Whole-cell Sugar Pattern Research Articles

Glycomyces halotolerans sp. nov., a novel actinomycete isolated from a hypersaline habitat in Xinjiang, China

A novel actinomycete strain, designated TRM 40137(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China, and subjected to a polyphasic taxonomic study. The strain was aerobic, Gram-positive and the optimum NaCl concentration for growth was 4-5% (w/v). Phylogenetic analysis showed that strain TRM 40137(T) has a 16S rRNA gene sequence similarity of 95.02% with the described species Glycomyces sambucus E71(T) and can be distinguished from all previously described representatives of the genus Glycomyces. The whole-cell sugar pattern consisted of xylose and galactose. The predominant menaquinone was MK-10(H(2)) and the major fatty acids were anteiso-C15:0 and anteiso-C17:0. The phospholipid pattern consists of phosphatidylglycerol, diphosphatidylglycerol, three unknown aminophospholipids and two unknown phospholipids. The G+C content of the genomic DNA was 68.8 mol%. A novel species Glycomyces halotolerans sp. nov. is proposed, with strain TRM 40137(T) (=CCTCC AA 2010013(T) = KCTC 19988(T)) as the type strain of G. halotolerans.

Micromonospora humi sp. nov., isolated from peat swamp forest soil

A novel actinomycete, strain P0402(T), was isolated from peat swamp forest soil collected in Thailand. Its taxonomic position was determined by using a polyphasic taxonomic approach. The chemotaxonomic characteristics of this strain matched those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole-cell sugar pattern D, phospholipid type II, and cellular fatty acid type 3b. Phylogenetic analysis based on 16S rRNA gene sequences revealed a close relationship between strain P0402(T) and Micromonospora coxensis JCM 13248(T) (99.0 % similarity), Micromonospora eburnea JCM 12345(T) (99.0 %), Micromonospora marina JCM 12870(T) (98.9 %), Micromonospora halophytica JCM 3125(T) (98.7 %), Micromonospora chalcea JCM 3031(T) (98.7 %), Micromonospora purpureochromogenes JCM 3156(T) (98.6 %) and Micromonospora aurantiaca JCM 10878(T) (98.5 %). It could be clearly distinguished from these type strains based on low levels of DNA-DNA relatedness and phenotypic differences. On the basis of the data presented, strain P0402(T) is suggested to represent a novel species of the genus Micromonospora, for which the name Micromonospora humi sp. nov. is proposed. The type strain is P0402(T) ( = JCM 15292(T) = PCU 315(T) = TISTR 1883(T)).

Actinopolyspora xinjiangensis sp. nov., a novel exteremely halophilic actinomycete isolated from a salt lake in Xinjiang, China

A novel halophilic, filamentous actinobacterium, designated TRM 40136(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain is aerobic, Gram-positive, halophilic, and the optimum NaCl concentration for growth is 10-15% (w/v). The whole-cell sugar pattern consists of xylose, glucose and arabinose. The predominant menaquinone is MK-6 (51.2%) and the major fatty acids are anteiso-C15:0 (35.2%), anteiso-C17:0 (15.9%) and iso-C15:0 (13.7%). The phospholipid pattern consists of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown phospholipids. The G+C content of the genomic DNA is 68.9mol%. Phylogenetic analysis showed that strain TRM 40136(T) had 16S rRNA gene sequence similarity of 96.1% with the closest described species Actinopolyspora mortivallis, and it can be distinguished from all species in the genus Actinopolyspora by using these data of polyphasic taxonomy study. On the basis of the polyphasic evidence, the strain TRM 40136(T) should be designated as a novel species of the genus Actinopolyspora for which the name Actinopolyspora xinjiangensis sp.nov. is proposed. The type strain is TRM 40136(T) (=CCTCC AA 209080(T)=KCTC 19656(T)).

