Family Pseudonocardiaceae Research Articles

Complete genome sequence of Saccharomonospora viridis type strain (P101T)

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer’s lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Actinophytocola oryzae gen. nov., sp. nov., isolated from the roots of Thai glutinous rice plants, a new member of the family Pseudonocardiaceae

A novel endophytic actinomycete, strain GMKU 367(T), was isolated from roots of Thai glutinous rice plants (Oryza sativa L. 'RD6') collected from Pathum Thani Rice Research Center, Pathum Thani province, Thailand. Strain GMKU 367(T) formed cylindrical spores on aerial mycelium, but sporangium-like structures and fragmentation of substrate mycelium were not observed. The cell-wall amino acids contained meso-diaminopimelic acid, alanine, glutamic acid and acetylated muramic acid. The whole-cell sugars were arabinose, galactose, mannose, rhamnose and ribose. Major fatty acids were iso-C(15 : 0), iso-C(16 : 0) and C(16 : 0). The diagnostic menaquinone was MK-9(H(4)). The polar phospholipids were phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The G+C content of the genomic DNA was 71.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequence data indicated that strain GMKU 367(T) differed from members of the family Pseudonocardiaceae. On the basis of the evidence presented in this polyphasic study, it is proposed that strain GMKU 367(T) represents a novel species in a new genus in the family Pseudonocardiaceae, with the name Actinophytocola oryzae gen. nov., sp. nov.; the type strain of Actinophytocola oryzae is GMKU 367(T) (=BCC 31372(T) =NBRC 105245(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)).

Pseudonocardia parietis sp. nov., from the indoor environment

A Gram-positive, rod-shaped, non-endospore-forming, mycelium-forming actinobacterium (04-St-002(T)) was isolated from the wall of an indoor environment colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 04-St-002(T) was shown to belong to the family Pseudonocardiaceae, and to be most closely related to Pseudonocardia antarctica (99.2 %) and Pseudonocardia alni (99.1 %). The major menaquinones were MK-8(H(4)) and MK-8(H(2)), the phospholipid type was PIII, and the polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylcholine. Moderate amounts of phosphatidylglycerol and an unknown polar lipid, L1, small or trace amounts of phosphatidylinositol, phosphatidylinositol-mannoside, three unknown lipids, two unknown phospholipids and four unknown glycolipids were also detected. The major fatty acids iso-C(16 : 0), iso-C(16 : 1), C(16 : 0) and C(16 : 1)omega7c supported the affiliation of strain 04-St-002(T) to the genus Pseudonocardia. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 04-St-002(T) from the two most closely related species, P. alni and P. antarctica. Strain 04-St-002(T) represents a novel species, for which the name Pseudonocardia parietis sp. nov. is proposed. The type strain is 04-St-002(T) (=DSM 45256(T)=CCM 7582(T)).

Sciscionella marina gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea

The taxonomic position of an actinomycete, designated SCSIO 00231(T), isolated from a sediment sample collected from the northern South China Sea, was determined by using a polyphasic approach. The organism formed fragmented substrate hyphae and sparse aerial mycelium on modified ISP 2 medium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain SCSIO 00231(T) fell into the family Pseudonocardiaceae, in which it formed a distinct lineage and was loosely associated with Thermocrispum municipale DSM 44069(T), with 93 % similarity. The other closest phylogenetic neighbours were Saccharopolyspora erythraea NRRL 2338(T) (92.6 % similarity) and Amycolatopsis sacchari DSM 44468(T) (93.1 % similarity). The isolate had cell-wall type IV (meso-diaminopimelic acid and whole-cell sugars arabinose, galactose and glucose) and phospholipid type III. The predominant menaquinone was MK-9(H(4)). The G+C content of the genomic DNA was 69 mol%. Based on these data, strain SCSIO 00231(T) can be readily distinguished from previously described organisms and represents a new genus within the family Pseudonocardiaceae. The name Sciscionella gen. nov. is proposed, with the novel species Sciscionella marina sp. nov. The type strain of Sciscionella marina is SCSIO 00231(T) (=KCTC 19433(T) =CCTCC AA208009(T)).

Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae

A novel actinomycete strain, YIM 0006(T), was isolated from soil of a tropical rainforest in northern Thailand. The isolate displayed the following characteristics: aerial mycelium is absent, short spore chains are formed directly on the substrate mycelium, contains meso-diaminopimelic acid, arabinose and galactose (cell-wall chemotype IV), the diagnostic phospholipid is phosphatidylcholine, MK-9(H(4)) is the predominant menaquinone and the G+C content of the genomic DNA is 69.0 mol%. Phylogenetic analysis and phenotypic characteristics showed that strain YIM 0006(T) belongs to the family Pseudonocardiaceae but can be distinguished from representatives of all genera classified in the family. The novel genus and species Actinomycetospora chiangmaiensis gen. nov., sp. nov. are proposed, with strain YIM 0006(T) (=CCTCC AA 205017(T) =DSM 45062(T)) as the type strain of Actinomycetospora chiangmaiensis.

Pseudonocardia tetrahydrofuranoxydans sp. nov.

A Gram-positive, rod-shaped, non-endospore-forming but mycelium-forming actinobacterium (strain K1(T)) was isolated from an enrichment culture containing tetrahydrofuran (THF) as the sole source of carbon. On the basis of its G+C content (71.3 mol%) and of 16S rRNA gene sequence similarity studies, strain K1(T) was shown to belong to the family Pseudonocardiaceae, most closely related to Pseudonocardia hydrocarbonoxydans (99.3 %), P. benzenivorans (98.8 %) and P. sulfidoxydans (98.3 %). The 16S rRNA gene sequence similarity to other Pseudonocardia species was less than 97 %. Chemotaxonomic data [major menaquinone MK-8(H(4)); major fatty acids C(16 : 0) iso, C(15 : 0) iso and C(17 : 1)omega6c] supported the affiliation of strain K1(T) to the genus Pseudonocardia. The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain K1(T) from the three species P. benzenivorans, P. sulfidoxydans and P. hydrocarbonoxydans, although all four organisms utilized THF. Strain K1(T) represents a novel species, for which the name Pseudonocardia tetrahydrofuranoxydans sp. nov. is proposed, with the type strain K1(T) (=DSM 44239(T)=CIP 109050(T)).

Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave

Two actinomycete strains, designated N7-3T and N4-6T, were isolated from a natural cave on Jeju Island, Republic of Korea, by using a dilution method, and were subjected to physiological, chemical and molecular characterization. The nearly complete sequences of the 16S rRNA gene were aligned and compared with those of representatives of the genus Amycolatopsis. Phylogenetic analysis showed that the organisms belong to the family Pseudonocardiaceae and formed two distinct lineages within the evolutionary radius of the genus Amycolatopsis. The chemotaxonomic and morphological properties support their classification in the genus Amycolatopsis. The 16S rRNA gene sequence data revealed that the closest relatives of strains N7-3T and N4-6T were Amycolatopsis sulphurea (97.9% similarity) and Amycolatopsis albidoflavus (98.7% similarity), respectively. The combination of physiological and genetic data supported the observation that the organisms could be distinguished from each other and from established species of the genus Amycolatopsis. The names Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov. are proposed for the two novel species, with N7-3T (= NRRL B-24427T = JCM 13280T) and N4-6T (= NRRL B-24428T = JCM 13279T) as the respective type strains.

Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil

Two actinomycete strains, 32U-2T and 32U-4, were isolated from a prairie soil in Minnesota and subjected to characterization by means of polyphasic taxonomy. The 16S rRNA gene sequences were determined following PCR amplification and cloning. A phylogenetic analysis, based on comparative analysis of 16S rRNA gene sequences, indicated that the organisms consistently formed a well-separated, distinct sub-branch within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. The levels of 16S rRNA sequence similarity between the isolates and the type strains of recognized Amycolatopsis species ranged from 94.1 to 97.9 %. The highest levels of sequence similarity were found between the isolates and Amycolatopsis coloradensis (97.6-97.9 %), Amycolatopsis alba and Amycolatopsis orientalis (97.3-97.6 %) and Amycolatopsis lurida (97.2-97.5 %). Chemotaxonomic characteristics supported the phylogenetic relationships between the organisms and members of the genus Amycolatopsis. However, a broad range of phenotypic and genetic data revealed that the isolates should be classified as novel species of the genus Amycolatopsis, for which the name Amycolatopsis minnesotensis sp. nov. is proposed. The type strain is 32U-2T (=KCCM 42246T = NRRL B-24435T).

Phylogenetic analysis of mutualistic filamentous bacteria associated with fungus-growing ants

The attine ant-microbe system is a quadripartite symbiosis, involving a complex set of mutualistic and parasitic associations. The symbiosis includes the fungus-growing ants (tribe Attini), the basidiomycetous fungi the ants cultivate for food, specialized microfungal parasites (in the genus Escovopsis) of the cultivar, and ant-associated mu tualistic filamentous bacteria that secrete antibiotics specifically targeted to suppress the growth of Escovopsis. In this study, we conduct the first phylogenetic analysis of the filamentous mutualistic bacteria (actinomycetes) associated with fungus-growing ants. The filamentous bacteria present on 3 genera of fungus-growing ants (Acromyrmex, Trachy myrmex, and Apterostigma) were isolated from 126 colonies. The isolated actinomycetes were grouped into 3 distinct morphological types. Each morphological type was specific to the ant genus from which it was isolated, suggesting some degree of host specificity. The phylogenetic position of the 3 morphotypes was estimated using 16S rDNA for representative strains. The 8 isolates of actinomycetes sequenced are in the family Pseudonocardiaceae (Actino mycetales) and belong to the genus Pseudonocardia. Transmission electron microscopy examination of the actino mycete associated with the cuticle of Acromyrmex sp. revealed bacterial cells with an outer electron-dense membrane, consistent with actinomycetes in the genus Pseudonocardia. Ant-associated Pseudonocardia isolates did not form a monophyletic group, suggesting multiple acquisitions of actinomycetes by fungus-growing ants over their evolutionary history.

Pseudonocardia benzenivorans sp. nov.

A Gram-positive, rod-shaped, non-spore-forming bacterium (B5(T)) was isolated from an enrichment culture that contained 1,2,3,5-tetrachlorobenzene as the sole source of carbon. On the basis of 16S rRNA gene sequence similarity studies, strain B5(T) was shown to belong to the family Pseudonocardiaceae and was related most closely to Pseudonocardia sulfidoxydans (98.8 %) and Pseudonocardia hydrocarbonoxydans (98.3 %). 16S rRNA gene sequence similarity to other Pseudonocardia species was <97 %. Chemotaxonomic data [major menaquinone, MK-8(H(4)); major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol; major fatty acids, C(16 : 0), iso-C(16 : 0) and iso-C(15 : 0)] supported the affiliation of strain B5(T) to the genus Pseudonocardia. The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain B5(T) from P. sulfidoxydans and P. hydrocarbonoxydans. Strain B5(T) therefore represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia benzenivorans sp. nov. is proposed, with the type strain B5(T) (=DSM 44703(T)=CIP 107928(T)).

Microbial degradation of aliphatic polyesters

AbstractPolyester‐degrading ability of actinomycetes obtained from culture collections was investigated by the formation of clear zones on polyester‐emulsified agar plates. Using 41 genera (43 strains) of actinomycetes with phylogenetic affiliations based on 16S rRNA sequences, poly(L‐lactide) (PLA)‐degraders were found to be limited to members of family Pseudonocardiaceae and related genera. On the other hand, poly(β‐hydroxybutyrate) (PHB)‐, polycaprolactone (PCL)‐, and poly(butylene succinate) (PBS)‐degraders were widely distributed in many families.

