Polyphasic characterization and genomic insights into Nocardioides turkmenicus sp. nov. isolated from a desert soil.

Strain KC13T, a novel desert-adapted, non-motile, Gram-stain-positive, rod-shaped, aerobic bacterium, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan and characterised by a polyphasic approach. Phylogenetic analysis based on 16S rRNA sequences revealed that strain KC13T was a member of the genus Nocardioides, and formed a distinct cluster with Nocardioides luteus DSM 43366T (99.3% sequence identity), Nocardioides albus DSM 43109T (98.9%), Nocardioides panzhihuensis DSM 26487T (98.3%) and Nocardioides albertanoniae DSM 25218T (97.9%). The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 85.8-91.0% and 30.2-35.9%, respectively, with the type strains of closely related species. The genome size of strain KC13T was 5.3 Mb with a DNA G + C content of 69.7%. Comprehensive genome analyses showed that strain KC13T, unlike its close relatives, had many genes associated with environmental adaptation. Strain KC13T was found to have chemotaxonomic and phenotypic characteristics of members of the genus Nocardioides and some differences from phylogenetic neighbours. Based on the chemotaxonomic, genomic, phenotypic and phylogenetic data, strain KC13T represents a novel species of the genus Nocardioides, for which the name Nocardioides turkmenicus sp. nov. is proposed, and the type strain is KC13T (= JCM 33525T = CGMCC 4.7619T).

Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis.

During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2 Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.

Saccharopolyspora soli sp. nov., isolated from Northern Cyprus soil.

A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain K220T, was isolated from soil collected from Cape Andreas (Zafer Burnu), Northern Cyprus, and subjected to a polyphasic taxonomic approach. The organism was shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Saccharopolyspora. 16S rRNA gene sequence analysis of strain K220T showed that it is closely related to the type strains of Saccharopolyspora maritima 3SS5-12 T, Saccharopolyspora kobensis JCM 9109 T and Saccharopolyspora hirsuta ATCC 27875 T with 97.6, 97.5 and 97.0% sequence similarity, respectively. In silico DNA-DNA hybridization and average nucleotide identity values between strain K220T and type strains of the genus Saccharopolyspora with publicly available genomes were 22.1-31.2% and 76.0-83.16%, respectively. The DNA G + C content of strain K220T was 68.3 mol%. The genome of strain K220T has genes associated with 24 biosynthetic gene clusters. The strain contained MK-9(H4) and iso-C16: 0 as the predominant respiratory quinone and fatty acid, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine. Based on evidence collected from the genotypic, phenotypic and phylogenetic analyses, strain K220T is considered to represent a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora soli sp. nov. is proposed. The type strain is K220T (= JCM 33912T = KCTC 49395T).

Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey.

An actinobacterium, designated 14C53T, was isolated from a soil sample on basaltic material from Samsun, Turkey. The growth ranges for NaCl concentration and pH of strain 14C53T were quite limited and the growth temperature range of the strain was 20-37 °C, with an optimum at 28 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain 14C53T was most closely related to Actinomadura geliboluensis A8036T (98.5 % similarity value), but in the phylogenetic tree, it formed a clade with Actinomadura alkaliterrae D310AT. The genome tree revealed a close relationship between the strain and Actinomadura pelletieri DSM 43383T. However, the digital DNA-DNA hybridization and average nucleotide identity values between strain 14C53T with Actinomadura geliboluensis A8036T and Actinomadura pelletieri DSM 43383T were 28.6-30.2 % and 84.3-85.5 %, respectively, and comparative analyses based on the genome sequences demonstrated that it represents a novel species of the genus Actinomadura. The genome size of strain 14C53T was approximately 9.0 Mb and the genomic DNA G+C content of the strain was 71.3 mol%. The major cellular fatty acids of strain 14C53T were C16 : 0 and iso-C16 : 0. Strain 14C53T contained meso-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H8) and MK-9(H6). Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Actinomadura soli sp. nov. is proposed, with 14C53T (=DSM 104447T=KCTC 39878T) as the type strain.

Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov., Saccharopolyspora terrae sp. nov. and their biotechnological potential revealed by genome analysis.