Amycolatopsis tucumanensis sp. nov., a copper-resistant actinobacterium isolated from polluted sediments

A novel actinomycete strain, ABO(T), isolated from copper-polluted sediments showed remarkable copper resistance as well as high bioaccumulation abilities. Classical taxonomic methods, including chemotaxonomy and molecular techniques, were used to characterize the isolate. Strain ABO(T) developed a honey-yellow substrate mycelium on all ISP media tested. Abundant, white, aerial mycelium was only formed on ISP 2, 5 and 7 and MM agar. Both types of hyphae fragmented into squarish rod-shaped elements. The aerial mycelium displayed spore-like structures with smooth surfaces in long, straight to flexuous chains. The organism has a type-IV cell wall lacking mycolic acids and type-A whole-cell sugar pattern (meso-diaminopimelic acid, arabinose and galactose) in addition to a phospholipid type-II profile. 16S rRNA gene sequence studies indicated that this organism is a member of the family Pseudonocardiaceae and that it forms a monophyletic clade with Amycolatopsis eurytherma NT202(T). The DNA-DNA relatedness of strain ABO(T) to A. eurytherma DSM 44348(T) was 39.5 %. It is evident from these genotypic and phenotypic data that strain ABO(T) represents a novel species in the genus Amycolatopsis, for which the name proposed is Amycolatopsis tucumanensis sp. nov. The type strain is ABO(T) (=DSM 45259(T) =LMG 24814(T)).

Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae

A novel halophilic actinobacterium, designated YIM 92370(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8-12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H(4)) and the major fatty acids were iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0). The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370(T) can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370(T) therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370(T) (=DSM 45210(T) =KCTC 19481(T)).

Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2(T) was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H(4)) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2(T) (=NRRL B-24463(T) =DSM 44720(T) =FERM P-16053(T) =JCM 10302(T) =NBRC 16184(T)).

Actinocatenispora thailandica gen. nov., sp. nov., a new member of the family Micromonosporaceae

Two actinomycete strains, TT2-10(T) and TT2-3, which produced long spore chains (more than 10 spores per chain), were isolated from peat swamp forest soil in Pattaloong Province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the family Micromonosporaceae, i.e. cell-wall chemotype II, muramic acid of the N-glycolyl type, whole-cell sugar pattern D and type II phospholipids. Analysis of the 16S rRNA gene sequences also indicated that these strains constitute a distinct lineage within the family Micromonosporaceae, sharing 91.3-93.8 % sequence similarity with members of this family. On the basis of their phenotypic and genotypic characteristics and their phylogenetic position, these strains represent a novel genus and species, for which the name Actinocatenispora thailandica gen. nov., sp. nov. is proposed. The type strain of Actinocatenispora thailandica is strain TT2-10(T) (=JCM 12343(T)=PCU 235(T)=DSM 44816(T)).

Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov.

During the course of a phylogenetic evaluation of Saccharothrix strains held in the ARS Culture Collection, it was discovered that Saccharothrix coeruleoviolacea NRRL B-24058(T) is unrelated to other species within this genus, and a polyphasic study was undertaken to clarify its taxonomic position. Strain NRRL B-24058(T) is observed to be phylogenetically separate from the genus Saccharothrix and is most closely related to the genus Actinoalloteichus. The strain exhibits chemotaxonomic properties that distinguish it from members of Actinoalloteichus, including a whole-cell sugar pattern consisting of galactose and ribose as diagnostic sugars, phosphatidylethanolamine, phosphatidylethanolamine containing 2-OH fatty acids and diphosphatidylglycerol as the predominant polar lipids and MK-9(H(4)) and MK-10(H(4)) as the only menaquinones observed. Strain NRRL B-24058(T) is distinct from other taxa within the suborder Pseudonocardineae and a new genus to be named Goodfellowia gen. nov. is proposed. The type species of this new genus is Goodfellowia coeruleoviolacea gen. nov., comb. nov., and the type strain is NRRL B-24058(T) (=DSM 43935(T) = INA 3564(T) = JCM 9110(T) = NBRC 14988(T) = VKM Ac-1083(T)).

Stackebrandtia nassauensis gen. nov., sp. nov. and emended description of the family Glycomycetaceae