Erratum: corrigendum: Fungus-growing ants use antibiotic-producing bacteria to control garden parasites

Nature 398, 701–704 (1999). We reported in this Letter that, on the basis of its cell-wall chemistry, the bacterium associated with the fungus-growing ant Acromyrmex octospinosus is in the genus Streptomyces (Streptomycetaceae: Actinomycetes). It has been brought to our attention by Nature that R. Wirth, T. Wagner, C. Kost, I. Bottcher, W.-R. Arendholz and M. Redenbach (manuscript submitted) do not find evidence of a specialized relationship between bacteria in the genus Streptomyces and fungus-growing ants in the genus Acromyrmex. Our ongoing molecular phylogenetic analyses reveal that the specialized symbiotic bacterium associated with Acromyrmex is not a species of Streptomyces, but is instead in the actinomycetous family Pseudonocardiaceae (C.R.C. and M. Cafaro, manuscript in preparation). This genus-level misidentification does not affect our other conclusions.

Development of cloning vectors and transformation methods for Amycolatopsis.

The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA- rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains.

Poly(L‐lactide)‐Degrading Activity in Various Actinomycetes

AbstractThe poly(L‐lactide) (PLA)‐degrading ability of actinomycetes obtained from culture collections was examined by the formation of clear zones on PLA‐emulsified agar plates. Using 41 genera (105 strains) of actinomycetes with phylogenetic affiliations based on 16S rRNA sequences, PLA degraders were found to be limited to members of the family Pseudonocardiaceae and related genera. They included Amycolatopsis, Saccharothrix, Lentzea, Kibdelosporangium, and Streptoalloteichus. A large number of PLA degraders were widely distributed within the genus Saccharothrix. Most strains forming clear zones on PLA‐emulsified agar plates also formed clear zones on silk fibroin agar plates. Saccharothrix species showed an ability to degrade PLA films and assimilate degradation products in liquid cultures. No significant change of the molecular weight and polydispersity (Mw/Mn) of the remaining film fragments was confirmed. After cultivation for two weeks, many irregular holes/pits on the surface of the film due to the colonization of microorganisms were observed by scanning electron microscopy.Scanning electron micrograph of the surface of PLA film: A. orientalis subsp. orientalis IFO 12362 after 14 d.magnified imageScanning electron micrograph of the surface of PLA film: A. orientalis subsp. orientalis IFO 12362 after 14 d.

Pseudonocardia spinosispora sp. nov., isolated from Korean soil.

A new strain of the genus Pseudonocardia, which was isolated from a Korean soil sample, is described. The organism shows distinct cultural characteristics in that it forms well-developed aerial mycelium that fragments into rod-shaped, spiny spores, and grows only in standing culture but not in shake culture. Substrate mycelium is sparse or absent in most media used. Phylogenetic analyses based on 16S rDNA sequences reveal that this isolate forms a distinct clade within the radiation encompassing the genera Pseudonocardia and Actinobispora of the family Pseudonocardiaceae. The affiliation to the genus Pseudonocardia is also supported by the cell chemistry, which is represented by the presence of meso-diaminopimelic acid, arabinose and galactose in the cell wall, tetrahydrogenated menaquinone with eight isoprene units as a predominant menaquinone, and phosphatidylcholine as a diagnostic phospholipid. The levels of 16S rDNA sequence similarity found between the isolate and the type strain of validly described species in the genus Pseudonocardia ranged from 94.8 to 96.3%. The organism is also readily differentiated from all of the validated species of the genus Pseudonocardia by means of a battery of phenotypic tests. The name proposed for the new species is Pseudonocardia spinosispora sp. nov. The type strain is LM 141T (= IMSNU 50581T = KCTC 9991T = NRRL B-24156T).