Exploration of unexplored habitats for novel actinobacteria with high bioactivity potential holds great promise in the search for novel entities. During the course of isolation of actinobacteria from desert soils, four actinobacteria, designated as 5K548T, 7K502T, 16K309T and 16K404T, were isolated from the Karakum Desert and their bioactivity potential as well as taxonomic provenances were revealed by comprehensive genome analyses. Pairwise sequence analyses of the 16S rRNA genes indicated that the four strains are representatives of putatively novel taxa within the prolific actinobacterial genus Saccharopolyspora. The strains have typical chemotaxonomic characteristics of the genus Saccharopolyspora by having meso-diaminopimelic acid as diagnostic diaminoacid, arabinose, galactose and ribose as whole-cell sugars. Consistent with this assignment, all of the isolates contained phosphatidylcholine in their polar lipid profiles and MK-9(H4) as the predominant menaquinone. The sizes of the genomes of the isolates ranged from 6.0 to 10.2 Mb and the associated G + C contents from 69.6 to 69.7 %. Polyphasic characterizations including determination of overall genome relatedness indices revealed that the strains are representatives of four novel species in the genus Saccharopolyspora. Consequently, isolates 5K548T, 7K502T, 16K404T and 16K309T are proposed as novel Saccharopolyspora species for which the names of Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov. and Saccharopolyspora terrae sp. nov. are proposed, respectively. Comprehensive genome analysis for biosynthetic gene clusters showed that the strains have high potential for novel secondary metabolites. Moreover, the strains harbour many antimicrobial resistance genes providing more evidence for their potentiality for bioactive metabolites.

Comprehensive genome analysis of a novel actinobacterium with high potential for biotechnological applications, Nonomuraea aridisoli sp. nov., isolated from desert soil.

During a study to isolate such actinobacteria with unique metabolic potential, a novel actinobacterium, designated KC333T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of the strain was investigated using a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was most closely related to Nonomuraea terrae CH32T (99.0% sequence similarity), Nonomuraea maritima FXJ7.203 T (98.9%), Nonomuraea candida HMC10T (98.7%) and Nonomuraea gerenzanensis ATCC 39727 T (98.6%), and is therefore considered to represent a member of the genus Nonomuraea. However, the average nucleotide identity and digital DNA-DNA hybridization based on whole-genome sequences between strain KC333T and close relatives demonstrated that it represents a novel species of the genus Nonomuraea. The major cellular fatty acids of strain KC333T were iso-C16: 0, C17:0 10-methyl and iso-C16: 0 2OH. Strain KC333T contained meso-diaminopimelic, mannose, madurose and ribose in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H4) and MK-9(H6). The genome size of strain KC333T is approximately 9.86 Mb, and the genomic DNA G + C content of the strain is 71.3%. In addition to the polyphasic characterisation, comprehensive genome analysis for gene clusters encoding carbohydrate-active enzymes and bioactive secondary metabolites as well as CRISPR-associated sequences revealed the high biotechnological potential of the strain. Based on evidence collected from the genotypic, phenotypic, and phylogenetic analyses, a novel species, Nonomuraea aridisoli sp. nov. is proposed with KC333T (= DSM 107062 T = JCM 32584 T = KCTC 49111 T) as the type strain.

Genomic insight into the Streptomyces aurantiacus clade: reclassification of Streptomyces ederensis as a later heterotypic synonym of Streptomyces umbrinus and Streptomyces glomeroaurantiacus as a later heterotypic synonym of Streptomyces aurantiacus.

The taxonomic relationships and genome features of the type strains in the Streptomyces aurantiacus clade, including Streptomyces aurantiacus, Streptomyces ederensis, Streptomyces glomeroaurantiacus, Streptomyces umbrinus, Streptomyces phaeochromogenes, Streptomyces dioscori and Streptomyces tauricus, were investigated. Type strains of these species shared high 16S rRNA gene sequence similarity to each other. Multilocus sequence analysis (MLSA) based on atpD, gyrB, recA, rpoB and trpB genes revealed that S. ederensis and S. umbrinus belong to the same species. Also, S. aurantiacus and S. glomeroaurantiacus belong to the same species, but the remaining species are not closely related to each other. MLSA results were verified by the results average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses; while the ANI and dDDH values between S. ederensis and S. umbrinus are 98.1 and 85.4 %, respectively, these values between S. aurantiacus and S. glomeroaurantiacus are 98.9 and 90.7 %, respectively. The presence of almost the same set of biosynthetic gene clusters and highly consistent phenotypic test results also supported the synonymy between S. ederensis and S. umbrinus, as well as between S. aurantiacus and S. glomeroaurantiacus. Therefore, S. ederensis should be reclassified as a later heterotypic synonym of S. umbrinus and S. glomeroaurantiacus should be reclassified as a later heterotypic synonym of S. aurantiacus.

