phylogenetic tree, this novel strain shared a branching point with M. hominis CIP 105731(T). The DNA G+C content was 66.5 mol% and DNA-DNA hybridization relatedness between NIO-1002(T), M. hominis CIP 105731(T) and M. testaceum KCTC 9103(T) was 39.0 ± 2.0% and 41.0 ± 2.0%, respectively. The major fatty acids were ai-C15 : 0, i-C16 : 0 and ai-C17 : 0 and the diamino acid in the cell-wall peptidoglycan of NIO-1002(T) was lysine. Data obtained from DNA-DNA hybridization and chemotaxonomic phenotypic analysis support the conclusion that strain NIO-1002(T) represents a novel species within the genus Microbacterium. The name Microbacterium enclense sp. nov. is proposed, with NIO-1002(T) ( = NCIM 5454(T) = DSM 25125(T) = CCTCC AB 2011120(T)) as the type strain.

Nonomuraea indica sp. nov., novel actinomycetes isolated from lime-stone open pit mine, India

A Gram-positive, aerobic, nonmotile actinomycete strain designated DRQ-2(T) was isolated from the soil sample collected from lime-stone open pit mine from the Gulbarga region, Karnataka province, India. Strain DRQ-2(T) was identified as a member of the genus Nonomuraea by a polyphasic approach. Strain DRQ-2(T) could be differentiated from other members of the genus Nonomuraea on the basis of physiology and 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity of strain DRQ-2(T) showed highest sequence similarity to Nonomuraea muscovyensis DSM 45913(T) (99.1%), N. salmonea DSM 43678(T) (98.2%) and N. maheshkhaliensis JCM 13929(T) with 98.0%, respectively. Chemotaxonomic properties showing predominant menaquinones of MK-9 (H4), MK-9(H2) and MK-9(H6), major polar lipids comprised diphosphatidylglycerol, phosphatidylmono methyl ethanolamine (PME), phosphatidylethanolamine (PE), hydroxy-PME (OH-PME), hydroxy PE (OH-PEE), phosphatidylglycerol (PG), ninhydrin-positive phosphoglycolipid and unknown phospholipid, fatty acids with major amounts of i-C16:0, ai-C15:0 and ai-C17:0 supported allocation of the strain to the genus Nonomuraea. Results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of strain DRQ-2(T) from closely related species. The genomic DNA G+C content of the organism was 72.5 mol%. On the basis of phenotypic, chemotypic and molecular characteristics, strain DRQ-2(T) represents a novel species of the genus Nonomuraea, for which the name N. indica sp. nov. is proposed, with type strain DRQ-2(T) (=NCIM 5480(T)= CCTCC AA 209050(T)).

Streptomyces chiangmaiensis sp. nov. and Streptomyces lannensis sp. nov., isolated from the South-East Asian stingless bee (Tetragonilla collina)

Two novel actinomycetes, strains TA4-1T and TA4-8T, were isolated from the South-East Asian stingless bee (Tetragonilla collina Smith 1857), collected from Chiang Mai Province, Thailand. The morphological and chemotaxonomic properties of strains TA4-1T and TA4-8T were consistent with the genus Streptomyces , i.e. the formation of aerial mycelia bearing spiral spore chains, the presence of the ll-isomer of diaminopimelic acid in cell walls, iso- and anteiso-branched fatty acids with carbon chain lengths 14–17 atoms as the major fatty acids and MK-9(H8) as the predominant menaquinone plus minor amounts of MK-9(H6) and MK-9(H10). Analysis of 16S rRNA gene sequences showed that strains TA4-1T and TA4-8T exhibited 98.8 and 98.1 % sequence similarity, respectively, with Streptomyces chromofuscus NRRL B-12175T and 98.9 % sequence similarity with each other. This study suggested that strains TA4-1T and TA4-8T were distinct from previously described species of the genus Streptomyces . In addition, the low degrees of DNA–DNA relatedness between the isolates and S. chromofuscus JCM 4354T warranted assigning strains TA4-1T and TA4-8T to two novel species. The names Streptomyces chiangmaiensis sp. nov. (type strain TA4-1T  = JCM 16577T  = TISTR 1981T) and Streptomyces lannensis sp. nov. (type strain TA4-8T  = JCM 16578T  = TISTR 1982T) are proposed. The species names indicate the geographical locations where the stingless bees reside.

Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C18 : 1ω9c, anteiso-C17 : 0 and C17 : 1ω8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) ( = DSM 45627(T) = KACC 16232(T)).

Proposal of Intrasporangium mesophilum sp. nov., and reclassification of Humihabitans oryzae Kageyama et al. 2007 as Intrasporangium oryzae comb. nov

A Gram-positive and aerobic bacterium, designated strain YIM 49065T, was isolated from rhizospheric soil of Jatropha curcas in Yunnan, China. This isolate formed branched and fragmented mycelia containing ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major cellular fatty acid profile was characterized by iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The DNA G+C content was 69.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequence demonstrated that strain YIM 49065T was closely associated with Intrasporangium calvum DSM 43043T and Humihabitans oryzae KV-657T, exhibiting 98.8 % and 98.6 % 16S rRNA gene sequence similarities, respectively. Furthermore, DNA–DNA hybridizations among strains YIM 49065T, I. calvum DSM 43043T and H. oryzae DSM 22331T indicated that this isolate represented a novel species in the genus Intrasporangium . On the basis of these data, we proposed one novel species, Intrasporangium mesophilum sp. nov., for strain YIM 49065T ( = DSM 23217T  = CCTCC AA 209077T). Additionally, the comparison of biochemical and phylogenetic characters supported the reclassification of Humihabitans oryzae as a separate species within the genus Intrasporangium , Intrasporangium oryzae comb. nov. (type strain KV-657T  = JCM 15924T  = NBRC 101802T  = NRRL B-24470T).

Intrasporangium chromatireducens sp. nov., a chromate-reducing actinobacterium isolated from manganese mining soil, and emended description of the genus Intrasporangium

A Gram-positive, aerobic actinobacterium with high chromate [Cr(VI)]-reducing ability, designated strain Q5-1T, was isolated from manganese mining soil in Hunan Province, central-south China. The organism formed branching hyphae and contained ll-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile was characterized by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The genomic DNA G+C content was 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q5-1T was closely related to Intrasporangium calvum DSM 43043T ( = NRRL B-3866T) and Humihabitans oryzae KV-657T ( = NRRL B-24470T) with similarities of 96.6 and 96.4 %, respectively. Comparison of phenotypic, biochemical and chemotaxonomic characters of strain Q5-1T and phylogenetically related strains revealed that the isolate represents a novel species of the genus Intrasporangium, for which the name Intrasporangium chromatireducens sp. nov. is proposed. The type strain is Q5-1T ( = KCTC 19811T = CCTCC AA 2010019T = CGMCC 1.10750T = NRRL B-59521T). An emended description of the genus Intrasporangium is also proposed.

Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov

A Gram-reaction-positive aerobic actinomycete, designated strain IM17-1(T), was isolated from a honey bee (Apis mellifera) hive in Chiang Mai Province, Thailand. The strain formed a branched substrate mycelium and mature aerial mycelium bore short chains of arthrospores with warty surfaces. The cell wall contained meso-2,6-diaminopimelic acid (cell-wall type III) and the whole cell sugars were fucose, galactose, glucose, madurose, mannose and ribose. The major isoprenoid quinone was hexahydrogenated menaquinone with nine isoprene units and the predominant cellular fatty acids were C₁₆:₀ (33.8 %), C₁₈:₁ω9c (32.7 %), summed feature 3 (C₁₆:₁ω7c and/or iso-C₁₅:₀ 2-OH) (8.7 %) and 10-methyl C₁₈:₀ (8.2 %). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. These morphological and chemotaxonomic characteristics were consistent with the classification of IM17-1(T) within the genus Actinomadura. Based on 16S rRNA gene sequence analysis, strain IM17-1(T) was closely related to the type strains of Actinomadura cremea subsp. cremea (98.1 %) and Actinomadura cremea subsp. rifamycini (98.6 %); however, it represented a distinct phylogenetic lineage from the other species within this genus. The unique genetic characteristics were reaffirmed by low levels of DNA-DNA relatedness between strain IM17-1(T) and the two most closely related type strains, A. cremea subsp. cremea JCM 3308(T) (56.5±4.9 %) and A. cremea subsp. rifamycini JCM 3309(T) (31.0±22.6 %), and further supported the proposal of IM17-1(T) as a novel species. Strain IM17-1(T) ( = JCM 16576(T)  = TISTR 1980(T)) thus represents a novel species of the genus Actinomadura, for which the name Actinomadura apis sp. nov. is proposed. In addition, the genotypic and phenotypic data suggested the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as a separate species, Actinomadura rifamycini sp. nov., comb. nov.