Amycolatopsis albidoflavus sp. nov.

The generic position of an actinomycete strain, 'Pseudonocardia sp.' IMSNU 22139, was investigated by the phylogenetic analysis of 16S rDNA sequence. Comparative studies of 16S rDNA sequences indicated that this organism consistently formed a distinct clade within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. This organism was also found to have chemotaxonomic properties consistent with those of the genus Amycolatopsis, which were represented by a type IV cell wall (meso-diaminopimelic acid, arabinose and galactose), a major menaquinone of MK-9(H4), a predominant fatty acid of 14-methylpentadecanoic acid, phosphatidylmethylethanolamine as a diagnostic phospholipid (a phospholipid type PII pattern) and DNA base composition of 68.5 mol% G+C. On the basis of physiological properties, cellular fatty acid profiles and its unique phylogenetic position, this organism is readily differentiated from all of the validly described species of the genus Amycolatopsis, and the name Amycolatopsis albidoflavus sp. nov. is proposed for it. The type strain is IMSNU 22139T (= KCTC 9471T = ATCC 53205T).

Actinoalloteichus cyanogriseus gen. nov., sp. nov.

Phylogenetic analysis of 'Actinoalloteichus cyanogriseus' based on its 16S rDNA sequence confirmed that the organism belongs to the family Pseudonocardiaceae. It contains glutamic acid, alanine and meso-diaminopimelic acid as cell wall amino acids, and menaquinone 9 (H4). Its taxonomic characteristics differ from those of the previously described organisms of the family Pseudonocardiaceae. On the basis of these morphological, physiological, chemotaxonomic and phylogenetic analyses, a new genus, Actinoalloteichus, is proposed, along with a new species, namely Actinoalloteichus cyanogriseus sp. nov. The type strain is A. cyanogriseus IFO 14455T (= AS 4.1159T = JCM 6095T).

Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov.

The generic position of two isolates from soils inside a gold mine cave in Kongju, Korea, was determined by 16S rDNA sequencing and chemotaxonomic characteristics. Phylogenetic analysis indicated that both of the isolates formed a clade with Lentzea albidocapillata and members of the genus Saccharothrix of the family Pseudonocardiaceae. The chemical composition of the isolates and of Lentzea albidocapillata was consistent with that of the genus Saccharothrix, which is characterized by a type III cell wall (the meso-isomer of diaminopimelic acid, and galactose and rhamnose as characteristic whole-cell sugars), MK-9(H4) as the major menaquinone, and a phospholipid type PII pattern (phosphatidylethanolamine as a diagnostic phospholipid). The combination of morphological features, chemotaxonomic characters and phylogenetic data supported the proposal that Lentzea albidocapillata, the only and type strain of the genus Lentzea, should be transferred to the genus Saccharothrix. On the basis of physiological properties, cellular fatty acid composition and DNA-DNA hybridization data, two new species within the genus Saccharothrix are proposed: Saccharothrix violacea sp. nov., type strain LM 036T (= IMSNU 50388T), and Saccharothrix albidocapillata comb. nov., type strain DSM 44073T (=IMSNU 21253T).

Phylogenetic analysis of the genera Pseudonocardia and Actinobispora based on 16S ribosomal DNA sequences.

The 16S rDNA sequences of 11 strains, nine type strains of validated Pseudonocardia species and Actinobispora yunnanensis, and two strains of unnamed Pseudonocardia species, were determined and compared with those of representatives of the family Pseudonocardiaceae. The phylogenetic analysis indicated that all of the validated species of the genera Pseudonocardia and Actinobispora consistently formed a monophyletic unit and separated well from the other genera of the family Pseudonocardiaceae. One unnamed Pseudonocardia strain was related to members of the genus Pseudonocardia, whereas the other unnamed Pseudonocardia strain formed a distinct clade within the radiation of the genus Amycolatopsis.