Streptomyces scabichelini sp. nov., isolated from soil.

A novel actinomycete, designated strain HC44T, was isolated from a soil sample collected from Hacibektas, Turkey, and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that HC44T clustered with members of the genus Streptomyces and the highest 16S rRNA gene sequence similarity values were obtained with Streptomyces vastus NBRC 13094T (97.6 %) and Streptomyces kalpinensis TRM 46509T (96.9 %). Multi-locus sequence analysis (MLSA) based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that the MLSA evolutionary distance value was 0.043 between strain HC44T and S. vastus NBRC 13094T. Whole-cell hydrolysates contained ll-diaminopimelic acid, glucose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content of the draft genome sequence, consisting of 11.2 Mbp, was 69.8 mol%. On the basis of polyphasic taxonomic evidence, strain HC44T represents a novel species of the genus Streptomyces, for which the name Streptomyces scabichelini sp. nov. is proposed. The type strain is HC44T (=DSM 106874T=KCTC 39872T).

Streptomyces boncukensis sp. nov., isolated from saltern soil.

A novel Gram-stain positive, aerobic, non-motile Actinobacterium, designated strain SB3404T, was isolated from saltern soil collected from Boncuk Saltern, Sungurlu-Çorum, Turkey, and subjected to a polyphasic taxonomic approach. The organism has shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis of strain SB3404T showed that it is closely related to Streptomyces albus NBRC 13014T (97.2% sequence similarity), Streptomyces xishensis YIM M 10378T (96.7%) and Streptomyces abyssalis YIM M 10400T (96.5%). The cell wall of the strain contained LL-diaminopimelic acid and the cell-wall sugars were glucose, mannose and ribose. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The major cellular fatty acids were found to be iso-C16:0, anteiso-C17:0 and anteiso-C15:0. Consequently, strain SB3404T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces boncukensis sp. nov. is proposed. The type strain is SB3404T (= KCTC 49371T = JCM 34018T).

Streptomyces coryli sp. nov., isolated from hazelnut orchard soil.

A novel actinobacteria, isolate A7024T, was isolated from commercial hazelnut orchard soil sample which was collected at Duzce, West Black Sea region, Turkey. A polyphasic taxonomic study was carried out to determine the status of this isolate. The phylogenetic tree reconstructed using the neighbour-joining algorithm based on 16S rRNA gene sequences indicated that isolate A7024T was positioned within the members of the genus Streptomyces with the highest sequence similarity (97.7 %) to Streptomyces cadmiisoli ZFG47T. The organism formed an extensively branched substrate and aerial hyphae which generated irregular rod-shaped spores with smooth-surfaces. The cell wall of strain A7024T contained ll-diaminopimelic. Glucose, mannose and ribose were detected as whole-cell sugars. Its polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and three unidentified glycolipids. Major menaquinones were MK-9(H6) and MK-9(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Strain A7024T had a genome size of 9.0 Mb with a genome G+C content of 71.5 mol%. The low level of 16S rRNA gene similarity, 19.3 ± 2.3% digital DNA-DNA hybridization and 76.94 % average nucleotide identity values, as well as some different phenotypic characteristics allowed the strain to be distinguished from the closely related type strains. Therefore, it is concluded that strain A7024T represents a novel species of the genus of Streptomyces, for which the name Streptomyces coryli sp. nov. is proposed. The type strain is A7024T (=DSM 42066T=KCTC 29102T=NRRL B-24888T).

Streptomyces boluensis sp. nov., isolated from lake sediment.

A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain YC537T, was isolated from lake sediment collected from Yenicaga Lake, Bolu, Turkey, and subjected to a polyphasic taxonomic approach. The organism had phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis of strain YC537T showed that it is closely related to the type strain of Streptomyces ziwulingensis F22T (97.9% sequence similarity), Streptomyces tauricus JCM 4837 T (97.7%) and Streptomyces beijiangensis NBRC 100044 T (97.6%). The cell wall of the strain contained LL-diaminopimelic acid and the cell-wall sugars were glucose, galactose and ribose. The major phospholipids of strain YC537T were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16:0, iso-C14:0, anteiso-C15:0 and iso-C15:0. Consequently, strain YC537T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces boluensis sp. nov. is proposed. The type strain is YC537T (= KCTC 39750 T = DSM 102303 T).