Nonomuraea maheshkhaliensis sp. nov., a novel actinomycete isolated from mangrove rhizosphere mud

A strain of Nonomuraea was isolated from Maheshkhali, Cox's Bazar, an unexplored region of Bangladesh. Strain 16-5-14(T) is a Gram-positive, aerobic, non-motile actinomycete that formed branched substrate and aerial mycelia. On the basis of 16S rRNA gene sequence similarity studies, strain 16-5-14(T) was shown to belong to the genus Nonomuraea, being most closely related to Nonomuraea kuesteri. Chemotaxonomic data supported allocation of the strain as a member of the genus Nonomuraea. The strain 16-5-14(T) contained MK-9(H(4)) as the major menaquinone, the polar lipid was phosphatidylethanolamine and major cellular fatty acids were observed as C(16 : 0 )(15.5%), iso-C(16 : 0) (13.8%) and 10-methyl C(17 : 0) (9.6%). Results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of strain 16-5-14(T) from closely related species N. kuesteri. Thus 16-5-14(T) represents a novel species of the genus Nonomuraea. On the basis of evaluation of the morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridization, Nonomuraea maheshkhaliensis sp. nov. (type strain, 16-5-14(T)=JCM 13929(T)=MTCC 8545(T)) is proposed.

Nonomuraea bangladeshensis sp. nov. and Nonomuraea coxensis sp. nov

Two novel bacterial strains were isolated from sandy soil from Cox's Bazar, Bangladesh. Strains 5-10-10(T) and 5-38-42(T) were Gram-positive, aerobic, non-motile actinomycetes that form branched substrate and aerial mycelium. On the basis of 16S rRNA gene sequence similarity studies, the novel strains were shown to belong to the genus Nonomuraea, being most closely related to Nonomuraea fastidiosa. Chemotaxonomic data supported the assignment of the novel strains as members of the genus Nonomuraea. Strain 5-10-10(T) contained MK-9(H(4)) and strain 5-38-42(T) contained MK-9(H(6)) and MK-9(H(4)) as the major menaquinones. Major polar lipids were phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The major cellular fatty acid for strain 5-10-10(T) was iso-C(16 : 0) (26.4 %); C(16 : 0) (17.4 %) was the major cellular fatty acid for strain 5-38-42(T). The results of DNA-DNA hybridization and physiological tests enabled strains 5-10-10(T) and 5-38-42(T) to be differentiated genotypically and phenotypically from each other and from the closely related species, N. fastidiosa. On the basis of these results, strains 5-10-10(T) and 5-38-42(T) represent two novel species of the genus Nonomuraea. Following an evaluation of morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridization experiments, the new isolates are proposed as two novel species, Nonomuraea bangladeshensis sp. nov. [type strain, 5-10-10(T) (=MTCC 8089(T)=JCM 13930(T))] and Nonomuraea coxensis sp. nov. [type strain, 5-38-42(T) (=MTCC 8090(T)=JCM 13931(T))].

Luedemannella gen. nov., a new member of the family Micromonosporaceae and description of Luedemannella helvata sp. nov. and Luedemannella flava sp. nov