During the course of a 16S rRNA gene sequence phylogenetic evaluation of putative Glycomyces strains, it was noted that strain NRRL B-16338(T) is phylogenetically nearest to the genus Glycomyces but apparently is not a member of this or any of the other currently described actinomycete genera. The strain was subjected to a polyphasic study using standard methods for chemotaxonomic, morphological and physiological evaluation. The strain exhibited chemotaxonomic characteristics distinct from Glycomyces in spite of having 16S rRNA gene sequence similarity of 92% with the described species of this genus. The whole-cell sugar pattern of NRRL B-16338(T) consisted of ribose and inositol, with traces of arabinose and mannose. The phospholipids observed were phosphatidylglycerol and diphosphatidylglycerol and menaquinones consisting of MK-10(H(4)), MK-10(H(6)), MK-11(H(4)) and MK-11(H(6)). A significant quantity (14.5%) of 17:0 anteiso 2-hydroxy fatty acid was observed in the fatty acid profile of this strain. These characteristics clearly differentiate NRRL B-16338(T) from members of the genus Glycomyces and it is proposed that the strain represents a new genus within the family Glycomycetaceae to be called Stackebrandtia gen. nov. The description of this family is emended to permit its inclusion. It is proposed that the type species of the genus should be named Stackebrandtia nassauensis. The type strain LLR-40K-21(T) (=NRRL B-16338(T)=DSM 44728(T)) was isolated from a soil sample from Nassau, Bahamas.

Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia.

Eleven motile spore-bearing actinomycetes were isolated from various plant samples and were studied to determine their taxonomic positions. The isolates showed colony appearance and morphology similar to those of the 'sporedome actinomycetes' previously described by L. G. Willoughby in 1969. Although the isolates showed variety in composition of isomers of 2,6-diaminopimelic acid in the cell walls and in whole-cell sugar patterns, all of the isolates were classified in the genus Kineosporia Pagani and Parenti 1978 emend. Itoh et al. 1989 on the basis of their morphological and other chemotaxonomic characteristics, i.e., menaquinone, phospholipid and cellular fatty acid compositions. This assignment to the genus was also supported by a phylogenetic analysis using the 16S rRNA gene sequences. By DNA-DNA hybridization experiment, five genospecies were recognized among the isolates, and one of them showed high levels with the type strain of the type species, Kineosporia aurantiaca, which is the sole member of the genus. These genospecies can be distinguished from each other by their cultural, physiological and biochemical characteristics, and the other four genospecies should be placed into four new species for which the names Kineosporia succinea (type strain I-273T = JCM 9957T), Kineosporia rhizophila (type strain I-449T = JCM 9960T), Kineosporia mikuniensis (type strain I-463T = JCM 9961T) and Kineosporia rhamnosa (type strain I-132T = JCM 9954T) are proposed.

New Subspecies of Genus Streptosporangium, Streptosporangium amethystogenes subsp. fukuiense subsp. nov.

Taxonomy of a soil isolate, strain AL-23456 which produces a hematopoietic cytokine inducer TAN-1511, was studied. The organism had branched substrate mycelia and spherical sporangia including nonmotile spores on the tips of sporangiophores arising from the aerial mycelia. The chemotaxonomic characteristics of this organism are as follows: the cell wall chemotype is type III (meso-diaminopimelic acid), the whole-cell sugar pattern is type B, the fatty acid pattern is type 3c, major menaquinones are MK-9(H2) and MK-9(H4), phospholipid type is type PIV, the N-acyl type of muramic acid in the cell wall is the acetyl type. These morphological and chemotaxonomic features suggested that the isolate belongs to the genus Streptosporangium.The isolate was compared with taxonomically most similar strain, Streptosporangium amethystogenes IFO 13986 by examining cultural and physiological properties, and a DNA-DNA hybridization technique. From the results, we propose a new subspecies, S. amethystogenes subsp. fukuiense, for the isolate. The type strain is strain AL-23456 (=IFO 15365).

Actinocorallia gen. nov., a New Genus of the Order Actinomycetales

One species of the new genus Actinocorallia, Actinocorallia herbida sp. nov., is described. The genus Actinocorallia is characterized by well-developed, branched, nonfragmented substrate mycelia. On the tips of unique coralloid sporophores, which arise from the substrate mycelia, long chains of nonmotile spores (more than 30 spores per chain) are borne. On rare occasions formation of coremia is observed. The chemotaxonomic characteristics of this organism are as follows: the cell wall chemotype is type III (meso-diaminopimelic acid), the whole-cell sugar pattern is type C (no diagnostic sugar type), the fatty acid pattern is type 1a (straight-chain saturated acids and monounsaturated acids), the predominant isoprenoid quinones are MK-9(H4) and MK-9(H6), phospholipid type PII (phosphatidylethanolamine) is present as the diagnostic polar lipid, the N-acyl type of muramic acid in the cell wall is the acetyl type, and the guanine-plus-cytosine content of the DNA is 73 mol%. The type strain of A. herbida is strain AL-50780 (= IFO 15485).