Shimazuella alba sp. nov. isolated from desert soil and emended description of the genus Shimazuella Park et al. 2007.

A novel, Gram-stain-positive bacterium, designated KC615T, was isolated from desert soil which was collected from the Karakum Desert, Turkmenistan. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence showed that isolate KC615T formed a monophyletic clade with Shimazuella kribbensis KCTC 9933T, sharing 98.2% similarity and polyphasic taxonomic studies confirmed the affiliation of the strain to the genus Shimazuella. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and hydroxy-phosphatidylethanolamine. The predominant menaquinones (> 10%) were MK-9(H4) and MK-10(H4). Major fatty acids were anteiso-C15:0, C20:0 and C18:0. The genomic DNA G + C content observed for strain KC615T was 38.5 mol%. Based on 16S rRNA gene similarity, DNA-DNA hybridization value, chemotaxonomic characteristics and differential physiological properties, strain KC615T is considered to represent a novel species within the genus Shimazuella, for which the name Shimazuella alba sp. nov. is proposed. The type strain is KC615T (= JCM 33532T = CGMCC 4.7616T).

Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov.

Three isolates, 5K138T, 8K307T and KC603T, with typical morphological characteristics of members of the genus Jiangella were obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliations of the strains. The strains showed chemotaxonomic properties consistent with their classification as representing members of the genus Jiangella such as ll-diaminopimelic acid in the cell wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as major polar lipids as well as MK-9(H4) as a major menaquinone. Pairwise sequence comparisons of the 16S rRNA genes showed that the strains were closely related to Jiangella alba DSM 45237T, Jiangella rhizosphaerae NEAU-YY265T and Jiangella mangrovi 3SM4-07T with higher than 99 % sequence identities. However, a combination of phenotypic and phylogenetic approaches as well as genome-based comparative analyses confirmed the taxonomic positions of these strains as representing distinct species within the genus Jiangella. Therefore, strains 5K138T, 8K307T and KC603T should each be classified as representing a novel species within the genus Jiangella, for which the names Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. are proposed, respectively. The type strains of the proposed novel species are as follows: Jiangella asiatica 5K138T (=JCM 33518T=CGMCC 4.7672T), Jiangella aurantiaca 8K307T (=JCM 33519T=CGMCC 4.7621T) and Jiangella ureilytica KC603T (=JCM 33520T=CGMCC 4.7618T).

Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material.

A Gram-stain-positive, aerobic, spore-forming actinobacterial strain, designated 160415T, was isolated from a surface soil sample, which was formed on basaltic parent material, collected from Samsun, Turkey. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 160415T clustered closely with species of the genus Nonomuraea, and showed the highest sequence similarity to Nonomuraea zeae NEAU-ND5T, Nonomuraea candida HMC10T and Nonomuraea turkmeniaca DSM 43926T with 99.1%, 98.9% and 98.7%, respectively. Chemotaxonomic properties including major menaquinones, diaminopimelic acid, sugar and phospholipid profiles also confirmed the affiliation of the strain to the genus Nonomuraea. The DNA G+C content of strain 160415T was 69.6 mol%. DNA-DNA hybridization and average nucleotide identity values between the strain and closely related type strains were less than the recommended cut-off values. On the basis of phylogenetic relationships, genotypic and phenotypic characterizations, strain 160415T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea basaltis sp. nov. is proposed. The type strain is 160415T (= KCTC 39875T = DSM 104309T).

Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae.

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora. In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili.

A novel actinobacterial strain, designated 13K301T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301T belongs to the genus Streptomyces and had highest sequence similarity to 'Streptomyces qaidamensis' S10T (99.2 %), Streptomyces flavovariabilis NRRL B-16367T (98.9 %) and Streptomyces phaeoluteigriseus DSM 41896T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA-DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H8) and MK-9(H6). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301T should be classified as representative of a novel species of the genus Streptomyces, for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301T (=DSM 106873T=KCTC 49110T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of Streptomyces galilaeus and Streptomyces bobili belong to a single species. It is, therefore, proposed that S. galilaeus be recognised as a heterotypic synonym of S. bobili for which an emended description is given.

Micromonospora deserti sp. nov., isolated from the Karakum Desert.

