Three new species of the genus Actinobispora of the family Pseudonocardiaceae, Actinobispora alaniniphila sp. nov., Actinobispora aurantiaca sp. nov. and Actinobispora xinjiangensis sp. nov

Pseudonocardia lacus sp. nov., An Actinomycete Isolated from a Lake Sediment Sample

A novel actinomycete strain, designated H11425T, was isolated from a sediment sample collected from Baihua Lake, Guizhou Province, PR China, and a polyphasic approach was employed to determine its taxonomic position. 16S rRNA gene sequence comparisons showed that strain H11425T is most closely related to Pseudonocardia sulfidoxydans JCM 10411T (97.9%) and Pseudonocardia kunmingensis JCM 32122T (97.8%). Both of phylogenetic analysis based on 16S rRNA gene sequence and phylogenomic analysis based on whole-genome sequence showed that strain H11425T formed a separate clade within the genus Pseudonocardia. The draft genome had a length of 8,059,576 bp with a G + C content of 74.5%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H11425T and its closely related Pseudonocardia species were 76.8-79.0%, 64.8-69.9% and 21.7-23.3%, respectively, which were significantly lower than the widely accepted species-defined threshold. Strain H11425T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. Mycolic acids were absent. The menaquinone was identifed as MK-8(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine, an unknown phospholipid and four unidentified aminophospholipids. The major fatty acids were iso-C16:0, iso-C14:0, iso H-C16:1 and iso-C16:0 2OH. On the basis of the taxonomic evidence, strain H11425T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia lacus sp. nov. is proposed. The type strain is H11425T (= JCM 34851T = CICC 25118T).

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

Introduction

Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value.

Methods

A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens.

Results

Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens.

Discussion

It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.

Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters

A novel actinomycete strain, designated S2-4^T, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene indicated that strain S2-4^T formed a unique clade next to that harboring Pseudonocardia dioxanivorans CB1190^T, which shared the highest sequence similarity (98.20%) with the new isolate. Phylogenetic analysis based on core genes of genomic sequences displayed a different scenario, exhibiting closer phylogenetic relationship of strain S2-4^T with several species with 16S rRNA gene sequence similarities ranging from 96.95 to 98.06%, which was confirmed by the phylogenetic tree reconstructed based on genomic sequences. Further, substantial differences between the genotypic properties of strain S2-4^T and its closest neighbors, including digital DNA-DNA hybridization, average nucleotide identity, and distribution patterns of biosynthetic gene clusters (BGC), indicated the taxonomic position of strain S2-4^T as a novel species of the genus Pseudonocardia. Accordingly, strain S2-4^T was observed to show a different distribution pattern of a predicted BGC encoding ectoine by comparative genomic analysis, which could be strongly linked to its unique habitat distinct from where its close neighbors were isolated. The major cellular fatty acids were iso-C_15:0, C_21:0, and iso-C_16:0. The predominant menaquinone was MK-8(H₄). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidyl-N-monomethylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, and two unidentified glycolipids. Here, we propose a novel species of the genus Pseudonocardia: Pseudonocardia humida sp. nov. with the type strain S2-4^T (= JCM 34291^T = CGMCC 4.7706^T).

A comprehensive study of eco-friendly natural pigment and its applications

Actinomycetes, a large group of filamentous bacteria account for 70–80% of secondary metabolites available commercially. The present investigation was undertaken with an aim to identify and characterize pigment from actinomycetes. Actinomycetes were isolated from rhizosphere soil samples collected from different regions of Madhya Pradesh state. Out of 85 actinomycetes, only 5 actinomycetes showed pigment production and based on diffusible pigment production ability one actinomycete ARITM02 was selected. The extraction of pigment was done by solvent extraction method using methanol and purified by TLC and column chromatography. The pigment was characterized by UV–Vis spectroscopy which showed the lamda maximum of 277.44. FTIR spectroscopy suggested various functional groups like amino group, amide group, hydroxide, benzene and lactone group. The Mass spectroscopy and NMR spectroscopy showed that the molecular mass of pigment is 621.7 and molecular formula is C34H43N3O8. The pigment was also tested for Antimicrobial activity against broad spectrum human pathogens, antioxidant test and toxicity test for safe use as a natural colorant in cosmetic, food, pharmaceutical and textile industries. The conclusion of study suggested that this novel pigment could be a versatile natural, safe and multipurpose.

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This study clearly describes about the characterization of pigment extracted from actinomycete ARITM02 which was isolated from rhizosphere soil.

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The selected isolate showed antimicrobial activity against bacteria, fungi and molds but no activity against dermatophytes.

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The study confirmed the basic biochemical nature of pigment which is similar to previous reported pigments.

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The pigment was characterized by UV–Vis spectroscopy, FTIR spectroscopy, Mass spectroscopy and NMR spectroscopy.

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The natural pigment is tested for Antimicrobial, antioxidant, anticancer and Allergy tests.

Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock

Eleven actinobacterial strains were isolated from a rock sample collected in the Atacama Desert. Molecular typing by BOX-PCR divided the strains into three clusters and showed that, although very similar, they were not clones. Three strains, ATK01, ATK03T and ATK17, each representing one of the defined BOX clusters, were chosen for further characterization. Phylogenetic analysis indicated that the strains were related to the genus Pseudonocardia and were recovered in a cluster together with Pseudonocardia bannensis YIM 63101T and Pseudonocardia xinjiangensis AS 4.1538T. Chemotaxonomic analyses confirmed their affiliation to the genus Pseudonocardia but differences were found between the new strains and their closest phylogenetic relatives. Physiological and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours supporting their status as a distinct species. Based on the overall data, it is proposed that strains ATK01, ATK03T and ATK17 represent a novel species of the genus Pseudonocardia for which the name Pseudonocardia nigra sp. nov. is proposed (type strain ATK03T=DSM 104088T=CECT 9183T).

Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

Selective isolation and distribution of Actinobispora strains in soil

A simplified enrichment method for selective isolation of Actinobispora strains from soil is described. Actinobispora spores were tolerant to dry-heat treatment at 110 degrees C for 15 min. Actinobispora was more resistant to 1 microgram/mL leucomycin, 1 microgram/mL novobiocin, and 0.5 microgram/mL tunicamycin than Streptomyces dominant in soil, which prevents selective isolation of Actinobispora. Percentages of Actinobispora colonies on the isolation plate were increased by addition of antibiotics and dry-heat treatment of the soil samples. By combining the techniques described above, this genus was isolated from 105 out of 574 soil samples (18% of the samples tested). It was recovered from the soil samples with pH values ranging 5.0 to 8.9, and 78% of strains were isolated from neutral soil (pH 6.0-8.0). A number of Actinobispora strains were isolated from various soils around the world. Actinobispora strains are widely distributed in the world at relatively high frequency.

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.