Amycolatopsis alba sp. nov., Isolated from Soil

A new Amycolatopsis species isolated from soil produces a new glycopeptide antibiotic related to vancomycin. Traditional taxonomic methods and contemporary fatty acid analysis techniques were used to establish the position of this species. The hyphae fragment extensively when the organism is cultured in liquid media. The organism is characterized by white aerial hyphae that bear long chains of cylindrical conidia. The reverse side is yellowish brown; a faint light brown soluble pigment is occasionally produced. The organism has a type IV cell wall (meso-diaminopimelic acid), a type A whole-cell sugar pattern, and a type PII phospholipid pattern. Mycolic acids are not present in whole-cell hydrolysates. The major menaquinone is MK-9(H4); there is also a minor amount of MK-8(H4). The name proposed for this new species is Amycolatopsis alba. The type strain is strain A83850 (= NRRL 18532).

Chemotaxonomic differentiation of coryneform bacteria isolated from biofilters.

Coryneform bacteria that were isolated from biofilters which are used for waste gas treatment of animal-rendering plant emissions were differentiated and partially identified by using chemotaxonomic methods. On the basis of the results of a numerical analysis of whole-cell fatty acid profiles, 79 isolates were divided into two major groups; the members of the first group contained saturated and monounsaturated fatty acids, whereas the members of the second group were characterized by iso- and anteiso-branched fatty acids. Division into subclusters was based mainly on quantitative differences in fatty acid composition and was confirmed by the results obtained for additional chemical markers (e.g., respiratory quinones, mycolic acids, polar lipids, cell wall amino acids, and whole-cell sugar patterns). By combining the results obtained for chemotaxonomic analyses that were performed for strains containing saturated and monounsaturated fatty acids, we were able to identify the genus Corynebacterium (two Corynebacterium species were differentiated on the basis of the occurrence of tuberculostearic acid), the genus Gordona, and the genus Mycobacterium. Among the strains that produced iso-anteiso fatty acid patterns, one subgroup was affiliated with the "nicotianae" group of the genus Arthrobacter; however, some strains contained a new combination of chemical markers. Peptidoglycan type A4 alpha, L-Lys-Gly-L-Glu was combined with menaquinones MK-7 and MK-8, whereas peptidoglycan type A4 alpha, L-Lys-L-Glu occurred together with MK-8 and MK-9. The second subgroup was characterized by a new type B peptidoglycan and MK-11, as well as small amounts of MK-12. Differentiation that was based first on chemotaxonomy and second on physiology gave reliable results. Thus, coryneform strains with new characteristics were isolated from biofilters.

Streptosporangium carneum sp. nov. Isolated from Soil

A new species of the genus Streptosporangium is described. This organism is characterized by light yellowish pink aerial hyphae bearing abundant sporangia which enclose many large, spherical, nonmotile spores. Cell walls of this new species contain meso-diaminopimelic acid, mannose, arabinose, and madurose (cell wall chemotype III and type B whole-cell sugar pattern); the cells contain phosphatidylinositol, diphosphatidylglycerol, and unknown glucosamine-containing phospholipids (phospholipid pattern type PIV), and they contain no mycolic acids. The major menaquinone detected was MK-9(H4); a minor amount of MK-9(H2) was also detected. Thus, this isolate has chemical and morphological properties that are consistent with the properties of the genus Streptosporangium. A comparison with previously described species of the genus Streptosporangium in which we used standard techniques plus fatty acid analyses indicated that this organism differs from previously described species. The name proposed for this new species is Streptosporangium carneum. The type strain is strain A84575 (= NRRL 18437). The description is based on a single isolate.

Saccharopolyspora spinosa sp. nov. Isolated from Soil Collected in a Sugar Mill Rum Still

A new Saccharopolyspora species isolated from soil collected in a sugar mill rum still is described. This organism is characterized by pale yellowish pink aerial hyphae that bear long chains of spores encased in distinctive spiny spore sheaths. Fragmentation occurs when the organism is cultured in liquid media. The new species contains meso-diaminopimelic acid, arabinose, and galactose (cell wall chemotype IV), has whole-cell sugar pattern type A, contains no mycolic acids, and contains phosphatidylcholine (phospholipid pattern type PIII). The single isolate has chemical and morphological properties consistent with the genus Saccharopolyspora. A comparison with previously described species of the genus in which we used standard techniques plus fatty acid analyses showed that this organism differs from previously described species. The name proposed for this new species is Saccharopolyspora spinosa. The type strain is strain A83543.1 (= NRRL 18395). The description is based on a single isolate.