Three actinomycete strains were isolated from soil samples collected in Bangladesh. The cultures formed spherical sporangia on short sporangiophores directly above the surface of the substrate mycelium. The sporangia developed singly or in clusters and each sporangium contained several nonmotile spherical to oval spores with a smooth surface. The strains 3-9(24)(T), 3-21(27) and 7-40(26)(T) contained meso-diaminopimelic acid in the cell walls, predominant menaquinone MK-9(H(6)) and MK-9(H(4)) and glucose, xylose, galactose, mannose, rhamnose, ribose and arabinose in the whole-cell hydrolysates. Diagnostic phospholipid is phosphatidylethanolamine and branched anteiso-C(17 : 0) (30.0-38.0%), anteiso-C(15 : 0) (12.5-14.0%), iso-C(16 : 0) (10.0-15.0%) and iso-C(15 : 0) (10.0-12.0%) were detected as the major cellular fatty acids. The acyl type of the peptidoglycan was glycolyl and mycolic acids were not detected. The G+C content of the DNA was 71 mol%. The chemotaxonomic data indicate that these strains belong to the family Micromonosporaceae. Phylogenetic analysis based on 16S rRNA gene sequence data suggested that the strains 3-9(24)(T), 3-21(27) and 7-40(26)(T) fall within the family Micromonosporaceae. On the basis of phylogenetic analysis and characteristic patterns of signature nucleotides as well as morphological and chemotaxonomic data, Luedemannella gen. nov. is proposed for our 3 isolates. DNA-DNA hybridization experiment and phenotypic characterization indicated that the new genus was constituted of 2 species, as Luedemannella helvata sp. nov. for the strain 3-9(24)(T) (=JCM 13249(T)=MTCC 8091(T)) and Luedemannella flava for the strain 7-40(26)(T) (=JCM 13250(T)=MTCC 8095(T)) in the family Micromonosporaceae.

Two new species of the genus Micromonospora: Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov., isolated from sandy soil

Two actinomycete strains, 2-19(6)(T) and 2-30-b(28)(T), which produced single, non-motile noduler to warty spore surfaces, were isolated from sandy soil in Chokoria, Cox's Bazar, Bangladesh. A polyphasic study was carried out to establish the taxonomic position of these strains. Morphological and chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora. Phylogenetic analysis using 16S rDNA sequences indicated that these strains should be classified in the genus Micromonospora. The 16S rDNA sequence of strain 2-19(6)(T )showed closest similarity to the type strains of M. mirobrigensis (98.9%) and M. carbonacea (98.8%), and the strain 2-30-b(28)(T) to the type strains of M. purpureochromogenes (99.4%), M. halophytica (99.3%) and M. aurantiaca (99.2%). Furthermore, a combination of DNA-DNA hybridization results and some differential physiological and biochemical properties indicated that these strains were distinguished from the phylogenetically closest relatives. These strains therefore represent two novel species, for which the name Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov. are proposed. The type strains are 2-19(6)(T) (=JCM 13247(T) =MTCC 8535(T)) and 2-30-b(28)(T) (=JCM 13248(T)=MTCC 8093(T)).

Kitasatospora sampliensis sp. nov., a novel actinobacterium isolated from soil of a sugar-cane field in India

Polyphasic characterization of an actinomycete strain VT-36T isolated from a sugar-cane field soil sample collected in Punjab State, India, revealed that the strain belongs to the genus Kitasatospora. The strain's chemotaxonomic characters and G+C content of DNA (76·5 mol%) were typical of members of the genus. Analysis of the 16S rRNA gene sequence supported the generic affiliation of the strain and showed that its closest phylogenetic relative was Kitasatospora putterlickiae F18-98T (=DSM 44665T) (98·3 % 16S rRNA gene sequence similarity). The similarities with type strains of all other Kitasatospora species were in the range 95·1–97·0 %. The results of DNA–DNA hybridization showed 54 % relatedness of the isolate and K. putterlickiae F18-98T. Based on the above data and the phenotypic differences from K. putterlickiae and other Kitasatospora species, it is proposed that the isolate should be classified as the type strain of a novel species, Kitasatospora sampliensis sp. nov., with strain VT-36T (=MTCC 6546T=DSM 44898T=JCM 13010T) as the type strain.

Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov., and transfer of Catellatospora citrea subsp. methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov

Three Gram-positive, aerobic, non-motile, mesophilic strains, designated 2-25(1)T, 2-29(17)T and 2-70(23)T, were isolated from sandy soil from Chokoria, Cox's Bazar, Bangladesh. The organisms produce short chains of non-motile spores that emerge singly or in tufts from vegetative hyphae on the surface of agar media. A comparative phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates formed a distinct clade within the evolutionary radiation of the family Micromonosporaceae and clustered with members of the genus Catellatospora. The nearest neighbours were Catellatospora citrea subsp. citrea and C. citrea subsp. methionotrophica. Chemotaxonomic data, such as the presence of meso- and 3-hydroxy-diaminopimelic acids, N-glycolyl type muramic acid, arabinose and xylose and glucose in whole-cell hydrolysates, phosphatidylethanolamine as a diagnostic phospholipid, a tetrahydrogenated menaquinone with 9 isoprene units as a major menaquinone and fatty acid profiles predominated by iso-branched hexadecanoic acid and iso-branched pentadecanoic acid, supported the affiliation of the novel isolates to the genus Catellatospora. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the novel isolates to be differentiated genotypically and phenotypically from the three recognized Catellatospora species. The three isolates therefore represent novel species for which the names Catellatospora chokoriensis sp. nov. [type strain 2-25(1)T=JCM 12950T=DSM 44900T], Catellatospora coxensis sp. nov. [type strain 2-29(17)T=JCM 12951T=DSM 44901T] and Catellatospora bangladeshensis sp. nov. [type strain 2-70(23)T=JCM 12949T=DSM 44899T], are proposed. DNA–DNA hybridization tests with C. citrea subsp. citrea and C. citrea subsp. methionotrophica, in combination with chemotaxonomic and physiological data, demonstrated that C. citrea subsp. methionotrophica should be elevated to a separate species for which the name Catellatospora methionotrophica sp. nov., comb. nov. is proposed (type strain JCM 7543T=DSM 44098T).

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).

Numerical and chemical classification of Streptosporangium and some related actinomycetes

One hundred and seventeen streptosporangia from soil were compared with marker strains of the family Streptosporangiaceae for many phenotypic properties. The data were examined using the Jaccard, pattern and simple matching coefficients with clustering achieved using average, complete and single linkage algorithms. Particular confidence was placed in the product of the pattern, average linkage analysis given the sharp definition of aggregate groups and clusters and a combination of low test error and high cophenetic correlation values. The test strains were assigned to five aggregate groups that were equated with the genera Streptosporangium (group A), Microbispora (group B), Planobispora and Planomonospora (Group C), Kutzneria (neé Streptosporangium viridogriseum (group D), and Microtetraspora (group E). The streptosporangia, both isolates and marker strains, were assigned to 5 major, 7 minor and 18 single membered clusters. Representative streptosporangia examined for chemical markers were characterised by the presence of meso-diaminopimelic acid in whole-organism hydrolysates, complex mixtures of straight- and branched chain fatty acids, di- and tetrahydrogenated menaquinones as predominant isoprenologues, and complex polar lipid patterns containing diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and uncharacterised components. The chemical and numerical data support the taxonomic integrity of the validly described species of Streptosporangium and suggest that the genus is markedly underspeciated.

Menaquinone composition in the classification and identification of aerobic actinomycetes

Menaquinones were the only isoprenoid quinones found in 36 strains representing different species of the genera Nocardia, Mycobacterium, Rhodococcus, Amycolatopsis, Saccharothrix, Streptomyces, Nocardiopsis and Actinomadura. Dihydrogenated menaquinones with nine isoprene units [MK-9(H2)] were the main components isolated from Mycobacterium. Dihydrogenated and tetrahydrogenated menaquinones with eight isoprene units were the predominant compounds identified in typical Rhodococcus and Nocardia strains, respectively. "Nocardia phenotolerans" differed from all of the other Nocardia species included in the study, in that it contained the MK-9(H2) [MK-8(H2)] menaquinone system. Nocardioform bacteria lacking mycolic acids contained tetrahydrogenated menaquinones with nine isoprene units as the main component. The Streptomyces strains studied exhibited complex mixtures of partially saturated menaquinones with nine isoprene units with the hexa- and/or octahydrogenated components predominating. Actinomadurae contained major amounts of hexahydrogenated menaquinones with nine isoprene units. In contrast, the single Nocardiopsis strain examined possessed complex mixtures of menaquinones with ten isoprene units, the dihydrogenated components being main constituents.