An isolate, 13K206T, with typical morphological characteristics of the genus Micromonospora was obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliation of the strain. The strain showed chemotaxonomical properties consistent with its classification in the genus Micromonospora such as meso- and 3-OH-A2pm in the cell-wall peptidoglycan, xylose in whole-cell hydrolysate and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was closely related to 'Micromonospora spongicola' S3-1T, Micromonospora nigra DSM 43818T and Micromonospora yasonensis DS3186T with sequence similarities of 98.6, 98.5 and 98.4 %, respectively. Digital DNA-DNA hybridization and average nucleotide identity analyses in addition to gyrB gene analysis confirmed the assignment of the strain to a novel species within the genus Micromonospora for which the name Micromonospora deserti sp. nov. is proposed. The type strain is 13K206T (=JCM 32583T=DSM 107532T). The DNA G+C content of the type strain is 72.4 mol%.

Polyphasic classification of Nonomuraea strains isolated from the Karakum Desert and description of Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov.

Five actinobacteria isolates, KC201T, KC401, KC310T, KC712T and 6K102T, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus Nonomuraea. The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus Nonomuraea. Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201T, KC310T, KC712T and 6K102T showed that these strains belonged to novel Nonomuraea species, the names proposed for these taxa are Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov., with the type strains KC310T (=CGMCC 4.7331T =DSM 102919T =KCTC 39774T), KC712T (=CGMCC 4.7334T =DSM 102925T =KCTC 39776), KC201T (=CGMCC 4.7339T =DSM 102917T =KCTC 39781T) and 6K102T (=CGMCC 4.7541T =JCM 32916), respectively.

Kribbella turkmenica sp. nov., isolated from the Karakum Desert.

A novel actinobacterial strain, designated 16K104T, was isolated from desert soil collected from the Karakum Desert and characterized using a polyphasic approach to clarify its taxonomic position. Strain 16K104T was found to have chemotaxonomic and morphological properties consistent with classification in the genus Kribbella. The strain shared the highest 16S rRNA gene sequence similarity with Kribbella albertanoniae BC640T (99.2 %), and formed a branch with Kribbella antibiotica YIM 31530T in the 16S rRNA gene phylogenetic tree. Multilocus sequence analysis (MLSA) using five housekeeping genes (gyrB, rpoB, relA, recA and atpD) for comparing the strain with all Kribbella type strains showed that the MLSA distances of strain 16K104T to the closely related type strains of the genus were much higher than the 0.04 threshold. The organism was found to contain ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were identified as ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C15:0, iso-C15 : 0 and iso-C17 : 0. The results of digital DNA-DNA hybridization and average nucleotide identity analyses, in addition to MLSA phylogenetic distances, confirmed that the strain represents a novel species of the genus Kribbella, for which the name Kribbella turkmenica sp. nov. is proposed. The type strain is 16K104T (=JCM 32914T=KCTC 49224T).

Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family Streptosporangiaceae isolated from the Karakum Desert.

A novel, Gram-positive, spore-forming actinomycete, designated strain 7K107T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. Strain 7K107T forms extensively branched substrate mycelia and aerial mycelia which differentiate into short chains of spores. The novel strain contains meso-diaminopimelic acid as the diagnostic wall amino acid and glucose, galactose, madurose and ribose as whole cell sugars. The predominant menaquinones were identified as MK-10(H4), MK-9(H4), MK-10(H6) and MK-9(H6). The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, glycolipids, phospholipids, unidentified lipids and an aminolipid. Major fatty acids were identified as C17:0 10-methyl and C14:0. The G + C content of the genomic DNA was determined to be 70.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is a member of the family Streptosporangiaceae. The strain shares high 16S rRNA gene sequence similarity (96.2%) with Sphaerisporangium album YIM 48782T followed by Sphaerisporangium corydalis NEAU-YHS15T (96.0%) and Nonomuraea candida HMC10T (95.9%). However, phylogenetic analyses based on 16S rRNA and gyrB genes, as well as whole genome comparison, confirmed the distinctiveness of the strain from closely related type strains of the genera Sphaerisporangium, Nonomuraea and Thermostaphylospora. On the basis of morphological, chemotaxonomic and phylogenetic as well as genomic analyses, strain 7K107T is concluded to represent a new genus within the family Streptosporangiaceae, for which the name Desertiactinospora gelatinilytica gen. nov., sp. nov is proposed. The type strain of D. gelatinilytica is 7K107T (= DSM 107423T = JCM 32585T = KCTC 49108T).