Kibdelosporangium philippinense sp. nov. Isolated from Soil

A new species of Kibdelosporangium is described. This organism is characterized by white aerial hyphae bearing long chains of smooth-walled spores and abundant sporangiumlike structures. The new species contains meso-diaminopimelic acid, arabinose, and galactose (type IV cell walls, type A whole-cell sugar pattern), phosphatidylethanolamine (type PII phospholipid pattern), and no mycolic acids. The single soil isolate has chemical and morphological properties consistent with the genus Kibdelosporangium. A comparison with previously described species of the genus Kibdelosporangium in which we used standard techniques, fatty acid profiles, and polypeptide banding fingerprints indicated that this strain is a new species. The name proposed for this new species is Kibdelosporangium philippinense. The type strain is strain A80407 (= NRRL 18198).

New Genus of the Actinomycetales: Kibdelosporangium aridum gen. nov., sp. nov.

A new actinomycete genus, Kibdelosporangium, is described. Members of this genus have type IV cell walls (meso-diaminopimelic acid, D-glutamic acid, DL-alanine, muramic acid, N-acetyl-D-glucosamine, D-galactose, and arabinose) and a type A whole-cell sugar pattern (D-galactose and arabinose) plus traces of madurose (3-O-methyl-D-galactose). No mycolic acids are present. The substrate mycelium has a tendency to fragment. The aerial mycelium bears long chains of spores, as well as sporangiumlike structures with well-defined walls. These sporangiumlike structures do not contain spores but germinate directly when they are placed on agar. The type strain of K. aridum is strain SK&F-AAD-216 (= ATCC 39323).

Glycomyces, a New Genus of the Actinomycetales

We describe two species of the new genus Glycomyces, Glycomyces harbinensis sp. nov. and Glycomyces rutgersensis sp. nov. Members of this genus are aerobic, produce nonfragmenting vegetative hyphae, and form chains of conidia on aerial sporophores. The cell walls are type II (meso-diaminopimelic acid and glycine are present), and the whole-cell sugar patterns are type D (xylose and arabinose are present). The phospholipid pattern of both species is type P-I (no nitrogenous phospholipids). The guanine-plus-cytosine content of the deoxyribonucleic acid ranges from 71 to 73 mol%. The type strain of type species G. harbinensis is strain NRRL 15337 (= LL-D05139), and the type strain of G. rutgersensis is strain NRRL B-16106 (= LL-I-20).

Chemical composition of cell-wall polysaccharides from leprosy-derived corynebacteria

The importance of cell-wall components for bacterial taxonomy has been repeatedly stressed [1,2]. Microorganisms of genera Corynebacterium, Mycobacterium and Nocardia (CMN group) have envelopes of similar structure and contain 3 kinds of polymers: peptidoglycan, arabinogalactan and mycolates [3,4]. Lechevalier and Lechevalier [5] have classified different genera of Actinomyces into 9 cell-wall types (I-IX) differing in the major amino acid constituents of their cell walls and 4 whole-cell sugar patterns (A-D) by analysis of cell hydrolysates. Cell-wall type IV and whole-cell sugar pattern type A, which are characteristic of the CMN group of microorganisms, are known to contain arabinose and galactose in the approximate ratio of 5 : 2. Two kinds of microorganisms have been recognized in human leprosy lesions: (a) Mycobacterium leprae, acid-fast Gram-positive, which does not replicate in vitro; and (b) some non-acid-fast Gram-positive bacteria which multiply in axenic culture and were previously indicated as 'diphtheroids' because of their resemblance to Corynebacterium diphtheriae (cf. refs. 6 and 7 for review). These microorganisms were recently characterized as true corynebacteria according to their DNA base composition (56 to 58% GC) [8] and mycolic acid structure (polyunsaturated corynomycolic acids) [10,13]. Consequently, 'diphtheroids' were renamed as 'leprosy derived corynebacteria' (LDC) according to Barksdale [11]. The aim of the present study was the purification and analysis of cell-wall polysaccharides of 3 LDC and 2 reference microorganisms, Corynebacterium hoffmannii and Mycobacterium smegmatis.