A Phylogenetic Analysis of the Family Pseudonocardiaceae and the Genera Actinokineospora and Saccharothrix with 16S rRNA Sequences and a Proposal To Combine the Genera Amycolata and Pseudonocardia in an Emended Genus Pseudonocardia

Warwick, S. I.; Bowen, Timothy; Mcveigh, H.; Tm, Embley

doi:10.1099/00207713-44-2-293

Cited by 190 publications

(141 citation statements)

References 52 publications

(53 reference statements)

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“…First dimension, left to right; second dimension bottom to top. similar to that reported for close relative P. alni (Evtushenko et al, 1989, Warwick et al 1994, whereas the other close relative, P. antarctica, contains phosphatidylethanolamine, distinguishing it from 04-St-002 T (Prabahar et al, 2004). The presence of phosphatidylinositol-mannoside has not been reported for either of these two species.…”

supporting

confidence: 63%

Pseudonocardia parietis sp. nov., from the indoor environment

Schafer

Busse²,

Kämpfer

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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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 v7c 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 (5DSM 45256 T 5CCM 7582 T ).The genus Pseudonocardia, originally proposed by Henssen (1957) for nocardioform actinomycetes that lack mycolate and have a type IV cell wall, reflected by the presence of meso-diaminopimelic acid and the sugars arabinose and galactose (Lechevalier & Lechevalier, 1980), comprises 28 species at the time of writing (Gu et al., 2006; Huang et al., 2002;Lee et al., 2000Lee et al., , 2001Lee et al., , 2002Lee et al., , 2004 Kämpfer & Kroppenstedt, 2004;Liu et al., 2006; Mahendra & AlvarezCohen, 2005;Qin et al., 2008).Strain 04-St-002 T was isolated from a wall colonized with moulds. After extraction of 1 g material sample for 15 min in 10 ml 0.9 % NaCl solution containing 0.01 % (v/v) Tween 80 and dilution on M79 agar (containing 10 g glucose, 10 g Bacto peptone, 2 g casein hydrolysate, 2 g yeast extract, 6 g NaCl, 15 g agar) for 2 weeks at 28 u C, the strain was maintained on M79 at 28 u C and showed a brown-coloured substrate mycelium. After a few days, a white aerial mycelium formed.Morphological properties, Gram-staining and cell morphology were observed by phase-contrast microscopy as described by Kämpfer & Kroppenstedt (2004). DNA isolation was performed with a commercial DNA extraction kit (GenElute Plant Genomic DNA kit; Sigma). Initially, the sample was prepared by a 1 min bead-beating step with 1 g 0.1 diameter Zirconia beads.Multiple sequence alignment and analysis of the data were performed using the software package MEGA version 4 (Tamura et al., 2007). Genetic distance calculations (distance options according to the Kimura two-parameter model), and clustering with the neighbour-joining (Fig. 1...

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supporting

confidence: 63%

Pseudonocardia parietis sp. nov., from the indoor environment

Schafer

Busse²,

Kämpfer

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…The polar lipids phosphatidylcholine and phosphatidylethanolamine, which are present in members of the genus Pseudonocardia, were not found in strains HKI 83T and HKI 84 (42).…”

Section: Discussionmentioning

confidence: 97%

Janibacter limosus gen. nov., sp. nov., a New Actinomycete with meso-Diaminopimelic Acid in the Cell Wall

Martin

Schümann

Rainey

et al. 1997

International Journal of Systematic Bacteriology

117

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New gram-positive bacteria were isolated from 1-year-old sludge from a wastewater treatment plant. The isolates are coccoid to rod-shaped, nonmotile aerobes that form neither spores nor mycelia. They are characterized by a peptidoglycan with directly cross-linked rneso-diaminopimelic acid (type Aly), by the presence of menaquinone MK-S(H,), and by the lack of mycolic acids. The strains have complex fatty acid patterns with i-C16:o and straight-chain saturated and unsaturated fatty acids as major components. The G+C content of the DNA is 70 mol%. The results of chemotaxonomic studies and a 16s ribosomal DNA sequence comparison support our proposal to assign these bacteria to a new genus, the genus Janibacter gen. nov.; the type species is Junibucter Zirnosus sp. nov., and the type strain of J. Zirnosus is strain HKI 83 (= DSM 11140).Both spore-forming and asporogenous actinomycetes have been screened during the last few years for useful bioactive compounds (13,39). The asporogenous organisms play important roles in mineralization of environmentally hazardous chemicals, such as polycyclic aromatic hydrocarbons (22), and in biotechnological production of natural products (23,26,29).To isolate new actinomycetes with new biological activities, we investigated several samples of soil, sludge, and sewage waste. A total of 168 strains were isolated from a 1-year-old sludge sample collected from a wastewater treatment plant. Two of these isolates were found to be markedly different from the other isolates and from previously described genera in their chemotaxonomic and their physiological features. In this paper these two strains are characterized phenotypically and phylogenetically. Below we propose the creation of a new genus, the genus Janibacter gen. nov., with one species, Janibacter limosus sp. nov., for these organisms. MATERIALS AND METHODSBacterial strains and cultural conditions. Strains HKI 83T (T = type strain) and HKI 84 were isolated from a 1-year-old sludge sample from the wastewater treatment plant near Jena, Thuringia, Germany, by the dilution plate technique on plate count agar (Difco Laboratories, Detroit, Mich.). General laboratory cultivation was performed at 28°C on solid rich medium (R medium) or in liquid R medium (43), which contained 1% (wtivol) Bacto Peptone (Difco), 0.5% (wt/vol) yeast extract, 0.5% (wt/vol) Casamino Acids, 0.2% (wthol) meat extract, 0.5% (wt/vol) malt extract, 0.2% (wtivol) glycerol. 0.1% (wt/vol) MgSO, -7H,O, and 0.005% (wt/vol) Tween 80 (pH 7.2). To determine the cellular fatty acids, strains were cultivated for 24 h in liquid tryptic soy broth (Difco) at 28°C.Morphological and physiological characteristics. Colony morphology on R medium and cell morphology at different ages were determined by stereomicroscopy and phase-contrast microscopy (Olympus, Tokyo, Japan). Nitrate reductase activity, urease activity, indole production, methyl red and Voges-Proskauer reactions, hydrogen sulfide production, and hydrolysis of esculin and Tween 80 were determined as described by Lanyi (...

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“…The results of chemotaxonomic and phylogenetic analysis of some related genera with wall chemotype IV and absence of mycolic acid, such as Saccharothrix, Amycolata, Kibdelosporangium, Actinokineospora, Pseudonocardia, Saccharomonospora and Amycolatopsis have been reported (Bowen et al, 1989;Embley et al, 1988a, b;Henssen et al, 1987;Kothe et al, 1989;Takeuchi et al, 1992;Warwick et al, 1994;Yassin et al, 1993). Ochi (1995) reported the results of amino acid sequence analysis of ribosomal protein AT-L30 of members of the family Pseudonocardiaceae.…”

Section: Introductionmentioning

confidence: 99%

“…Ochi (1995) reported the results of amino acid sequence analysis of ribosomal protein AT-L30 of members of the family Pseudonocardiaceae. Warwick et al (1994) reported the phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix. These authors indicated that Amycolatopsis, Saccharomonospora, Pseudonocardia, Amycolata, Saccharopolyspora and Kibdelosporangium should be placed in the family Pseudonocardiaceae.…”

Section: Introductionmentioning

confidence: 99%